Annual Report EPFL School of Life Sciences

SV 

2007 

Annual Report EPFL School of Life Sciences 

EPFL-SV | SV Building | Station 19 | CH 1015 Lausanne | http://sv.epfl.ch

PREAMBLE 

Biomedical research will increasingly rely on quantitative approaches and high-end technologies, 

and the future of life sciences lies at the crossroads of biology, basic sciences, informatics and 

engineering. Accordingly, the EPFL School of Life Sciences trains a new breed of researchers 

whose combined skills in these various fields are set to address fundamental biological questions 

and to attack the major medical problems of our times with the true spirit of systems biologists. 

The School of Life Sciences hosts more than forty research groups that apply this philosophy to 

cancer, infectious diseases and mental or neurological disorders, pushing for integrated 

approaches that span a range of disciplines from functional genomics to high-tech bioengineering, 

and from computer neurosciences to structural modeling. 

A bachelor, “Life Sciences and Technology”, two masters, “Life Sciences and Technology” and 

“Bioengineering and Biotechnology”, and three Ph.D. programs, “Biotechnology and 

Bioengineering”, “Neurosciences” and “Molecular biology of cancer and infection”, constitute the 

educational arms of our school, hosting some six hundred students from all geographic and 

scientific horizons. 

Our growing ties with other schools at the EPFL and other Institutions in the Lemanic region 

through joined research and educational programs, the upcoming graduation of our first class of 

master students, and the imminent opening of another building dedicated to life sciences are 

some of the marks of very exciting times for our faculty! 

Professor Didier Trono 

Professor & Dean of the School of Life Sciences 

Ecole Polytechnique Fédérale de Lausanne (Switzerland) 

http://sv.epfl.ch

MAIN SCIENTIFIC EVENTS 

AUGUST 2007 

The second EPFL Life Science Symposium 2007 on 'Neurosciences : Molecules, Systems and Diseases' 

On this occasion, the European Debiopharm Life Sciences Award presented to Dr Zoltan Nusser, researcher 

at the Experimental Medicine Institute, part of the Hungarian Science Academy 

JULY-SEPTEMBER 2007 

Our School of Life Sciences organizing the Summer Research Scholar Program, offering, each year, in 

collaboration with the nearby University of Lausanne (UNIL), intensive research training opportunites to 

undergraduate students interested in research careers in the life sciences 

SEPTEMBER 2007 

The EPFL, leading two of the eight ambitious research projects of ‘Systems X’, the Swiss Initiative in 

Systems Biology, member of the worldwide systems biology network 

PUBLIC-ORIENTED EVENTS 

MARCH 2007 

Participation of BMI research groups to the ‘Brain Awareness Week’ at the national and international levels 

MAY 2007 

Lab visits for the Swiss ‘Gene Days’ 

JUNE 2007 

First SV Inaugural Lecturers by Yann Barrandon and Denis Duboule 

OCTOBER 2007 

London Serpentine Gallery Experiment Marathon – Participation of Olaf Blanke 

HONORS – AWARDS – ANNOUNCEMENTS 

‣ Allergan announces its acquisition of Endoart, a leading Swiss developer of remote-controlled medical 

devices, founded by Nikos Stergiopulos, chair of Hemodynamics and Cardiovascular Technology (LHTC) 

‣ The Alliance Award 2006 granted to Henry Markram, Tania Rinaldi, Karina Kulangara, Brandi Mattson, 

Maria Toledo Rodriguez and Kamila Markram, of the BMI, for the 'Methods for treating and/or preventing 

pervasive developmental disorders in a subject' invention; this invention was selected among all inventions 

registered in 2006 by the EPFL Industrial Relations Office 

‣ Stewart Cole, Director GHI, elected to The Royal Society, the UK’s prestigious national Academy of 

Sciences 

‣ Matthias Lutolf, Head of the Stem Cell Bioengineering Lab, won one of the 20 European Young 

Investigator Awards (EURYI); the candidates were selected on the basis of their future potential and on their 

academic and research excellence 

‣ Stewart Cole, Director GHI, receives grant from the Bill and Melinda Gates Foundation 

‣ On the occasion of the EPFL Journée Magistrale : two junior researchers from the EPFL School of Life 

Sciences on stage : a member of Melody Swartz' group, Jacquie Shields was awarded the prestigious Latsis 

International Foundation Award; Tania Rinaldi, PhD in Henry Markram's group was granted the D. N. 

Chorafas Foundation's Prize 

‣ The KPMG Tomorrow's Market Award to one of our junior researcher and PhD candidate, Sai Reddy, 

presented on the occasion of the EPFL Innovation Day 

‣ Merck Serono, a division of Merck KGaA, and EPFL announced the signing of a research collaboration 

agreement in the areas of Neuroscience, Oncology and Drug Delivery; under this agreement, three Merck 

Serono-endowed Chairs will be created at EPFL: in neurodegenerative diseases, such as Alzheimer's and 

Parkinson's; in cancer, in the framework of the Swiss Institute for Experimental Cancer Research (ISREC); 

and in innovative drug delivery technologies, for instance nanoparticle vaccines 

‣ The creation of a world center for vaccine research was announced in Lausanne by Dr. Ch. Kleiber, the 

Switzerland's Secretary of State for Education and Research; aids, tuberculosis and malaria will be at the 

heart of the work done by the Swiss Institute for Vaccine Research (ISRV) to start operating in 2008; the 

Swiss federal government is chipping in CHF5 million for the institute, which groups researchers from the 

University of Lausanne, the EPFL and the Ludwig Institute among other institutions; the Swiss government 

decided to provide the funding after the Bill and Melinda Gates Foundation provided a SFr15 million grant to 

CHUV (Lausanne University Hospital) for similar vaccine research 

Back to the Table of Contents

THE UNDERGRADUATE STUDIES 

The Life Sciences curriculum aims at educating a new generation of engineers who can master the 

technical and scientific skills needed for studying life and developing the biomedical techno-logies of 

tomorrow. This educational program, established under the direction of Prof. William F. Pralong, M. D., is 

unique in Switzerland and Europe. 

Bachelor’s program (3 years) 

The first two years provide basic courses followed throughout EPFL, such as analysis, linear algebra, 

physics, chemistry (general and organic), and numerical methods. Specific courses in Life Sciences begin 

with biochemistry, cellular, molecular and developmental biology. In the first two years, life sciences courses 

make up less than 20% of the total academic load. 

In the third year, are integrated engineering courses (signals and systems, electronic and electrical 

systems) and typical life sciences courses such as genetics, immunology, and functional genomics applied 

to biological development, bio-computing, neuroscience, molecular biology, systems biology via the study of 

human physiology. Practices in physiology also give the opportunity to apply the engineering and biological 

knowledge acquired up to this point. 

During the third year, the Students orient their training by choosing some of their credits in one of the 

specializations offered at the masters’ program. This includes a bachelor project either in bioengineering and 

biotechnology or in neurosciences and molecular medicine. 

Master’s program (2 years) 

• Master in Life Science and Technology includes several specializations. Among these are 

neurosciences, molecular medicine, and bio-computing. Each specialization is made up of 15 

credits of obligatory courses + 15 credits of optional courses, and/or 

• Master in Biotechnology and Bioengineering, includes 2 specializations in Biotechnology and 

Bioengineering. Each one requires taking 15 specific and obligatory credits together with 15 

optional credits. An additional specialization is offered as minor in Biomedical engineering 

constituted of 22 optional credits with the obligatory project of 8 credits. This specialization is 

organized with the school of Engineering 

Both degree programs share a common basic curriculum that aims to provide Students with the knowledge 

of the modern technologies used in the life sciences such as imaging, bio-computing and optical systems 

applied to biology. In addition, courses in management and economics and applied laws and ethics for the 

life sciences are offered. A large portion of the master program (60 credits) is dedicated to laboratory work 

and projects. 

THE GRADUATE STUDIES 

All three graduate programs comprise a combination of coursework, laboratory based research, in-house 

seminars, and national or international conferences. 

The Doctoral Program in Biotechnology and Bioengineering aims at providing doctoral students with the 

education necessary to be leaders in the fast-growing industrial and academic biotechnology and 

bioengineering sectors, i.e. a depth of knowledge and competence in their specific research area as well as 

a breadth of knowledge in biology, bioengineering and biotechnology. These program themes include: 

genomics and proteomics, biomolecular engineering and biomaterials, stem cell biotechnology, cell and 

process engineering, biochemical engineering, orthopaedic engineering, biomechanics, mechanobiology, 

cell biophysics, computational biology, biomedical imaging as well as molecular, cell and tissue engineering 

The Doctoral Program in Neuroscience provides its students with training from the genetic to the 

behavioural level including molecular, cellular, cognitive, and computational neuroscience. Students 

matriculate in the highly dynamic and interdisciplinary environment of the EPFL's Brain Mind Institute of the 

FSV. The program is further strengthened by research and training opportunities in collaboration with the 

Universities of Lausanne and Geneva 

The Doctoral Program in Molecular Biology of Cancer and Infection is a joint program between the 

Swiss Institute for Experimental Cancer Research (ISREC-EPFL) and the Global Health Institute (GHI- 

EPFL). The program provides training and research opportunities to highly motivated doctoral Students in 

key areas of modern biology in Lausanne, Switzerland. Highly qualified applicants worldwide are chosen 

twice a year through a competitive selection procedure 


OUR CORE FACILITIES & TECHNOLOGY PLATFORMS 

To enhance the training and research capabilities of its students and scientists, EPFL and the School of 

Life Sciences have made significant investment over the past few years to establish state-of-the-art 

technology platforms and core facilities. These facilities are directed and managed by dedicated teams of 

highly trained and experienced staff and are run on a fee-for-service basis. They offer training, access to 

technology, assistance with experimental design and high level data analysis, and collaborations. 

In addition, scientists from our School of Life Sciences closely collaborate with other services in the 

Lemanic region, including the ‘Center for Biomedical Imaging’ and the ‘Lake Geneva Area Genomics Core 

Facility’ 

Currently, the following Life Sciences related core facilities and technology platforms have been 

established at the EPFL School of Life Sciences: 

BIOIMAGING & OPTICS 

Head: Dr Nathalie Garin 

HISTOLOGY 

Head: Dr Jessica Dessimoz 

BIOMOLECULAR SCREENING 

Head: Dr Gerardo Turcatti 

BIOINFORMATICS & BIOSTATISTICS 

Head: Dr Jacques Rougemont 

FLOW CYTOMETRY 

Head: Dr Joanna Roberts 

BIO-ELECTRON MICROSCOPY 

Head of CIME BIO-EM: Dr Graham Knott 

PROTEIN EXPRESSION 

Head: Dr David Hacker 

CENTER FOR THE STUDY OF LIVING SYSTEMS 

Head: Dr Marcel Gyger 

PROTEOMICS 

Head: Dr Marc Moniatte 

TRANSGENIC TECHNOLOGIES 

Head: Dr Friedrich Beermann 


BMI - THE BRAIN MIND INSTITUTE 

The Brain Mind Institute is dedicated to exploring the emergence of higher brain function across multiple 

levels ranging from gene expression to cognition and covering multiple brain regions. Constructed on a 

foundation of futuristic technology, in a manner that can be recurrently interconnected with labs around 

the world, it has the vision to go beyond established concepts. The spectrum of BMI’s faculty projects 

spans across several domains of the neurosciences, including: Molecular Neuroscience, Cellular 

Neuroscience, Systems Neuroscience, Behavioral Neuroscience, Cognitive Neuroscience, Computational 

Neuroscience, and, in collaboration with clinical partners, the neurobiological bases of Neurological and 

Psychiatric diseases. The BMI laboratories are equipped with state-of-the-art equipment, techniques and 

approaches 

RESEARCH GROUPS 

AEBISCHER LAB 

Patrick Aebischer 

Full Professor 

Head of lab (PI) 

http://len.epfl.ch 

TEAM MEMBERS 

Ursula Alves-Zwahlen,Administrative Assistant 

Samareh Azeredo da Silveira Lajaunias, PhD Student 

Jean-Charles Bensadou,Senior Scientist 

Nicolas Bouche, Engineer 

Delphine Charvin, Postdoctoral Fellow 

Carine Ciron, Postdoctoral Fellow 

Philippe Colin,Technician 

Philippe Coune,PhD Student 

Julien Dusonchet, PhD Student 

Meret Gaugler, PhD Student 

Anne Maillard, Technician 

Osiris Marroquin Belaunzaran, PhD Student 

Roberto Mastroeni, Scientific Collaborator 

Vivianne Padrun, Chief Technician 

Fabienne Pidoux, Technician 

Emilda Pino, PhD Student 

Katarzyna Piorkowska, PhD Student 

Cédric Raoul, Postdoctoral Fellow 

Christel Sadeghi, Technician 

Bernard Schneider, Senior Scientist 

Veronica Setola, Postdoctoral Fellow 

Christopher Towne, PhD Student 

Romain Zufferey, Senior Scientist 

INTRODUCTION 

The main focus of the Laboratory of Neurodegenerative Studies is to develop gene therapy 

approaches for the treatment of neurodegenerative diseases such as Parkinson’s disease, Alzheimer’s 

disease and amyotrophic lateral sclerosis. Our laboratory is also implicated in the development of new 

animal models based on virus-mediated overexpression or silencing of genes involved in 

neurodegenerative diseases. For both gene therapy and development of models, viral vectors such as 

lentivirus and adeno-associated virus are produced and used in our laboratory. For therapeutic purposes, 

the technique of genetically engineered encapsulated cells allowing the localized secretion of various 

proteins as well as drug-testing are also widely implemented. The functional effects are characterized 

through the use of a wide variety of techniques including behavioural assessment, in vivo imaging 

techniques, morphological analysis and biochemical measurements. 

DESCRIPTION OF RESEARCH PROJECTS IN 2007 

- To generate genetic models of Parkinson’s (PD) and Alzheimer’s (AD) diseases using viral vectors 

expressing mutated forms of human genes 

- To evaluate the mechanisms of toxicity and aggregation in vivo of amyloidogenic proteins in the central 

nervous system 

- To assess various therapeutic approaches (using viral vectors, encapsulation technique or by drugtesting) 

in genetically-based animal models of neurodegenerative disorders 

- To test the silencing of mutated human forms of superoxide dismutase 1 (SOD1) as a therapeutic 

approach in animal models of amyotrophic lateral sclerosis (ALS) using various routes of administration

- To characterize the beneficial effect of the neurotrophic factor glial cell line-derived neurotrophic factor 

(GDNF) using the cell encapsulation technique in animal models of PD 

- To develop and characterize new cell lines to optimize the cell encapsulation technique for clinical 

applications 

- To design new viral constructs using inducible promoters to allow the reversibility of transgene 

expression 

MAIN RESULTS OBTAINED IN 2007 

- Lentiviral vectors have been validated as potential valuable gene transfer tools for midbrain 

dopaminergic neurons in both rats and mice (Déglon et al. 2000; Bensadoun et al. 2000) 

- Lentiviral vectors carrying protective genes have been successfully tested in murine models of 

motoneuron diseases (Azzouz et al. 2000; Hottinger et al 2000; Guillot et al. 2004) 

- Neurodegeneration in primate models of Parkinson’s disease have been prevented by lentiviral vector 

delivery of GDNF (Kordower et al. 2000) 

- Development of cells and tools to improve cell encapsulation technique (Schneider et al. 2001/2003; 

Rinsch et al. 2001; Sommer et al. 2002; Schwenter et al. 2003/2004) 

- Lentiviral vectors carrying protective genes have been successfully used in rodent to mimic or treat 

animal models of Huntington’s disease (Pereira de Almeida et al. 2001/2002; Bensadoun et al. 2001; 

Régulier et al. 2002; Zala et al. 2004; Perrin et al. 2007) 

- Development of a rat lentiviral-based model of Parkinson’s disease using synuclein and therapeutic 

investigations (Lo Bianco et al. 2002/2004) 

- Lentiviral-mediated RNA interference (Abbas-Terki et al. 2002) 

- Wld s -mediated protection of dopaminergic fibers in an animal model of Parkinson disease (Sajadi et al. 

2004) 

- Effect of lentiviral-mediated silencing of SOD1 on disease onset and progression in a mouse model 

of ALS (Raoul et al. 2005/2006) 

- Conditional gene expression and knockdown in vivo using viral vectors (Szulc et al. 2006) 

- Transient striatal delivery of GDNF via encapsulated cells leads to sustained behavioral improvement in 

a bilateral model of Parkinson disease (Sajadi et al. 2006) 

2006-2007 PUBLICATIONS 

B.L. Schneider, C.R. Seehus, E.E. Capowski, P. Aebischer, S.-C. Zhang, C.N. Svendsen. Overexpression 

of α-synuclein in human neural progenitors leads to specific changes in fate and 

differentiation. Hum Mol Genet, 16:651-666, 2007 

P. Aebischer, A.C. Kato. Playing defense against Lou Gehrig’s disease. Scientific American, November, 

86-93, 2007 

S. Palfi, E. Brouillet, B. Jarraya, J. Bloch, C. Jan, M. Shim, F. Condé, X.-J. Li, P. Aebischer, Ph. Hantraye, 

N. Déglon. Expression of mutated huntingtin fragment in the putament is sufficient to produce abnormal 

movement in non-human primates. Mol Ther, 15:1444-1451, 2007 

Consiglio, S. Martino, D. Dolcetta, G. Cusella, M. Conese, S. Marchesini, G. Benaglia, L. Wrabetz, A. 

Orlacchio, N. Déglon, P. Aebischer, G. M. Severini, C. Bordignon. Metabolic correction in 

oligodendrocytes derived from metachromatic leukodystrophy mouse model by using encapsulated 

recombinant myoblasts. J Neurol Sci, 255:7-16, 2007 

M. Suzuki, J. McHugh, C. Tork, B. Shelley, S.M. Klein, P. Aebischer, C.N. Svendsen. GDNF secreting 

human neural progenitor cells protect dying motor neurons, but not their projection to muscle in a rat 

model of familial ALS. PLoS ONE, 8:e689, 2007 

V. Perrin, E. Régulier, T. Abbas-Terki, R. Hassig, E. Brouillet, P. Aebischer, R. Lüthi-Carter, N. Déglon. 

Neuroprotection by Hsp104 and Hsp27 in lentiviral-based rat models of Huntington’s disease. Mol Ther, 

15:903-911, 2007 

M. Wiznerowicz, J. Jakobsso, J. Szulc, S.Liao, A. Quazzola, F. Beermann, P. Aebischer, D. Trono. 

The Krab repressor domain can trigger de novo promoter methylation during mouse early embryogenesis. 

J Biol Chem, 282 : 34535-34541, 2007 

E.E. Capowski, B.L. Schneider, A.D. Ebert, C.R. Sehus, R. Zufferey, P. Aebischer, C. Svensen. 

Lentiviral vector-mediated genetic modification of human neural progenitor cells for ex-vivo gene therapy. 

J Neurosci Meth, 163 : 338-349, 2007

J. Szulc, P. Aebischer. Conditional gene expression and knockdown using lentivirus vectors encoding 

shRNA. Methods in Molecular Biology, 434 : 291-309, 2007 

Szulc, J., Wiznerowicz, M., Sauvain, M.O., Trono, D., and Aebischer, P. (2006). A versatile tool for 

conditional gene expression and knockdown. Nat. Methods. 3(2): 109-116 

Raoul, C., Buhler, E., Sadeghi, C., Jacquier, A., Aebischer, P., Pettmann, B., Henderson, C.E., and 

Haase, G. (2006). Chronic activation in presymptomatic amyotrophic lateral sclerosis (ALS) mice of a 

feedback loop involving Fas, Dax, and FasL. Proc. Natl. Acad. Sci. USA. 103(15): 6007-6012 

Raoul, C., Barker, S.D., and Aebischer, P. (2006). Viral-based modelling and correction of 

neurodegenerative diseases by RNA interference. Gene Ther. 13(6): 487-495 

Sajadi, A., Bensadoun, J.C., Schneider, B.L., Lo Bianco, C., and Aebischer, P. (2006). Transient striatal 

delivery of GDNF via encapsulated cells leads to sustained behavioral improvement in a bilateral model of 

Parkinson disease. Neurobiol. Dis. 22(1): 119-129 

Blanco-Bose, W.E., Schneider, B.L., and Aebischer, P. (2006). Inducing tolerance to a soluble foreign 

antigen by encapsulated cell transplants. Mol. Ther. 13(2): 447-456 

Ridet JL, Bensadoun JC, Deglon N, Aebischer P, Zurn AD. (2006). Lentivirus-mediated expression 

of glutathione peroxidase: neuroprotection in murine models of Parkinson’s disease. Neurobiol. 

Dis. 21(1): 29-34 

Pardo, R., Colin, E., Régulier, E., Aebischer, P., Deglon, N., Humbert, S., and Saudou, F. (2006). 

Inhibition of calcineurin by FK506 protects against polyglutamine-huntingtin toxicity through an increase of 

huntingtin phosphorylation at S421. J. Neurosci. 26(5): 1635-1645 

Modeling of Parkinson disease by over-expression of pathogenic proteins in the rat substantia nigra: protein 

aggregation and neurotoxicity in response to a phosphorylation mutant of human α-synuclein 

(Azeredo da Silveira Lajaunias S. et al., submitted) 


BLANKE LAB 

Olaf Blanke 

Tenure Track Assistant Professor 


http://lnco.epfl.ch 

TEAM MEMBERS 

Shahar Arzy, PhD Student 

Jane Aspel,Visiting Postdoctoral Fellow 

Christelle Bachofner, Visiting Stud./Research Assist. 

Sebastian Dieguez, PhD Student 

Pär Halje, PhD Student 

Silvio Ionta, Visiting postdoc 

Oliver Kannape, Visiting Stud./Research Assist. 

Bigna Lenggenhager, PhD Student 

Christophe Lopez, Postdoctoral Fellow 

Manuel Mercier, PhD Student 

Michael Mouthon, Undergraduate (MA)-Student 

Nate Newby, Engineer 

Leila Overney, Postdoctoral Fellow 

Caroline Rheiner, Administrative Assistant 

Jakob Scherer, Undergraduate (MA)-Student 

Lars Schwabe, DFG Postdoctoral Fellow 

Tej Tadi, PhD Student 

INTRODUCTION 

Research at the Laboratory of Cognitive Neuroscience is carried out by a multidisciplinary team of 

biologists, psychologists, medical doctors, physicists, engineers and computer scientists. 

We focus our investigations on the functional and neural mechanisms of body perception corporeal 

awareness and self consciousness. Projects rely on the investigation of healthy subjects as well as 

neurological patients (who suffer from selective neurocognitive deficits and illusions) by combining 

psychophysical and cognitive paradigms with state of the art neuroimaging techniques such as intracranial 

EEG surface EEG fMRI and Virtual Reality. 

DESCRIPTION OF RESEARCH PROJECTS AND MAIN RESULTS OBTAINED IN 2007 

With several major publications our research has elucidated how bodily self-consciousness relates to 

multisensory global bodily processing and brain activation in temporo-parietal and extrastriate cortex. This 

included studies in neurological patients and in healthy participants. Our interdisciplinary expertise - 

bridging cognitive neurology, experimental epileptology, intracranial electrophysiology, experimental 

psychology and neuroimaging - has recently been extended to engineering-based approaches to 

cognition building a virtual reality (VR) neuroimaging platform with a portable 256 channel EEG system 

(VR-EEG). This VR-EEG platform allows us to carry out cognitive experiments in highly realistic, 

ecologically valid environments that close the perception-action loop while the participants’ brain activity 

(and soon also of brain damaged neurological patients) is continually monitored. Next to studying the 

neural mechanisms of bodily self consciousness experimentally we expect this novel technological 

amalgam to also become a key research technique in the larger field of the cognitive neurosciences, as 

well as the adjacent fields of virtual reality and presence research. Key collaborations for projects on this 

VR platform have been established locally at EPFL as well as with leading European computer scientists. 


Arzy S, Mohr C, Michel CM, Blanke O. (2007) Duration not strength of TPJ activation predicts schizotypy. 

NeuroImage 35: 326-333 

Lenggenhager B, Tadi T, Metzinger T, Blanke O. (2007a) Video ergo sum. Manipulating bodily selfconsciousness. 

Science 317: 1096-1099. Editorial/News of the Week in the issue Science (2007) 317: 

1020-1021 

Lenggenhager B, Lopez C, Blanke O. (2007b) Influence of galvanic vestibular stimulation on egocentric 

and object-based mental transformations. Exp Brain Res. (2008) 184: 211-221. Epub 2007 Aug. 24 

Brooks A, Van der Zwan R, Billard A, Petraska B, Clarke S, Blanke O (2007) Auditory motion influences 

biological motion perception. Neuropsychologia 45: 523-530 

Blanke O, Arzy S, Overney L (in press) Deficient mental own-body imagery in a neurological patient with 

out-of-body experiences due to cervical spinal cord injury. Cortex. 2008 [Epub ahead of print]

Blanke O, Adriani M, Brooks A, Mercier M, Spinelli L, Lavanchy L, Safran AB, Landis T (2007) Three 

distinct types of deficient form-from-motion perception following unilateral posterior brain damage. 

Neuropsychologia 45: 644-653 

Fischer C, Overney L, Fauve X, Blanke O, Rhyner M, Herzog M, Bourban P, Månson JA (2007) What 

mechanical and dynamic properties should alpine skis possess Ratings by advanced and expert skiers. 

J Sports Sci 19:1-10 

Arzy S, Seeck M, Spinelli L, Ortigue S, Blanke O. (2006) Induction of an illusory shadow person. Nature 

443: 287 

Arzy S, Thut G, Mohr C, Michel CM, Blanke O. (2006) Neural correlates of embodiment. Distinct 

contributions of temporo-parietal junction and extrastriate body area. J Neurosci 26: 8074-8081 

Brugger P, Regard M, Blanke O, Landis T. (2006) Polyopic heautoscopy. Cortex 42:666-674 

Arzy S, Petit L, Landis T, Blanke O (2006) Neural mechanisms of embodiment. asomatognosia due to 

premotor cortex damage. Arch Neurol 63:1022-1025 

Mohr C, Blanke O, Brugger P (2006) Perceptual aberrations impair mental own body transformations. 

Behavioural Neuroscience 120: 528-534 

Ortigue S, Landis T, Megevand P, Blanke O. (2006) Representational neglect for personal and 

extrapersonal space: A double dissociation. Neurology 66: 1414-1417 

Seeck M, Pegna AS, Seghier M, Ortigue S, Khateb A, Spinelli L, Lazeyras F, Blanke O, Deonna, T, 

Landis T, Villemure JG. (2006) Cortical language localization: Is fMRI superior to electrical cortical 

stimulation Neurology 66: 592-594 


FRAERING LAB 

TEAM MEMBERS 

Lorene Aeschbach, Technician 

Matthias Cacquevel, Postdoctoral Fellow 

Charlotte Egger, Postdoctoral Fellow 

Jemila Houacine, PhD Student 

Marie-Isabelle Magold, PhD Student 

Fabien Ruef, Research Assistant 


Fang Wu, Postdoctoral Fellow 

Patrick Fraering 


since August 2007 

Head of Lab (PI) 

http://fraering-lab.epfl.ch 

INTRODUCTION 

The Laboratory of Molecular and Cellular Biology of Alzheimer’s Disease is focusing on 

understanding the molecular mechanisms that lead to Alzheimer’s disease with the aim of identifying new 

therapeutic targets to safely treat the disease by using both genomic and proteomic approaches. 


Alzheimer’s medications approved by the U.S. Food and Drug Administration (FDA) may temporarily delay memory 

decline for some individuals, but none of the currently approved drugs is known to stop the underlying degeneration of 

brain cells. Accelerating insight into the biology of the disease, including a detailed understanding of the biochemistry of γ- 

secretase (which is directly implicated in the production of the amyloidogenic Aβ peptides), may offer promising targets for 

a new generation of treatments to prevent, slow or even reverse damage to nerve cells. 

Purification and characterization of Human γ-secretase 

γ-Secretase is a protein complex composed of four integral membrane proteins (presenilin (PS), Nicastrin, Pen-2, and 

Aph-1), with presenilin constituting the catalytic component and the other 3 proteins acting as necessary cofactors. 

Because prokaryotic systems are not appropriate for the overexpression of physiological γ-secretase for structural 

studies, we purified intact, proteolytically active γ-secretase complexes from Chinese hamster ovary (CHO) cells that 

stably over-express human PS1, Aph-1 and Pen-2 in the presence of high levels of endogenous NCT (designated γ-30 

cells). 

Three dimensional structure of γ-Secretase 

Because γ-secretase is a complex enzyme that contains at least 18 transmembrane domains, crystallographic 

approaches are difficult and remote. Thus, we used electron microscopy (EM) and single particle image analysis on the 

purified enzyme to generate the first 3D reconstruction of γ-secretase. We found that purified, active γ-secretase is an 

elongated globular structure, with the longest dimension being 120A° (in the membrane) and the other two dimensions 

perpendicular to the long axis being about 70-80 A° each. A cut open view (Fig. below) revealed the most dramatic 

feature of the structure being the presence of a low-density central chamber. The shape of the chamber is irregular, with 

a diameter of 20-40 A°. At the display threshold, we observe two openings to the interior chamber: one of 20 A° size 

(designated H1) facing up toward the exterior of the cell, and the other about 10 A° in size (designated H2) facing down 

toward the cytoplasm. 

3D structure of the γ-secretase complex. (A) A cut-open view of γ-secretase from the side reveals a large central chamber, one 

opening (H1) facing up toward the exterior of the cell, and one (H2) facing down toward the cytoplasm. Two weak-density lateral 

regions are labeled with asterisks. (B) Side views generated by rotating the map around a vertical (top) and a horizontal axis 

(bottom).

The most enigmatic feature of γ-secretase and other intramembrane proteases is their location within the 

hydrophobic environment of the membrane and their requirement for water molecules to accomplish 

peptide bond hydrolysis. How γ-secretase releases its two cleavage products into distinct subcellular 

compartments has also been mysterious. Our 3D structure of γ-secretase provides plausible explanations 

for these questions. The observed interior chamber and apical and basal pores would allow the entry of 

water molecules and their sequestration from the lipid surround by the proteinaceous microenvironment 

provided by the many transmembrane domains. The two thin-density regions in the transmembrane 

portion may represent sites which could be opened up transiently to enable entrance of the α-helically 

conformed substrates, i.e., the TMDs of various single transmembrane proteins (step I = substrate 

binding). After a substrate (e.g., C99 of APP or the analogous N∆E fragment of Notch) enters the 

proteinaceous central chamber and undergoes hydrolysis by the two aspartate-containing catalytic site in 

PS (step II = substrate entrance/cleavage), the cleavage product that includes the extracellular half of the 

substrate’s TMD (e.g., Aβ or Np3) could be released through the H1 channel to the extracellular surface, 

whereas the product that includes the cytoplasmic half of the substrate’s TMD plus the intracellular 

domain (e.g., AICD or NICD) could be released through the H2 channel to the cytoplasm (step III = 

products release). 

Model for intramembrane processing of membrane proteins. The 

membrane-bound 99-residue C-terminal fragment of amyloid precursor 

protein (APP-C99) serves as a substrate for γ-secretase, which catalyzes an 

unusual proteolysis within the transmembrane region to generate the toxic 

amyloid-beta peptides (Aβ) and release the APP intracellular domain 

(AICD). 

High-resolution crystal structure of Human γ-secretase 

The limited amount of purified γ-secretase that can be produced using currently available cell lines and 

procedures has prevented the achievement of a high-resolution crystal structure by X-ray crystallography 

or 2D crystallization. We recently generated and characterized a new mammalian cell line (S-20) that 

overexpresses strikingly high levels of γ-secretase (~4-5-fold higher in the new S-20 cells than in our 

previously described γ-30 cells, and ~17-fold higher in the S-20 cells than in the untransfected parental 

CHO cells). We then used these cells to develop a rapid protocol for the high-grade purification of 

proteolytically active γ-secretase. In conclusion, the new S-20 cell line combined with our rapid protocol for 

scaling up the production of active and homogenous γ-secretase particles represents a necessary and 

significant step towards new biochemical and structural insights of this biologically and therapeutically 

important protease.

γ-Secretase substrate selectivity 

γ-Secretase substrates including APP and Notch are involved in many crucial physiological functions such 

as the regulation of the immune system, memory, and synaptic plasticity. Thus, a central concern about 

inhibiting γ-secretase to lower Aβ production in AD is that this should also interfere with Notch processing 

and lead to severe toxicity because of interference with cell differentiation. Indeed, significant adverse 

effects of γ-secretase inhibitors caused by blocking Notch signaling have been described in preclinical 

animal studies. To chronically prevent the accumulation of Aγ deposits by inhibiting γ-secretase without 

adversely affecting its other physiological functions, it remains a major goal to identify γ-secretase 

inhibitors that discriminate between APP and the processing of Notch. 

We have identified several compounds that regulate the cleavage specificity of γ-secretase. Whatever the 

precise biochemical mechanism, our findings are pharmacologically relevant and could have major 

therapeutic implications. Apparently, the γ-secretase complex can be directly affected in a way that allows 

selective inhibition of Aγ production without interfering with Notch proteolysis. Thus, the disturbing specter 

of Notch-associated toxicities previously reported upon in vivo administration of γ-secretase inhibitors may 

be avoidable, making this protease a much more attractive therapeutic target for the prevention and/or 

treatment of AD. 


Vlado K. Lazarov*, Patrick C. Fraering*, Zhiqiang Chen, Wenjuan Ye, Michael S. Wolfe, Dennis J. Selkoe 

and Huilin Li. Electron microscopic structure of purified, active γ-secretase reveals an aqueaous 

intramembrane chamber and two pores. Proc Natl Acad Sci USA, 2006;103:6889-6894. * The two 

authors participated equally to this work 

Patrick C. Fraering. Structural and Functional Determinants of γ-Secretase, an Intramembrane Protease 

Implicated in Alzheimer's Disease, Current Genomics, Volume 8, Number 8, December 2007 


GERSTNER LAB 

Wulfram Gerstner 



Double appointment in the School of 

Computer & Communication Sciences 

& in the School of Life Sciences 

http://lcn.epfl.ch 

TEAM MEMBERS 

Laurent Badel, PhD Student 

Claudia Clopath,PhD Student 

Nicolas Fremaux, PhD Student 

Guillaume Hennequin,PhD Student 

Vincent Hirschi, Scientific Assistant 

Gediminas Luksys,PhD Student 

Nicolas Marcille,PhD Student 

Chantal Mellier,Administrative Assistant 

Eilif Muller, Postdoctoral Fellow 

Richard Naud, PhD Student 

Denis Sheynikhovich,Postdoctoral Fellow 

Christian Tomm, PhD Student 

Eleni Vasilaki,Postdoctoral Fellow 

Lorric Ziegler, PhD Student 

INTRODUCTION 

The activities at the Laboratory of Computational Neuroscience focus on the following questions 

centered around temporal aspects of information processing in the brain. 

Models of spiking neurons. In contrast to most artificial neural networks, real neurons 

communicate with short pulses. How could the brain use pulse coding for information 

processing What are the dynamical properties of networks of spiking neurons 

Spike-timing dependent learning rules. Recent experiments show that the change of a 

synaptic weight from a neuron i to a neuron j depends on the relative timing of the pulses of 

neurons i and j. What are the computational consequences of such asymmetric learning rules 

How can we model these changes in an efficient way How can we stabilize memories formed by 

synaptic changes 

Spatial Representation and Models of the Hippocampus. Neurons in the hippocampus of the 

rat show activity that depends on the spatial location of the animal. What could be the use of 

spatial representations for navigation How can we understand place fields from visual input and 

path integration How can learning be incorporated in spatial representations Can complex 

‘cognitive’ navigation be understood from simple principles 


Models of spiking neurons 

More than 200 labs around the world routinely use integrate-and-fire type neuron models as a basis for 

network simulation or mathematical analysis. We wanted to check whether this class of models is a valid 

description of neuronal behaviour. To this end, we compared simple spiking neuron models of the 

integrate-and-fire type with experimental measurements (made available to us through collaborations 

within the BMI and outside BMI) on pyramidal neurons in slices during injection of time dependent 

currents (current clam) or conductances (dynamic clamp). Our results (Jolivet et al., 2006) show that 

these simple neuron models can predict spike times of real neurons with a precision of 2 ms and 

subthreshold voltage traces with 2mV precision, thus justifying a posteriori existing models. Moreover we 

have proposed, based on these experiments, variants of simple neuron models that include refractoriness 

or adaptation (Brette and Gerstner, 2005; Badel et al. 2008).

Spike-timing dependent learning rules 

We have been involved in models of Spike-timing-dependent plasticity since 1993, even well before the first 

experimental results were published. During recent years we have tried to adapt the models to better describe 

experimental facts, in particular the fact that the amount of potentiation depends on the frequency of spike pairings, 

and not only the number of pairs (Pfister and Gerstner, 2006). Moreover, we have asked how models of Spike- 

Timing-Dependent Plasticity can explain receptive field formation and memory and found an interesting connection 

of spiking models to the classical model of Bienenstock-Cooper-Munro (Toyoizumi et al. 2005). 

Spatial representation and Models of the hippocampus 

Rats use different navigation strategies depending on the type of input and the task paradigm. We have used our 

model of hippocampal place cells and reinforcement learning to account for published experimental data on Morris 

Water maze navigation with fixed or random start conditions, or food relocalisation in rectangular boxes and 

connected these behavioural findings via modelling with electrophysiological findings on grid cells and place cells 

(Arleo and Gerstner, 2000; Chavarriaga et al. 2005). 


M.H. Herzog and M. Esfeld and W. Gerstner (2007). Neural Networks 20:1054-1056 

T. Toyoizumi, J.-P. Pfister, K. Aihara, and W. Gerstner (2007). Optimality Model of Unsupervised Spike- 

Timing Dependent Plasticity: Synaptic Memory and Weight Distribution Neural Computation, 19: 639- 

671 

C. Clopath, R. Jolivet, A. Rauch, H.-R. Lüscher and W. Gerstner (2007). Predicting neuronal activity with 

simple models of the threshold type: Adaptive Exponential Integrate-and-Fire model with two 

compartments. Neurocomputing 70: 1668-1673 

Pfister, J.P. and Gerstner, W. (2006).Triplets of Spikes in a Model of Spike Timing-Dependent Plasticity. 

J. Neurosci., 26: 9673 – 9682. 

Pfister, J.P., Toyoizumi, T., Barber, D. and Gerstner, W. (2006). Optimal Spike-Timing Dependent 

Plasticity for Precise Action Potential Firing in supervised learning. Neural Computation 18:1309 – 1339 

Pfister, J.P. and Gerstner, W. (2006). Beyond Pair-Based STDP: a Phenomenological Rule for Spike 

Triplet and Frequency Effects. Available from: NIPS*2005 Online papers http://books.nips.cc/nips18.html. 

IN: Advances in Neural Information Processing Systems 18}, Y. Weiss and B. Schölkopf and J. Platt, MIT 

Press, Cambridge, pp 1083 – 1090 

Richardson, M.J.E. and Gerstner, W. (2006).Statistics of subthreshold neuronal voltage fluctuations due to 

conductance-based synaptic shot noise Chaos 16:026106 

Jolivet, R., Rauch, A.,Lüscher, H.R. and Gerstner, W. (2006). Integrate-and-Fire models with adaptation are good 

enough Available from: NIPS*2005 Online papers http://books.nips.cc/nips18.html. IN: Advances in Neural 

Information Processing Systems 18}, Y. Weiss and B. Schölkopf and J. Platt,MIT Press, Cambridge, pp. 595 – 602 

Jolivet, R., Rauch, A., Lüscher, H.R. and Gerstner, W. (2006). Predicting spike timing of neocortical 

pyramidal neurons by simple threshold models, Journal of Computational Neuroscience 21:35 – 49 

Aviel, Y. and Gerstner, W.(2006).From spiking neurons to rate models: a cascade model as an 

approximation to spiking neuron models with refractoriness. Phys. Rev. E 73, 051908 

Badel, L., Gerstner, W. and Richardson, M.J.E. (2006). Dependence of the spike-triggered average 

voltage on membrane response properties, Neurocomputing, Volume 69, 1062 – 1065

HADJIKHANI GROUP 

TEAM MEMBERS 

Anthony Lissot, Postdoctoral Fellow 

Karine Metrailler, Research Coordinator 

Britt Russo, PhD Student 

Nils Rettby, Master Student 


Nouchine Hadjikhani, PhD 

SNSF Professor, Group Leader 

http://bmi.epfl.ch/ 

INTRODUCTION 

The theme of our research is the neuroanatomical bases of emotional, social and cognitive difficulties in 

autism. To address these questions, we use behavioral data acquisition as well as anatomical and 

functional brain imaging in young adults with high functioning autism or Asperger syndrome. 


We are in particular interested in trying to find biomarkers of autism and in exploring whether cognitive 

behavioral training may induce brain plasticity together with improvement in symptomatology. 

2007 PUBLICATIONS 

DaSilva AF, Granziera C, Snyder J, Hadjikhani N. Thickening in the Somatosensory Cortex of Migraine 

Patients. Neurology 2007;69:1990-1995 

Vincent M, Hadjikhani N. Migraine aura and related phenomena: beyond scotomata and scintillations. 

Cephalagia 2007;27(12):1368-1377 

Whitcher B, Wisco JJ, Hadjikhani N, Tuch DS. Statistical Group Comparison of Diffusion Tensors via 

Multivariate Hypothesis Testing. Magnetic Resonance in Medicine 2007;57:1065-1074 

Vincent M, Hadjikhani N. The cerebellum and migraine. Headache 2007;47:820-833 

DaSilva AF, Granziera C, Snyder J, Tuch DS, Vincent M, Hadjikhani N. Interictal alterations of the 

trigeminal somatosensory pathway and PAG in migraine. Neuroreport 2007;18(4)301-305 

Hadjikhani N, Joseph RM, Snyder J, Tager-Flusberg H. Abnormal activation of the social brain during face 

perception in autism. Human Brain Mapping. 2007;28:441-449 


HERZOG LAB 

Michael Herzog 

Associate Professor 


http://lpsy.epfl.ch 

TEAM MEMBERS 

Kristoffer Aberg, PhD Student 

Marco Boi, PhD, Student 

Anne-Sylvie Crisinel, MA-Student 

Laure Dayer, Administrative Assistant 

Hermens Frouke, Postdoctoral Fellow 

Plomp Gijs, Postdoctoral Fellow 

Tom Otto, PhD Student 

Leila Overney, Postdoctoral Fellow 

Marc Repnow, Engineer 

Maya Roinishvili, Visiting Postdoctoral Fellow 

Johannes Rüter , PhD Student 

Toni Saarela. PhD Student 

Bilge Sayim, PhD Student 

Frank Scharnowski, PhD Student 

Ghose Tandra, Visiting Postdoctoral Fellow 

Elisa Tartaglia, PhD Student 

INTRODUCTION 

In the Laboratory of Psychophysics, we investigate basic mechanisms of visual information processing 

in human observers. 

Main topics of research are: feature binding and integration, contextual modulation, time course of 

information processing, and perceptual learning. Visual information processing is also investigated in 

schizophrenic patients and sportsmen. 

The main goal of our research is to characterize the interplay of spatial integration and temporal binding 

processes with the help of psychophysics, TMS, EEG, mathematical modelling, and clinical investigations. 


Perception is not immediate. Visual information processing usually takes a considerable time before a 

decision is made and a conscious percept is elicited. Recent results using TMS have shown that this 

period can be as long as 400ms even though stimuli were presented for a very short time (e.g. 60ms). 

Why so long We postulate that already the early visual brain performs much more complex processing 

than previously thought. Experimentally, we have shown evidence for non-retinotopic feature processing 

delicate timing in spatio-temporal masking and puzzling spatial effects in simultaneous masking. All these 

results challenge the usual descriptions of early visual information processing in terms of static spatial 

mechanisms such as lateral inhibition and pooling of information. On the other hand, further masking 

experiments have shown that most alternative temporal models fall short to explain even the temporal 

aspects of visual processing. Therefore, in order to understand the first 400 ms of visual information 

processing, we propose that spatial and temporal aspect of vision should not be split up into separate 

research areas but rather be studied and modeled together. 


Herzog M.H., Estfeld M., Gerstner W. (2007). Consciousness & the small network argument. 

Neural Networks 20, 1054-1056. (for commentaries see Taylor 2007a & 2007b) 

Bachmann T., Elliott M., Herzog M., Vorberg D. (2007). Visual perception in a snapshot. 

Psychological Research 71, 615-617 

Herzog M.H., Scharnowski F., Hermens F. (2007). Long lasting effects of unmasking in a feature fusion 

paradigm. Psychological Research 71, 653-658 

Scharnowski F., Hermens F., Herzog M.H. (2007). Bloch's law and the dynamics of feature fusion. 

Vision Research 47, 2444-2452 

Fischer C., Overney L.S., Fauve M., Blanke O., Rhyner H., Herzog M.H., Bourban P.E., Manson J.A. 

(2007). What static and dynamic properties should slalom skis posses Judgements by advanced and 

expert skiers. Journal of Sports Sciences 25(14), 1567-1576 

Otto T.U. (2007). Grouping based feature attribution in metacontrast masking. Advances in Cognitive 

Psychology 3(1-2), 107-109 

Hermens F., Ernst U. (2007). Visual backward masking: Modeling spatial and temporal aspects. 

Advances in Cognitive Psychology 3 (1-2), 93-105.

Herzog M.H. (2007). Spatial processing and visual backward masking. Advances in Cognitive 

Psychology 3(1-2), 85-92 

Ansorge U., Francis G., Herzog M.H., Ogmen H. (2007). Visual masking and the dynamics of human 

perception cognition and conciousness. A century of progress a contemporary synthesis and future 

directions. Advances in Cognitive Psychology 3(1-2), 1-8. 

Hermens F., Herzog M.H. (2007). The effects of the global structure of the mask in visual backward 

masking. Vision Research 3, 85-92 

Schutze C., Bongard I., Marbach S., Brand A., Herzog M.H. (2007). Collinear contextual suppression in 

schizophrenic patients. Psychiatry Research 15, 237-243 

Scharnowski F., Hermens F., Kammer T., Ogmen H., Herzog M.H. (2007). Feature fusion reveals slow 

and fast visual memories. Journal of Cognitive Neurosciences 19(4), 632-641 

Malania M., Herzog M.H., Westheimer G. (2007). Grouping of contextual elements that affect vernier 

thresholds. Journal of Vision Vol 7 No 2 Art 1 

Duangudom V., Francis G., Herzog M.H. (2007). What is the strength of a mask in visual metacontrast 

masking Journal of Vision Vol 7 No 1 Art 7 

Weiskopf N., Sitaram R., Josephs O., Veit R., Scharnowski F., Goebel R., Birbaumer N., Deichmann R., 

Mathiak K. (2007). Real-time functional magnetic resonance imaging: Methods and applications. 

Magnetic Resonance Imaging 25, 989-1003 

Otto T.U., Ogmen H., & Herzog M.H. (2006). The flight path of the phoenix-The visible trace of invisible 

elements in human vision. Journal of Vision, 6(10), 1079-1086 

Herzog M.H., Ewald K.R.F., Hermens F., Fahle M. (2006). Reverse feedback induces position and 

orientation specific changes. Vision Research, 46, 3761-3770 

Herzog M.H., Lesemann E., Eurich, C.W. (2006). Spatial interactions determine temporal feature 

integration as revealed by unmasking. Advances in Cognitive Psychology, 2, 77-85 

Otto T., Herzog M.H., Fahle M., Zhaoping L. (2006). Perceptual learning with spatial uncertainties. 

Vision Research, 46, 32233233 

Ogmen H., Otto T., Herzog M.H. (2006). Perceptual grouping induces non-retinotopic feature attribution in 

human vision. Vision Research, 46, 32343242 


LASHUEL LAB 

Hilal Lashuel 



http://nmnf.epfl.ch 

TEAM MEMBERS 

Tristan Bolmont, Postdoctoral Fellow 


Saviana Di Giovanni, Postdoctoral Fellow 

Farah El-Turk, PhD Student 

Bruno Fauvet, Master Student 

Valerie Grimminger, Postdoctoral Fellow 

Martial Mbefo Kamdem, Research Associate 

Hajer Ouertatani-Sakouhi, PhD Student 

Katerini Paleologou, Postdoctoral Fellow 

Asad Qureshi, PhD Student 

David Virtel, PhD Student 

Adrian Schmid, Postdoctoral Fellow 

INTRODUCTION 

The Laboratory of Molecular Neurobiology and Functional Neuroproteomics is working at the 

interace of chemistry and biology: 

Research efforts in the Lashuel’s laboratory cover the following topics: 

- Elucidating the structural basis of amyloid-associated toxicity in neurodegenerative diseases, 

including Alzheimer's, Parkinson's, and Huntington's disease 

- Understanding the role of quaternary structure in protein function and disease 

- developing novel chemical and physical approaches and tools to monitor and control protein 

misfolding and protein aggregation in vitro and in vivo 

- developing cellular models of neurodegeneration in Parkinson’s disease; 

- developing novel therapeutic strategies based on modulating protein aggregation and clearance 

- Exploiting amyloid fibril formation for constructing polypeptide materials with potential applications in 

biotechnology and medicine. 


Research efforts in our laboratory focus on understanding the role of protein aggregation, more 

specifically amyloid fibril formation, in the pathogenesis of neurodegenerative diseases, including 

Alzheimer's disease, Parkinson's disease, and Huntington disease. In particular, we are working on 

defining the biochemical mechanism of amyloid fibril formation of two amyloidogenic proteins, α-synuclein 

and amyloid- (Aβ), and how they contribute to each of their respective diseases, Parkinson's and 

Alzheimer's diseases. Using a multifaceted approaches that employ tools from chemistry, biophysics, 

structural biology, and molecular and cell biology, our group is working to elucidate the structural basis of 

amyloid toxicity in neurodegenerative diseases. A detailed understanding of the mechanism of amyloid 

fibril formation and its relation to disease pathology should contribute to our understanding of the 

mechanism of pathogenesis and the identification of therapeutic targets for treating and/or preventing 

these devastating diseases. 

We take a reductionist approach, focused on the structure of the various protein aggregates on the 

amyloid pathway and the dynamics of their interconversion in vitro, to establish potential links between 

protein aggregation in vitro and toxicity. An array of biophysical techniques are employed to probe in 

detail the quaternary (analytical ultracentrifugation, molecular electron microscopy, scanning electron 

microscopy) and tertiary (circular dichroism, fluorescence) structural changes associated with the 

conversion of these proteins from their normal state into β-sheet rich toxic aggregates, including low 

molecular weight oligomers, protofibrils and fibrils. We plan take advantage of genetic (e.g. autosomal 

dominant mutations that cause familial disease and haplotyes that are linked to risk) and pathologic 

findings to guide the design of our experiments.

In addition to mechanistic in vitro studies, we are focusing on developing screening approaches to identify 

drug-like molecule that can be used to perturb amyloid fibril formation and neurotoxicity in vitro and in 

vivo. In addition to providing potential drug candidate, this approach will identify drug-like molecules that 

could be used as tools "molecular probes" to elucidate the role of amyloid fibril formation in α-synuclein 

and Aβ pathogenesis in cell culture and in animal models of the disease. A detailed understanding of the 

mechanism of amyloid fibril formation and its relation to disease pathology should contribute to our 

understanding of the mechanism of pathogenesis and the identification of therapeutic targets for treating 

and/or preventing these devastating diseases. 


Mimna R., Camus M-S., Schmid A., Tuchscherer G., Lashuel HA*, Mutter M*. “Switch Peptides: 

Disruption of amyloid fibrils through controlled induction of β-sheet to α-helix transformation”. 

Angewandte Chemie, 2007, 46, 2681-2684 

Follmer, C, Romao L, Einsiedler C, Porto T, Alves-Lara F, Lashuel HA, Lansbury PT, Neto VM, Silva JL, 

and Foguel D. “ Dopamine affects the stability, hydration and packing of protofibrils and fibrils of wildtype 

and variants of alpha-synuclein”. Biochemistry, 2007, 46, 472-482 

Tuchscherer G., Chandravarkar A., Camus MS, Berard J., Schmid A., Bhubaneswar M, Murat K, Mimna 

R, Lashuel HA., Mutter M. “Switch peptides as folding precursors in self-assembling peptides and 

amyloid fibrillogenesis”. Biopolymers, 2007, 88, 2, 239-252 

Fredenburg RA., Rospigliosi C., Meray R., Kessler JC., Lashuel HA, Eliezer D., and Lansbury PT Jr. 

“The Impact of the E46K Mutation on the Properties of alpha-synuclein in its Monomeric and Oligomeric 

States”. Biochemistry, 2007, 46, 7107-7118 

Chafekar SM., Malda H., Merkx M., Meijer BW., Lashuel HA., Baas F., Scheper W*. “Coupling of KLVFF 

to dendrimers strongly potentiates inhibition of β-amyloid aggregation”. Chembiochem, 

2007 Oct 15;8(15):1857-64 

Lansbury PT* and Lashuel HA*. “A century-old debate on protein aggregation and neurodegeneration 

enters the clinic. Nature, 2006, 443, 774-779 

Lashuel HA* and Harald Hirling. “Rescuing defective vesicular trafficking protects against α-synuclein 

toxicity in cellular and animal models of Parkinson’s disease. ACS Chemical Biology, 2006, 1(7), 1, 

420–424 

Lashuel HA* and Lansbury PT*. "Are amyloid diseases caused by protein aggregates that mimic 

bacterial pore-forming toxins" Quarterly Review of Biophysics. 2006, 39 (2), 1-35 

Saucede L., Santos SD., Chandravarkar A., Mandal B., Murat K., Camus, M-S., Berard, J., Grouzmann, 

E., Adrian M., Dubochet J., Lopez J., Lashuel HA., Tuchscherer GT., Mutter M. “ “Switch Peptides: 

From Conformational Studies to Alzaheimer’s Disease”. CHIMIA, 2006, 60, 199-202 


LUTHI-CARTER LAB 

Ruth Luthi-Carter 



http://lngf.epfl.ch 

TEAM MEMBERS 


Meredith Dixon,Technician 

Ozgun Gokce,PhD Student 

Ana Jovicic, PhD Student 

Alexandre Kuhn,Postdoctoral Fellow 

Valerie Perrin,Postdoctoral Fellow 

Maria Rey,Technician 

Nikita Rudinskiy,PhD Student 

Heike Runne,PhD Student 

David Taylor, Postdoctoral Fellow 

INTRODUCTION 

A primary focus of the Functional Neurogenomics Laboratory is to understand the molecular bases for 

the loss of neuronal function in neurodegenerative diseases. Our studies are centered around diseaserelated 

perturbations of neurotransmitter signaling and transcription. 

One major emphasis of our current studies is the pathogenesis of Huntington's disease and other 

polyglutamine disorders. These diseases result from dominantly inherited trinucleotide expansion 

mutations. Despite the known origin of these disorders the disease course is currently intractable. Thus, a 

more detailed understanding of the disease process is urgently warranted. 

In parallel with our efforts to better understand and treat neurodegenerative illnesses, we consider what 

the perturbations observed in disease can reveal about the brain’s normal function. We are currently 

examining the contributions of particular individual and functionally related sets of molecules to 

neurotransmitter signaling and neuronal survival. 


Transcriptomic analysis of human Huntington’s disease (HD) brain 

Perturbations in transcription have been implicated as an essential pathogenic mechanism of Huntington’s 

disease and related disorders. Although predictions based on models of disease have been building for a 

number of years, the present study has provided the first opportunity to assess the validity of these 

hypotheses with bona fide disease samples. Using laser-capture microdissection combined with 

microarray analyses, we confirmed gene expression changes in HD-affected neurons at an mRNA/cell 

level. These analyses elucidated a novel regional specificity of disease-related mRNA changes and a 

prominent effect on neurotransmitter-related signaling processes. A manuscript describing this work was 

published in 2006 (Hodges et al., Hum. Mol Genet. 15:965-977). Additional studies examining progressive 

neuron-specific HD effects are ongoing. 

Modeling transcriptional dysregulation in HD mice 

Achieving a mechanistic understanding of disease and initiating preclinical therapeutic trials necessitate 

the study of huntingtin toxicity and its remedy in model systems. To allow the engagement of appropriate 

experimental paradigms, Huntington’s disease models need to be validated in terms of how they 

recapitulate a particular aspect of human disease. In order to examine transcriptome-related effects of 

mutant huntingtin, we compared striatal mRNA profiles from seven genetic mouse models of disease to 

that of postmortem human HD caudate using microarray analysis. Transgenic models expressing short N- 

terminal fragments of mutant huntingtin (R6/1 and R6/2 mice) exhibited the most rapid effects on gene 

expression, consistent with previous studies. Although changes in the brains of HD models expressing 

full-length mutant huntingtin took longer to appear, 15-month and 22-month CHL2 Q150/Q150 , 18-month 

Hdh Q92/Q92 and 2-year-old YAC128 animals also exhibited significant HD-like mRNA signatures. When the 

affected genes were compared across models, a robust concordance was observed. Importantly, changes 

concordant across multiple lines of mice were also in excellent agreement with the mRNA changes seen 

in human HD caudate. Although it was expected that the expression of full-length huntingtin transprotein 

might result in unique gene expression changes compared to those caused by expression of an N- 

terminal huntingtin fragment, no discernable differences between full-length and fragment models were 

detected. There was, however, an overall concordance between transcriptomic signature and disease 

stage. The combined analysis of mouse and human HD transcriptomes provides an important chronology 

of mutant huntingtin's gene expression effects.

These results of these were published in August 2007 (Kuhn et al., Hum. Mol Genet. 16:1845-1861). 

Mechanistic studies of mutant huntingtin's effects on gene expression are in progress. 

Common mechanisms of transcriptional dysregulation in polyglutamine disorders 

Neurodegenerative disorders resulting from expansion of polyglutamine repeats in proteins are a 

compelling context in which to understand neuronal transcriptional regulation. It has been shown that the 

polyglutamine expansion in such disease-causing proteins can lead to aberrant protein-protein 

interactions with multiple components of the transcriptional machinery of neuronal cells. In Huntington’s 

disease (HD), aberrant interaction partners include general transcription factors, chromatin remodeling 

factors, DNA-binding transcription factors, and co-activators and co-repressors. In cell and animal models 

of HD, pharmacological agents which affect various steps in transcriptional regulation have shown 

promise as candidate therapeutics. The causative mutation in spinocerebellar ataxia type 17 (SCA-17) 

has recently been determined to be a polyglutamine expansion in the TATA-binding protein, a widely 

utilized component of the basal transcriptional machinery. Given that SCA-17 and HD share common 

etiologic and pathologic features, we propose to perform detailed comparative analyses of their effects on 

neuronal gene expression. This project is being carried out in collaboration with the Institute of Genomics 

and Integrative Biology in Delhi as a part of the Indo Swiss Joint Research Programme. 

Neuron- and glia-specific gene expression 

The brain is a complex organ comprised of many sophisticated and heterogeneous cell types. In order to 

refine our understanding of the development, function, and dysfunction of these various cell populations, 

we need to understand their distinct molecular signatures. In addition to considering cell ratios and cellspecific 

gene expression in healthy neural tissue, it is important for understanding the cellular and 

molecular processes underlying brain diseases. In our laboratory, this issue has come to our attention in 

the context of neurodegenerative disease gene expression profiles, where dynamic changes in cell ratios 

often accompany the disease process. We have recently collected gene expression signatures of specific 

neural subtypes. We are now studying the promoter sequences of the corresponding genes in order to 

elucidate the mechanisms by which cell type-specific regulation is achieved. 

Identification of potential HD biomarkers 

The identification of biomarkers that can be used to track the progression of Huntington’s disease in a 

sensitive fashion would be a tremendous aid to therapeutic trials. Transcriptomic studies of brain tissues 

from HD patients and HD model systems demonstrate a large disease-related effect on gene expression. 

Therefore, measures of gene expression could be useful state markers for HD. We are working to identify 

candidate HD gene expression biomarkers in peripheral blood samples of human HD patients. A panel of 

several dozen candidate markers, including those encoded by a number of immune response and 

apoptotic pathway genes, has been recently testing. Quantitative real-time PCR assays showed that the 

expression of one of these mRNAs, IER3, correlates with disease stage (as described in Runne et al., 

2007 Proc. Natl. Acad. Sci. U.S.A. 104:14424-14429). 

Neuronal calcium sensors as regulators of neuronal signaling and survival 

EF-hand calcium binding proteins are known to be important mediators in brain functions including longterm 

plasticity, excitatory neurotransmission, transcription, and neuronal survival. However, the functions 

of the specialized neuronal calcium sensor (NCS) proteins and their role in the brains of higher 

vertebrates have been poorly defined to date. Hippocalcin is an NCS protein enriched in the medium spiny 

neurons of the striatum, and is downregulated in the caudate nucleus of patients with Huntington’s 

disease. We are conducting studies to examine the calcium-dependent role of hippocalcin in regulating 

neurotransmitter signaling and neuronal survival. This project is funded by the Swiss National Science 

Foundation. 

Use of HD differential expression data to identify novel neurotherapeutics 

We have employed microarray gene expression profiling to examine the cellular pathways disrupted by 

mutant huntingtin and other expanded polyglutamine proteins. These experiments have provided a new 

set of molecular targets for possible therapeutic intervention. We are currently determining whether 

individual polyglutamine-induced gene expression changes are contributory (i.e. they exacerbate disease 

progression) or protective (i.e. they curb disease progression). We are currently implementing genetic and 

pharmacologic strategies to distinguish between beneficial and detrimental changes in an in vitro model of HD. 

This project is supported in part by an FP6 European Training grant and an award from the Swiss TELETHON.

Modulation of sirtuins and other nutritionally accessible regulators of gene expression 

Decreasing neurodegeneration (increasing survival) of mature brain neurons is a rational strategy for 

improving cognitive health. Dietary compounds have shown a high potential for extending cellular 

longevity. One major mechanism of nutrition-related lifespan extension is the regulation of gene 

expression. Although diet-related benefits to neural function are unquestionable, there is astonishingly 

little data on the potential gene substrates of dietary effects in neuronal cells. 

In this project, we will explore whether dietary or pharmaolocgic modulation of sirtuins or other 

endogenous transcriptional regulators can improve neuronal function. This project currently receives 

support through the EPFL-Nestec Alliance.


Luthi-Carter, R. (2008) Huntington's and other polyglutamine diseases: many effects of single gene 

mutations. Drug Discov. Today: Dis. Mech. [doi:10.1016/j.ddmec.2007.10.002] 

Kuhn, A., Hodges, A., Strand., A., Hunter, J.M., Goldstein, D.R., Aragaki, A.K., Hughes, G., Sengstag, 

T., Kooperberg, C., Cha, J.-H.J., Hannan, A.J., Dunnett, S.B., Ferrante, R.J., Albin, R., Bates, G., 

Shelbourne, P., Detloff, P., Delorenzi, M., Augood, S.J., Faull, R.L.M., Olson, J.M., Jones, L. and 

Luthi-Carter, R. (2007) Mutant huntingtin's effects on striatal gene expresssion in mice recapitulate 

changes observed in human Huntington's disease brain and do not differ with mutant huntingtin length or 

wild-type huntingtin dosage. Hum. Mol. Genet. 16, 1845-1861 

Runne, H., Kuhn, A., Wild, E.J., Pratyaksha, W., Kristiansen, M., Isaacs, J., Régulier, E., Delorenzi, 

M., Tabrizi, S.* and Luthi-Carter, R.* (2007) Analysis of potential transcriptomic biomarkers for 

Huntington's disease in peripheral blood. Proc. Natl. Acad. Sci. U.S.A.. 104, 14424-14429 

Stack, E.C., Dedeoglu, A., Smith, K.M., Cormier, K., Kubilus, J.K., Bogdanov, M., Matson, W.R., Yang, L., 

Jenkins, B.G., Luthi-Carter, R., Kowall, N.W., Hersch, S.M., Beal, M.F., Ferrante, R.J. (2007) 

Neuroprotective effects of synaptic modulation in Huntington's disease R6/2 mice. J. Neurosci. 

27, 12908-12915 

Perrin, V., Régulier, E., Abbas-Terki, T., Hassig, R., Brouillet, W., Aebiseher, P., Luthi-Carter, R. and 

Déglon, N. (2007) Neuroprotection by Hsp104 and Hsp27 in lentiviral-based models of Huntington's 

disease. Mol. Therapy 15, 903-911 

Stack, E., Del Signore, S.J., Luthi-Carter, R., Soh, B.Y., Goldstein, D.R., Matson, S., Goodrich, 

S., Markey, A.L., Cormier, K., Hagerty, S.W., Smith, K., Ryu, H., Ferrante, R.J. (2007) Modulation of 

Nucleosome dynamics in Huntington's disease. Hum. Mol. Genet. 16, 1164-1175 

Hodges, A.H., Strand, A.D., Aragaki, A.K., Kuhn, A., Sengstag, T., Hughes, G., Elliston, L.A., Hartog, 

C., Goldstein, D.R. Thu, D., Hollingsworth, Z.R., Collin, F., Synek, B., Holmans, P.A., Young, 

A.B., Wexler, N.S., Delorenzi, M., Kooperberg, C., Augood, S.J., Faull, R.L., Olson, J.M., Jones, L., 

Luthi-Carter, R. (2006) Regional and cellular gene expression changes in human Huntington's disease 

brain. Hum. Mol. Genet. 15(6):965-977 

Jones, L. Goldstein, D.R., Hughes,G.P., Strand, A., Collin, F., Dunnett, S.B., Kooperberg, C.L., Aragaki, 

A., Olson, J.M., Augood, S.A., Faull, R.L.M., Luthi-Carter, R., Moskvina, V. and Hodges, A.K. (2006). 

Assessment of the relationship between pre-chip and post-chip quality measures for Affymetrix GeneChip 

expression data. BMC Bioinformatics 7:211 

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Genomics 87(2):200-207 


MAGISTRETTI LAB 

Pierre Magistretti 


Pierre Magistretti 


Joint Chair EPFL / UNIL-CHUV 


Co-Director BMI 

http://bmi.epfl.ch 

TEAM MEMBERS 

Igor Allaman, Senior Postdoctoral Fellow 

Cendrine Barrière, Technician 

Maxime Baud, MD/PhD Student 

Mireille Bélanger, Postdoctoral Fellow 

Sophie Burlet, Postdoctoral Fellow 

Julie Chenal, Postdoctoral Fellow 

Elsy Dunand, Technician 

Gabriele Grenningloh, Senior Scientist 

Renaud Jolivet, Postdoctoral Fellow 

Pascal Jourdain, Postdoctoral Fellow 

Sylvain Lengacher, Senior Postdoctoral Fellow 

Pierre Marquet, Senior Postdoctoral Fellow 

Maud Marti Favre, Technician 

Corinne Moratal, Technician 

Julia Parafita, PhD Student 

Hélène Perreten, PhD Student 

Jean-Marie Petit, Senior Postdoctoral Fellow 

Benjamin Rappaz, PhD Student 

INTRODUCTION 

The Laboratory of Neuroenergetics and Cellular Dynamics has two main lines of research: the 

principal one is to try to understand the cellular and molecular mechanisms of neurometabolic coupling, 

namely the processes by which appropriate energy substrates are delivered to neurons where and when 

they are active. Our studies ongoing now for two decades have identified the interactions between 

neurons and glial cells (astrocytes) as the basis of neurometabolic coupling. Elucidation of these 

mechanisms is essential to understand the basis of the signals detected by functional brain imaging 

techniques, which visualize changes in blood flow, glucose utilization or oxygen consumption in register 

with synaptic activity. We are also interested in understanding the bases of neurometabolic coupling in 

other aspects of brain function and dysfunction, such as learning and memory, the sleep-wake cycle, as 

well as neurodegeneration. Accordingly, we are now addressing the issue of "metabolic plasticity". Indeed, 

it is very likely that metabolic adaptations do occur in register with the functional and structural changes 

that occur during synaptic plasticity. We are currently studying transcriptionally-regulated adaptations in 

the level of expression of certain genes of brain energy metabolism in relation to neuronal plasticity as 

observed during learning, the sleep-wake cycle and certain pathological conditions such as 

neuroinflammation and neurodegeneration. 

The second line of research is represented by a neurophotonics project, which is implemented through a 

joint effort with the Advanced Photonics Laboratory at the STI Faculty, to develop a new type of 

microscope using different optical modalities. In particular we are centering our initial efforts in combining 

a novel optical method, digital holographic microscopy with fluorescence microscopy and 

electrophysiology, each one of these techniques providing unique information on neuronal structure and 

function. We are particularly interested in studying dynamic cellular processes such as those that are at 

the basis of neuronal plasticity. Indeed, digital holographic microscopy allows the non-invasive, on-line, 

three-dimensional visualization of cells with a spatial resolution in the order of the nanometer and a 

millisecond temporal resolution. 

Pierre Magistretti is also pursuing a theoretical work in collaboration with psychoanalysts, to explore the 

possible relevance of certain experimental findings in the neurosciences with psychoanalytical concepts. 

A particular emphasis is put on plasticity and basal brain energy utilization. 


Since the group has moved to the EPFL in 2005, the main focus of our research is the investigation of the 

molecular and cellular determinants that underlie the plasticity of neuron-glia metabolic coupling. We have 

now identified and begun to characterize at least three conditions in which the metabolic profile of the 

neuron-astrocyte metabolic coupling undergoes adaptations: synaptic plasticity underlying spatial 

learning, the sleep-wake cycle and exposure to a pro-inflammatory environment (cytokines and betaamyloid).

Metabolic plasticity during learning 

Regarding metabolic plasticity as a concomitant of synaptic plasticity that characterizes learning, we are 

well underway in the metabolic mapping, in terms of 2-deoxyglucose autoradiography, of the changes in 

glucose utilization that occur during a spatial learning task (eight-arm radial maze). Thus we have 

observed that the areas of increase in 2-DG utilization evolve over the eight-day learning period and 

during recall, thus providing a metabolic map of the areas in which changes in neuron-glia metabolic 

coupling are likely to occur. After completing the mapping phase which we are conducting with the aid of a 

new unbiased image-analysis and 3-dimensional reconstruction method that we have developed in 

collaboration with Prof Jean-Philippe Thiran from the signal processing laboratory at EPFL, we will 

perform laser capture microdissection in the microregions of interest and analyze by QRT-PCR the level 

of expression of a selected number of genes which we know are central to the neuron-glia metabolic 

coupling. We have already preliminary results indicating the feasibility of this approach. This project has 

the potential to contribute to identify the role of metabolic adaptations in plasticity and learning and to 

clarify the molecular and cellular nature of the mechanisms that underlie the changes in functional brain 

imaging profiles that have been observed in learning paradigms. 

Metabolic plasticity during the sleep-wake cycle 

Regarding metabolic plasticity during the sleep-wake cycle we are drawing on our initial observations 

indicating marked changes in the level of expression of a gene encoding for a key enzyme in glycogen 

metabolism, namely Protein Targeting to Glycogen (PTG). The level of expression of PTG, which 

regulates an astrocyte-specific process such as glycogen resynthesis, is indeed markedly increased by 

sleep deprivation, as is the activity of glycogen synthase, indicating that following sleep deprivation, the 

metabolic profile of the cortex is in a glycogen-synthesizing mode. We are currently exploring the effect of 

pharmacological agents that interfere with glycogen metabolism on sleep-wake cycle and sleep 

architecture. We have indeed set up a complete animal sleep laboratory at EPFL which is now fully 

operational. We are also undertaking an extensive regional analysis of the level of expression of a panel 

of selected genes which we know are key for neuron-glia metabolic coupling, following various types of 

sleep deprivation, namely pharmacological, behavioral and also using a new cage that we have 

developed which allows to produce conditions for non-stressful sleep fragmentation, a condition that more 

closely resembles human perturbations of sleep. 

Metabolic plasticity in response to a pro-inflammatory environment (Pro-inflammatory cytokines 

and beta-amyloid) 

Local alterations of brain energy metabolism and oxidative stress are features of neurodegenerative 

disorders, notably of Alzheimer’s disease (AD). Both amyloid peptide and inflammation mediators have 

been shown to play a significant role in AD pathogenesis. Considering the role of astrocytes in brain 

energy metabolism, we are interested to investigate the effects of pro-inflammatory cytokines (TNFα and 

Il-1ß) and beta-amyloid (Aß) on glucose metabolism in these cells. Using primary cultures of cortical 

astrocytes, we have found that pro-inflammatory cytokines and beta-amyloid, markedly modify, in a 

transcriptionally-regulated manner, the metabolic profile of astrocytes. Essentially a pro-inflammatory 

environment results in a marked increase in glucose utilization; however this "extra" glucose is neither 

stored as glycogen nor released as lactate, but is processed through the TCA cycle and in the pentose 

phosphate pathway (PPP). Modulation of PPP appears of particular interest as this is the key metabolic 

pathway for the generation of reducing equivalents (NADPH) which are essential factors for scavenging 

reactive oxygen species, known to be critically involved in neurodegeneration. These observations thus 

provide an initial link between perturbations of neuroenergetics with neurodegeneration. 

Regarding amyloid we have made the puzzling observation that its effects on energy metabolism are 

dependent on its state of aggregation and on internalization of the peptide by astrocytes. We intend to 

study the molecular and signaling mechanisms that couple internalization of a pathological protein, 

activation of the proteasome and induction of genes regulating energy metabolism. This line of research 

has, among other potential pathophysiogical implications, interesting ramifications to link the amyloid 

hypothesis of Alzheimer’s disease with the metabolic and functional brain imaging findings that 

characterize the disease.

Digital holographic microscopy (DHM) 

The DHM phase signal provides information about both cell morphology and the optical properties of the 

intracellular compartment. We have therefore developed a decoupling procedure that allows to obtain 

from the phase signals, separately information about cell morphology (volume, shape, nano-movements) 

and about the intracellular refractive index, which is mostly dependent on the intracellular protein 

concentration. By combining electrophysiological recordings with the decoupling procedure we have 

observed that neuronal activity induces a phase signal. In experiments performed on the HEK cell line, 

transfected to express specifically the GABAA receptor we have established a quantitative relationship 

between Cl - currents and the phase signals (phase-voltage curve analogous to current-voltage curve). 

Glutamate application to cultured neurons also elicits a receptor-specific phase signal which is due to 

water fluxes accompanying transmembrane ionic fluxes. 

An interesting development of this optical method will be to visualize activity-dependent phase signals to 

analyse the dynamics of network activity in vitro as the holographic approach allows to capture 

instantaneously the information across the network. 


Aubert A, Pellerin L, Magistretti PJ, Costalat R.(2007). A coherent neurobiological framework for functional 

neuroimaging provided by a model integrating compartmentalized energy metabolism. Proc Natl Acad 

Sci U S A. 104(10):4188-4193 

Granziera C, Thevenet J, Price M, Wiegler K, Magistretti PJ, Badaut J, Hirt L. (2007). Thrombin-induced 

ischemic tolerance is prevented by inhibiting c-jun N-terminal kinase. Brain Res. 1148:217-25 

Kovacs KA, Steullet P, Steinmann M, Do KQ, Magistretti PJ, Halfon O, Cardinaux JR. (2007) 

TORC1 is a calcium- and cAMP-sensitive coincidence detector involved in hippocampal long-term 

synaptic plasticity. Proc Natl Acad Sci U S A. 104(11): 4700-4705 

Laughton JD, Bittar P, Charnay Y, Pellerin L, Kovari E, Magistretti PJ, Bouras C. (2007). 

Metabolic compartmentalization in the human cortex and hippocampus: evidence for a cell- and regionspecific 

localization of lactate dehydrogenase 5 and pyruvate dehydrogenase. BMC Neurosci. 23 (8) 35 

Badaut J, Brunet JF, Petit JM, Guérin CF, Magistretti PJ, Regli L. (2007). Induction of brain 

aquaporin 9 (AQP9) in catecholaminergic neurons in diabetic rats. Brain Res. Nov 7; [Epub ahead of 

print] 

Colomb T., Montfort F., Kuhn J., Aspert N., Cuche E., Marian A., Charriere F., Bourquin S., Marquet P., 

Depeursinge C. (2006). Numerical parametric lens for shifting, magnification, and complete aberration 

compensation in digital holographic microscopy. J Opt Soc Am A Opt Image Sci Vis. 23 (12):3177-90 

Charriere F., Colomb T., Montfort F., Cuche E., Marquet P., Depeursinge C. (2006). Shot-noise influence 

on the reconstructed phase image signal-to-noise ratio in digital holographic microscopy. 

Appl Opt. 45(29):7667-73 

Montfort F., Colomb T., Charriere F., Kuhn J., Marquet P., Cuche E., Herminjard S., Depeursinge C. 

(2006). Submicrometer optical tomography by multiple-wavelength digital holographic microscopy. 

Appl Opt. 45 (32):8209-17 

Montfort F., Charriere F., Colomb T., Cuche E., Marquet P., Depeursinge C. (2006) Purely numerical 

compensation for microscope objective phase curvature in digital holographic microscopy: influence of 

digital phase mask position. J Opt Soc Am A Opt Image Sci Vis. 23 (11):2944-53 

Colomb T., Cuche E., Charriere F., Kuhn J., Aspert N., Montfort F., Marquet P., Depeursinge C. (2006). 

Automatic procedure for aberration compensation in digital holographic microscopy and applications to 

specimen shape compensation. Appl Opt. 45(5):851-63 

Charriere F., Kuhn J., Colomb T., Montfort F., Cuche E., Emery Y., Weible K., Marquet P., Depeursinge C. 

(2006). Characterization of microlenses by digital holographic microscopy. Appl Opt. 45(5):829-35 

Charriere F., Marian A., Montfort F., Kuehn J., Colomb T., Cuche E., Marquet P., Depeursinge C. (2006). 

Cell refractive index tomography by digital holographic microscopy. Opt Lett. 31(2):178-80 

Charrière F., Pavillon N., Colomb T., Depeursinge C., Heger T. J., Mitchell E. A. D, Marquet P. and 

Rappaz B. (2006). Living specimen tomography by digital holographic microscopy: morphometry of testate 

amoeba. Opt Exp. 14(16):7005-7013

Colomb T., Kuehn J., Charrière F., Depeursinge C., Marquet P., Aspert N. (2006). Total aberrations 

compensation in digital holographic microscopy with a reference conjugated hologram. 

Opt Exp. 14(10):4300-4306 

Kovacs K.A., Steinmann M., Magistretti P.J., Halfon O., Cardinaux J.R. (2006). C/EBPbeta couples 

dopamine signalling to substance P precursor gene expression in striatal neurons. J Neurochem. 

98(5):1390-9 

Morgenthaler F.D., Kraftsik R., Catsicas S., Magistretti P.J. Chatton J.Y. (2006). Glucose and lactate are 

equally effective in energizing activity-dependent synaptic vesicle turnover in purified cortical neurons. 

Neuroscience 141:157-65 

Chiry O., Pellerin L., Monnet-Tschudi F., Fishbein W.N., Merezhinskaya N., Magistretti P.J., Clarke S. 

(2006). Expression of the monocarboxylate transporter MCT1 in the adult human brain cortex. 

Brain Res. 1070:65-70 

Bondallaz P., Barbier A., Soehrman S., Grenningloh G., Riederer B.M. (2006.) The control of microtubule 

stability in vitro and in transfected cells by MAP1B and SCG10. Cell Motil Cytoskeleton 63:681-95 

Vega I.E., Hamano T., Propost J.A., Grenningloh G., Yen S.H. (2006). Taxol and tau overexpression 

induced calpain-dependent degradation of the microtubule-destabilizing protein SCG10. Exp Neurol. 

202:152-60 

Voria I, Hauser J., Axis A., Schenker M., Bichet S., Kuntzer T., Grenningloh G., Barakat-Walter I. (2006). 

Improved sciatic nerve regeneration by local thyroid hormone treatment in adult rat is accompanied by 

increased expression of SCG10. Exp Neurol. 197:258-67 

Confocal image of a mouse cortical astrocyte. 

Green fluorescence indicates Glial Fibrillary Acidic Protein (GFAP), a selective 

marker of the cytoskeleton of astrocytes. Mitochondria are labelled in red with the 

dye Mitotracker. The cell nucleus is labelled with the dye DAPI, producing a blue 

fluorescence. 


MARKRAM LAB 

Henry Markram 



Co-Director BMI 

http://bmi.epfl.ch/LNMC.html 

TEAM MEMBERS 

Katia Antoniello, Technician 

Debasree Banerjee, Student grant holder 

Flavien Beaud, Student-Assistant 

Thomas K. Berger, PhD Student 

Jean Philippe Boquete, Technician 

Alexandra Boussommier, Student Assistant 

Pierre Bou Fayssal, Student-Assistant 

Audrey Ducret, Technician Apprentist 

Christiane Debono, Administrative Assistant 

Luca Gambazzi, PhD Student 

Michele Giugliano, Postdoctoral Fellow 

Raphael Holzer, Postdoctoral Fellow 

Asif Muhammad Jan, PhD Student 

Georges Khazen, PhD Student 

Deborah La Mendola, Technician 

Delphine Langlet, Technician 

Jean-Vincent Le Bé, PhD Student 

Antoine Lecoultre, Technician Apprentist 

Tamara Merk, Technician Apprentist 

Rodrigo Perin de Campos, PhD Student 

Michele Pignatelli, PhD Student 

Plucinotta Matteo, Student-Assistant 

Imad Riachi, PhD Student 

Guillaume Ridoux, Student-Assistant 

Sandrine Romand, PhD Student 

Eulalie Sauthier, Student-Assistant 

Barry Sefton, Postdoctoral Fellow 

Guilherme Silva, PhD student 

INTRODUCTION 

The Laboratory of Neural Microcircuitry adopts a multidisciplinary approach to the structure and 

function of the neocortex. The neocortex constitutes nearly 80% of the human brain and is made of a 

repeating stereotypical microcircuit of neurons. This neural microcircuit lies at the heart of the information 

processing capability of the neocortex, the capability of mammals to adapt to a rapidly changing 

environment, memory, and higher cognitive functions. 

The goal of the laboratory has been to derive the blue print for this microcircuit. The neocortical 

microcircuit exhibits omnipotent computational capabilities, meaning that the same microcircuit of neurons 

can simultaneously partake in an unrestricted number of tasks. This capability allows the neocortex to be 

parcellated into multiple overlapping functional vertical columns (0.3-0.5 m in diameter) that form the 

foundation of functional compartmentalization of the neocortex. In order to derive the blueprint of this 

microcircuit, we study the components (the neurons) of the microcircuit, how the neurons are 

interconnected (anatomical properties of connections), and the functional structure of the microcircuitry 

(physiological & plasticity properties of connections). A neocortical column contains several thousand 

neurons interconnected in a precise and intricate manner. 

To study the different types of single neurons we employ whole-cell patch clamp studies in neocortical 

slices to obtain the electrophysiological profile of neurons, to aspirate cytoplasm for single cell multiplex 

RT-PCR studies and to load the neurons with dyes to allow subsequent 3D anatomical computer 

reconstruction of each neuron. This approach enables us to derive the electrophysiological behaviour, the 

anatomical structure, as well as the genetic basis of the anatomy and physiology of each type of cell. The 

microcircuit contains at least 9 major anatomical classes of cells, 15 major electrophysiological classes 

and 20 major molecular classes. Precise anatomical and physiological rules also operate to connect the 

different types of neurons. In order to derive these rules, we obtain multiple patch-clamp recordings from 

pre-selected neurons. This allows repeated analysis of the major connections and derivation of the 

signatures of connectivity as well as the physiological and plasticity principles for these connections.

The laboratory has also developed a multidisciplinary approach to studying diseases such as Autism. We 

have developed an insult-based animal model of Autism (the Valproic acid animal model) and study the 

gene expression changes (using DNA microarray analysis, multiplex RT-PCR and qRT-PCR), protein 

expression (using immunostaining approaches, Western Blotting), single molecule dysfunction (ion 

channel screening), synaptic malfunctioning (using multineuron patch-clamping), circuit malfunctioning 

(multi-electrode array stimulation and recording), whole brain malfunctioning (using in vivo multi-unit 

recordings) and behavioural alterations (using a battery of behavioural tests). 

Neocortical microcircuitry 

LNMC has studied extensively the microcircuitry of layer 6 and layer 1 of the somatosensory neocortex as 

well as a specific subset of callosal projecting layer 5 neurons in order to better understand the types of 

neurons and their connections. In addition, LNMC has studied the di-synaptic connections between 

pyramidal neurons via interneurons and the differences in the layer 5 circuitries between various 

neocortical areas with an emphasis on the specializations found in the medial prefrontal cortex. LNMC has 

also examined extensively the molecular distinctions between neocortical neurons. 

Synaptic organization and plasticity 

LNMC has studied the principles that govern how neurons choose their targets. The first study showed 

that the axonal arbour promiscuously forms close axo-dendritic touches with virtually all neighbouring 

neurons, but forms boutons with only a subset of all potential targets. In a second study we found that 

activity can cause these connections to form and disappear – the first reporting of microcircuit plasticity. 

Current studies are further examining the rules driving the connections between neurons and the 

mechanism underlying these rules. In more recent studies LNMC used the first 12 neuron patch-clamp 

system to study the statistical connectivity patterns in neural microcircuits to study how these patterns 

deviate from randomness for excitatory and inhibitory circuits. 

Gene expression in neocortical neurons 

LNMC conducted an exhaustive study to examine the correlated changes in electrical morphological and 

gene expression of layer 5 pyramidal neurons during development (from P9 to P60). This study is in the 

last phases and could yield crucial insight into the transcriptome dynamics underlying changes in neuron 

structure and function. 

Informatics 

LNMC has been in charge of assembling the reverse engineered data to be data based for the Blue Brain 

Project and to drive experiments to fill gaps and control the quality of data. The database is now the most 

comprehensive database on a microcircuit possible allowing the BBP to reconstruct the first version of a 

neocortical column. 

Iterations between simulations and experiments 

LNMC is engaged in the BBP in the sense that the experimenters also carry our experiments or provide 

data to be used by the BBP team for calibrating the reconstructed and simulated circuit. Predictions of 

structural and functional principles from the model can now also be rapidly tested experimentally. 

Computation 

Aside from the computational projects within BBP, in the initial stages of LNMC, the lab was focused on 

understanding how the brain can compute when electrical states are continuously changing. This gave 

rise to the novel concept called “Liquid Computing”, which is equivalent to high entropy computing or 

computing of transient states of activity. The core finding here was that a neural network can generate a 

consistent and meaningful output even though the underlying electrical states are constantly changing. 

This finding is now widely examined in the computational and robotics fields as it provides a universal 

approach to perform real-time computing on time series data. 

Animal model of autism 

LNMC in collaboration with LGC of Carmen Sandi, validated and established the insult-based, valproic 

acid, animal model of autism and applied the multi-omics approach in an attempt to determine the core 

molecular, cellular, synaptic, circuit, systems and behavioural alterations. The study found that animals of 

this model, displayed the core symptoms of autism as reported from humans, and made a major new 

discovery that these animals display severe abnormalities in fear processing, where fear memories are 

enhanced, prolonged and resist extinction. The in vitro brain slice experiments revealed that the 

neocortical microcircuitry was hyper-reactive and that the hyper-reactivity was due to hyper-connected 

circuits. The study also found that the circuits were hyper-plastic and found a massive enhancement of 

NMDA receptors and Calcium meditated signalling pathways. Based on these results LNMC proposed a 

radically new theory of autism called “The Intense World Syndrome” in which the world of the Autistic child 

is proposed to be painfully intense and aversive which could explain may of the symptoms of Autism 

without relying of a theory of mental retardation and poor brain function.


Calì C, Berger TK, Pignatelli M, Carleton A, Markram H, Giugliano M. Inferring connection proximity 

in networks of electrically coupled cells by subthreshold frequency response analysis. J Comput 

Neurosci. 2007 Nov 28; [Epub ahead of print] 

Rinaldi T, Kulangara K, Antoniello K, Markram H. Elevated NMDA receptor levels and enhanced 

postsynaptic long-term potentiation induced by prenatal exposure to valproic acid. Proc Natl Acad Sci 

U S A. 2007 Aug 14;104(33):13501-6. 

Rinaldi T, Silberberg G, Markram H. Hyperconnectivity of Local Neocortical Microcircuitry Induced 

by Prenatal Exposure to Valproic Acid. Cereb Cortex. 2007 Jul 17; [Epub ahead of print] 

Mazzatenta A, Giugliano M, Campidelli S, Gambazzi L, Businaro L, Markram H, Prato M, Ballerini L. 

Interfacing neurons with carbon nanotubes: electrical signal transfer and synaptic stimulation in cultured 

brain circuits. J Neurosci. 2007 Jun 27;27(26):6931-6 

Markram K, Rinaldi T, Mendola DL, Sandi C, Markram H. Abnormal Fear Conditioning and Amygdala 

Processing in an Animal Model of Autism. Neuropsychopharmacology. 2007 May 16; [Epub ahead of 

print] 

Silberberg G, Markram H. Disynaptic inhibition between neocortical pyramidal cells mediated by Martinotti 

cells. Neuron. 2007 Mar 1;53(5):735-46 

Le Bé JV, Markram H. A new mechanism for memory: neuronal networks rewiring in the young rat 

neocortex. Med Sci (Paris). 2006 Dec;22(12):1031-3. French 

Le Bé JV, Silberberg G, Wang Y, Markram H. Morphological, electrophysiological, and synaptic properties 

of corticocallosal pyramidal cells in the neonatal rat neocortex. Cereb Cortex. 2007 Sep;17(9):2204-13. 

Epub 2006 Nov 23 

Migliore M, Cannia C, Lytton WW, Markram H, Hines ML. Parallel network simulations with Neuron. 

J Comput Neurosci. 2006 Oct;21(2):119-29 

Markram H., Rinaldi T., Markram K. The Intense World Syndrome – an alternative hypothesis for Autism. 

Frontiers in Neuroscience, 1,1:77-96, 2007 

Shaul Druckmann, Yoav Banitt, Albert Gidon, Felix Schurmann, Henry Markram and Idan Segev A novel 

multiple objective optimization framework for constraining conductance-based neuron models by 

experimental data. Frontiers in Neuroscience, 1,1:7-18, 2007 

Haroon Anwar, Imad Riachi, Sean Hill, Felix Schürmann and Henry Markram An approach to capturing 

neuron morphological diversity. Neuronal Modeling. MIT Press. (E. DeSchutter, Ed.). 2007 

Michael Hines; Hubert Eichner; Felix Schuermann. Neuron splitting in compute-bound parallel network 

simulations enables runtime scaling with twice as many processors. J. Computational Neuroscience, in 

press 

Michael Hines, Henry Markram and Felix Schürmann Fully Implicit Parallel Simulation of Single Neurons, 

J. Computational Neuroscience, in press 

J. Kozloski, K. Sfyrakis, S. Hill, F. Schurmann & H. Markram Identifying, tabulating, and analyzing 

contacts between branched neuron morphologies. IBM J. RES. & DEV. VOL. 52 NO. 1/2 2008 

Markram H. Bioinformatics: industrializing neuroscience.Nature. 2007 Jan 11;445(7124):160-1 

Arsiero, M., Luscher, H-R., Lundstrom, B.N., and Giugliano, M (2007). The Impact of Input Fluctuations on 

the Frequency-Current Relationships of Layer 5 Pyramidal Neurons in the Rat Medial Prefrontal Cortex, 

Journal of Neuroscience 27(12), 3274-84 

Mazzatenta, A., Giugliano, M., Campidelli, S., Gambazzi, L., Businaro, L., Markram, H., Prato, M., 

Ballerini, L. (2007). Interfacing Neurons with Carbon Nanotubes: Electrical Signal Transfer and Synaptic 

Stimulation in Cultured Brain Circuits. Journal of Neuroscience 27(26), 6931-6 

Arsiero, M., Lüscher, H.-R. and Giugliano, M. (2007). Real-time Closed-Loop Electrophysiology: towards 

new frontiers in in vitro investigations in the Neurosciences. Arch. Ital. Biol. 145(3-4):193-209

Wang Y, Markram H, Goodman PH, Berger TK, Ma J, Goldman-Rakic PS. Heterogeneity in the pyramidal 

network of the medial prefrontal cortex. Nature Neurosci. 2006 Apr;9(4):534-42 

Migliore M, Cannia C, Lytton WW, Markram H, Hines ML. Parallel network simulations with NEURON. 


Le Be JV, Markram H. A new mechanism for memory: neuronal networks rewiring in the young rat 

neocortex (in French) Med Sci (Paris). 2006 Dec;22(12):1031-3 

Le Be JV, Silberberg G, Wang Y, Markram H. Morphological, Electrophysiological, and Synaptic 

Properties 

of Corticocallosal Pyramidal Cells in the Neonatal Rat Neocortex. Cereb Cortex. 2006 Nov 23 (Epub, 

ahead of print) 

Le Be JV, Markram H. Spontaneous and evoked synaptic rewiring in the neonatal neocortex. Proc Natl 

Acad Sci U S A. 2006 Aug 29;103(35):13214-9 

Berger T., Luscher, H-R and Guiliano, M (2006). Transient Rhythmic Activity in the Somatosensory Cortex 

Evoked by Distributed Input in vitro. Neuroscience 140(4), 1401-13 


BLUE BRAIN PROJECT 

Henry Markram 


Director BBP 

http://bluebrainproject.epfl.ch 

TEAM MEMBERS 

Joyce Abou-Jaoudé, Grand undergr. Student 

Jie Bao, Grant undergrad. Student 

Nikolai Chapochnikov, Grant undergr. Student 

Christiane Debono, Administrative Assistant 

Shaul Druckmann, affiliated PhD Student 

Laurent Francioli, internship Student 

Albert Gidon, affiliated PhD Student 

Ahmed Taher Hany, Grand undergr. Student 

Etay Hay, affiliated PhD Student 

Juan Hernando-Vieites, affiliated PhD Student 

Sean Hill, Postdoctoral Fellow (IBM) 

Guillaume Jacot, Student Assistant 

Asif Jan, PhD Student 

Srinivasan Karthik, Grant undergr. Student 

James G. King, Engineer 

Sebastien Lasserre, PhD Student 

Aurélien Macé, Grant undergraduate Student 

Othman Muhamad Razib, Grant undergr. Student 

Rajnish Ranjan, PhD Student 

Srikanth Ramaswamy, PhD Student 

Imad Riachi, PhD Student 

Philippe Rochat, Postdoctoral Fellow 

Alvaro Rodriguez Dominguez, Grant undergrad. Student 

Felix Schürmann, Postdoctoral Fellow 

Konstantinos Sfyrakis, Postdoctoral Fellow 

Thomas Tränkler, Grant undergraduate Student 

INTRODUCTION 

The Blue Brain Project began in July 2005 as a collaboration between Professor Henry Markram from 

the Brain Mind Institute at the EPFL (Ecole Polytechnique Fédérale de Lausanne) School of Life Sciences 

and International Business Machines (IBM), aimed at modeling the neocortical column. The neocortical 

column represents the basic functional unit of the cerebral cortex in mammals that underlies nearly all 

sensory and cognitive processing. These units are repeated millions of times across the cortex, with the 

basic structure remaining the same from the mouse to man. From its origins – IBM’s BlueGene/L 

supercomputer and 10 years of experimental data from Professor Markram’s laboratory and – the project 

has grown to include an international multidisciplinary team of experimentalists, modelers and computer 

scientists. 

By the end of 2007 a simulation-based research process has been developed to generate a cellular-level 

model of a 2-week-old rat somatosensory neocortex based on extensive experimental data. The 10,000 

threedimensional model neurons were placed in the neocortical volume (550 μm in diameter by 1,200 μm 

high) and arranged in 6 layers according to their morphological and electrical properties. The cells have 

model ion channels, determined by gene expression data, distributed along their membrane surfaces to 

reproduce the experimentally observed diversity of electrical firing properties seen in cortical pyramidal 

cells and interneurons. Potential synaptic locations between cells are identified through a touch detection 

process that searches for axons and dendrites in proximity to each other. Functional synapses are placed 

according to experimental observations of the probability of synaptic interactions between different cell 

types. The entire circuit, once constructed, is run through a barrage of tests to calibrate the network 

circuitry according to experimental data. This includes systematic checks of the ion channels, electrical 

behavior of neurons, composition of the column, patterns of connectivity and behavior of monosynaptic 

and polysynaptic pathways. The model network is then run through a series of test protocols evaluating its 

capacity for replicating network level phenomena. 


• A new modeling framework for the automatic, on-demand construction of neural circuits built 

from biological data. 

• A new simulation and calibration process that automatically and systematically analyzes the 

biological accuracy and consistency of each revision of the model. 

• The first cellular-level neocortical column model built entirely from biological data that can now 

serve as a key tool for simulation-based research in neuroscience.


Anwar, H., Riachi, I., Hill, S., Schürmann, F. and Markam, H., 2008. An approach to capturing neuron 

morphological diversity. In: DeSchutter, E. (Ed.), Neuronal Modeling. MIT Press 

Druckmann, S., Banitt, Y., Gideon, A., Schürmann, F., Markam, H. and Segev, I., 2007. A novel multiple 

objective optimization framework for constraining conductance-based neuron models by experimental 

data. Frontiers in Neuroscience. 1, 7-18 

Hines, M. L., Eichner, H. and Schürmann, F., 2008a. Neuron splitting in compute-bound parallel network 

simulations enables runtime scaling with twice as many processors. J Comput Neurosci. 25, 203-210. 

Hines, M. L., Markram, H. and Schürmann, F., 2008b. Fully implicit parallel simulation of single neurons. 

J Comput Neurosci. 

Kozloski, J., Sfyrakis, K., Hill, S., Schürmann, F., Peck, C. and Markram, H., 2008. Identifying, tabulating, 

and analyzing contacts between branched neuron morphologies. IBM Journal of Research and 

Development. 52 

Markram H. The Blue Brain Project. Nature Reviews Neuroscience 2006 7(2):153-60 

Wang Y, Markram H, Goodman PH, Berger TK, Ma J, Goldman-Rakic PS. Heterogeneity in the pyramidal 

network of the medial prefrontal cortex. Nature Neurosci. 2006 Apr;9(4):534-42 

Migliore M, Cannia C, Lytton WW, Markram H, Hines ML. Parallel network simulations with NEURON. 


Le Be JV, Markram H. A new mechanism for memory: neuronal networks rewiring in the young 

rat neocortex (in French) Med Sci (Paris). 2006 Dec;22(12):1031-3 

Le Be JV, Silberberg G, Wang Y, Markram H. Morphological, Electrophysiological, and Synaptic 

Properties of Corticocallosal Pyramidal Cells in the Neonatal Rat Neocortex. Cereb Cortex. 2006 Nov 23 

Le Be JV, Markram H. Spontaneous and evoked synaptic rewiring in the neonatal neocortex. 

Proc Natl Acad Sci U S A. 2006 Aug 29;103(35):13214-9 

Sitting inside a neocortical column: Shown is a subsetA subset 

of neurons from a neocortical column simulation of the Blue 

Brain Project. The false colors represent the membrane voltage 

across the individual neurons; white represents spiking. 

(courtesy BBP/EPFL) 


PETERSEN LAB 

TEAM MEMBERS 

Rachel Aronoff, Postdoctoral Fellow 

Michael Avermann, PhD Student 

Sylvain Crochet, Postdoctoral Fellow 

Luc Gentet, Postdoctoral Fellow 

Sandrine Lefort, PhD Student 

Celine Matéo, PhD Student 

Ferenc Matyas, Postdoctoral Fellow 

James Poulet, Postdoctoral Fellow 


Carl Petersen 



http://lsens.epfl.ch 

INTRODUCTION 

The Laboratory of Sensory Processing investigates synaptic mechanisms of sensory perception and 

associative learning. Experiments in mice investigate cortical processing of sensory input, focusing on the 

signalling pathway from the mystacial whiskers to the somatosensory barrel cortex. The goal is to 

understand coding, development and plasticity of perceptions at the level of individual neurons and their 

synaptic interactions within a well-defined signalling pathway. 

. 


Very basic questions remain unanswered regarding brain function during behaviour. Over the last 5 years, 

we have contributed to current knowledge of cortical function relating to whisker-sensation through wholecell 

recordings and imaging in awake behaving mice. 

Brain states 

Crochet & Petersen (2006) reported the first membrane potential recordings during quantified 

sensorimotor behaviour. We found that behaviour profoundly regulates membrane potential dynamics and 

defines distinct brain states during quiet and active periods. Sensory processing of whisker stimuli was 

strongly regulated by brain state. 

Sensorimotor integration 

Ferezou et al. (2006 2007) reported the first voltage-sensitive imaging data from awake behaving rodents. 

We found that even a single brief whisker deflection causes a highly dynamic and distributed sensory 

response in both somatosensory and motor cortex. Sensory processing in motor cortex may contribute to 

the active acquisition of sensory information. 

Coding 

In layer 2/3 of the mouse barrel cortex we find that most neurons fire very few action potentials but all 

show prominent subthreshold membrane potential changes. Subthreshold membrane potential 

depolarisations are correlated in nearby neurons. Specific sensory information is therefore likely to be 

encoded in action potentials, whereas subthreshold potentials may relate to capacity for associative 

learning. 


Petersen CCH (2007) “Higher Nervous Functions”. Chapter 9 in “Lecture Notes on Human Physiology”. 

Edited by Ole Petersen. Published by Blackwell 

Petersen CCH (2007) “Sensory Systems”. Chapter 6 in “Lecture Notes on Human Physiology”. Edited by 

Ole Petersen. Published by Blackwell 

Borgdorff AJ, Poulet JFA, Petersen CCH (2007) Facilitating sensory responses in developing mouse 

somatosensory barrel cortex. J Neurophysiol 97: 2992-3003 

Accolla R, Bathellier B, Petersen CCH, Carleton A (2007) Differential spatial representation of taste 

modalities in the rat gustatory cortex. J Neurosci 27: 1396-1404

Berger T, Borgdorff AJ, Crochet S, Neubauer FB, Lefort S, Fauvet B, Ferezou I, Carleton A, Luscher HR, 

Petersen CCH (2007) Combined voltage and calcium epifluorescence imaging in vitro and in vivo reveals 

subthreshold and suprathreshold dynamics of mouse barrel cortex. J Neurophysiol 97: 3751-3762 

Petersen CCH (2007) The functional organization of the barrel cortex. Neuron 56: 339-355 

Ferezou I, Haiss F, Gentet LJ, Aronoff R, Weber B, Petersen CCH (2007) Spatiotemporal dynamics 

of cortical sensorimotor integration in behaving mice. Neuron 56: 907-923 

Petersen CCH (2006) “Advances in understanding cortical function through combined voltage-sensitive 

dye imaging, whole-cell recordings and analysis of cellular morphology.” Chapter 14 in “Neuroanatomical 

Tract-Tracing 3: molecular, neurons, and systems”. Edited by Laszlo Zaborszky. Floris Wouterlood and 

Jose Lanciego. Published by Springer 

Ferezou I, Bolea S, Petersen CCH (2006) Visualizing the cortical representation of whisker touch: voltagesensitive 

dye imaging in freely moving mice. Neuron 50: 617-629 

Crochet S, Petersen CCH (2006) Correlating whisker behavior with membrane potential in barrel cortex of 

awake mice. Nat Neurosci 9: 608-610 

Aronoff R, Petersen CCH (2006) Controlled and localized genetic manipulation in the brain. 

J Cell Mol Med 10: 333-352 

Petersen CCH (2006) Advances in understanding cortical function through combined voltage-sensitive 

dye imaging, whole-cell recordings, and analysis of cellular morphology. Chapter 14 in Neuroanatomical 

Tract-Tracing 3. Edited by Laszlo Zaborsky, Floris Wouterlood and Jose Lanciego. Published by Springer 

© Neuron (Cell Press) - Ferezou et al. (2007) Neuron 56: 907-923. 

This figure illustrates a cortical sensory response imaged with 

voltage-sensitive dye to a single whisker deflection which began in 

the primary somatosensory barrel cortex and subsequently excited 

the whisker motor cortex. 


SANDI LAB 

Carmen Sandi 



http://lgc.epfl.ch 

TEAM MEMBERS 

Reto Bisaz, PhD Student 

Jorge E. Castro ,PhD Student 

Marjorie Clerc, Technician 

Conboy Lisa, Post Doctoral Fellow 

Cordero M. IsabeP, ost-Doc 

Gantelet Emilien, Postdoctoral Fellow 

Larsen Marianne H., Postdoctoral Fellow 

Gediminas Luksys, PhD Student 

Marquez Cristina, Postdoctoral Fellow 

Rossetti Clara, Technician 

Salehi Basira, PhD Student 

Siegmund Coralie, Technician 

Steinmann Ioana, Administrative Assistant 

Marjan Timmer, PhD Student 

VISITING SCIENTIST 

Prof. Nan Sui, Chinese Academy of Sciences 

INTRODUCTION 

The Laboratory of Behavioural Genetics focuses on the interactions between stress and cognitive 

function, with a focus on learning and memory processes and on psychiatric disorders. Projects in the lab 

can be classified in three main research lines: (i) understanding the contribution of stress to cognitive 

function; (ii) elucidating the mechanisms involved in the negative impact of chronic stress on brain function 

and cognition; and (iii) searching for novel cognitive enhancers. 


Role of synaptic proteins in the facilitating effects of stress in learning 

This subproject focuses on the involvement of synaptic proteins [particularly glutamate receptors, AMPA 

(GluR1, GluR2, GluR3) and NMDA (NR1, NR2A, NR2B) receptor subunits membrane trafficking, and 

neural cell adhesion molecules (NCAM isoforms; PSA-NCAM)], in hippocampus and amygdala, in the 

facilitating effects of stress in spatial learning. We have selected two intrinsic stress conditions that lead to 

a differential learning rate in the water maze: training mice at two different water temperatures (i.e., 22 or 

30°C). Mice trained at 22°C display a better performance than mice trained at 30°C (appropriate control 

groups allowed to discharge a lack of motivation in 30°C-trained animals). The better learning of these 

animals is accompanied by a rapid translocation of GluR2/3 receptor subunits to the synaptic 

compartment, whereas the slower learning rate of 30°C-trained mice is related to a decrease in the 

synaptic localization of NR2A receptor subunit. The stress hormones glucocorticoids are required for the 

facilitating effect of stress on memory formation and for the synaptic insertion of GluR2/3 subunits. In vitro, 

corticosterone also induces the trafficking of GluR2 receptors to the cell membrane. These findings 

provide a molecular substrate for the interactions between stress and cognitive function. 

The impact of stress on the establishment of social memories: gene expression studies 

We have developed an animal model in which stress has important and long-lasting influences on social 

relationships by amplifying the persistence of the memory for the social status that is established in a first 

encounter between conspecifics. In our model, if a male rat is exposed to a stressful aversive experience 

and shortly afterwards briefly confronted with an unfamiliar male rat, the stressed rat eventually becomes 

the submissive one and their hierarchical relationship becomes long-lasting. Such stable hierarchy 

contrasts with evidence of a lack of long-term memory for the social status in animals that undergo the 

same experiences but are not submitted to prior stress. A series of experiments allowed us to propose 

that stress potentiates a hierarchy-linked recognition memory between “specific” individuals through 

mechanisms that involve de novo protein synthesis. These results implicate stress among the key 

mechanisms contributing to create social imbalance and highlight memory mechanisms as key mediators 

of stress-induced long-term establishment of social rank. We have now identified a down-regulation of 

oxytocin receptors in the medial amygdala as a mechanism linked to stress-induction of submissive 

behavior, while an upregulation of vasopressin receptors in the lateral septum is associated with dominant 

status. These changes in gene expression were observed at 3h after hierarchy establishment and, 

respectively, correlated with corticosterone and testosterone plasma levels. Current studies are addressed 

to assess long-term changes (1 week after the first encounter) in gene expression in this model system.

Behavioral /‘personality’ traits stress coping and vulnerability to stress 

From an evolutionary point of view, the physiological stress response has being selected for its ability to 

provide the individual with a pattern of quick reactions that help coping with potential dangers. 

Behavioral/’personality’ traits have also evolved for their adaptive value under specific situations. Both in 

humans and rodents (among many other animals), there is a considerable variation in the way individuals 

react to stress. We exploit variation in outbred rats to search for relevant ‘personality’ factors that could 

account for a differential neurobiological predisposition to cope with stress, to learn under stress, and to 

display either resilience or vulnerability to psychopathology when confronted with excessive or sustained 

stressful situations. We have found that clustering individuals according to meaningful behavioral traits 

helps predicting how they will solve spatial and reversal learning situations, as well as their vulnerability to 

be affected in specific behavioral and mood-related domains after exposure to chronic stress. We have 

identified ‘trait anxiety’ in rats as a good predictor factor for the development of stress-related cognitive 

deficits. Moreover, the subset of more affected individuals at the behavioral level was found to show the 

greatest reduction in hippocampal neurogenesis after chronic stress. 

Role of NCAM in memory formation 

Polysialylation of the neural cell adhesion molecule (PSA-NCAM) is expressed in brain regions that play 

key roles in learning and emotion. We have investigated the functional implication of PSA-NCAM in 

different types of learning. Upregulation of PSA-NCAM was observed in the rat hippocampus following 

training in hippocampus-dependent tasks. In contextual fear learning, such upregulation was confined to 

the dorsal hippocampus. Upregulation of amygdaloid PSA-NCAM was found in rats trained in the 

amygdala-dependent auditory fear conditioning task. Specific removal of PSA through microinfusion of the 

enzyme endoneuraminidase-N in the dorsal (but not ventral) hippocampus impaired contextual fear 

conditioning, without affecting auditory conditioning. However, cleavage of PSA in the amygdala failed to 

affect fear conditioning processes. A similar pattern of results was obtained using mice deficient for the 

gene polysialyltransferase ST8SiaIV/PST, the enzyme that attaches PSA to NCAM in adulthood. These 

mice showed normal auditory fear conditioning, but were impaired in spatial and reversal learning. 

Altogether, these findings suggest a key role for PSA-NCAM in associative types of learning that require 

complex computations and, hence, in brain regions (such as dorsal hippocampus and prefrontal cortex) 

that sustain such functions. They also indicate a lack of requirement of PSA-NCAM for non-associative or 

simpler operations proposed to occur in the amygdala and the ventral hippocampus during defensive 

behavior. Overall, these results suggest that whereas PSA-NCAM is critical for cognitive flexibility and 

learning involving complex associations, it is not a necessary requirement for those physiological functions 

essential for survival that are either innately hardwired or acquired very rapidly. 


Lopez-Fernandez M.A. Montaron M.F. Varea E. Rougon G., Venero C. Abrous D.N. and Sandi C. (2007). 

Upregulation of polysialylated neural cell adhesion molecule in the dorsal hippocampus after contextual 

fear conditioning is involved in long-term memory formation. J. Neurosci. 27:4552-4561 

Cordero M.I. and Sandi C. (2007). Stress amplifies memory for social hierarchy. Front. Neurosci. 

1:175-184 

Markram K. Gerardy-Schahn R. and Sandi C. (2007). Selective learning and memory impairments in mice 

deficient for polysialylated NCAM in adulthood. Neuroscience 144:788-796 

Markram K. Lopez-Fernandez M.A. Abrous D.N. and Sandi C. (2007). Amygdala upregulation of NCAM 

polysialylation induced by fear conditioning is not required for fear memory processes. Neurobiol. Learn. 

Mem. 87:573-582 

Markram K. Rinaldi T. La Mendola D. Sandi C. and Markram H. (2007). Abnormal fear conditioning and 

amygdala processing in an animal model of autism. Neuropsychopharmacology May 16; [Epub ahead 

of print] PMID:17507914 

Sandi C. and Bisaz R. (2007). A model for the involvement of neural cell adhesion molecules in stressrelated 

mood disorders. Neuroendocrinology 85:158-176 

Sandi C. and Pinelo-Nava M.T. (2007). Stress and Memory: Behavioral effects and neurobiological 

mechanisms. Neural Plast. ID 78970 

Luksys G. Knuesel J. Sheynikhovich D. Sandi C. and Gerstner W. (2006). Effects of stress and genetic 

background on meta-parameter dynamics in reinforcement. Advances in Neural Information Processing 

Systems 19 eds. B. Schölkopf J.C. Platt and T. Hofmann MIT Press Cambridge MA 

Toledo-Rodriguez M. and Sandi C. (2007). Stress before puberty exerts a sex- and age-related impact on 

auditory and contextual fear conditioning in the rat. Neural Plast. ID 71203

Rizhova L. Klementiev B. Venero C. Cambon K. Sandi C. Vershinina E Vaudano E. Berezin V. and Bock 

E. (2007). Effects of P2 a peptide derived from a homophilic binding site in NCAM on learning and 

memory in rats. Neuroscience 149:931-942 

Borcel E. Perez-Alvarez L. Herrero A.I. Brionne T. Varea E. Berezin V. Bock E. Sandi C. and Venero C. 

(2007). Chronic stress in adulthood impairs spatial memory and the survival of newborn hippocampal cells 

in aging animals: prevention by FGL a mimetic peptide of NCAM. Behav. Pharmacol. 

Sandi, C. and Touyarot, K. (2006) Mid-life stress and cognitive deficits during early aging in rats: Individual 

differences and hippocampal correlates. Neurobiol. Aging 27:128-140 

Venero, C., Herrero, A.I., Touyarot, K., Cambon, K., López-Fernández, M.A, Berezin, V., Bock, V. and 

Sandi, C. (2006) Hippocampal upregulation of NCAM expression and polysialylation plays a key role on 

spatial memory. Eur. J. Neurosci. 23:1585-1595 

Herrero, A.I., Sandi, C. and Venero, C. (2006) Individual differences in anxiety trait are related to spatial 

learning abilities and hippocampal expression of mineralocorticoid receptors. Neurobiol. Learn. Mem. 

86:150-159 

López-Grancha, M., López-Crespo, G., Venero, C., Cañadas, F., Sánchez-Santed, F., Sandi, C. and 

Flores, P. (2006) Differences in corticosterone level due to inter-food interval length: implications for 

schedule-induced polydipsia. Horm. Behav. 49:166-172 

Donohue, H.S., Gabbott, P.L.A., Davies, H.A., Rodríguez, J.J., Cordero, M.I., Sandi, C., Colyer, F.M. and 

Stewart, M.G. (2006) Volume measurements show that synaptic density is unchanged in CA1 rat 

hippocampus after chronic restraint stress but post-synaptic density size increases. Neuroscience 

140:597-606 

Immunolabelling of new cell in the 

hippocampal dentate gyrus 


SCHNEGGENBURGER LAB 

TEAM MEMBERS 


Zhizhong Dong Postdoctoral Fellow 

Ozgur Genc, PhD Student 

Juan Goutman, Postfoctoral Fellow 

Yunyun Han, PhD Student 

Olexey Kochubey, Postdoctoral Fellow 

Martin Müller, PhD Student (external) 

Heather Murray, Technician 

Le Xiao, PhD Student 

Ralf Schneggenburger 




INTRODUCTION 

Nerve cells are connected to each other in intricate neuronal networks, and communicate with each other 

at synapses via the process of chemical synaptic transmission. Thus, understanding how synaptic 

transmission is regulated by neuronal activity during short- and long-term plasticity is an important aspect 

of information processing in neuronal networks. At most chemical synapses, transmission originates at the 

presynaptic nerve terminal by the quantal release of neurotransmitter, and presynaptic factors, such as 

the availability of readily-releasable vesicles, and presynaptic Ca 2+ buffering and Ca 2+ signalling influence 

the probability of transmitter release, synaptic strength, and short-term plasticity. Therefore, our main 

interest lies in understanding the cellular and molecular mechanisms that regulate Ca 2+ signalling and 

Ca 2+ dependent vesicle fusion in the nerve terminal, and the factors that regulate the probability of 

transmitter release. 

In order to study presynaptic signalling mechanisms, we use a mammalian CNS synapse with a giant 

presynaptic terminal, the calyx of Held (see Figure). The unusually large size of the calyx of Held allows 

us to make direct whole-cell patch-clamp recordings from this nerve terminal, a technique that we have 

combined with presynaptic Ca 2+ imaging and Ca 2+ uncaging. This has allowed us and other groups to gain 

insight into presynaptic Ca 2+ signalling and transmitter release with a resolution that cannot be achieved at 

other CNS synapses. We have shown previously that the Ca 2+ sensitivity of vesicle fusion is significantly 

higher than what was assumed before (Schneggenburger & Neher, 2000), and that intracellular second 

messengers, like diacylglycerol, can directly enhance the Ca 2+ sensitivity of the vesicle fusion machinery 

(Lou et al., 2005). To investigate the role of specific proteins in the Ca 2+ -sensing that precedes vesicle 

fusion, the Laboratory of Synaptic Mechanisms uses virus-mediated overexpression of Synaptotagmin 

and other presynatic proteins, and genetically modified mouse lines in collaborative studies. 

(A) The calyx of Held is a giant excitatory 

(glutamatergic) nerve terminal formed by 

globular bushy cells in the anterior ventral 

cochlear nucleus (aVCN). The axons of these 

cells project to the contralateral 'medial nucleus 

of the trapezoid body' (MNTB), where they form 

large calyx-like endings on MNTB neurons. 

(B) Scheme of a calyx of Held. Most MNTB 

neurons receive only a single, large calyx of 

Held. A calyx of Held can contain between 300 - 

600 active zones. We exploit the large diameter 

of this giant synaptic nerve terminal (~ 10 - 15 

µm) to perform direct presynaptic patch-clamp 

and Ca 2+ imaging experiments.

In another line of research, we study mechanisms that guarantee the maintenance of nerve terminal 

function. Nerve terminals can be located at long distances (millimetres or more) from their parent soma. It 

is likely that nerve terminals contain a specific protein re-folding apparatus, like heat-shock cognate 

proteins that are directed to the nerve terminal via cystein-string-protein (CSP), to guarantee the 

continuous functioning of SNAREs and other presynaptic proteins during repeated rounds of exo- and 

endocytosis. We investigate the role of CSP in the survival, Ca 2+ signalling and membrane recycling at the 

calyx of Held nerve terminal. In addition, we have begun to study the role of CSP and related proteins for 

dopamine release from nigrostriatal nerve terminals. 

Finally, we aim at identifying genes that determine the synaptic connectivity pattern in the brain. Each 

nerve cell in the brain can contact as many as 1000 other nerve cells both via local, and via long-range 

synaptic connections. The specificity of the innervated target neurons, and the size and release probability 

of synapses formed on target cells is thus crucial for setting up the correct synaptic connectivity in the 

brain. We aim to identify molecules involved in determining synapse size in the auditory brainstem by a 

functional genomics approach. 


Molecular mechanisms of fast- and slow transmitter release 

We have shown that stimulating the calyx of Held by Ca 2+ uncaging evokes two distinct kinetic component 

of transmitter release (Wölfel, Lou & Schneggenburger 2007; J. Neuroscience). Because Ca 2+ uncaging 

creates a spatially uniform intracellular Ca 2+ signal, the observation of two kinetic components of release 

shows that intrinsic mechanism(s), such as the existence of two readily-releasable (sub)pools with 

different Ca 2+ sensitivities, or else an "a posteriori" reduction of Ca 2+ sensitivity after the onset of the 

stimulus determines fast- and slow release at synapses. We are following-up on this study by investigating 

the role of Synaptotagmin-2 (Syt-2), the likely Ca 2+ sensor at the calyx of Held (see below), for the fast 

phase of Ca 2+ -driven vesicle fusion. We use in-vivo sh-RNA knock-down approaches, adenovirusmediated 

overexpression, and a Syt-2 k.o. mouse to investigate the role of Syt-2, and specific domains 

of Syt-2 for the fast phase of neurotransmitter release. 

Using a newly established method of single-cell qPCR in combination with whole-cell recordings of 

globular bushy cells (which generate calyces of Held), we have studied the isoform-expression pattern of 

a large family of presynaptic proteins, the Synaptotagmins (Le Xiao; in collaboration with Prof. Ruth Lüthi- 

Carter and Heike Runne; LNGF). We observe a strong expression of Syt-2 and Syt-11 in these neurons, 

whereas Syt-1 is only weakly expressed, or absent. Thus, Syt-2 is the best candidate for a fast 

Ca 2+ sensor at the calyx of Held, which also agrees with recently published work by others (Sun et al, 

2007). 

We are also studying whether an increase in the intrinsic Ca 2+ sensitivity of transmitter release 

accompanies developmental changes in Ca 2+ - secretion coupling at the calyx of Held. To this end, we 

have extended presynaptic Ca 2+ uncaging in paired pre- and postsynaptic recordings to P13-P14 rats (Dr. 

A. Kochubey, Yunyun Han). However, we do not see a significant change in the intrinsic Ca 2+ sensitivity 

of vesicle fusion in this age range (Kochubey, Han & Schneggenburger, submitted). 

Presynaptic Ca 2+ signalling and the interaction of synaptic depression and facilitation 

The calyx of Held is a depressing synapse because repetitive stimulation leads to the depression of EPSC 

amplitudes over a wide range of stimulation frequencies. We showed previously, though, that synaptic 

facilitation is also present at the calyx of Held, and can be studied under conditions of a reduced initial 

release probability. We could show recently that synaptic facilitation has an extremely fast decay time 

constant (~ 30 - 50 ms) that is controlled by Ca 2+ binding to Parvalbumin, an endogenous Ca 2+ binding 

protein present in the calyx of Held (Müller, Felmy, Schwaller & Schneggenburger 2007; J. Neuroscience). 

Martin Müller has more recently found evidence for an interaction between depression and facilitation of 

transmitter release. He found that increasing the frequency of synaptic stimulation from a nearphysiological 

background frequency (10 - 20 Hz) to higher values (100 - 200 Hz) leads to a transient 

increase in transmitter release caused by facilitation. Thus, net depression can be overcome by short-term 

facilitation even at a strongly depressing synapse (Müller et al., in preparation). This finding is important 

for our understanding of synaptic signalling during trains of physiological activity at the calyx of Held 

synapse. 

Signalling mechanisms in presynaptic potentiation and second-messenger modulation of transmitter release 

Post-tetanic potentiation (PTP) is a use-dependent increase of synaptic strength which is driven by 

'residual' Ca 2+ in the nerve terminal, but the signalling mechanisms which underlie this and related forms 

of synaptic potentiation are not fully understood. We recently showed that activation of protein kinase-C 

(PKC) plays an important role during PTP, and we showed that activated PKC mainly acts by increasing 

the Ca 2+ sensitivity of vesicle fusion, thereby enhancing the transmitter release probability (Korogod, Lou 

and Schneggenburger 2007, PNAS).

We have also investigated the molecular mechanisms by which the diacylglycerol (DAG) analogues, 

phorbol esters, potentiate spontaneous- and Ca 2+ evoked release. Using a knock-in mice with disrupted 

DAG binding to the C1-domain of munc-13 (the munc-13 H567K mutant), we showed that both PKC and 

Munc-13 are involved in the phorbol ester-mediated potentiation of transmitter release (Lou, Korogod, 

Brose & Schneggenburger 2008, J. Neuroscience 28: 8257). 

Mechanisms of nerve terminal maturation and - degeneration 

We hypothesize that the presynaptic phenotype of cystein-string-protein (CSP) knock-out mice which we 

have established previously (Fernandez-Chacon, Wölfel et al. 2004, Neuron) represents a loss-of-function 

of an essential co-chaperone activity of CSP in the nerve terminal. Using the calyx of Held as a model 

system, we are now investigating in more detail the presynaptic signalling mechanisms that are impaired 

in CSP -/- mice. Specifically, we investigate whether presynaptic Ca 2+ currents, Ca 2+ buffering or - 

extrusion, the number and/or Ca 2+ sensitivity of readily-releasable vesicles, and membrane re-uptake 

might be primarily impaired in CSP -/- mice, with the aim to identify possible target proteins which are 

most sensitive to the removal of CSP (Yunyun Han, Dr. Zhizhong Dong). 

In a separate project line, we are investigating whether loss of CSP also leads to a misfunction of 

dopamine release from nigrostriatal terminals. Dopamine release in the striatum is vital to the functioning 

of the basal ganglia motor system, and degeneration of dopaminergic neurons in the Substantia nigra 

occurs in Parkinson's Disease. We are using amperometric detection of dopamine in striatal slices to 

investigate whether dopamine release is especially vulnerable to removal of CSP (Dr. Zhizhong Dong; 

Ogur Genc). 

Identifying candidate genes that determine the development of the calyx of Held 

In this ongoing research project, we use genomics methods to compare the gene expression in various 

nuclei of the auditory brainstem, with the aim to identify genes with potentials roles in the development of 

the calyx of Held (Le Xiao). The giant "calyx of Held" synapse is formed within a few days during early 

postnatal development, but the molecular and activity-dependent cues that play a role in calyx 

development are unknown. Identifying signalling molecules in calyx of Held development will allow us to 

understand the regulation of synapse size in the brain, an important parameter that determines the 

strength of synaptic signal processing. 


Müller, M., Felmy, F., Schwaller, B., Schneggenburger, R. (2007). Parvalbumin is a mobile presynaptic 

Ca 2+ -buffer in the calyx of Held that accelerates the decay of Ca 2+ and short-term facilitation. 

J. Neuroscience 27 : 2261-2271 

Wölfel, M., Lou, X., Schneggenburger, R. (2007). A mechanism intrinsic to the vesicle fusion machinery 

determines fast and slow transmitter release at a large CNS synapse. J. Neuroscience 27: 3198-3210 

Korogod, N., Lou, X., Schneggenburger, R. (2007). Posttetanic potentiation critically depends on an 

enhanced Ca 2+ sensitivity of vesicle fusion mediated by presynaptic PKC. Proc. Natl. Acad. Sci. USA 

104: 15923-15928 

Schneggenburger, R. and Forsythe, I.F. (2006) The calyx of Held. Cell Tissue Res. 326: 311-337 

(Review) 


HIRLING GROUP 

TEAM MEMBERS 

Ahmed Boucharaba, Postdoctoral Fellow 

Liliane Glauser, Technician 

Michel Kropf, PhD Student 

Karina Kulangara, PhD Student 

Charles Roduit, PhD Student 

Harald Hirling, PhD 

Group Leader 


INTRODUCTION 

Our group is working on the synaptic transmission between nerve cells. In particular, we are interested in 

the molecular mechanisms that insert neurotransmitter receptors into the cell surface of the postsynaptic 

neurons in order to become receptive for the neurotransmitter liberated by the presynaptic neuron. 

Regulating the number of surface neurotransmitter receptors is a major principle of synaptic plasticity 

underlying learning and memory. 


We have been developing a new labeling technique that allows to attach fluorophores or biotin to different 

subunits of a receptor on a living cell. This technique is now used to study receptors following their 

internalization. A new postdoc in the group started a project to analyze receptor trafficking upon different 

types of NMDA receptor stimulations, and he has been using the new labeling technique. 

In addition, a PhD student from UNIL has been co-supervised by Dr Hirling on a project on canine 

distemper virus infection of neurons and the resulting alterations in glutamatergic transmission and 

excitotoxicity. He has finished this study in the course of 2007.


Brunner, J.-M., Plattet, P., Majcherczyk, P., Zurbriggen, A., Wittek, R. and Hirling, H. (2007). 

Canine distemper virus infection of primary hippocampal cells induces increase in extracellular 

glutamate and neurodegeneration. J. Neurochem., 103:1184-1195 

Yersin, A., Hirling, H., Kasas, S., Roduit, C., Kulangara, K., Dietler, G., Lafont, F., Catsicas, S. 

and Steiner, P. (2007) Elastic properties of the cell surface and trafficking of single AMPA 

receptors in living primary hippocampal neurons. Biophys. J., 92(12):4482-4489 

Kulangara, K., Kropf, M., Glauser, L., Magnin, S., Alberi, S., Yersin, A. and Hirling, H. (2007). 

Phosphorylation of GRIP1 regulates surface expression of glutamate receptors. J. Biol. Chem. 

282 (4):2395-2404 

Brissoni, B., Agostini, L., Kropf, M., Martinon, F., Swoboda, V., Lippens, S., Everett, H., Aebi, 

N., Janssens, S., Meylan, E., Felbermann-Corti, M., Hirling, H., Gruenberg, J, Tschopp, J and 

Burns, K. (2006). Intracellular trafficking of Interleukin-1 receptor I requires Tollip. 

Curr. Biology, 16:2265-2270 

Genoud, C., Quariauxx, C., Steiner, P., Hirling, H., Welker, E. and Knott, G.W. (2006). Plasticity 

of astrocyte coverage and glutamate transmporter expression in adult mouse cortex. 

PLoS Biology, 4:e343 


IBI - THE INSTITUTE OF BIOENGINEERING 

The Institute of Bioengineering serves as a focus point for research in the basic biological sciences 

using quantitative and systems analyses as well as translation of the biological and biochemical sciences 

into therapeutics and diagnostics. In pursuit of basic biological mechanisms, IBI faculty investigate 

questions such as how the cellular microenvironment controls cellular differentiation and morphogenetic 

processes, how stem cell processes such as self-renewal and differentiation are determined, how cell 

migration and trafficking in complex environments is modulated, how complex biological networks such as 

metabolism, gene expression and protein trafficking are regulated, and how biophysical and biomolecular 

signals interact in control of cellular behavior. In pursuit of translation, IBI faculty develop novel 

technologies in areas including interventional and diagnostic biomedical microdevices, synthetic and 

biosynthetic biomaterials for delivery of small molecule drugs, proteins and DNA, materials in 

bionanotechnology, immunotherapy based on active biomolecules and nanomaterials, tissue engineering 

for therapeutics as well as physiological modelling based on biomolecular and stem cell approaches, and 

novel molecules for photodynamic therapy 


BARRANDON LAB 

Yann Barrandon 


Joint Chair 

EPFL / UNIL-CHUV 


http://ldcs.epfl.ch 

TEAM MEMBERS 

Alexandro Amici, PhD Student EPFL 

Fahd Azzabi, PhD Student EPFL 

Paola Bonfanti, MD, PhD Student EPFL 

Michel Brouard, MD, PhD, Postdoctoral Fellow CHUV 

Marco Burki, Research Assistant, CHUV-COP 

Vincent Cattin, MD, PhD Student EPFL 

Line Chapuis, Research Assistant EPFL 

Stéphanie Claudinot, Postdoctoral Fellow CHUV 

Alexandra Delacour, Postdoctoral Fellow 

Marc-André Demierre, Driver CHUV-COP 

Nicolas Fête, Postdoctoral Fellow EPFL 

Nicolas Grasset, MD, PhD Student EPFL 

François Gorostidi, MD, PhD Student EPFL-CHUV 

Stéphanie Lathion, Postdoctoral Fellow CHUV 

Daniel Littman, PhD Student EPFL 

Louis Mercier, Research Assistant CHUV 

Melissa Maggioni, PhD Student EPFL 

Johannes Mosig, PhD Student EPFL 

Daisuke Namba,senior Postdoctoral Fellow EPFL 

Takahiro Nakamura, MD, Postdoctoral Fellow 

Michael Nicolas, Postdoctoral Fellow 

Katrin Petermann, undergraduate Student EPFL 

Ariane Rochat, PhD, group leader CHUV 

Emmanuelle Savioz-Dayer, Clinic Tral Assistant CHUV 

Guillaume Saurais, undergraduate Student EPFL 

Liliane Schnell, Research Assistant CHUV 

Céline Tobler, PhD Student, EPFL 

Fujio Toki, Postdoctoral Fellow EPFL 

Jeanne Vannod, Research Assistant EPFL 

Steeve Vermot, Research Assistant CHUV 

Alexandra Vitiello, Administrative Assistant EPFL 

Christelle Volorio, Postdoctoral Fellow CHUV 

INTRODUCTION 

The joint chair (EPFL/UNIL-CHUV) of Stem Cell Dynamics is involved in fundamental and translational 

stem cell research to bring stem cells from bench to bedside. 


Squamous epithelia are from ectodermal, mesodermal and endodermal origin. They include the epidermis (the 

outer part of the skin), the epidermal appendages, the epithelia lining the oral cavity, the oesophagus, the vagina 

and the anal canal, and the ocular surface. All squamous epithelia are self-renewing and are thought to contain 

stem cells. Most importantly, squamous epithelia have an extensive capacity to repair when wounded, and are 

bound to cancer transformation when chronically aggressed (i.e. skin carcinoma are among the most frequent 

human cancers, carcinoma of the larynx in smokers). Interestingly, non-stratified epithelia like the epithelium of the 

trachea can undergo epidermal metaplasia, a condition that favors cancer transformation.

We have investigated the relationship that exists among stem cells of stratified epithelia at the cellular and 

the molecular levels, our working hypothesis being that stem cells of squamous epithelia are closely 

related, if not identical. We have accumulated compiling evidences that stem cells of stratified epithelia 

can respond equally to skin morphogenetic signals, further strengthening the hypothesis that stratified 

epithelia, including the thymic epithelium, contain stem cells that are closely related. We are now 

investigating the molecular mechanisms that control stem cell fate in squamous epithelia. 

We have actively pursued the development of a large animal model to evaluate the fate of transplanted 

autologous keratinocyte stem cells and the generation of epidermal appendages (EuroStemCell), and we 

have continued our efforts toward the gene therapy of Recessive Dystrophic Epidermolysis Bullosa using 

autologous keratinocyte stem cells genetically corrected ex vivo (Therapeuskin). In parallel, we are 

collaborating with several of our EPFL colleagues to model hair follicle and corneal renewal (in 

collaboration with Freddy Radtke, J-P Thiran, Théo Lasser and Georges Abou Jaoudé). 


Majo, F., Rochat, A., Nicolas, M., Abou Jaoudé, G., Barrandon, Y. (2008). Oligopotent stem cells are 

distributed throughout the mammalian ocular surface. Nature In press 

Gurtner, G. C., Werner, S., Barrandon, Y., Longaker, M. T. (2008). Wound repair and regeneration. 

Nature 453: 314-21 

Feutz, A.C., Barrandon, Y., Monard, D. (2008). Control of thrombin signaling through PI3K is a 

mechanism underlying plasticity between hair follicle dermal sheath and papilla cells. J Cell Sci 121: 

1435-43 

Grisel, P., Meinhardt, A., Lehr, H. A., Kappenberger, L., Barrandon, Y., Vassalli, G. (2008). The MRL 

mouse repairs both cryogenic and ischemic myocardial infarcts with scar. Cardiovasc Pathol 17: 14-22 

Nakamura, T., Ohtsuka, T., Sekiyama, E., Cooper, L. J., Kokubu, H., Fullwood, N. J, Barrandon, Y., 

Kageyama, R. (2008). Hes1 Regulates Corneal Development and the Function of Corneal Epithelial 

Stem/progenitor Cells. Stem Cells 26(5): 1265-74 

Vauclair*, S., Majo*, F., Durham, A. D., Ghyselinck, N. B., Barrandon, Y., Radtke, F. (2007). Corneal 

epithelial cell fate is maintained during repair by Notch1 signaling via the regulation of vitamin A 

metabolism. Dev Cell 13 (2), 242 -53. Co-first authors 

Barrandon, Y. (2007). Crossing boundaries: stem cells, holoclones, and the fundamentals of squamous 

epithelial renewal. Cornea 26: S10-2 

Barrandon, Y. (2007). Genetic manipulation of skin stem cells: success, hope, and challenges ahead. 

Mol Ther 15 (3), 443-4 

Linderholm, P., Vannod, J., Barrandon, Y., Renaud, P. (2007). Bipolar resistivity profiling of 3D tissue 

culture. Biosens Bioelectron 22: 789-96 

Mitsiadis, T. A., Barrandon, O., Rochat, A., Barrandon, Y., De Bari, C. (2007). Stem cell niches in 

mammals. Exp Cell Res 313: 3377-85 

Rochat, A., Claudinot, S., Nicolas, M., Barrandon, Y. (2007). Stem cells and skin engineering. Swiss Med 

Wkly 137: Suppl 155, 49S-54S 

Linderholm, P., Braschler, T., Vannod, J., Barrandon, Y., Brouard, M., Renaud, P. (2006). Twodimensional 

impedance imaging of cell migration and epithelial stratification. Lab Chip 6 : 1155-62 

Majo, F., Barrandon, Y., Othenin-Girard, P., Toublanc, M., Hoang-Xuan, T. (2006). Corneal epithelial 

diseases related to limbal stem cell deficiency. J Fr Ophtalmol 29 (9), 1060-9 

Rea, MA., Zhou, L., Gin, Q., Barrandon, Y., Easley, KW., Gungner, SF., Phillips, MA., Holland, WS., 

Gumerlock, PH., Rocke, DM., Rice, RH. (2006). Spontaneous immortalization of human epidermal cells 

with naturally elevated telomerase. J Invest Dermatol 126 (11), 2507-15 

Wong, CE., Paratore, C., Dours-Zimmermann, MT., Rochat, A., Pietri, T., Suter, U., Zimmermann, DR., 

Dufour, S., Thiery, JP., Meijer, D., Beermann, F., Barrandon, Y., Sommer, L. (2006). Neural crest-derived 

cells with stem cell features can be traced back to multiple lineages in the adult skin. J Cell Biol 175 (6), 

1005-15

Confocal microscopy of cultivated human thymic epithelial cells; Ki67 (red), nuclear staining (blue) pan keratin (green) 


DAL PERARO LAB 

TEAM MEMBERS 

Matteo Thomas De Giacomi, PhD Student 

Christina Mattsson, Administrative Assistant 

Matteo Dal Peraro 


Since November 2007 


http://lbm.epfl.ch 

FORMER HOME INSTITUTION 

The University of Pennsylvania (UPenn) 

Philadelphia, USA 

INTRODUCTION 

In the Laboratory for Biomolecular Modeling we use and develop molecular modeling techniques in 

order to investigate complex biological systems, in particular their function emerging from structure. Our 

main targets are bacterial and viral systems and their mechanism of resistance towards natural and 

clinical drugs. We are developing new multiscale schemes able to extend the time-scale and size-scale of 

current molecular simulations in order to tackle problems such as the assembly of large macromolecular 

complexes and the design of improved remedies for pathogenic infections. 

DESCRIPTION OF RESEARCH ACTIVITIES AND MAIN RESULTS OBTAINED IN 2007 

In the last decade the advances in the field of computational biology have greatly improved the structural 

and mechanistic knowledge of biological systems at the atomistic level, shedding light on issues that are 

often experimentally inaccessible. Although the current computational power along with state-of-the-art 

implementations allow application of such techniques to study the evolution of large systems for long 

times, it remains generally unfeasible to reach dimensions and dynamical scales that are significant to 

most of the biological processes both in vitro and in vivo. 

Schemes for a coarse-grained description of proteins, nucleic acids and membranes in molecular 

simulations have been recently developed to overcome this limitation. However, they all sacrifice the 

possibility to produce atomistic-detailed models, which is a crucial requirement when studying phenomena 

involving molecular recognition entitled to control complex pathways. Thus, the integration of different 

scales of description, such as coarse-grained and all-atom Hamiltonians, in what is commonly called 

multiscale framework, has recently turned out as a promising strategy able to guarantee the accurate 

description of molecular interactions. Multiscale techniques allow, in fact, the expansion of the time-scale 

and size-scale of current simulations bridging the resolution and dimensionality gap between in silico and 

in vivo – in vitro experiments. These novel features are important for tackling problems such as proteinligand 

recognition and protein-protein interactions in large macromolecular networks, and for efficiently 

integrating experimental inputs in computational atomistic models of biological machines. 

Within this framework, we are currently developing new multiscale schemes for molecular simulations. 

The main idea is based on the partition of the system in regions treated with different accuracy, e.g. 

preserving the atomistic detail where the chemical interactions are important and coarse-graining degrees 

of freedom where they are not relevant for the specific problem of interest. The method has the advantage 

to largely enhance the sampling power of standard molecular simulations, and to preserve the accuracy of 

the calculation. In particular, we have introduced a robust scheme to evaluate electrostatic interactions in 

proteins that uses topological information coming from the 3D structure to reconstruct the full electrostatic 

field from a multipolar expansion of the centers of charge (see Figure). The new scheme is not expensive 

in terms of CPU time, and it is robust with respect to protein dynamics. It has been successfully applied (i) 

to ligand binding recognition (where electrostatics at localized active sites is crucial, (see Figure), (ii) to the 

study of structural rearrangements that might happen in macromolecular assembly and protein networks 

dynamics, and (iii) to the study of protein-protein interactions.


N. B. Publications issued in the frame of the University of Pennsylvania 

Calhoun, J. R., Liu, W., Spiegel, K., Dal Peraro, M., Klein, M. L., Valentine, K. G., Wand, A. J. and 

DeGrado W. F. (2008). Solution NMR structure of a designed metalloprotein and complementary 

molecular dynamics refinement. Structure. 16(2): 210-215 

J. Moran-Barrio, J. M. Gonzalez, M. N. Lisa, A. L. Costello, M. Dal Peraro, P. Carloni, B. Bennett, D. L. 

Tierney, A. S. Limansky, A. M. Viale, and A. J. Vila. (2007). The metallo b-lactamase GOB is a mono- 

Zn(II) enzyme with a novel active site. J Biol Chem, 282(25):18286-18293 

M. De Vivo, B. Ensing, M. Dal Peraro, G. A. Gomez, D. W. Christianson, and M. L. Klein. (2007). Proton 

shuttles and phosphatase activity in soluble epoxide hydrolase. J Am Chem Soc, 129(2):387-394 

M. Dal Peraro, A. J. Vila, P. Carloni, and M. L. Klein. (2007). Role of zinc content on the catalytic 

efficiency of B1 metallo beta-lactamases. J Am Chem Soc, 129(10):2808-2816 

M. Dal Peraro, K. Spiegel, G. Lamoureux, M. D. Vivo, W. F. DeGrado, and M. L. Klein. (2007). Modeling 

the charge distribution at metal sites in proteins for molecular dynamics simulations. 

J Struct Biol, 157(3):444-453 

M. Dal Peraro, P. Ruggerone, S. Raugei, F. L. Gervasio, and P. Carloni. (2007). Investigating biological 

systems using first principles Car-Parrinello molecular dynamics simulations. Curr Opin Struc Biol, 

17(2):149-156. 

D. Bucher, S. Raugei, L. Guidoni, M. Dal Peraro, U. Rothlisberger, P. Carloni, and M. L. Klein. (2006). 

Polarization effects and charge transfer in the KcsA potassium channel. Biophys Chem, 124(3):292-301 

© ACS 

Multiscale description of molecular interactions. ADP moiety (in space-filled 

representation) at the binding site of actin (represented in gray ribbon). Ligand-protein 

interactions are described using a classical all-atom force field within a first shell surrounding 

ADP (depicted in balls-and-sticks representation), whereas the long-range electrostatic 

contribution of the rest of the protein is coarse-grained using a multipolar expansion for the 

contribution of the peptide backbone (yellow dipoles) and the polar side chains (not shown). 

Such an approach has the advantage to largely speed up the computational time needed for a 

given simulation (up to 30 times faster), while preserving the accuracy of the calculation. 


DEPLANCKE LAB 

TEAM MEMBERS 

Julien Bryois, Master Student 

Korneel Hens, Postdoctoral Fellow 

Christina Mattsson, Administrative Assistant 

Jovan Simicevic, PhD Student (since 2008) 

Bart Deplancke 


Since November 2007 


http://deplancke-lab.epfl.ch 


The University of Massachusetts Medical School, 

Worcester, USA (UMassMed)) 

INTRODUCTION 

Gene regulatory networks play a vital role in metazoan development and function, and deregulation of 

these networks is often implicated in disease. The interactions between genes and their respective 

regulatory transcription factors (TFs) that form the basis of gene regulatory networks have however been 

poorly characterized. This is because the transcriptional function of most metazoan TFs, which denotes 

the regulatory elements they bind to, the genes they regulate, the transcriptional consequence of their 

DNA interactions, and the transcriptional complexes in which they function, remains unknown. 

The overall goal of our Laboratory of Systems Biology and Genetics is to reverse engineer the gene 

regulatory networks that control metazoan development and function. 

Our main research goals are : 

- to identify the regulatory elements that control mammalian gene expression, and the TFs that bind to 

them using high-throughput technologies 

- to model the dynamic properties of gene regulatory circuitries to make predictions on how specific 

regulatory networks will behave under different physiological or pathological conditions such as cancer, 

neurodegenerative diseases, and the metabolic syndrome 

- to develop novel and innovative tools to detect and monitor protein-DNA interactions in vivo. 


The recent availability of genomic resources for multiple model organisms has permitted the development 

of novel methodologies that probe gene regulatory networks at a systems rather than at the individual 

gene level. During my post-doctoral research, we developed such a method (Deplancke et al. Genome 

Res., 2004), based on the conventional yeast one-hybrid (Y1H) assay, that complements current TFcentered 

gene regulatory network mapping techniques such as ChIP-chip. 

A key break-through in the development of this patented high-throughput protein-DNA interaction 

detection method was the generation of a screening library that solely consists of TFs specific for the 

metazoan organism of interest, which significantly increases the efficiency of Y1H screens. In 2007, we 

have been further transforming our Y1H system to increase its overall capacity and simplify the pipeline. 

For this purpose, we developed a novel Steiner triple system-based smart-pooling strategy, which allows 

the simple and rapid testing of the majority of TFs of specific model organisms using two simple screens 

(e.g. Vermeirssen, Deplancke et al., Nature Meth., 2007). The versatility of the strategy should also allow 

a straight-forward adaptation to screen TFs in other systems and, likely, other biomolecules and assays 

as well. 

In 2008, our laboratory aims to further increase the throughput of our system to tackle the transcriptional 

complexity inherent of mammalian organisms. We will implement an automatic liquid handling platform to 

perform Y1H screens in 384 instead of the manual 96 well plate format that is used today. Our main goal 

is to initiate the mapping of mouse gene regulatory networks for which we are currently building a 

comprehensive TF resource.


N. B. Publications issued in the frame of the University of Massachusetts Medical School, W. 

A. Mukhopadhyay*, B. Deplancke*, A.J.M. Walhout, H.A. Tissenbaum. Chromatin immunoprecipitation 

(ChIP) coupled to detection by quantitative real-time PCR to study transcription factor binding to DNA in 

Caenorhabditis elegans. Nature Protocols, 3:698-709, 2008. (*, shared first authorship) 

V. Vermeirssen*, B. Deplancke*, I. Barrasa*, J.S. Reece-Hoyes*, N.J. Martinez, H.E. Arda, C.A. Grove, 

A.J.M. Walhout. A C. elegans transcription factor array and Steiner Triple System-based smart pools: 

high-performance tools for transcription regulatory network mapping, Nature Methods, 4:659-664, 2007. 

(*, shared first authorship) 

B. Deplancke, V. Vermeirssen, H.E. Arda, N.J. Martinez, A.J.M. Walhout. Gateway-compatible yeast onehybrid 

screens. Cold Spring Harbor Protocols, October 2006. 

B. Deplancke, A. Mukhopadhyay, W. Ao, A.M. Elewa, C.A. Grove, N.J. Martinez, R. Sequerra, L. 

Doucette-Stamm, J.S. Reece-Hoyes, I.A. Hope, H.A. Tissenbaum, S.E. Mango, A.J.M. Walhout. A genecentered, 

C. elegans protein-DNA interaction network, Cell, 125:1193-1205, 2006. 

Preview: Farkas IJ, Beg QK, Oltvai ZN. Exploring transcriptional regulatory networks in the worm. Cell, 

125:1032-4, 2006. 

Y. Wang, S.W. Oh, B. Deplancke, J. Luo, A.J.M. Walhout, H.A. Tissenbaum. C. elegans 14-3-3 proteins 

regulate life span and interact with SIR-2.1 and DAF-16/FOXO. Mechanisms of Aging and 

Development, 127:741-7, 2006. 


HUBBELL LAB 

Jeffrey A. Hubbell 



http://lmrp.epfl.ch 

TEAM MEMBERS 

Myriam Adam, Scientist 

Catharina Adelöw, PhD Student 

Nela Anguelova, Scientific Collaborator 

Carol Anne Bonzon, Administrative Assistant 

Peter Frey, Scientific Advisor (UNIL Professor) 

Jay A. Gantz, Trainee (F.W. Olin College of Eng.) 

Urara Hasegawa, Postdoctoral Fellow 

Nathan Hammond, trainee (MIT) 

Jong Eun Ihm, PhD Student 

Yun Suk Jo, PhD Student 

Peter Käuper, Scientist 

Stephane Kontos, PhD Student 

Iraklis Kourtis, PhD Student (jointly with LMBM) 

Thomas Krähenbühl, PhD Student 

Hans Mattias Larsson, Master Student 

Seung Tae Lee, Postdoctoral Fellow 

Leslie Julie, Trainee (Rice University) 

Kristen Lorentz, PhD Student 

Mateo Ricardo Losada, PhD Student 

Redouan Mahou, PhD Student 

Mikaël Martino, PhD Student 

Lionel Micol, PhD Student 

Mayumi Mochizuki, Postdoctoral Fellow 

Conlin O'Neil, PhD Student 

Miriella Pasquier, Laboratory Assistant 

Jennifer Patterson, Postdoctoral Fellow 

Rubin Berek Pisarek, PhD Student 

Ana-Maria Popa, PhD Student (CSEM Neuchâtel) 

Brian Pullin, PhD Student 

Sai Reddy, PhD Student 

Dominique André Rothenfluh, PhD Student 

Catherine Schütz, PhD Student 

Eleonora Simeoni, Scientist 

Stephanie Traub, Trainee 

André Van der Vlies, Postdoctoral Fellow 

Diana Velluto, Postdoctoral Fellow 

Loïc Wagnière, Apprentice chemistry Lab. Assistant 

Christine Wandrey, PhD, MER 

Lirong Yang, PhD Student 

INTRODUCTION 

The Laboratory for Regenerative Medicine and Pharmacobiology operates at the interface of the 

chemical and biological sciences, developing novel materials for use in regenerative medicine, in drug 

delivery, in nonviral delivery for gene drugs, and in vaccines and immunotherapeutics. We envision novel 

synthetic and biological materials based on designed physicochemical or biological activity, we synthesize 

or recombinantly express these materials, and we evaluate them in realistic three-dimensional culture 

models or in animal models of disease. As examples of our areas of interest and our approaches, we 

engineer variant forms of growth factors and biomaterial matrices for use in inducing angiogenesis and 

triggering other cellular behaviors in skin, bone, and in particular bladder and urinary tract repair; we 

develop novel polyelectrolytes and study their characteristics in solution and as polyelectrolyte complexes 

and applications in bio-encapsulation; we develop novel polymers for delivering hydrophobic drugs in 

cancer and immunotherapy; we develop novel polymers for delivering nucleotide and gene drugs; and we 

develop nanoparticle technology for vaccines and immunotherapeutics. 


Regenerative medicine 

The laboratory made exciting advances in engineering matrix-bound morphogens for conjugation in 

biomaterial matrices for tissue repair and regeneration: IGF-1 variants for use in smooth muscle, VEGF-A 

variants for inducing angiogenesis, fibronectin variants for supporting stem cell differentiation in bone 

repair, and FGF-18 variants for cartilage repair.

Drug and gene delivery 

Chemists, biologists and bioengineers collaborated to push our approaches with block copolymers 

forward in delivering small molecule drugs (such as paclitaxel in cancer, cyclosporine A in 

immunosuppression) and gene-based drugs (both siRNA and plasmid DNA in vitro and in vivo). Polymers 

have been developed to carry these diverse payloads, both alone and in combination. Approaches for 

targeting nanoparticles to tissues such as cartilage were developed. 

Vaccines and immunotherapeutics 

In collaboration with the Laboratory for Mechanobiology and Morphogenesis (Prof. M.A. Swartz), the 

laboratory demonstrated that nanoparticles can be used as a vaccine platform for targeting cells in the 

lymph nodes. This, combined with advanced design of the polymeric nanoparticle surface, may enable a 

new generation of vaccines, highly stable and very economical, for use in both the developing and the 

developed world. The team has demonstrated that ultra-small particles, smaller than biological particles, 

can be swept into the lymphatics within a few minutes of injection, drain to the lymph nodes, and are 

collected there for antigen presentation. 


Bourdillon, D., Freitag, R. & Wandrey, C. Association and temperature-induced phase transition studied 

by analytical ultracentrifugation. Progr. Colloid Polym. Sci 2006, 150-157 (2007 

Cerritelli, S., Velluto, D. & Hubbell, J.A. PEG-SS-PPS: Reduction-sensitive disulfide block copolymer 

vesicles for intracellular drug delivery. Biomacromolecules 8, 1966-1972 (2007) 

Ehrbar, M., Rizzi, S.C., Hlushchuk, R., Djonov, V., Zisch, A.H., Hubbell, J.A., Weber, F.E. & Lutolf, M.P. 

Enzymatic formation of modular cell-instructive fibrin analogs for tissue engineering. Biomaterials 28, 

3856-3866 (2007) 

Ehrbar, M., Rizzi, S.C., Schoenmakers, R.G., San Miguel, B., Hubbell, J.A., Weber, F.E. & Lutolf, M.P. 

Biomolecular hydrogels formed and degraded via site-specific enzymatic reactions. Biomacromolecules 

8, 3000-3007 (2007) 

Hubbell, J.A. Matrix-bound growth factors in tissue repair. Swiss Medical Weekly 137, Suppl. 155: 172S- 

176S (2007) 

Malinova, V. & Wandrey, C. Loading polyelectrolytes onto porous microspheres: Impact of molecular and 

electrochemical parameters. J. Phys. Chem. B 111, 8494-8501 (2007) 

Mercanzini, A., Reddy, S.T., Velluto, D., O'Neil, C.P., Maillard, A., Bensadoun, J.C., Bertsch, A., Hubbell, 

J.A. & Renaud, P. Controlled releaes drug coatings on flexible neural probes. Conf. Proc. IEEE Eng. 

Med. Biol. Soc. 1, 6612-6615 (2007) 

Oberson, C., Boubaker, A., Ramseyer, P., Meyrat, B.F. & Frey, P. Endoscopic and surgical treatment,of 

vesico-ureteral reflux in children. Swiss Medical Weekly 137, 471-475 (2007) 

Panayitou, M., Pohner, C., Vandevyver, C., Wandrey, C., Hilbrig, F. & Freitag, R. Synthesis and 

characterisation of thermo-responsive poly(N,N '-diethylacrylamide) microgels. Reactive & Functional 

Polymers 67, 807-819 (2007) 

Raeber, G.P., Lutolf, M.P. & Hubbell, J.A. Mechanisms of 3-D migration and matrix remodeling of 

fibroblasts within artificial ECMs. Acta Biomater. 3, 615-629 (2007) 

Ramseyer, P., Meagher-Villemure, K., Burki, M. & Frey, P. (Poly)acrylonitrile-based hydrogel as a 

therapeutic bulking agent in urology. Biomaterials 28, 1185-1190 (2007) 

Reddy, S.T., van der Vlies, A.J., Simeoni, E., Angeli, V., Randolph, G.J., O'Neill, C.P., Lee, L.K., Swartz, 

M.A. & Hubbell, J.A. Exploiting lymphatic transport and complement activation in nanoparticle vaccines. 

Nat. Biotechnol. 25, 1159-1164 (2007) 

Rintoul, I. & Wandrey, C. Magnetic field effects on the free radical solution polymerization of acrylamide. 

Polymer 48, 1903-1914 (2007) 

Roman, I., Vilalta, M., Rodriguez, J., Matthies, A.M., Srouji, S., Livne, E., Hubbell, J.A., Rubio, N. & 

Blanco, J. Analysis of progenitor cell-scaffold combinations by in vivo non-invasive photonic imaging. 

Biomaterials 28, 2718-2728 (2007)

Segura, T. & Hubbell, J.A. Synthesis and in vitro characterization of an ABC triblock copolymer for siRNA 

delivery. Bioconj. Chem. 18, 736-745 (2007) 

Segura, T., Schmokel, H. & Hubbell, J.A. RNA interference targeting hypoxia inducible factor 1 alpha 

reduces post-operative adhesions in rats. J. Surg. Res. 141, 162-170 (2007) 

Walpoth, B.H., Zammaretti, P., Cikirikcioglu, M., Khabiri, E., Djebaili, M.K., Pache, J.C., Tille, J.C., 

Aggoun, Y., Morel, D., Kalangos, A., Hubbell, J.A. & Zisch, A.H. Enhanced intimal thickening of expanded 

polytetrafluoroethylene grafts coated with fibrin or fibrin-releasing vascular endothelial growth factor in the 

pig carotid artery interposition model. J. Thorac. Cardiovasc. Surg. 133, 1163-1170 (2007) 

Billinger, M., Buddenberg, F., Hubbell, J.A., Elbert, D.L., Schaffner, T., Mettler, D., Windecker, S., Meier, 

B. & Hess, O.M. Polymer stent coating for prevention of neointimal hyperplasia. J. Invasive Cardiol. 18, 

423-426 (2006) 

Bourdillon, D., Hunkeler, D. & Wandrey, C. The analytical ultracentrifuce for the characteriation of 

polydisperse polyelectrolytes. Progr. Colloid Polym. Sci 2006, 141-149 (2006) 

Danielsson, C., Ruault, S., Basset-Dardare, A. & Frey, P. Modified collagen fleece, a scaffold for 

transplantation of human bladder smooth muscle cells. Biomaterials 27, 1054-1060 (2006) 

Danielsson, C., Ruault, S., Simonet, M., Neuenschwander, P. & Frey, P. Polyesterurethane foam scaffold 

for smooth muscle cell tissue engineering. Biomaterials 27, 1410-1415 (2006) 

Hubbell, J.A. 3D engineered ECM analogues for studying cell behaviour and engineering tissue healing. 

J. Anat. 209, 567-568 (2006) 

Hubbell, J.A. Matrix-bound growth factors in tissue repair. Swiss Medical Weekly 136, 387-391 (2006) 

Hubbell, J.A. Multifunctional polyplexes as locally triggerable nonviral vectors. Gene Ther. 13, 1371-1372 

(2006) 

Lussi, J.W., Falconnet, D., Hubbell, J.A., Textor, M. & Csucs, G. Pattern stability under cell culture 

conditions - A comparative study of patterning methods based on PLL-g-PEG background passivation. 

Biomaterials 27, 2534-2541 (2006) 

Missirlis, D., Hubbell, J.A. & Tirelli, N. Thermally-induced glass formation from hydrogel nanoparticles. 

Soft Matter 2, 1067-1075 (2006) 

Missirlis, D., Kawamura, R., Tirelli, N. & Hubbell, J.A. Doxorubicin encapsulation and diffusional release 

from stable, polymeric, hydrogel nanoparticles. Eur. J. Pharm. Sci. 29, 120-129 (2006) 

Paolo, E.R., Stoetter, H., Cotting, J., Frey, P., Gebri, M., Beck-Popovic, M., Tolsa, J.F., Fanconi, S. & 

Pannatier, A. Unlicensed and off-label drug use in a Swiss paediatric university hospital - A pilot study. 

Swiss Medical Weekly 136, 218-222 (2006) 

Reddy, S.T., Rehor, A., Schmoekel, H.G., Hubbell, J.A. & Swartz, M.A. In vivo targeting of dendritic cells 

in lymph nodes with poly(propylene sulfide) nanoparticles. J. Controlled Release 112, 26-34 (2006) 

Reddy, S.T., Swartz, M.A. & Hubbell, J.A. Targeting dendritic cells with biomaterials: developing the next 

generation of vaccines. Trends Immunol. 27, 573-579 (2006) 

Reidy, M., Zihlmann, P., Hubbell, J.A. & Hall, H. Activation of cell-survival transcription factor NF kappa B 

in L1Ig6-stimulated endothelial cells. J. Biomed. Mater. Res. 77A, 542-550 (2006) 

Rizzi, S.C., Ehrbar, M., Halstenberg, S., Raeber, G.P., Schmoekel, H.G., Hagenmuller, H., Muller, R., 

Weber, F.E. & Hubbell, J.A. Recombinant protein-co-PEG networks as cell-adhesive and proteolytically 

degradable hydrogel matrixes. Part II: Biofunctional characteristics. Biomacromolecules 7, 3019-3029 

(2006) 

Trentin, D., Hall, H., Wechsler, S. & Hubbell, J.A. Peptide-matrix-mediated gene transfer of an oxygeninsensitive 

hypoxia-inducible factor-1 alpha variant for local induction of angiogenesis. Proc. Natl. Acad. 

Sci. U. S. A. 103, 2506-2511 (2006)

Wandrey, C. Polyelectrolytes - Functionality by synergism of electrostatic interaction and chain 

architecture. Kgk-Kautschuk Gummi Kunststoffe 59, 669-677 (2006) 

Zisch, A.H., Ehrbar, M., Hubbell, J., Raeber, G., Schnell, C. & Walpoth, B. Biomimetic materials for 

injectable tissue engineering: studies of acute, lasting and unexpected angiogenesis response. FASEB J. 

20, A20-A21 (2006) 


LUTOLF LAB 

TEAM MEMBERS 

Myriam Cordey, Postdoctoral Fellow 

Steffen Cosson, Masters Student 

Samy Gobaa, Postdoctoral Fellow 

Stefan Kobel, PhD Student 

Monika Limacher, Masters Student 

Katarzyna Mosiewicz, PhD Student 

Andrea Negro, Masters Student 

Chiara Paviolo, Masters Student 

Adrian Ranga, PhD Student 

Chia Tan, Masters Student 

Matthias Lutolf 


Since February 2007 


http://lscb.epfl.ch 


Stanford University, School of Medicine, Ca., USA 

INTRODUCTION 

Tissue homeostasis and regeneration are critically dependent on a limited number of adult stem cells, 

their self-renewal capability and their commitment to differentiated cells. Due to these unique properties, 

stem cells hold enormous potential for the treatment of many diseases. Despite extensive research on 

elucidating molecular stem cell regulation, significant hurdles need to be overcome before stem cells can 

be used for therapy. Arguably one of the greatest challenges is controlling stem cell behavior outside of 

the body, as this would for example allow expanding them to sufficient numbers. Adult stem cells reside in 

specialized niches, comprised of complex mixtures of extracellular cues delivered by support cells in close 

proximity. Niches protect stem cells from rapid differentiation and regulate the delicate balance between 

self-renewal and differentiation. The mechanisms by which niches regulate stem cells remain poorly 

defined in mammals, mainly because of the difficulties in manipulating these intricate microenvironments 

in vivo. 

Research in the Laboratory of Stem Cell Bioengineering is at interface of stem cell biology and 

biomolecular engineering to gain fundamental insight into how protein components of tissue-specific 

microenvironments, termed niches, control the behavior of multipotent adult stem cells. 

We develop novel technologies to biochemically and structurally deconstruct in vivo niches, and 

reconstruct them in vitro, creating well-defined artificial stem cell niches as novel paradigms to decipher 

adult stem cell regulation. We are using these platforms as tools to probe the biochemical stem cell-niche 

crosstalk. This research will yield insights into the dynamics of stem cell fate changes in response to 

extrinsic protein signals, and may spawn new strategies for stem cell-based therapies. 


The main LSCB goals in 2007 (start up: February 2007) have been: 

- Recruitment of strong team members, 

- Acquisition and installation of key lab infrastructure, 

- Acquisition of substantial amount research funding, 

- Start of experimental activities. 

These goals have been achieved. 


N. B. Publications issued in the frame of Stanford University, School of Medicine 

Lutolf, M.P. and Blau, H.M., Control of adult stem cell function by their niche and by bioengineered 

artificial niches, Book chapter, Advances in Tissue Engineering, in press 

Lutolf, M.P. and Hubbell, J.A., Synthetic biomaterials as cell-responsive artificial extracellular matrices, 

Book chapter, Advances in Tissue Engineering, in press 

Ehrbar, M., Rizzi, S.C., Schoenmakers, R., Hubbell, J.A., Weber, F.E., Lutolf, M.P. (2007) Biomolecular 

Hydrogels Formed and Degraded via Site-Specific Enzymatic Reactions. Biomacromolecules. 8 (10), 

3000 -3007

Raeber, G.P., Lutolf, M.P. and Hubbell, J.A. (2007) Fibroblasts preferentially migrate in the direction of 

principal strain, Biomechanics and Modeling in Mechanobiology. Jul 7; DOI 10.1007/s10237-007- 

0090-1 

Ehrbar, M., Rizzi, S.C., Hlushchuk, R., Djonov, V., Zisch, A.H., Hubbell, J.A., Weber, F.E., and Lutolf, M.P. 

(2007) Enzymatic formation of modular cell-instructive synthetic fibrin analogs for tissue engineering. 

Biomaterials. 2007 Sep;28(26):3856-66 

Raeber, G.P., Lutolf, M.P. and Hubbell, J.A. (2007) Mechanisms of 3-D migration and matrix remodeling 

of fibroblasts within artificial ECMs. Acta Biomaterialia. Sep;3(5):615-29 


STERGIOPULOS LAB 

Nikolaos Stergiopulos 



http://lhtc.epfl.ch 

TEAM MEMBERS 

Luca Augsburger, PhD Student 

Michel Bachmann, Engineer 

Rafaela Fernandes da Silva, Postdoctoral Fellow 

Edouard Fonck, PhD Student 

Alec Ginggen, PhD Student 

Philippe Reymond, PhD Student 

Rana Saitta-Rezakhaniha, PhD Student 

Tamina Sissoko, Administrative Assistant 

Sylvain Roy, PhD Student 

Tyler Thatcher, PhD Student 

Alkiviadis Tsamis, PhD Student 

INTRODUCTION 

The Laboratory of Hemodynamics and Cardiovascular Technology (LHTC) focuses on the relation 

between blood flow and the development, progression and regression of cardiovascular disease. 

Development of vascular implants and non-invasive or mini-invasive technologies for the diagnosis and 

treatment of cardiovascular disease is also a major objective. 


Hemodynamics 

We studied the effect of compliance on isolated porcine carotids perfused ex vivo under physiological 

flows and we showed that reduced cyclic stretch leads to endothelial disfunction and further accentuates 

the effects of plaque-prone hemodynamics 

We analyzed the major determinants of pressure transfer from a peripheral artery (clinical measurement 

site) to the aorta and we found out that the most influencial parameter is the local wave speed. This ay let 

us improve or personalize the transfer function characteristics as applied on a “per patient” basis. 

Vascular Mechanics 

We studied alterations in histology and biomechanical properties of the human thoracic and abdominal 

aorta. We applied our in house developed constituent-based strain energy function to analyze the 

contribution of the different wall components on the apparent biomechanical properties of the aorta during 

aging. We found that a significant part of the compliance decrease with aging is attributed to profound 

changes in the collagen engagement properties. Collagen appears to engage at less stretch and more 

abruptly, leading thus to a stiffer aorta. 

We developed a theoretical model for the prediction of wall remodelling in response to acute hypertension. 

Stress-driven geometrical remodelling and compliance-driven collagen remodelling laws were applied to 

yield the remodelling rate equations describing the evolution of geometry and material properties. 

Plausible results in good agreement with experimental data show that the model, despite its simplicity, 

provides an interesting theoretical basis for studying wall remodelling dynamics. 


Westerhof BE, Guelen I, Stok WJ, Wesseling KH, Spaan JA, Westerhof N, Bos WJ, and Stergiopulos N. 

Arterial pressure transfer characteristics: effects of travel time. Am J Physiol Heart Circ Physiol 292: 

H800-807, 2007 

Tugulu S, Silacci P, Stergiopulos N, and Klok HA. RGD-Functionalized polymer brushes as substrates for 

the integrin specific adhesion of human umbilical vein endothelial cells. Biomaterials 28: 2536-2546, 

2007 

Jegger D, Mallik AS, Nasratullah M, Jeanrenaud X, da Silva R, Tevaearai H, von Segesser LK, and 

Stergiopulos N. The effect of a myocardial infarction on the normalized time-varying elastance curve. 

J Appl Physiol 102: 1123-1129, 2007 

Fonck E, Prod'hom G, Roy S, Augsburger L, Rufenacht DA, and Stergiopulos N. Effect of elastin 

degradation on carotid wall mechanics as assessed by a constituent-based biomechanical model. 

Am J Physiol Heart Circ Physiol 292: H2754-2763, 2007 

Jegger D, da Silva RF, Lartaud I, Gaillard V, Jeanrenaud X, Nasratullah M, von Segesser LK, Atkinson J, 

Segers P, Tevaearai H, and Stergiopulos N. Effects of an aging vascular model on healthy and diseased 

hearts. Am J Physiol Heart Circ Physiol 293: H1334-1343, 2007

Thacher T, Gambillara V, Da Silva R, Montorzi G, Stergiopulos N, and Silacci P. Oscillatory shear stress 

and reduced compliance impair vascular functions. Clin Hemorheol Microcirc 37: 121-130, 2007 

Zulliger MA and Stergiopulos N. Structural strain energy function applied to the ageing of the human 

aorta. J Biomech 40: 3061-3069, 2007 

Tsamis A and Stergiopulos N. Arterial Remodeling in Response to Hypertension Using a Constituentbased 

Model. Am J Physiol Heart Circ Physiol 293: H3130-3139, 2007 

da Silva RF, Chambaz C, Stergiopulos N, Hayoz D, and Silacci P. Transcriptional and post-transcriptional 

regulation of preproendothelin-1 by plaque-prone hemodynamics. Atherosclerosis 194: 383-390, 2007 

Jegger D, Jeanrenaud X, Nasratullah M, Chassot PG, Mallik A, Tevaearai H, von Segesser LK, Segers P, 

and Stergiopulos N. Noninvasive Doppler-derived myocardial performance index in rats with myocardial 

infarction: validation and correlation by conductance catheter. Am J Physiol Heart Circ Physiol 

290: H1540-1548, 2006 

Jegger D, da Silva R, Jeanrenaud X, Nasratullah M, Tevaearai H, von Segesser LK, Segers P, Gaillard V, 

Atkinson J, Lartaud I, and Stergiopulos N. Ventricular-arterial coupling in a rat model of reduced arterial 

compliance provoked by hypervitaminosis D and nicotine. Am J Physiol Heart Circ Physiol 291: H1942- 

1951, 2006 

Gambillara V, Chambaz C, Montorzi G, Roy S, Stergiopulos N, and Silacci P. Plaque-prone 

hemodynamics impair endothelial function in pig carotid arteries. Am J Physiol Heart Circ Physiol 

290: H2320-2328, 2006 

Claessens TE, Georgakopoulos D, Afanasyeva M, Vermeersch SJ, Millar HD, Stergiopulos N, Westerhof 

N, Verdonck PR, and Segers P. Nonlinear isochrones in murine left ventricular pressure-volume loops: 

how well does the time-varying elastance concept hold Am J Physiol Heart Circ Physiol 290: H1474- 

1483, 2006 

Flow and pressure waveforms as measured in vivo with MRI and applanation 

tonometry in a group of young volunteers (top panels) as compared to 

predictions of a generalized 1-D model of the entire systemic circulation. All 

features are reproduced faithfully, giving solid evidence that the 1-D model can 

capture and reproduce well the pressure and flow wave propagation phenomena 

in the arterial tree. 


SWARTZ LAB 

Melody Swartz 



http://lmbm.epfl.ch 

TEAM MEMBERS 

Marie Ballester, Master Student 

Véronique Borel, Technician 

James Brandon Dixon, Postdoctoral Fellow 

Mark Fleury, PhD Student 

Didier Foretay, Technician 

Ulrike Haessler, PhD Student 

Amine Issa, PhD Student 

Iraklis Kourtis, PhD Student 

Ingrid Margot, Administrative Assistant 

Dimana Miteva, PhD Student 

Jan Overney, PhD Student 

Miriella Pasquier, Technician 

Sandeep Rangunathan, Master Student 

Sai Reddy, PhD student 

Joseph Rutkowski, PhD Student 

Elena Seminati, Erasmus Student (Polit. di Milano) 

Adrian Chung-Kai Shieh, Postdoctoral Fellow 

Jacqueline Shields, Postdoctoral Fellow 

Alice Anna Tomei, PhD student 

Carolyn Yong, PhD Student 

INTRODUCTION 

Cancer metastasis, lymphedema, lipid transport, and immune cell function all depend on lymphatic 

function or dysfunction, and are all tied to interstitial fluid balance and transport. The lymphatic system is 

part of the circulation; it drains fluid, solutes, and macromolecules from the interstitial space and returns 

them to the blood. It also is a critical component of the immune system; immune cells traffic through 

lymphatic vessels and reside in lymph nodes, where they communicate with each other and can become 

activated. Cancer cells also utilize lymphatic vessels, and likely interstitial flow, to spread to distant sites 

throughout the body. Lymphedema occurs when lymphatic function is not optimal, and causes irreversible 

tissue remodeling that becomes exacerbated with time and for which there is no cure or treatment, other 

than massage and bandaging. Finally, since lymphatic vessels drain lipids (in the form of chylomicrons) 

from the gut, they play important roles in lipid trafficking and possibly metabolism. Despite its importance, 

the regulatory biology of lymphatic function is poorly understood. Furthermore, lymphatic drug delivery 

holds great potential because of localized targeting of lymph nodes, where one might target metastasized 

cancer cells, deliver imaging agents, or deliver immunomodulatory drugs to immune cells; this great 

potential is underexploited. 


Morphogenesis and directional cell migration processes are typically thought of strictly in terms of 

diffusional models – cells migrating up concentration gradients of growth factors and cytokines. We have 

determined, first based on theoretical considerations and then by experimentation in vitro and in vivo, that 

this model is only a part if the picture, and potentially a small part. In 2007, we have focused considerable 

attention on understanding how convection, in particular flow in the interstitium between the blood 

capillaries and the lymphatic capillaries, can induce morphogenetic processes such as blood- and 

lymphangiogenesis, and tumor and dendritic cell migration into the lymphatics. We determined that the 

same biophysical phenomena control these diverse physiological and pathophysiological processes. 

Essentially, we determined that cells can sense the direction of flow by emitting their own morphogens, 

and then sensing how interstitial flow biases the concentration gradients of these signals; when the 

signals are matrix-binding, this phenomenon can be amplified, by flow bias of both the signal and the cellderived 

proteases that liberate the signal from its bound state. 

As an example of how this phenomenon operates, we showed that tumor cells find and migrate toward the 

lymphatics, their primary route of escape in tumor metastasis, by sensing flow via self-secreted CCR7 

ligands (Shields et al, Cancer Cell, 2007), and also that dendritic cells do the same (unpublished). Dogma 

held that they migrated toward directional signals secreted by the lymphatics, but analysis of this concept 

based on first principles revealed flaws, in that the rate of diffusion away from the lymphatics is 

considerably slower than the rate of convection back into the lymphatics (flow is always in the direction of 

the lymphatics). Thus this new mechanism can explain how immune cells and tumor cells can efficiently 

home to the nearest draining lymphatic vessel.

We also completed a study to elucidate the relative effects of biomechanical (fluid flow) and biochemical 

signaling in lymphangiogenesis (Goldman et al, FASEB J, 2007). VEGFR-2 and VEGFR-3 are both 

receptors for VEGF-C and VEGF-D (the most potent activators of lymphangiogenesis), and it was not 

clear whether these receptors were redundant for VEGF-C signaling or whether they had cooperative 

signaling roles. Using a novel wound-healing model of adult lymphangiogenesis in the mouse with 

function blocking antibodies, we first showed that fluid flow was an organizational cue in 

lymphangiogenesis, and that once lymphatic endothelial cell growth was initiated, lymphatic organization 

could proceed apparently unaltered without VEGFR-3. Then we demonstrated that VEGFR-3 and 

VEGFR-2 were both required for lymphatic proliferation and migration, early growth cues in 

lymphangiogenesis, while only one or the other (but not both) for lymphatic organization. Instead, 

interstitial flow was required and necessary for lymphatic endothelial organization into functional vessels. 

This has implications in strategies to either block or enhance lymphatic growth, both of which are being 

explored therapeutically to treat tumor metastases (e.g., blocking VEGFR-3) or attempting to enhance 

lymphatic growth to treat lymphedema patients. 

In 2007, we also continued our work with in vitro lymphangiogenesis using interstitial flow and matrixbound 

growth factors to characterize differences between modulators of blood and lymphatic 

angiogenesis in vitro (Helm et al, Biotech & Bioeng, 2007). Specifically we showed that the morphologies 

of each depend strongly on the matrices used, and that each requires different matrices, despite their 

similarities in vitro. This has important implications for tissue engineering of blood and lympahtic 

capillaries and is the first to characterize such differences. Also, along the lines of slow interstitial fluid flow 

through a 3D matrix, we completed a computational study to determine the relationship between average 

velocity and shear and pressure forces on matrix vs cells (Pedersen et al, J Biomech). We found that peak 

shear stresses were much higher than previously thought, and that the architecture of the matrix strongly 

dictates the stresses felt by a cell. This would explain local matrix remodeling to stress-shield the cells and 

also provides guides for estimating the stresses imposed by interstitial flow used in our other studies. 

Finally, together with the Laboratory for Regenerative Medicine and Pharmacobiology, we explored in 

2007 means by which to exploit the phenomenon of interstitial flow to target immunotherapeutics into the 

lymphatics and thus to the lymph node (Reddy et al, Nature Biotechnol, 2007). We determined that 

ultrasmall polymer nanoparticles, ca. 20 nm in diameter, were capable of being swept into the lymphatics 

by interstitial flow. Using this approach, we could deliver antigen to the dendritic cells in the lymph nodes 

much more efficiently than any other known approach. Furthermore, when the surface of the nanoparticle 

was complement-activating and coupled to a model antigen, an immune response could be potently 

elicited (antibody titers and T cell response). This opens the door for new approaches to vaccines for both 

infectious diseases and cancer.


ST Reddy, AJ van der Vlies, E Simeoni, V Angeli, GJ Randolph, MA Swartz, and JA Hubbell (2007). 

Exploiting lymphatic transport and complement activation in nanoparticle vaccines. Nature Biotechnol. 

25(10):1159-64 

JD Shields, ME Fleury, C Yong, AA Tomei, GJ Randolph, and MA Swartz (2007). Autologous chemotaxis 

as a mechanism of tumor cell homing to lymphatics via interstitial flow and autocrine CCR7 signaling. 

Cancer Cell 11:526-538. comment J. Cell Biol. 178:4) 

AL Thawgawng, RS Ruoff, MA Swartz, and MR Glucksberg (2007). An ultra-thin PDMS membrane as a 

bio/micro-nano interface: fabrication and characterization. Biomed Microdevices. 9(4):587-95 

ME Fleury and MA Swartz (2007). Interstitial flow and its effects in soft tissues. Annu. Rev. Biomed. Eng. 

9:229-56 

J Goldman, JM Rutkowski, JD Shields, MC Pasquier, Y Cui, HG Schmoekel, S Wiley, DJ Hicklin, B 

Pytowksi, and MA Swartz (2007). Cooperative and redundant roles of VEGFR-3 and VEGFR-2 signaling 

in adult lymphangiogenesis. FASEB J. 21(4):1003-12 

J Goldman, KA Conley, A Raehl, DM Bondy, B Pytowski, MA Swartz, JM Rutkowksi, DB Jaroch, and EL 

Ongstad (2007). Regulation of lymphatic capillary regeneration by interstitial flow in skin. Am. J. Physiol, 

Heart Circ. Physiol. 292(5):H2176-83 

AL Thawgawng, MA Swartz, MR Glucksberg, and RS Ruoff (2007). Bond-detach lithography: A method 

for micro/nanolithography by precision PDMS patterning. Small 3 (1): 132-138 

JM Rutkowski and MA Swartz (2007). A driving force for change: Interstitial flow as a morphoregulator. 

Trends Cell Biol. 17(1):44-50 

CE Helm, AH Zisch, and MA Swartz (2007). Engineered blood and lymphatic capillaries in 3D VEGFfibrin-collagen 

matrices with interstitial flow. Biotech. Bioeng. 96(1):167-176 

JA Pedersen, F Boschetti, and MA Swartz (2007). Effects of extracellular matrix architecture on velocity 

and shear stress profiles on cells within a 3-D collagen matrix. J. Biomech. 40:1484-92 

ST Reddy, MA Swartz, and JA Hubbell (2006). Targeting dendritic cells with biomaterials: Developing the 

next generation of vaccines. Trends Immunol. 7(12):573-9 

ST Reddy, DA Berk , RK Jain , and MA Swartz (2006). A sensitive in vivo model for quantifying interstitial 

transport of injected macromolecules and nanoparticles. J. Appl. Physiol. 101(4):1162-9 

MM Choe, AA Tomei, and MA Swartz (2006). 3D culture model of the human airway mucosa. 

Nature Protocols 1:357-362 

JM Rutkowski, M Moya, J Johannes, J Goldman, and MA Swartz (2006). Secondary lymphedema in the 

mouse tail: lymphatic hyperplasia, VEGF-C upregulation, and the protective role of MMP-9. Microvasc. 

Res. 72:161-171 

JM Rutkowski, KC Boardman, and MA Swartz (2006). Characterization of lymphangiogenesis in a model 

of adult skin regeneration. Am. J. Physiol. Heart Circ. Physiol. 291: H1402–H1410 

ME Fleury, KC Boardman, and MA Swartz (2006). Autologous morphogen gradients by subtle interstitial 

flow and matrix interactions. Biophys. J. 91(1) 113–121 

MM Choe, PHS Sporn, and MA Swartz (2006). Extracellular matrix remodeling by dynamic strain in a 3D 

airway wall model. Am. J. Resp. Cell Mol. Biol. 35(3):306-13 

LG Griffith and MA Swartz (2006). Capturing complex 3D tissue physiology in vitro. Nature Rev. Mol. Cell 

Biol. 7:211-224 

ST Reddy, A Rehor, HG Schmoekel, JA Hubbell, and MA Swartz (2006). Targeting dendritic cells in lymph 

nodes with PPS-PEG nanoparticles. J. Contr. Rel. 112(1):26-34 

CP Ng and MA Swartz. (2006). Mechanisms of interstitial flow-induced remodeling of fibroblast-collagen 

cultures. Ann. Biomed. Eng. 34(3):446-54 

LG Griffith, MA Swartz, and RT Tranquillo (2006). Education for careers in tissue engineering and 

regenerative medicine. Ann. Biomed. Eng. 34(2):265-9 


WURM LAB 

Florian A. Wurm 



http://lbtc.epfl.ch 

Protein Expression Core Facility 

http://pecf.epfl.ch 

TEAM MEMBERS 

Adam Myriam, Senior Scientist 

Bachmann Virginie, Technical Assistant 

Backliwal Gaurav, PhD Student 

Baldi Lucia, Senior Scientist 

Cevey Jean, Technical Assistant 

Chenuet Sébastien, PhD Student 

Cole Harriet, Trainee, HESSO Sion 

Delegrange Fanny, PhD Student 

Divorne Marie-France, Administrative Assistant 

Fernandez Garcia Isabel, Trainee 

Engelhardt Eva Maria, PhD Student 

Elsenary Faisal, Trainee, HESSO Sion 

Hacker David, Senior Scientist 

Kiseljak Divor, Internship Student 

Küttel Ivan, Trainee, HES-SO Sion 

Meerschman Carine, Technician 

Nallet Sophie, PhD Student 

Oberbek Agata, PhD Student 

Stettler Matthieu, PhD Student 

Wulhfard Sarah, PhD Student 

Zhang Xiaowei, PhD Student 

INTRODUCTION 

Mammalian cells are now considered the most versatile and productive host system for the manufacture 

of recombinant proteins for pharmaceutical applications. In support of this economically important area, 

the goal of the Laboratory of Cellular Biotechnology (LBTC) is to develop new technologies for (i) the 

large-scale production of recombinant proteins by transient transfection of mammalian cells, (ii) the rapid 

generation of high-producing recombinant cell lines, and (iii) the scalable cultivation of mammalian cells in 

serum-free suspension by orbital shaking. 

EQUIPMENT 

We have a fully functional top-of-the-line cell culture bioreactor facility including 3-, 28- and 150-L stirredtank 

bioreactors with accessory sterilization equipment. We also have numerous shaker and incubator 

systems for suspension cell cultivation using orbital shaking. We have developed “scale-down” systems 

for suspension cultures that are crucial for high-throughput applications for research on bioprocess 

conditions. More recently, orbital shaker technology has been scaled-up to 2’000 L with a custom-made 

research bioreactor. We have also developed orbitally shaken helical track bioreactors at both small- and 

large-scale. 


Large-scale transient gene expression 

With our two main production hosts, Chinese hamster ovary (CHO) and human embryo kidney (HEK 293) 

cells, we are developing novel methods to increase transient protein production following DNA delivery 

with the cationic polymer polyethylenimine (PEI). For both cell lines, we discovered that by controlling cell 

growth after transfection, either by exposure to sub-optimal temperatures (CHO) or to a combination of 

negative cell cycle regulators (HEK 293), we could enhance the transient production of recombinant 

proteins. In turn, these findings meant that it was possible to perform transfections at high cell densities 

since the lack of cell growth substantially reduced nutrient limitations of the medium. We now can achieve 

transient recombinant protein yields in 100 mg/L range with these two host cell lines. This technology has 

been applied to the first transient production of a recombinant subunit vaccine against a human pathogen 

through a project funded by the Swiss Innovation Agency KTI/CTI. 

Generation of high-producing cell lines 

The establishment of recombinant CHO-derived cell lines remains a time-consuming and labor-intensive 

process. We are attempting to make this process more efficient by improving gene delivery and genetic 

selection methods. We have characterized many cell lines derived from either chemical (PEI and calcium 

phosphate) or physical (microinjection) DNA delivery methods. Among these gene transfer methods, only 

microinjection allows the experimenter to control of the amount and timing of DNA delivery into the nucleus. We 

have also explored methods to quickly select cell lines and determine their stability of recombinant protein 

expression. Many of these cell lines have been evaluated at the cytogenetic level through a collaboration with 

researchers at the CHUV in Lausanne. The results have provided new insights into the kinetics of DNA 

integration in CHO-derived cell lines.

Orbital shaking technology for the cultivation of animal cells in suspension 

We have developed novel disposable bioreactor systems using orbital shaking technology to reduce the 

cost and shorten the time needed for recombinant protein production. This recently developed technology 

has been successfully scaled up to 100 L and is being tested at the 2’000 L scale in a custom-designed 

disposable bioreactor. As a twist on the same theme, we have developed a new mixing strategy using 

orbitally shaken helical track bioreactors. We have demonstrated that the helical track on the inside wall 

of the cylindrical container enhances fluid mixing and gas transfer in orbitally shaken cultures. We are 

actively engaged in studying cell physiology, fluid dynamics, and process control in these systems. 

Cellular activity is influenced in a major way by such “simple” external factors as pH, oxygen level, 

osmolarity, ionic strength, and temperature. Also, gas transfer, mixing, shear force, and medium viscosity 

play enormous roles in determining cellular capacity for protein production. These aspects are particularly 

relevant in large-scale bioreactors. This project has been funded through the Swiss Innovation Agency 

KTI/CTI. 

Our experience with mammalian cell culture allowed us to be involved in a EU-funded tissue engineering 

project aimed at the preparation of biologically compatible scaffolds for the growth of human urinary tract 

epithelial cells. Recombinant CHO cell lines expressing extracellular matrix proteins were cultivated on 

various polymers for deposition of the protein product on the polymer; the CHO cells were then removed 

and epithelial cells seeded and expanded on the polymer. 

The LBTC has been the home of the Protein Expression Core Facility (PECF) since its creation in 

2006. The PECF provides services for recombinant protein expression from both mammalian and 

bacterial hosts, scale-up of hybridoma cultures for monoclonal antibody production, and affinity protein 

purification. 

Two 5-L cultures of suspension-adapted CHO cells 

on an orbital shaker in 10-L disposable biotainers. 

We are developing orbital shaking technology as an 

economical and highly efficient approach for the 

research-scale production of recombinant proteins. 

The batch cultivation of a stable cell line in such a 

system allowed us to obtain between 100 and 500 

mg of recombinant protein in 10 days. 

(Stettler et al. 2007). 


Stettler M, Zhang X, Hacker DL, De Jesus M, Wurm FM. Novel orbital shake bioreactors for transient 

production of CHO derived IgGs. Biotechnol Prog. 2007 Nov-Dec;23(6):1340-6

Wurm FM. Manufacturing of biopharmaceuticals and implications for biosimilars. Kidney Blood Press 

Res. 2007;30 Suppl 1:6-8 

Hildinger M, Baldi L, Stettler M, Wurm FM. High-titer, serum-free production of adeno-associated virus 

vectors by polyethyleneimine-mediated plasmid transfection in mammalian suspension cells. 

Biotechnol Lett. 2007 Nov; 29 (11):1713-21 

Ehrmann K, Pataky K, Stettler M, Wurm FM, Brugger J, Besse PA, Popovic R. NMR spectroscopy and 

perfusion of mammalian cells using surface microprobes. Lab Chip. 2007 Mar;7(3):381-3 

Ehrmann K, Saillen N, Vincent F, Stettler M, Jordan M, Wurm FM, Besse PA, Popovic R. Microfabricated 

solenoids and Helmholtz coils for NMR spectroscopy of mammalian cells. Lab Chip. 2007 Mar; 7(3):373- 

80 

Muller N, Derouazi M, Van Tilborgh F, Wulhfard S, Hacker DL, Jordan M, Wurm FM. Scalable transient 

gene expression in Chinese hamster ovary cells in instrumented and non-instrumented cultivation 

systems. Biotechnol Lett. 2007 May; 29(5):703-11 

Baldi L, Hacker DL, Adam M, Wurm FM. Recombinant protein production by large-scale transient gene 

expression in mammalian cells: state of the art and future perspectives. Biotechnol Lett. 2007 May; 

29(5):677-84 

Bertschinger M, Backliwal G, Schertenleib A, Jordan M, Hacker DL, Wurm FM. Disassembly of 

polyethylenimine-DNA particles in vitro: implications for polyethylenimine-mediated DNA delivery. 

J Control Release. 2006 Nov; 116(1):96-104 

Grosjean F, Bertschinger M, Hacker DL, Wurm FM. Multiple glycerol shocks increase the calcium 

phosphate transfection of non-synchronized CHO cells. Biotechnol Lett. 2006 Nov; 28(22):1827-33 

Lehnert, T., Nguyen, D., Baldi, L., and Gijs, M.A. Glass reflow on 3-dimensional micro-apertures for 

electrophysiological measurements on-chip. Microfluidics and Nanofluidics. 2007, 3 (1) 109-17 

Bertschinger M, Burki C, Backliwal G, Hacker DL, Jordan M, Wurm FM. Polyethylenimine-based quality 

control assay for plasmid DNA. Anal Biochem. 2006 Sep 15; 356(2):309-11 

Stettler M, Jaccard N, Hacker D, De Jesus M, Wurm FM, Jordan M. New disposable tubes for rapid and 

precise biomass assessment for suspension cultures of mammalian cells. Biotechnol Bioeng. 2006 Dec 

20; 95(6):1228-33 

Derouazi M, Flaction R, Girard P, de Jesus M, Jordan M, Wurm FM. Generation of recombinant Chinese 

hamster ovary cell lines by microinjection. Biotechnol Lett. 2006 Mar; 28(6):373-82 

Derouazi M, Martinet D, Besuchet Schmutz N, Flaction R, Wicht M, Bertschinger M, Hacker DL, 

Beckmann JS, Wurm FM. Genetic characterization of CHO production host DG44 and derivative 

recombinant cell lines. Biochem Biophys Res Commun. 2006 Feb 24; 340(4):1069-77 

Hacker, D.L., Cohen, L., Muller, N., Thanh, H.-P., Derow, E., Ritter, G., and Wurm, F.M. (2007). 

Development of a transient mammalian expression process for the production of cancer testis antigen NY- 

ESO-1, pp. 125-128. In Cell Technology for Cell Products. R. Smith (Ed.). Springer, Dordrecht, 

The Netherlands 

Bertschinger, M., Hacker, D., and Wurm, F.M. (2007). The role of the sumoylation pathway in transient 

and stable recombinant protein expression in Chinese hamster ovary cells, pp. 129-132. 

In Cell Technology for Cell Products. R. Smith (Ed.). Springer, Dordrecht, The Netherlands 

Derouazi, M., Martinet, D., Besuchet, N., Flaction, R., Wicht, M., Bertschinger, M., Hacker, D., Beckmann, 

J., and Wurm, F.M. (2007). Stability and cytogenetic characterization of recombinant CHO cell lines 

established by microinjection and calcium phosphate transfection, pp. 443-446. In Cell Technology for 

Cell Products. R. Smith (Ed.). Springer, Dordrecht, The Netherlands 

Stettler, M., DeJesus, M., Ouertatani-Sakouhi, H., Engelhardt, E.-M., Muller, N., Chenuet, S., 

Bertschinger, M., Baldi, L., Hacker, D., Jordan, M., and Wurm, F.M. (2007). 1000 non-instrumented 

bioreactors in a week, pp. 489-495. In Cell Technology for Cell Products. R. Smith (Ed.). Springer, 

Dordrecht, The Netherlands 

Hacker, D.L., and Wurm, F.M. (2007). Protein production in mammalian cells. In The Encyclopedia of 

Life Sciences, John Wiley and Sons, New York 


IBI – CO-AFFILIATED RESEARCH GROUPS - SCHOOL OF BASIC SCIENCES 

HATZIMANIKATIS LAB 

TEAM MEMBERS 

Ljubisa Miskovic, Postdoctoral Fellow 

Romero Luis Miery Teran, Research Assistant 

Marilisa Neri, Postdoctoral Fellow 

Vassily Hatzimanikatis 



http://lcsb.epfl.ch 

INTRODUCTION 

The members of the Laboratory of Computational Systems Biotechnology (LCSB) develop and apply 

mathematical and computational methods for the study of complex cellular processes, such as metabolic 

pathways, signal transduction networks, and genetic networks. 


The PI and members of the LCSB led the development and publication of the first genome-scale 

thermodynamic analysis of a microorganism (E. coli). They also developed a thermodynamics-based 

metabolic flux analysis method. 

Bioinformatics, 21 (8), 1603-1609 (2005) 


N. B. 2006 research work carried out partially at Northwestern University and at the EPFL 

Adam M. Feist, Chris S. Henry, Jennifer L. Reed, Markus Krummenacker, A. R. Joyce, Peter D. Karp, 

Linda J. Broadbelt, Vassily Hatzimanikatis, and Bernhard O. Palsson. (2007) A genome-scale metabolic 

reconstruction for Escherichia coli K-12 MG1655 that accounts for 1261 ORFs and thermodynamic 

information. Molecular Systems Biology, 3: Art. No. 121 

C.S. Henry, L.J. Broadbelt, V. Hatzimanikatis. (2007) Thermodynamics-based Metabolic Flux Analysis, 

Biophysical Journal, 92 (5), 1792-1805 (2007) 

Hermioni Zouridis and Vassily Hatzimanikatis. (2007). A model for protein translation: Polysome selforganization 

leads to maximum protein synthesis rates. Biophysical Journal, 92 (3), 717-730 

Reuben Thomas, Carlos J. Paredes, Sanjay Mehrotra, Eleftherios T. Papoutsakis and Vassily 

Hatzimanikatis. (2007) A model-based optimization framework for the inference of regulatory interactions 

using time-course DNA microarray expression data. BMC Bioinformatics, 8:22

C. S. Henry, M. D. Jankowski, L. J. Broadbelt and V. Hatzimanikatis. (2006). Genome-scale 

Thermodynamics Analysis of E. coli metabolism. Biophysical Journal, 90 (4), 1453-1461 

A. Mehra and V. Hatzimanikatis.(2006) An algorithmic framework for genome-wide modeling and analysis 

of translation networks. Biophysical Journal, 90 (4), 1136-1146 

Joanna Gonzalez-Lergier, Linda J. Broadbelt and Vassily Hatzimanikatis (2006) Analysis of the Maximum 

Theoretical Yield for the Synthesis of Erythromycin Precursors in Escherichia coli. Biotechnology and 

Bioengineering, 95 (4), 638-644 

T. R. Rieger, R. I. Morimoto and V. Hatzimanikatis. (2006) Bistability can explain threshold phenomena in 

protein aggregation both in vitro and in vivo. Biophysical Journal, 90 (3), 886-895 

L. Wang and V. Hatzimanikatis (2006) Metabolic Engineering Under Uncertainty. I: Framework 

Development. Metabolic Engineering, 8 (2), 133-141 

L. Wang and V. Hatzimanikatis (2006) Metabolic Engineering Under Uncertainty. II: Analysis of Central 

Carbon Metabolism in S. cerevisiae. Metabolic Engineering, 8 (2), 142-159 


JOHNSSON LAB 

Kai Johnsson 



http://isic.epfl.ch/ 

TEAM MEMBERS 

Sambashiva Banala, PhD Student 

Michael Bannwarth, Postdoctoral Fellow 

Karolina Bojkowska, PhD Student 

Matthias Brun, Phd Student 

Christopher Chidley, PhD Student 

Claudia Gasparini, Administrative Assistant 

Arnaud Gautier, Postdoctoral Fellow 

Marlon Hinner, Postdoctoral Fellow 

Damien Maurel, Postdoctoral Fellow 

Evelyne Muller, Postdoctoral Fellow 

Simone Schmitt, Postdoctoral Fellow 

Agostina Ruggiu, PhD Student 

INTRODUCTION 

The availability of the complete genome sequence of an organism presents the exciting opportunity to 

characterize the entire set of its encoded proteins. Confronted with the large numbers of genes of 

unknown function there is an urgent and generally acknowledged need to develop innovative approaches 

to study protein function in vivo and in vitro. The research undertaken at the Laboratory of Protein 

Engineering addresses this need by developing and applying chemical approaches to characterize the 

movement, interactions and chemical microenvironment of proteins inside the living cell and in vitro. We 

have introduced two general methods for the covalent and specific labelling of fusion proteins with 

chemically diverse compounds that open up new ways of studying and manipulating proteins. Current 

projects focus on the further development of these and similar approaches and their application to 

selected biological problems that cannot be resolved by traditional approaches. 


We have introduced a method for the simultaneous labelling of proteins in living cells. We have introduced 

a method for the selective crosslinking of fusion proteins in living cells as tool to study protein-protein 

interactions. We have introduced a new method for in vitro protein evolution based on a covalent chemical 

genotype-phenotype linkage. 


Chemical probes shed light on fusion proteins Helen O’Hare, Kai Johnsson, Arnaud Gautier, Current 

Opinions in Structural Biology, 17, 488-94 (2007) 

A Covalent Chemical Genotype-Phenotype Linkage for in vitro Protein Evolution Viktor Stein, India Sielaff, 

Kai Johnsson, Florian Hollfelder, ChemBioChem, 8, 2191-2194 (2007) 

Chemical tools for biomolecular imaging” Nils Johnsson, Kai Johnsson, ACS Chemical Biology, 2, 31-38 

(2007) 

Inducing and sensing protein-protein interactions in living cells via selective crosslinking Guillaume 

Lemercier, Susanne Gendreizig, Maik Kindermann, Kai Johnsson, 

Angewandte Chemie, 46, 4281-4285 (2007) 

Evolving the substrate specificity of O 6 -alkylguanine-DNA alkyltransferase through loop insertion for 

applications in molecular imaging” Christian Heinis, Simone Schmitt, Maik Kindermann, Guillaume Godin, 

Kai Johnsson, ACS Chemical Biology, 1, 575-584 (2006) 

Post-translational covalent labeling reveals heterogeneous mobility of individual G protein-coupled 

receptors in living cells, Michael Prummer, Bruno H. Meyer, R. Franzini, Jean-Manuel Segura, Nathalie 

George, Kai Johnsson, Horst Vogel, ChemBioChem 7, 908-11 (2006)

Chimeric streptavidins with reduced valencies Guillaume Lemercier, Kai Johnsson, 

Nature Methods 3, 247-8 (2006) 

Directed evolution of O 6 -alkylguanine-DNA alkyltransferase for applications in protein labeling” Thomas 

Gronemeyer, Christopher Chidley, Alexandre Juillerat, Christian Heinis and Kai Johnsson, Protein Eng. 

Des. Sel. 19, 309-318 (2006), 

FRET imaging reveals that functional neurokinin-1 receptors are monomeric and reside in membrane 

microdomains of live cells” Bruno H. Meyer, Jean-Manuel Segura, Karen L. Martinez, Ruud Hovius, 

Nathalie George, Kai Johnsson, Horst Vogel, Proc. Natl. Acad. Sci., 103, 2138-43 (2006) 

Covalent labeling of cell surface proteins for in vivo FRET studies Bruno H. Meyer, Karen L. Martinez, 

Jean-Manuel Segura, Pedro Pascoal, Ruud Hovius, Nathalie George, Kai Johnsson, Horst Vogel, FEBS 

Lett. 580, 1654-8 (2006) 

Protein function microarrays based on self-immobilizing and self-labeling fusion proteins India Sielaff, 

Anke Arnold, Guillaume Godin, Stefano Tugulu, Harm-Anton Klok and Kai Johnsson, ChemBioChem, 7, 

194-202 (2006) 

Simultaneous and specific pulse-chase labeling 

of different cell wall proteins in budding yeast 


IBI – CO-AFFILIATED RESEARCH GROUPS - SCHOOL OF ENGINEERING 

AMINIAM LAB 

Kamiar Aminian 

Adjunct Professor 


http://lmam.epfl.ch 

TEAM MEMBERS 

Danielle Alvarez, Administrative Asssistant 

Brian Coley, PhD Student 

Julien Chardonnens, PhD Student 

Julien Favre, PhD Student 

Raluca Lidia Ganea, PhD Student 

Jean Gramiger, Technician 

Anisoara Ionescu, Scientific Collaborator 

Albin Kujawa, Technician 

Benoît Le Callennec, Postdoctoral Fellow 

Pascal Morel, Technician 

R Hossein ouhani, Phd Student 

Arash Salarian, Postdoctoral Fellow 

Shimba Saccio, Trainee 

MEDICAL ADVISOR 

Brigitte Jolles-Haeberli, Adjunct Professor 

INTRODUCTION 

The translational research in the Laboratory of Movement Analysis and Measurement aims to move 

engineering research into clinical applications. We are particularly interested to characterize the changes 

in movement ability in terms of type of pathology: osteoarthritis, pain and movement disorder, etc. Our 

research consists in measuring and modelling human body movements and postures in everyday 

conditions. We develop wearable technology for long-term monitoring of physical activity and gait analysis 

by recording biomechanical signals detected by body fixed sensors. We use advanced signal processing 

to devise new methods for activity recognition, to extract disease related features hidden in human 

movement and to classify movement disorders by modelling the dynamics of human movement. 

The following clinical fields involving the locomotion system are concerned: 

Outcome evaluation in orthopaedics and Sport Biomechanics 

Providing objective assessment of gait and motor function changes after treatment, performance 

evaluation in athletes and sport injury prevention. This activity is supported by a convention between 

EPFL and “Division de l’appareil locomoteur” (DAL) of the Lausanne University Hospital (CHUV). 

Fall prevention in elderly 

Objective evaluation of risk of fall and change of motor function with age, design of new tools for 

rehabilitation in aging population. 

Neurology and movement disorders 

Accurate and early detection of movement disorder such as Parkinson disease, wearable and in home 

monitoring of disease progression. 

Physical activity and Quality of Life 

Providing new insight in both the disability and the decreased QoL associated with a large variety of 

disorders and their treatment, understanding how symptoms vary over the course of days or week. 

LAB FACILITIES 

EPFL-DAL Gait lab in CHUV, camera based motion capture system, force-plate, pressure insoles, inertial 

sensors, Electromygram monitor, bi-canal fluoroscopy and Radio Stereometric Analysis (RSA). 


Outcome evaluation in orthopaedics and Sport Biomechanics 

Shoulder function has been evaluated during daily activity in healthy subjects and in patients before and 

after surgery. We have shown the improvement of shoulder mobility (frequency and intensity) and its 

“endurance” (higher arm position with longer period) after surgery

By performing spatial and temporal synchronization of our measurements systems (camera, force-plate, 

pedobarograph and inertial sensors) we have provided a comprehensive study of multi-segment foot 

kinematics and have shown that foot kinematics can be accurately measured by these instruments using 

three segments. 

We have designed and validated a new ambulatory system to measure accurately knee joint orientation 

using body fixed inertial sensors. We have analyzed knee joints function in ACL-deficient patients before 

and after reconstructive surgery. 

Simulated ski jump has been studied in lab, and a new method has been devised for body posture 

orientation reconstruction using five inertial sensors worn by the athlete. We have reached a precision of 

1° during in-run phase and 2° during takeoff. 

Fall prevention in elderly 

By grouping elderly subjects into fit and frail groups, we have shown that the two groups differ significantly 

in many characteristics, including measures of falls-efficacy, functional, gait, and mobility performance. 

Preliminary analyses confirmed our hypothesis that subjects in the lower quartile of falls efficacy had 

about twice higher odds to qualify for frail/pre-frail status, independent of gait speed and variability, 

comorbidity, and functional status. 

The “complexity of the movement” has been assessed by the fractal dimension of the kinematics pattern 

of trunk motion during Sit-to Stand/Stand-to-Sit transitions. This complexity differed significantly when 

comparing fit and frail elderly persons, confirming our initial hypothesis that complexity of kinematical 

pattern during postural transfer could objectively discriminate between subjects with various health 

conditions, including frail subjects prone to falls. 

Neurology and movement disorders 

Long-term physical activity was reliably monitored in Duchenne Muscular Dystrophy (DMD) patients in 

their home environment and showed a trend towards improvement after steroid treatment. The time spent 

“on feet” (walking & standing) and the number of 2 minutes continuous walking episodes increased 

significantly. Fractal analysis of the sequence of daily walking periods revealed a more structured pattern 

after treatment suggesting a kind of improved temporal organization (distribution of long walking episodes 

over the monitoring time). 

We have designed a totally automatic and instrumented method for analysis of “Get up and Go test” in 

Parkinsonian patients. This included detection and analysis of gait, sit-to-stand and turning phases. Some 

of the parameters measured by our method showed significant differences between patients and controls 

and some of them showed signs of evolution of Parkinson’s during 12 th month. 

Physical activity and Quality of Life 

Although quantitative physical activity data is, to some extent, available for people living in western 

countries there is no such information regarding rural areas in emerging countries. We have designed a 

new wearable device usable in rough environment such as the rural conditions that prevail in Ifakara, 

Tanzania. A comparative analysis in Tanzanian farmers showed a higher physical activity in men as the 

time percent spent walking and the total number of steps were higher for men. However, physical activity 

parameters which can be associated with working tasks showed comparable figures between men and 

women. The nonlinear analysis shows that the fluctuations of physical activity patterns display fractal 

temporal organization characterized by power law decaying temporal correlations.


A. Salarian, H. Russmann, F. Vingerhoets , P. R. Burkhard, K Aminian, Ambulatory monitoring of physical 

activities in patients with Parkinson’s disease , IEEE Transactions on Biomedical Engineering, 2296- 

2299, 2007 

ED. de Bruin, B. Najafi, K. Murer, D. Uebelhart, K. Aminian, Quantification of everyday motor function in a 

geriatric population, Journal of Rehabilitation Research and Development, 44, 417-428, 2007 

W. Zijsltra, K. Aminian, Mobility assessment in older people; new possibilities and challenges, 

Eur J Aging, 4, 3-12, 2007 

B. Coley, BM. Jolles, A. Farron, A. Bourgeois, F. Nussbaumer, C. Pichonnaz, K. Aminian, Outcome 

Evaluation in Shoulder Surgery using 3D Kinematics Sensors, Gait & Posture, 25, 523-532, 2007 

A. Salarian, H. Russmann, C. Wider, P. R. Burkhard, F. Vingerhoets , K Aminian, Quantification of tremor 

and bradykinesia in Parkinson’s disease using a novel ambulatory monitoring system, 

IEEE Transactions on Biomedical Engineering, 54, 313-322, 2007 

J Favre, F Luthi, BM Jolles, O Siegrist, B Najafi, K. Aminian, A new ambulatory system for comparative 

evaluation of the three dimensional knee kinematics, applied to anterior cruciate ligament injuries, journal 

of Knee Surgery, Sports Traumatology, Arthroscopy, 14, 592–604, 2006 

V. Dubost, F. Herrmann, RW Kressig, K. Aminian, B. Najafi, O. Beauchet. Relationships between dualtask-related 

changes in stride velocity and stride time in healthy older adults, Human Movement science, 

25, 372-382, 2006 

J. Favre, BM. Jolles, O. Siegrist, K. Aminian, 'Quaternion based fusion of gyroscopes and accelerometers 

to improve 3D angles measurement', Electronics letters, 42, 612, 2006 

H. Dejnabadi, BM Jolles, E. Casanova, P. Fua, K. Aminian, Estimation and Visualization of Sagittal 

Kinematics of Lower Limbs Orientation using Body-Fixed Sensors, IEEE Transactions on Biomedical 

Engineering, 53, 1385-1393, 2006 

K. Aminian, Human movement capture and their clinical applications, Invited Chapter in “Computational 

Intelligence for Movement Sciences: Neural Networks, Support Vector Machines and other Emerging 

Techniques ”, Editors: Begg, RK and Palaniswami, M. Idea Group Inc., USA, Chapter 3, 101-138, 2006 

U. Lindemann , C. Becker, I. Unnewehr, R. Muche, K. Aminian, H. Dejnabadi, Th. Nikolaus, W. Puhl, K. 

Huch, KE. Dreinhöfer, Gait analysis and WOMAC are complementary in assessing functional outcome in 

total hip replacement, Clin. Rehabil., 20, 5, 413-420, 2006 


PIOLETTI LAB 

Dominique Pioletti 



http://lbo.epfl.ch 

TEAM MEMBERS 

Martin Aeberhard, Scientific Collaborator 

Ana Borges de Couraça, PhD Student 

Miguel Gortchacow, PhD Student 

Sandra Jaccoud, Lab Technician 

Francesco Merlini, Engineer 

Virginie Kokocinski, Administrative Assistant 

Nathalie Krattinger, Postdoctoal Fellow 

Lee Ann Laurent-Applegate, Group Leader 

Aurélie Quintin, PhD Student 

Silvio Ramondetti, Scientific Assistant 

Alireza Roshan Ghias, PhD Student 

Corinne Scaletta, Lab Technician 

Vincent Stadelmann, PhD Student 

Alexandre Terrier, Group Leader 

Arne Vogel, PhD Student 

MEDICAL ADVISORS 

Farron Alain - Schizas Constantin 

Zambelli Pierre-Yves 

VISITING SCIENTIST 

Tenorio Holanda Diene Maria 

INTRODUCTION 

The Lab of Biomechanical Orthopedics (LBO) has four field of research: tissue engineering of musculoskeletal 

tissues, implant and joints biomechanics, drug delivery system and mechano-biology. 

A combination of biomechanical and biological approaches is used to describe and understand the 

different clinical problems of interest such as bone loss following total joint arthroplasty, arthritis or 

intervertebral disc degeneration. Based on these analysis, original solutions are developed such as fetal 

cell therapy, scaffold with high mechanical properties or orthopaedic implant used as drug delivery 

system. 

A strong collaboration exists between the LBO and the “Département de l’Appareil Locomoteur (DAL)” at 

the CHUV allowing a translation of research results to clinical applications. 


The feasibility of using fetal cells for bone tissue engineering was demonstrated in an in vivo study. In 

parallel, a biomechanical analysis of an in vivo study in sheep demonstrated that the permeability value of 

a bone scaffold has to be controlled to favor an osteoinduction. 

Based on a biomechanical model, it was possible to propose a drug concentration on an implant to induce 

an optimal osteointegration and this concentration has been validated by an in vivo study. 

The numerical musculoskeletal model of the shoulder previously developed in the lab has been extended 

to predict the mobility, the force, and the pressure of the glenohumeral joint with anatomical and nonanatomical 

prostheses. Different improvements of these prostheses have been proposed. Several 

methods have been tested to better estimate the muscular activity during typical movements. The 

methods acquired for the shoulder have been reused to develop a musculoskeletal model of the knee 

joint. This knee model has been used to evaluate the biomechanical consequences of ACL rupture. 


N. A. Ramaniraka, P. Saunier, O. Siegrist and D.P. Pioletti Biomechanical evaluation of intra-articular and 

extra-articular procedures in anterior cruciate ligament reconstruction: A finite element analysis. 

Clinical Biomechanics, 22(3), 336-343 (2007) 

A. Quintin, N. Hirt-Buri, C. Scaletta, C. Schizas, D.P. Pioletti and L.A. Applegate Consistency of fetal cell 

banks for research and clinical use. Cell Transplantation, 16, 675-684 (2007) 

A. Terrier, A. Vogel, M. Capezzali and A. Farron. An algorithm to allow humerus translation in the 

indeterminate problem of shoulder abduction. Medical Engineering & Physics, 22(6), 645-651 (2007) 

A. Terrier, A. Reist, A. Vogel and A. Farron Effect of supraspinatus deficiency on humerus translation and 

glenohumeral contact force during abduction. Clinical Biomechanics, 22(6), 645-651 (2007)

G. Georgiou, L. Mathieu, D.P. Pioletti, P.-E. Bourban, J.-A. Månson, J.C. Knowles and S.N. Nazhat 

Polylactic acid-phosphate glass composite foams as scaffolds for tissue engineering. 

J Biomed Mater Res B, 80-B, 322-331 (2007) 

D. P. Pioletti, M.O. Montjovent, P.Y. Zambelli and L. Applegate Bone tissue engineering using fetal cell 

therapy. Swiss Medical Weekly, 136, 557-560 (2006) 

Y. T. Konttinen, T.M. Wright, R. Trebse, M. Takagi, M. Silbermann, J. Salo, C. Rieker, D.P. Pioletti, T. 

Ogino, L. Nordsletten, R. Lappalainen, W. Jiranek, S.B. Goodman, E. Gomez-Barrena, K.D. Draenert and 

P. Aspenberg Total joint replacement and aseptic loosening. Helix Review Series Rheumatology, 

11, 98-102 (2006) 

A. Farron, A. Terrier and P. Büchler Risks of loosening of a prosthetic glenoid implanted in retroversion. 

Journal of Shoulder and Elbow Surgery, 15(4), 521 (2006) 

A. Terrier, P. Büchler and A. Farron Influence of glenohumeral conformity on glenoid stresses after total 

shoulder arthroplasty Journal of Shoulder and Elbow Surgery, 15(4), 512-520 (2006) 

B. Peter, O. Gauthier, S. Laib, B. Bujoli, J. Guicheux, P. Janvier, G.H. van Lenthe, R. Muller, P.Y. 

Zambelli, J.M. Bouler and D.P. Pioletti Local delivery of bisphosphonate from coated orthopedic implants 

increases implants mechanical stability in osteoporotic rats. J Biomed Mater Res A, 76(1), 133-43 (2006) 

L.M. Mathieu, T.L. Mueller, P.E. Bourban, D.P. Pioletti, R. Muller and J.A. Manson Architecture and 

properties of anisotropic polymer composite scaffolds for bone tissue engineering. Biomaterials, 27(6), 

905-16 (2006) 

Contact pressure on the polyethylene component for the anatomical (top) and reversed (bottom) prosthesis every 

30 degrees of abduction in the scapular plane. The contact pressure on the reversed polyethylene cup is 20 times 

lower and mainly located on its inferior aspect. 

Histological femoral sections of 4 

different mice 2 months after 

implantation in their condyles of a 

scaffold with and without human fetal 

bone cells. Black indicates new bone 

formation. 


PSALTIS LAB 

TEAM MEMBERS 

James Adleman, PhD Student 

Jae-Woo Choi, PhD Student 

Alexandre Goy, PhD Student 

Rachel Grange, Postdoctoral Fellow 

Chia-Lung Hsieh, PhD Student 

Konstantinos Makris, Postdoctoral Fellow 

Carole Loeffen Berthet, Administrative Assistant 

Ye Pu, Postdoctoral Fellow 

Wuzhou Song, PhD Student 

Andreas Vasdekis, Postdoctoral Fellow 

Demetri Psaltis 



Dean of the School of Engineering 

http://lo.epfl.ch 


California Institute of Technology (Caltech), 

Pasadena, Ca., USA 

INTRODUCTION 

The Optics Laboratory is mainly active in optofluidic devices, imaging applications with nanoparticles 

markers and nonlinear optics. 


Optofluidics 

Fluids are used to synthesize novel optical systems. The optical properties of fluids can be modified by 

chemical synthesis relatively easily and the insertion of fluids in the optical path specifies or adapts the 

functionality of the optical system. One of the approaches we are pursuing is the integration of microfluidic 

circuits with photonic structures that contain voids into which fluids are injected. Another approach is the 

use of colloidal solutions of nanoparticles. Electrical fields or light beams redistribute the nanoparticles and 

modify the optical properties of the structure. Liquid dyes injected into microfluidic chips provide the optical 

gain necessary for building a dye laser on a chip. We develop molecular photonics for lab-on-a-chip 

applications, where the light source is integrated for imaging or sensing. We develop lasers, based on 

fluidics and organic dyes. The gain is in the fluid and is optically pumped. The fabrication is a critical point, 

to this end we have developed PDMS fabrication capabilities and nano-lithography using the electron 

beam. 

Imaging applications with nanoparticles as markers 

Second harmonic generation (SHG) from nanoparticles is opening new types of imaging applications. 

Those nanoparticles can be used as markers to label biological cells and allow for better detection 

techniques. In contrast to fluorescent markers such as green fluorescent protein (GFP) or quantum dots 

(QD), both limited by photobleaching, Second Harmonic Radiation IMaging Probe (SHRIMP) emits a 

stable signal over a long time owing to the lack of real energy state transition. The femtosecond response 

allows for observing fast dynamic process, such as protein conformation. Moreover the coherent nature of 

SHG enables us to capture three-dimensional (3D) information in single frame by recording hologram at 

the doubled optical frequency. We worked with BaTiO 3 and LiNbO 3 nanoparticles as well as KNbO 3 

nanowires. 

Nonlinear optics 

We are studying theoretical and experimental nonlinear propagation of femtosecond pulses in 3-D media. 

The nonlinearity produces very distinctive diffraction patterns such as self focusing and solitary waves 

(waves that remain stable as the beam propagates). The research is mainly on nonlinear optics with 

evanescent waves, filament formation, modulation and transverse instabilities, non-paraxial nonlinear 

optics with emphasis in subwavelength imaging and nonlinear wave propagation in fluidic devices.


N.B. All 2006 publications issued in the frame of Caltech 

Theory of resonantly enanced near-field imaging, Tsang M, Psaltis D, Optics Express, Vol.15 (19), 

pp 11959-11970, Sep 2007 

Optical parametric generation in periodically poled KTi0P04 via extended phase matching, Pu Y, Wu J, 

Tsang M, Psaltis D, Applied Physics Letters, Vol 91 (13): Article 131120, Sep 24, 2007 

Nanoimprinted circular grating distributed feedback dye laser, Chen Y, Li Z, Zhang Z, Psaltis D, Scherer 

A, Applied Physics Letters, Vol. 90, Article 051109, Jul 31, 2007 

Trapping of dielectric particles with light-induced space-charge fields, Eggert HA, Kuhnert FY, Buse K, 

Adleman JR, Psaltis D, Applied Physics Letters, Vol. 90, Article 241909, Jun 12, 2007 

Modulational instability in nonlinearity-managed optical media, Centurion M, Porter MA, Pu Y, Kevrekidis 

PG, Frantzeskakis DJ, Psaltis D, Phys. Rev. A, Vol. 75, Article 063804, Jun 5, 2007 

Optofluidic distributed feedback dye lasers, Li Z, Psaltis D, IEEE Journal of Selected Topics in 

Quantum Electronics, Vol. 13, No. 2, Mar/Apr 2007 

Linear and logarithmic capacities in associative neural networks, Venkatesh S, Psaltis D, 

IEEE Transactions on Information Theory, Vol. 53, No. 2, p. 854, Feb 2007 

Trapping and storage of particles in electroactive microwells, Cordovez B, Psaltis D, Erickson D, 

Applied Physics Letters, Vol. 90, No. 2, Art. No. 024102, Jan 2007 

Modulational Instability in a Layered Kerr Medium: Theory and Experiment, Centurion M, Porter MA, Pu 

Y, Kevrekidis PG, Frantzeskakis DJ, Psaltis D, Pys. Rev, Let., Vol. 97, No. 234101, pp 234101-1 to 

234101-4, Dec 2006 

Slanted hole array beam profiler (SHArP)- a high-resolution portable beam profiler based on linear 

aperture array, Cui XQ, Heng X, Wu JG, Yaqoob Z, Scherer A, Psaltis D, Yang C, Optics Letters, Vol. 

31, No. 21, pp 3161-3163, Nov 2006 

Characterization of Light Collection Through a Subwavelength Aperture From a Point Source 

Heng X, Cui X, Knapp DW, Wu J, Yaqoob Z, McDowell EJ, Psaltis D, Yang C, Optics Express, Vol. 14, 

No. 22, pp 19411-10425, Oct 2006 

Mechanically tunable optofluidic distributed feedback dye laser, Li Z, Zhang Z, Scherer A, Psaltis D, 

Optics Express, Vol. 14, No. 22, pp 10494-10499, Oct 2006 

Optical detection of asymmetric bacteria utilizing electro orientation, Choi J-W, Pu A, Psaltis D, 

Optics Express, Vol 14, Issue 21, pp 9780-9785, Oct 2006 

Optofluidic microscopy--a method for implementing a high resolution optical microscope 

on a chip, Heng X, Erickson D, Baugh LR, Yaqoob Z, Sternberg PW, Psaltis D, Yang C 

Lab on a Chip, No. 6, pp 1274-1276, October 2006 

Holographic capture of femtosecond pulse propagation, Centurion M, Pu Y, Psaltis D 

J. Appl Phys. 100, 063104, 2006 

Reflectionless evanescent-wave amplification by two dielectric planar waveguides, Psaltis D, Mankei 

Tsang, Optics Letters, Vol 31, No 18, pp 2741-2743, September 2006 

Developing optofluidic technology through the fusion of microfluidics and optics, Psaltis D, Quake SR, 

Yang CH, NATURE, Vol. 442 No 27, pp 371-386, July 2006 

Nonlinearity Management in Optics: Experiment, Theory, and Simulation, Centurion M, Porter MA, 

Kevrekidis PG, Psaltis D, Phys. Rev. Let., Vol. 97, No. 033903, pp 033903-3 to 033903-4, July 2006 

Optofluidics can create small, cheap biophotonic devices, with Yang CH, Psaltis D, Laser Focus World, 

pp 85-88, July 2006 

Holographic grating formation in a colloidal suspension of silver nanoparticles, Adleman JR, Eggert HA, 

Buse K, Psaltis D, Optics Letters, Vol.. 31, No. 4, pp 447-449, Feb 2006

Single mode optofluidic distributed feedback dye laser, Li ZY, Zhang ZY, Emery T, Scherer A, Psaltis D, 

Optics Express, Vol. 14, No. 2 pp 696-701, Jan 2006 

Nanofluidic tuning of photonic crystals circuits, Erickson D, Rockwood T, Emery T, Scherer A, Psaltis D, 

Optics Letters, Vol. 31, No. 1, pp 59-61, Jan 2006 

Optofluidic DFB dye laser 

A liquid waveguide cavity with first order Bragg gratings are embedded inside the PDMS 

chip. It can be simply integrated into lab-on-a-chip system exhibits the advantage of low 

cost, compact size, wide wavelength choice and good beam quality. 


GHI - THE GLOBAL HEALTH INSTITUTE 

The Global Health Institute has been created to contribute to the understanding, diagnosis, prevention 

and treatment of infectious diseases, which still claim 18 million lives each year worldwide and account for 

half of the deaths in developing countries. The GHI’s present activities reflect the Institute’s future 

ambitions. Basic mechanisms of host-pathogen interactions and innate immunity towards pathogens are 

being studied using multidisciplinary approaches. Crucial world health issues, like tuberculosis and 

HIV/AIDS, are being tackled. These include understanding, and hopefully counteracting, the persistence 

of Mycobacterium tuberculosis, the causative agent of tuberculosis, or designing drugs to treat this 

disease. Mechanisms of HIV infection and use of this virus in gene therapy approaches are also the 

subject of intense research. All these studies benefit greatly from the innovative and integrated nature of 

the EPFL campus, which provides expertise and training in quantitative and systems biology, and allows 

the use of novel techniques in the field of life sciences. As the still young Institute continues to grow, these 

efforts will be extended to more pathogenic bacteria and viruses as well as to parasites, responsible for 

other major diseases such as malaria 


COLE LAB 

Stewart Cole 


Since June 2007 


Director GHI 

http://cole-lab.epfl.ch 

TEAM MEMBERS 

Philippe Busso, Lab technician 

Jeffrey Chen, Postdoctoral Fellow 

Elizabeth Fullam, Postdoctoral Fellow 

Ravi Gupta, external Student 

Ruben Hartkoorn, Postdoctoral Fellow 

Adamandia Kapopoulou, Postdoctoral Fellow 

Gaëlle Kolly, Student 

Suzanne Lamy, Administrative Assistant 

Jocelyne Lew, Scientific Assistant 

Sophie Magnet, Postdoctoral Fellow 

Iain Old, Project Manager 

Florence Pojer, Postdoctoral Fellow 

Claudia Sala, Postdoctoral Fellow 

Patricia Schneider, Lab Technician 

Swapna Uplekar, PhD Student 


Unité de Génétique Moléculaire Bactérienne 

Institut Pasteur, France 

INTRODUCTION 

A multidisciplinary approach is being used at the Laboratory of Microbial Pathogenesis to tackle major 

public health problems such as tuberculosis (TB) and leprosy. The unit comprises experts in genomics, 

functional genomics, bioinformatics, biochemistry, chemistry and structural biology. Using genome biology 

as a platform we are actively involved in discovering new drugs to treat TB and believe that knowledge 

gained through discovery must be broadly and swiftly disseminated. Given the global importance of the 

TB problem, we are trying to strike the correct balance between competition and collaboration. 


TB Drug Discovery 

The Cole laboratory at EPFL is leading a major effort to discover new drugs for the treatment of 

tuberculosis (TB) as part of an Integrated Project funded by the European Commission for five years from 

January 2006. The New Medicines for Tuberculosis Project, NM4TB, NM4TB aims to discover and 

develop new drugs for the treatment of TB through an integrated approach implemented by a team, that 

combines some of Europe's leading academic TB researchers, with a major pharmaceutical company and 

three SMEs, all with a strong commitment to discovering new anti-infective agents. NM4TB has a 

comprehensive portfolio of potential and validated targets plus several novel, proprietary anti-TB agents in 

its pipeline.

In collaboration with the Biomolecular Screening Platform, led by Dr. Gerardo Turcatti, we are conducting 

innovative whole cell and target-based screens of chemical libraries in order to identify lead compounds. 

These are characterized in terms of their IC50 for the target and MIC for M. tuberculosis; potential 

mutagenicity and cytotoxicity are then evaluated before conducting further pharmacological tests such as 

microsomal stability, cytochrome P450 inhibition and protein binding. Below we describe briefly some of 

the areas under study. 

Signal transduction, phosphorelays and cell wall biosynthesis in M. tuberculosis 

There is mounting evidence that cell growth and elongation is controled by a phosphorelay involving 

serine-threonine protein kinases (STPK) and phosphatases, and forkhead-associated proteins that 

recognize phospho-threonine residues. See figure. We are intensively investigating the biological function 

of PknB, and trying to identify the ligand for this essential receptor kinase, a potential therapeutic target for 

new TB drugs. Downstream signalling partners have been identified and their physiological roles are 

being uncovered. Several enzymes catalysing key steps in cell wall biogenesis are also being intensively 

investigated. 

Protein secretion and pathogenicity 

The ESX-1 protein secretion system is the major virulence determinant operating in M. tuberculosis and 

has been lost by the vaccine strains M. bovis BCG and M. microti. ESX-1 is required for the export of 

small helical-hairpin proteins belonging to the ESAT-6 family as well as other effector proteins of unknown 

function. ESX-1 mediates host cell entry of tubercle bacilli and triggers intercell spread. We are using an 

integrated approach to establish the organisation, architecture and function of this ATP-driven secretory 

apparatus and consider that, despite its non-essentiality, it represents an attractive target for chemical 

biology and drug discovery. 

A regulatory map of the M. tuberculosis genome 

We have adopted an integrated approach to studying gene regulation by using chromatinimmunoprecipitation 

of DNA-binding proteins in conjunction with high density oliogonucleotide-based 

microarrays to map the genome. This is shedding new light on various aspects of the physiology and 

behavior of tubercle bacilli and represents a useful adjunct to transcriptomics in drug discovery, 

particularly in providing clues to mechanism of action. Regulatory information is being incorporated into 

TubercuList, the genome server dedicated to M. tuberculosis http://genolist.pasteur.fr/TubercuList/, for 

which we are the official curators. 

Phylogeography and immunodiagnosis of leprosy 

Despite the massive and highly successful implementation of mulitidrug therapy by the World Health 

Organisation, leprosy remains a serious public health problem in several countries probably due to our 

inability to identify infectious cases early enough. One of our goals is the development of an 

epidemiological tool to monitor transmission of the disease. This uses comparative genomics, particularly 

SNP (single nucleotide polymorphism) and VNTR (variable number tandem repeat analysis of patient 

isolates, to monitor the phylogeography of leprosy. Immunodiagnostic approaches are also being pursued 

in an attempt to establish a test capable of distinguishing between exposure to Mycobacterium leprae and 

infection. 

Gene knock-out 

Essentiality 

Gene knockdown 

Vulnerability 

Druggability 

Chemically tangible startpoint 

Target inhibition 

Stops microbial 

growth 

Efficacy in mice 

Implies cidality 

Efficacy 

in man 

Drug target validation pipeline showing the increasing levels of confidence 


N. B. Unless clearly stated (e.g. : ‘2007, EPFL’) all publications issued in the frame of the Institut Pasteur 

Stinear, T. P., T. Seemann, S. Pidot, W. Frigui, G. Reysset, T. Garnier, G. Meurice, D. Simon, C. 

Bouchier, L. Ma, M. Tichit, J. L. Porter, J. Ryan, P. D. R. Johnson, J. K. Davies, JenkinG.A., P. L. C. 

Small, L. M. Jones, F. Tekaia, F. Laval, M. Daffé, J. Parkhill & S. T. Cole, (2007) Recent adaptation to a 

changed environment inferred from the genome of Mycobacterium ulcerans, the causative agent of Buruli 

ulcer. Genome Res 17: 1-9

Shepard, W., A. Haouz, M. Graña, A. Buschiazzo, J. M. Betton, S. T. Cole & P. M. Alzari, (2007) 

The crystal structure of Rv0813c from Mycobacterium tuberculosis reveals a new family of fatty acid 

binding protein-like proteins in bacteria. J. Bacteriol. 189: 1899-1904 

Prado, S., V. Toum, B. Saint-Joanis, S. Michel, M. Koch, S. T. Cole, F. Tillequin & Y. L. Janin, (2007) 

Antimycobacterial Benzofuro[3,2-f]chromenes from a 5-bromochrome-6-ol. Synthesis 10: 1566-1570 

Prado, S., Y. L. Janin, B. Saint-Joanis, V. Huteau, P. Brodin, S. Michel, M. Koch, S. T. Cole, F. Tillequin & 

P.-E. Bost, (2007) Synthesis and antimycobacterial evaluation of benzofurobenzopyran analogues. 

Bioorg Med Chem 15: 2177-2186 

Marsollier, L., E. Deniaux, P. Brodin, A. Marot, C. M. Wondje, J. P. Saint-Andre, A. Chauty, C. Johnson, 

F. Tekaia, E. Yeramian, P. Legras, B. Carbonnelle, G. Reysset, S. Eyangoh, G. Milon, S. T. Cole & J. 

Aubry, (2007) Protection against Mycobacterium ulcerans lesion development by exposure to aquatic 

insect saliva. PLoS medicine 4: e64 

Marsollier, L., P. Brodin, M. Jackson, J. Kordulakova, P. Tafelmeyer, E. Carbonnelle, J. Aubry, G. Milon, 

P. Legras, J. P. Andre, C. Leroy, J. Cottin, M. L. Guillou, G. Reysset & S. T. Cole, (2007) Impact of 

Mycobacterium ulcerans biofilm on transmissibility to ecological niches and Buruli ulcer pathogenesis. 

PLoS pathogens 3: e62 

Marsollier, L., J. P. Andre, W. Frigui, G. Reysset, G. Milon, B. Carbonnelle, J. Aubry & S. T. Cole, (2007) 

Early trafficking events of Mycobacterium ulcerans within Naucoris cimicoides. Cell Microbiol 9: 347-355 

Grana, M., A. Haouz, A. Buschiazzo, I. Miras, A. Wehenkel, V. Bondet, W. Shepard, F. Schaeffer, S. T. 

Cole & P. M. Alzari, (2007) The crystal structure of M. leprae ML2640c defines a large family of putative 

S-adenosylmethionine-dependent methyltransferases in mycobacteria. Protein Sci 16: 1896-1904 

de Jonge, M. I., T. P. Stinear, S. T. Cole & R. Brosch, (2007) The mycobacteria: a postgenomic view. In: 

Bacterial pathogenomics. M. J. Pallen, K. E. Nelson & G. M. Preston (eds). Washington, DC: ASM Press, 

pp. 49-89 

de Jonge, M. I., G. Pehau-Arnaudet, M. M. Fretz, F. Romain, D. Bottai, P. Brodin, N. Honore, G. Marchal, 

W. Jiskoot, P. England, S. T. Cole & R. Brosch, (2007) ESAT-6 from Mycobacterium tuberculosis 

dissociates from its putative chaperone CFP-10 under acidic conditions and exhibits membrane-lysing 

activity. J Bacteriol 189: 6028-6034 

Coutanceau, E., J. Decalf, A. Martino, A. Babon, N. Winter, S. T. Cole, M. L. Albert & C. Demangel, 

(2007) Selective suppression of dendritic cell functions by Mycobacterium ulcerans toxin mycolactone. J 

Exp Med 204: 1395-1403 

Cole, S. T. & P. M. Alzari, (2007, EPFL) Towards new tuberculosis drugs. Biochemical Society 

transactions 35: 1321-1324 

Chesne-Seck, M. L., N. Barilone, F. Boudou, J. G. Asensio, P. E. Kolattukudy, C. Martin, S. T. Cole, B. 

Gicquel, D. N. Gopaul & M. Jackson, (2007) A point mutation in the two-component regulator PhoP-PhoR 

accounts for the absence of polyketide-derived acyltrehaloses but not that of phthiocerol dimycocerosates 

in Mycobacterium tuberculosis H37Ra. J Bacteriol 

Casenghi, M., S. T. Cole & C. F. Nathan, (2007, EPFL) New approaches to filling the gap in tuberculosis 

drug discovery. PLoS medicine 4: e293 

Brosch, R., S. V. Gordon, T. Garnier, K. Eiglmeier, W. Frigui, P. Valenti, S. Dos Santos, S. Duthoy, C. 

Lacroix, C. Garcia-Pelayo, J. K. Inwald, P. Golby, J. Nunez Garcia, R. G. Hewinson, M. A. Behr, M. A. 

Quail, C. Churcher, B. G. Barrell, J. Parkhill & S. T. Cole, (2007) Genome plasticity of BCG and impact on 

vaccine efficacy. Proc Natl Acad Sci U S A 104: 5596–5601 

Schumann, G., S. Schleier, I. Rosenkrands, N. Nehmann, S. Halbich, P. F. Zipfel, M. I. de Jonge, S. T. 

Cole, T. Munder & U. Mollmann, (2006) Mycobacterium tuberculosis secreted protein ESAT-6 interacts 

with the human protein syntenin-1. Centr Eur J Biol 1: 183-202 

Saint-Joanis, B., C. Demangel, M. Jackson, P. Brodin, L. Marsollier, H. Boshoff & S. T. Cole, (2006) 

Inactivation of Rv2525c, a Substrate of the Twin Arginine Translocation (Tat) System of Mycobacterium 

tuberculosis, Increases {beta}-Lactam Susceptibility and Virulence. J Bacteriol 188: 6669-6679

Prado, S., H. Ledeit, S. Michel, M. Koch, J. C. Darbord, S. T. Cole, F. Tillequin & P. Brodin, (2006) 

Benzofuro[3,2-f][1]benzopyrans: A new class of antitubercular agents. Bioorg Med Chem 14: 5423-5428 

Marsollier, L., J. P. Andre, W. Frigui, G. Reysset, G. Milon, B. Carbonnelle, J. Aubry & S. T. Cole, (2006) 

Early trafficking events of Mycobacterium ulcerans within Naucoris cimicoides. Cell Microbiol 9: 347-355 

Majlessi, L., M. Simsova, Z. Jarvis, P. Brodin, M. J. Rojas, C. Bauche, C. Nouze, D. Ladant, S. T. Cole, P. 

Sebo & C. Leclerc, (2006) An increase in antimycobacterial Th1-cell responses by prime-boost protocols 

of immunization does not enhance protection against tuberculosis. Infect Immun 74: 2128-2137 

Fernandez, P., B. Saint-Joanis, N. Barilone, M. Jackson, B. Gicquel, S. T. Cole & P. M. Alzari, (2006) The 

Ser/Thr protein kinase PknB is essential to sustain mycobacterial growth. J Bacteriol 188: 7778-7784 

Coutanceau, E., P. Legras, L. Marsollier, G. Reysset, S. T. Cole & C. Demangel, (2006) Immunogenicity 

of Mycobacterium ulcerans Hsp65 and protective efficacy of a Mycobacterium leprae Hsp65-based DNA 

vaccine against Buruli ulcer. Microbes Infect 

Brodin, P., L. Majlessi, L. Marsollier, M. I. de Jonge, D. Bottai, C. Demangel, J. Hinds, O. Neyrolles, P. D. 

Butcher, C. Leclerc, S. T. Cole & R. Brosch, (2006) Dissection of ESAT-6 system 1 of Mycobacterium 

tuberculosis and Impact on immunogenicity and virulence. Infect Immun 74: 88-98 

Araoz, R., N. Honoré, S. Cho, J. P. Kim, S. N. Cho, M. Monot, C. Demangel, P. J. Brennan & S. T. Cole, 

(2006) Antigen discovery: a postgenomic approach to leprosy diagnosis. Infect Immun 74: 175-182 

Araoz, R., N. Honore, S. Banu, C. Demangel, Y. Cissoko, C. Arama, M. K. Uddin, S. K. Hadi, M. Monot, 

S. N. Cho, B. Ji, P. J. Brennan, S. Sow & S. T. Cole, (2006) Towards an immunodiagnostic test for 

leprosy. Microbes Infect 8: 2270-2276 


LEMAÎTRE LAB 

TEAM MEMBERS 

Jean-PhilippeBoquet, Lab Technician 

Nichole Broderick, Scientific Collaborator 

Nicolas Buchon, Scientific Collaborator 

Véronique Bulliard, Administative Assistant 

Délia Glangetas, Lab Assistant 

Aurélien Guillou, Scientific Assistant 

Onya Opota, Scientific Collaborator 

David Welchman, Scientific Collaborator 

Bruno Lemaître 


Since July 2007 


http://lemaitrelab.epfl.ch 


CNRS Molecular Genetics Center, Gif-sur-Yvette, 

France 

INTRODUCTION 

Our group studies the molecular basis of microbial infection and corresponding host defence responses 

using Drosophila as a model system. Analysing how insects combat microbial infection might be relevant 

to our understanding of infectious processes and innate host defence in vertebrates. 


Regulation of antimicrobial peptide gene expression by the Toll and Imd pathways 

Two signalling pathways, Imd (Immune deficiency) and Toll, controlling the expression of antimicrobial 

peptides in Drosophila in response to microbial infection have been identified. We have used genetic 

screens to extend our understanding of how these pathways activate immune responses as well as to 

determine how the host recognizes and distinguishes between different microbial pathogens. RNAi and 

loss-of-function analysis were recently used to demonstrate the role of DIAP2 (Inhibitor of Apoptosis 2) in 

this pathway. Our results underline the similarities between the Imd pathway and the TNFα receptor 

pathway that mediates NF-κB innate immune response in vertebrates. We have recently performed a 

large extensive RNAi screen for serine proteases acting upstream of the Toll pathway. This allowed us to 

identify 5 new serine proteases involved in Toll activation by Gram-positive bacteria including SPE 

(Spatzle Processing Enzyme) that is involved in the cleavage of the Toll ligand Spatzle. 

Bacterial sensing in Drosophila 

We are analyzing the mechanisms used by Drosophila to detect bacteria during a course of an infection. 

Using highly purified bacterial compounds we were able to show that Gram-negative diaminopimelic acidtype 

peptidoglycan (DAP-type peptidoglycan) is the most potent inducer of the Imd pathway and that the 

Toll pathway is predominantly activated by Gram-positive Lysine-type peptidoglycan. Therefore, 

Drosophila’s ability to discriminate between Gram-positive and Gram-negative bacteria therefore, does not 

rely on lipopolysacharid detection but rather on the recognition of specific forms of PGs. Recently, we 

have demonstrated a key role for amidase Peptidoglycan Recognition Proteins (PGRPs) in controlling the 

level of Imd pathway activity by degrading peptidoglycan. PGRP-LB is an efficient amidase that remove 

peptides from the glycan chains, thereby converting Gram-negative peptidoglycan into non-immunostimulatory 

fragments. Interestingly, PGRP-LB encodes a secreted protein and is regulated by the Imd 

pathway. The presence of PGRP-LB in the hemolymph establishes a negative feedback loop that ensures 

an appropriate level of immune activation in response to bacterial infection. 

Post-Genomic analysis of Drosophila immune responses 

In an effort to identify new Drosophila genes involved in the immune response, we have compared the 

genome-wide expression profile of Imd and Toll deficient adult flies to wild-type flies in response to 

microbial infection using high-density oligonucleotide arrays. This microarray study served as the starting 

point of several post-genomic analyses. The power of this approach is illustrated by the recent 

characterization by our group of an immune-responsive serpin (Serpin 27A) and of several serine 

proteases that play important roles in the melanisation reaction (an arthropod specific immune defence) 

as well as a novel immune-responsive clotting factor called Fondue.

The gut immune response 

In Drosophila, antimicrobial peptide genes are also produced in the gut in response to oral bacterial 

infection. We have investigated in more detail recognition mechanisms underlying the gut immune 

response. We first showed that antimicrobial peptide genes gene induction in the gut is mediated by the 

Imd pathway through the recognition of Gram-negative peptidoglycans by PGRP-LC in a similar manner 

to the activation of Imd in the fat body. The mechanisms by which endogenous non-pathogenic gut 

commensals are distinguished from pathogenic bacteria are not understood and are the focus of intense 

study in mucosal immunology. We have demonstrated the role of the amidase PGRP gene PGRP-LB in 

the tolerance to commensals. We hypothesized that gut commensal bacteria have a low division rate and 

release only low amounts of peptidoglycan that can readily be hydrolyzed by amidase PGRPs, whereas 

infectious bacteria release large amounts of peptidoglycan while proliferating. Thus amidase PGRPs 

down-regulate the immune response and determine the immune reactivity of the fly. We are currently 

investigating the molecular mechanisms underlying the gut immune defence. 

Host-pathogen interactions in Drosophila 

To date most of our knowledge on the Drosophila immune response is based on the analysis of host 

reactions following injection of non-pathogenic bacteria into the hemolymph of Drosophila larvae or adults. 

Over the last years we have developed the use of natural infections of Drosophila with natural pathogens 

to dissect host responses. Recently, we isolated Pseudomonas entomophila (P. entomophila), a natural 

bacterial pathogen of Drosophila, from flies sampled in Guadeloupe. We showed that P. entomophila 

induces a systemic immune response in Drosophila larvae and causes food uptake blockage after oral 

infection. Importantly. Insertional mutagenesis identified 45 P. entomophila genes required to infect and/or 

to kill Drosophila. The genome of P. entomophila was sequenced in collaboration with Genoscope (Evry) 

revealing the existence of several putative bacterial virulence factors required for infection. We are now 

using bacterial genetics to characterize the strategies used by these bacteria to survive in their host. The 

use of P. entomophila was also pivotal in the demonstration that Drosophila is capable of activating an 

immune response adapted to specific invaders and the relevance of gut immune responses to fight 

infection. 


N. B. All 2006-2007 publications issued in the frame of the CNRS Molecular Genetics Center 

Romeo, Y. and Lemaitre, B. (2008, EPFL). Drosophila Immunity: Methods for monitoring the activity of 

Toll and Imd signalling pathway. Methods in Molecular Biology vol 415 Innate Immunity. Edited by 

Jonathan Ewbank and Eric Vivier Humana Press p379-402 

Leulier F, and Lemaitre B. (2008, EPFL) Toll-like receptors - taking an evolutionary approach. Nature 

Review Genetics;9(3):165-78 

Lemaitre B, Hoffmann J. 

25 697-743 

(2007) The Host Defense of Drosophila melanogaster. Annu Rev Immunol. 

Muniz CA, Jaillard D, Lemaitre B. Boccard F.(2007) Erwinia carotovora Evf antagonizes the elimination 

of bacteria in the gut of Drosophila larvae. Cell Microbiol. Cell Microbiol, 9 (1) 106-119 

Bangham J, Jiggins F, Lemaitre B. (2006) Insect immunity: the post-genomic era. Immunity. 

2006 Jul;25(1):1-5 

Brun, S., Vidal, S., Spellman, P., Ueda, R., Tricoire, H., and Lemaitre, B. 2006. The MAPKKK Mekk1 

regulates the expression of Turandot stress genes in response to septic injury in Drosophila. Genes to 

Cells 11. 397-407 

Jang IH, Chosa N, Kim SH, Nam HJ, Lemaitre B, Ochiai M, Kambris Z, Brun S, Hashimoto C, Ashida M, 

Brey PT, Lee WJ. (2006) A spatzle-processing enzyme required for toll signaling activation in Drosophila 

innate immunity. Dev Cell. 10 (1) :45-55 

Kambris, K., Brun, S., Jang, I.-H., Nam, H.-J., Romeo, Y., Takahashi, K., Lee, W., Ueda, R., and Lemaitre, 

B. 2006. A large-scale in vivo RNAi screen identifies five new serine proteases required for Toll activation 

during the Drosophila immune response. Current Biology 6(8):808-13 

Liehl P, Blight M, Vodovar N, Boccard F, Lemaitre B (2006) Prevalence of local immune response against 

oral infection in a Drosophila/Pseudomonas infection model. PLoS Pathog 2(6): e56 

Leulier F, Lhocine N, Lemaitre B, Meier P. (2006) The Drosophila IAP DIAP2 Functions in Innate Immunity 

and is Essential to Resist Gram-negative Bacterial Infection. Mol Cell Biol. 26: 7821-7831

Scherfer, S., Qazi, M.R., Takahashi, K., Ueda, R., Dushay, M.S., U., T., and Lemaitre, B. 2006. The Toll 

immune-regulated Drosophila protein Fondue is involved in hemolymph clotting. Dev Biol 295(1):156-63 

Vodovar, N., Vallenet, D., Cruveiller, S., Rouy, Z., Barbe, V., Acosta, C., Cattolico, L., Jubin, C., Lajus, A., 

Segurens, B., Vacherie, B., Wincker, P., Weissenbach, J., Lemaitre, B., Médigue, C., and Boccard, F. 

2006. The complete genome sequence of the entomopatogenic and metabolically versatile soil bacterium 

Pseudomonas entomophila. Nature Biotech 4(6):673-9 

Zaidman-Remy A., Hervé M., Poidevin M., Pili-Floury S., Kim M-S, Blanot D., Oh B.H., Ueda R., 

Mengin-Lecreulx D. and B. Lemaitre. (2006) The Drosophila amidase PGRP-LB adjusts the immune 

response to bacterial infection, Immunity 24(4):463-73 

A model of Imd pathway activation by Gram-negative bacteria. A balance 

between peptidoglycan (PGN) sensing through the receptor PGRP-LC and 

peptidoglycan degradation through the amidase PGRP-LB determines the 

level of activation of the Imd pathway during bacterial infection 

A bacterial strain (expressing GFP) persisting in the midgut of 

Drosophila larvae 


MCKINNEY LAB 

John McKinney 


Since June 2007 


http://mckinney-lab.epfl.ch 

TEAM MEMBERS 

Cyntia de Piano, PhD Student 

Neeraj Dhar, Senior Scientist 

Meltem Elitas, PhD Student 

Sonia Garcia, Lab Technician 

Suzanne Lamy, Administrative Assistant 

Manisha Lotlikar, PhD Student (Rockefeller) 

Jean-Bernard Nobs, Master Student 

Frederick Ross, PhD Student (Rockefeller) 

Anna De Graff Tischler, Postdoctoral Fellow 

Hongqian Yang, external Student 

Muhittin Emre Özdemir, PhD Student 

Yuichi Wakamoto, Postdoctoral Fellow 


Rockefeller University, N. Y., USA 

INTRODUCTION 

Most bacterial infections come and go in a matter of days or weeks, but tuberculosis (TB) persists for the 

lifetime of the host. Although effective anti-tuberculosis therapy has been available since the 1950s, 

successful treatment requires administration of multiple antibiotics for six months or longer, a regimen that 

most TB patients are unable or unwilling to complete without close supervision. Although the liveattenuated 

Bacille Calmette Guérin (BCG) vaccine has been widely administered since the 1920s, the 

protective efficacy of BCG in clinical trials has been highly variable and generally poor. The development 

of new and more effective interventions hinges on an improved understanding of the mechanisms that 

control TB persistence, pathogenesis, and protection. 

In the Laboratory of Bacteriology, we study the persistence mechanisms that are responsible for the 

recalcitrance of the TB bacillus (Mycobacterium tuberculosis) to host immunity and antimicrobial therapy. 

Our research is focused in four areas: 

Counter-immunity 

Host immunity is usually sufficient to contain M. tuberculosis infection, but not to eradicate infection. We 

seek to identify the strategies that M. tuberculosis deploys to evade or counter the impact of the host 

immune response. 

In vivo metabolism 

Central metabolism has recently emerged as an attractive target for antimicrobial drug discovery. We seek 

to identify the metabolic pathways that are required for M. tuberculosis growth and persistence during 

infection of the mammalian host. 

Antibiotic tolerance 

TB is notoriously refractory to antimicrobial therapy. We seek to elucidate the mechanistic basis of M. 

tuberculosis persistence in the antibiotic-treated host, and the epigenetic basis of cell-to-cell variation in 

sensitivity to antibiotics. 

Growth control. M. tuberculosis is also notorious for its slow intrinsic growth rate (doubling time: 20-24 

hours). We seek to understand why M. tuberculosis grows so slowly and to identify the physiologic 

adaptations that are required for slow growth. 

Our experimental approaches include molecular genetics, tissue culture and animal infection models, 

computational modeling, mass spectrometry, microfluidics, and time-lapse fluorescence microscopy. In 

collaboration with our partners in EPFL's School of Engineering, we are developing new tools to analyze 

the time evolution of bacterial phenotypes at single-cell resolution. 


The Laboratory of Bacteriology was established in EPFL's School of Life Sciences in July 2007. Our 

principal goal in relocating to EPFL was to establish new and multidisciplinary lines of research in 

mycobacteriology. Towards that goal, we have established collaborations with our new colleagues in 

EPFL's School of Engineering and School of Basic Sciences. These collaborations have greatly expanded the 

range of technical approaches that we apply to our research. The new lines of research in our lab include computational 

modeling, mass spectrometry, microfluidics, microelectromechanical systems, and automated time-lapse microscopy.


N. B. All publications issued in the frame of the Rockefeller University, N. Y. 

Upton, A. and McKinney, J.D. (2007). Role of the methylcitrate cycle in propionate metabolism and 

detoxification in Mycobacterium smegmatis. Microbiology 153(12):3973-3982 

Dhar, N. and McKinney, J.D. (2007). Microbial phenotypic heterogeneity and antibiotic tolerance. 

Curr. Opin. Microbiol. 10(1):30-38 

Gould, T.A., van de Langemheen, H., Muñoz-Elías, E.J., McKinney, J.D. and Sacchettini, J.C. (2006). 

Dual role of isocitrate lyase 1 in the glyoxylate and methylcitrate cycles in Mycobacterium tuberculosis. 

Mol. Microbiol. 61(4):940-947 

Timm, J., Kurepina, N., Kreiswirth, B.N., Post, F.A., Walther, G.B., Wainwright, H.C., Bekker, L.G., Kaplan, 

G. and McKinney, J.D. (2006). A multidrug-resistant, acr1-deficient clinical isolate of Mycobacterium 

tuberculosis is unimpaired for replication in macrophages. J. Infect. Dis. 193(12):1703-1710 

Muñoz-Elías, E.J. and McKinney, J.D. (2006). Carbon metabolism of intracellular bacteria. 

Cell. Microbiol. 8(1):10-22 

Owens, R.M., Hsu, F.F., VanderVen, B.C., Purdy, G.E., Hesteande, E., Giannakas, P., Sacchettini, J.C., 

McKinney, J.D., Hill, P.J., Belisle, J.T., Butcher, B.A., Pethe, K. and Russell, D.G. (2006). M. tuberculosis 

Rv2252 encodes a diacylglycerol kinase involved in the biosynthesis of phosphatidylinositol mannosides 

(PIMs). Mol. Microbiol. 60(5):1152-1163 

Muñoz-Elías, E.J., Upton, A., Cherian, J. and McKinney, J.D. (2006). Role of the methylcitrate cycle in 

M. tuberculosis metabolism, intracellular growth, and virulence. Mol. Microbiol. 60:1109-1122 

This image shows a time-lapse microscopy image (1,000X) of a microcolony of 

mycobacteria expressing green fluorescent protein (GFP). The bacteria were 

grown in a continuous-flow microfluidic device and exposed to the antituberculosis 

drug isoniazid (INH) for 8.5 hr. 


TRONO LAB 

Didier Trono, MD 



Dean of the School of Life Sciences 

http://tronolab.epfl.ch 

TEAM MEMBERS 

Daniel Bach Gonzalez, Postdoctoral Fellow 

Isabelle Barde, Postdoctoral Fellow 

Karolina Bojkowska, PhD student 

Yannick Bulliard, PhD student 

Andrea Corsinotti, PhD student 

Alexander Peter Dörr, Postdoctoral Fellow 

Lena Farneman Andersson, Administrative Assistant 

Anna Groner, PhD student 

Johan Jakobsson, Postoctoral Fellow 

Stephanie Jost, PhD student 

Alexandra Liagre Quazzola, Technician 

Pierre Maillard, PhD Student 

Sylvain Meylan, PhD Student 

Sujana Nylakonda, Technician 

Simon Quenneville, Postdoctoral Fellow 

Shyam Sunder Reddy Peddy, PhD Student 

Sylviane Reymond, Technician 

Severine Reynard, Technician 

Helen Mary Rowe, Postdoctoral Fellow 

Francesca Santoni di Si , Posdoctoral Fellow 

Fatima Serhan, Postoctoral Fellow 

Priscilla Turelli, Research Associate 

Sonia Verp, Technician 

INTRODUCTION 

Retroelements constitute important evolutionary forces for the genome of higher organisms, yet their 

uncontrolled spread, whether from endogenous loci or within the context of viral infections, can cause 

diseases such as cancer, hepatitis and AIDS. Correspondingly, a variety of host-encoded activities limit 

this process, belonging to a line of defense commonly called intrinsic or innate immunity, which notably 

contributes to taming endogenous retroelements and to restricting the cross-species transmission of 

retroviruses. Our work aims at characterizing the relationship between retroelements and their hosts, and 

at shedding light on regulatory mechanisms that shape the expression of mammalian genomes. 


The delicate equilibrium between retroelements and higher organisms 

Retroelements not only comprise deadly human pathogens such as HIV or HBV, but they also are 

responsible for almost half of the DNA contained in the genome of higher organisms. Sophisticated 

mechanisms are thus at play in their control, which include transcriptional silencing by DNA methylation, 

post-transcriptional silencing by RNA interference and inhibition by cellular proteins such as 

polynucleotide cytidine deaminases (CDAs) of the APOBEC family or tripartite motif proteins such as 

TRIM5α. We previously demonstrated that APOBEC proteins can be broadly active antiretroviral factors 

that act by lethally editing the nascent minus strand DNA product of reverse transcription, and that they 

can also block HBV. Our recent work has explored the molecular mechanisms of action of these antivirals, 

asking in which physiological framework they act as factors of innate immunity against HIV and HBV, and 

how they contribute to the control of endogenous retroelements. One result of this ongoing work is the 

demonstration that, in spite of evidence suggesting such a model, APOBEC family members are not 

essential contributors to the control of HBV by interferons. In parallel, we have been investigating TRIM5α, 

a restriction factor that limits the cross-species transmission of primate lentiviruses and prevents infection 

of human cells by so-called N- but not B- or NB-tropic strains of murine leukemia virus (MLV). Through a 

mutation-based functional analysis of TRIM5α-mediated MLV restriction, we found that changes at 

tyrosine 336 of human TRIM5α, within the variable region 1 of its C-terminal PRYSPRY domain, can 

expand its activity to B-MLV and to the NB-tropic Moloney MLV. Conversely, we observed that the escape 

of MLV from restriction by wild-type or mutants forms of huTRIM5α can be achieved through 

interdependent changes at positions 82, 109, 110 and 117 of the viral capsid. Together, our results 

support a model in which TRIM5α-mediated retroviral restriction results from the direct binding of the 

antiviral PRYSPRY domain to the viral capsid, and can be prevented by interferences exerted by critical 

residues on either one of these two partners. Our ongoing work capitalizes on these results to examine 

the modalities of HIV recognition by TRIM5α, and seeks to identify the cellular cofactors of this antiviral 

effector.

Lentiviral vectors to probe transcriptional regulation 

We pioneered the development of lentiviral vectors and contributed to the demonstration that these gene 

delivery vehicles have great potential for both basic research and human therapeutics. Lentiviral vectors 

are increasingly used for the generation of transgenic animals by infection of zygotes or early blastocysts, 

and we performed and in-depth characterization of this procedure and its outcome. By measuring the 

frequency of germ line transmission of individual proviruses resulting from lentivector-mediated infection of 

fertilized mouse oocytes, we determined that integration most often occurs at the one- or two-cells stage, 

hence that the degree of genotypic mosaicism in the resulting transgenic animals is minimal. Furthermore, 

by mapping hundreds proviral integration sites in transgenic mice obtained by this technique, we found 

that integration favors genes expressed in early blastomeres. This suggests that, as previously noted in 

other settings, lentiviral vectors integrate preferentially into regions of the genome that are transcriptionally 

active or poised for activation. Our current effort, conducted in collaboration with Denis Duboule’s and 

Stylianos Antonarakis’ groups, exploits lentivector-mediated transgenesis to identify cis-acting DNA 

elements that govern limb development and regulate the expression of genes involved in Down’s 

syndrome. In parallel, we are fine-tuning lentiviral vectors for the gene therapy of chronic granulomatous 

disease, a genetic form of immunodeficiency. 

KRAB zinc finger proteins and epigenetic regulation 

The human genome contains more than four-hundred genes coding for KRAB (Krüppel-associated box) 

zinc finger proteins (KRAB-ZFPs), and comparative sequence analyses indicate that this family of 

epigenetic repressors is vertebrate-specific. While large variations between organisms suggest a role in 

speciation, no gene target of KRAB-ZFPs has been unequivocally identified and the physiological roles of 

these regulators remain essentially unknown. Nevertheless, extensive in vitro molecular analyses have 

revealed that their conserved KRAB domain recruits the KAP1 (KRAB-associated protein 1) corepressor 

(also known as TRIM28, TIF1β or KRIP-1), which in turn serves as a scaffold for a multimolecular histoneand 

DNA-modifying complex that silences transcription by triggering the formation of heterochromatin. In 

some tissue culture systems, KAP1 appears to partake in cell-cycle regulation and DNA-damage 

response, while a KAP1 knockout is early embryonic lethal in the mouse. We previously exploited 

KRAB/KAP1-mediated epigenetic repression to achieve in vivo controllable transgenesis and knockdown 

by combining doxycycline-regulated KRAB-containing fusion proteins and lentiviral vectors. This led us to 

discover that KRAB/KAP1 can promote de novo promoter methylation when tethered to the vicinity of 

Cp-G-rich DNA during the first few days of mouse embryogenesis. We are currently asking whether this 

epigenetic regulatory system is involved in the wave of DNA methylation that characterizes the 

mammalian early embryonic period, and notably results in the control of endogenous retroelements. We 

are also proceeding to a characterization of the genomic modalities of KRAB/KAP1 epigenetic regulation, 

and examining the role of this system in various somatic tissues. 


D. Bach, S. Peddy, B. Mangeat, A. Lakkaraju , K. Strub and D. Trono (2008). Characterization 

of APOBEC3G binding to 7SL RNA. Retrovirology 5: 54 (Epub ahead of print) 

F. Diaz-Griffero, M. perron, K. McGee-Estrada, R. Hanna, P.V. Maillard, D. Trono and J. Sodroski (2008). 

A human TRIM5a B30.2/SPRY domain mutant gains the ability to restrict and prematurely uncoat B-tropic 

murine leukemia virus. Virology (Epub ahead of print) 

M.-O-. Sauvain, A. Dorr, B. Stevenson, A. Quazzola, F. Naef, M. Wiznerowicz, F. Schütz, V. Jongeneel, 

D. Duboule, F. Spitz and D. Trono (2008). Genotypic features of lentiviral transgenic mice. J. Virol. 

82: 7111-7119 

P. Turelli, A. Quazzola, S. Verp, S. Jost and D. Trono (2008). APOBEC3-independent IFN-induced viral 

clearance in Hepatitis B virus transgenic mice. J. Virol. 82: 6585-6590 

N. Genoud, D. Ott, N. Prinz, P. Schwartz, U. Suter, D. Trono and A. Aguzzi (2008). Antiprion prophylacis 

by gene transfer of soluble prion antagonist. Am. J. Pathol. 172: 1287-1296 

P. Maillard, S. Reynard, F. Serhan, P. Turelli and D. Trono (2007). Interfering residues narrow down 

the spectrum of MLV restriction by human TRIM5a. PLoS Pathog. 3 (12) 

M. Wiznerowicz, J. Jakobsson, J. Szulc, S. Liao, A. Quazzola, F. Beermann, P. Aebischer and D. Trono 

(2007). The KRAB repressor domain can trigger de novo promoter methylation during mouse early 

embryogenesis. J. Biol. Chem. 282:34535-34541 

A.G. Dayer, B. Jenny, M.O. Sauvain, G. Potter, P. Salmon, E. Zgraggen, M. Kanemitsu, E. Gascon, 

S. Sizonenko, D. Trono, J.Z. Kiss (2007). Expression of FGF-2 in neural progenitor cells enhances their 

potential for cellular brain repair in the rodent cortex. Brain 130: 2962-2976

S. Jost, P. Turelli, B. Mangeat, U. Protzer and Didier Trono (2007). Induction of antiviral cytidine 

deaminases does not explain the inhibition of hepatitis B virus replication by interferons in hepatoma 

cells. J. Virol. 81: 10588-10596 

A. Malaschicheva, B. Kanzler, E. Tolnukova, D. Trono and A. Tomilin (2007). Lentiviruses for lineagespecific 

gene manipulation. Genesis 45: 4565-459 

M.B. Asparuhova, G. Marti. S. Liu. F. Serhan, D. Trono and D. Schumperli (2007). Inhibition of 

HIV1 multiplication by a modified U7 snRNA inducing Tat and Rev exon skipping. J. Gene Med. 9: 323- 

334 

K.L. Zhang, B. Mangeat, M. Ortiz, V. Zoete, D. Trono, A. Telenti and O. Michielin (2007). Model structure 

of human APOBEC3. PLosONE 2: e378 

A. Rideau, B. Mangeat, T. Matthes, D. Trono and P. Beris, 2007. Molecular mechanism of hepcidin 

deficiency in a patient with juvenile hemochromatosis. Haematologica 97: 27-28 

A. Fodor, C. Harel, L. Fodor, M. Armoni, P. Salmon, D. Trono and E. Karnieli, 2007. Adult rat liver cells 

transdifferentiated with lentiviral IPF1 vectors reverse diabetes in mice: an ex vivo gene therapy approach. 

Diabetologia 50: 121-130 

M. Wiznerowicz, J. Szulc and D. Trono, 2006. Tuning silence: conditional systems for RNA interference. 

Nat. Meth. 3: 682-688 

Y. Bulliard, M. Wiznerowicz, I. Barde and D. Trono, 2006. KRAB can repress lentivirus proviral 

transcription independently of integration site. J. Biol. Chem. 281:35742-35746 

T. Nguyen, J. Birraux, B. Wildhaber, A. Myara, F. Trivin, C. Le Coultre, D. Trono and C. Chardot. 2006. Ex 

vivo lentivirus transduction and immediate transplantation of uncultured hepatocytes for treating 

hyperbilirubinemic Gunn rat. Transplantation, 82: 794-803 

Y. Ariumi, F. Serhan, P. Turelli, A. Telenti and D. Trono, 2006. The integrase interactor 1 (INI1) proteins 

facilitate Tat-mediated human immunodeficiency virus type 1 transcription. Retrovirology 3: 47 

P. Salmon and D. Trono (2006). Production and titration of lentiviral vectors. Curr. Protoc. Hum. Genet. 

Chapter 12, unit 12.10 

M. Eberhardt, P. Salmon, M.A. von Mach, J.G. Hengstler, M. Brulport, P. Linscheid, D. Seboek, J. 

Oberholzer, A. Barbero, I. Martin, B. Muller, D. Trono and H. Zulewski, 2006. Multipotential nestin and Isl- 

1 positive mesenchymal stem cells isolated from human pancreatic islets. Biochem. Biophys. Res. 

Commun. 345: 1167-1176 

Y. Ariumi and D. Trono, 2006. The Ataxia-Telangiectasia-Mutated (ATM) protein can enhance human 

immunodeficiency virus type 1 replication by stimulating Rev function. J. Virol. 80: 2445-2452 

J. Szulc, M. Wiznerowicz, M.-O. Sauvain, D. Trono and P. Aebischer, 2006. A highly versatile tool for 

conditional gene expression and knockdown. Nat. Meth. 3: 109-116 

K. Nadra, S.I. Anghel, E. Joye, N. Soon Tan, S. Basu-Modak, D. Trono, W. Wahli and B. Desvergne, 

2006. Differentiation of trophoblast giant cells and their metabolic functions are depeendent on 

peroxisome proliferator-activated receptor b/d. Mol. Cell. Biol. 26 : 3266-3281 

Drug-controllable 

transgenesis 

SIN 

Ubiquit 

Gene X SIN 

SIN 

TiSpec 

Gene X SIN 

Ubiquitous 

Tissue-specific 

TR-KRAB 

SIN 

P3 SIN 

shRNA 

SIN 

P3 ** 

SIN 

shRNA 

Drug-controllable 

knockdown 


VAN DER GOOT LAB 

Gisou van der Goot 



http://vdg.epfl.ch 

TEAM MEMBERS 

Laurence Abrami, Research Associate 

Mirko Bischofberger, PhD Student 

Valérie Burger, Administrative Assistant 

Julie Charolais Thoenig, Postdoctoral Fellow 

Julie Deuquet, PhD Student 

Barbara Freche, Postdoctoral Fellow 

Manuel Gonzalez, PhD Student 

Luc Henry, Trainee 

Ioan Iacovache, PhD Student 

Béatrice Kunz, Technician 

Céline Lafourcade, Postdoctoral Fellow 

Radhakrishnan Panatala, Trainee 

Lucile Pernot, Postdoctoral Fellow 

Nuria Reig, Postdoctoral Fellow 

Suzanne Salvi, Technician 

INTRODUCTION 

The effort of our laboratory is focused on understanding the molecular and cellular mode of action of 

bacterial protein toxins, such as pore-forming toxins or anthrax toxin, which are major determinants of 

human infectious diseases. We have recently broadened these studies to understanding the physiological 

role and the cell biology of the anthrax toxin receptors and their partner proteins. Our work lies at the 

frontier of cell biology and cellular microbiology and bacterial toxins provide us with a powerful tool to 

study basic cellular processes, in addition to their role as virulence factors. 


Our major findings during the year 2007 have come from our work on the anthrax toxin and its receptors. 

The anthrax toxin is composed of three polypeptide chains: the rotective antigen (PA), the lethal factor 

(LF) and the edema factor (EF). LF is a zinc dependent metalloprotease that cleaves all MAP kinase 

kinases ; EF is a calmodulin dependent adenylate cyclase that is responsible for the edema observed in 

anthrax patients ; PA has no enzymatic activity and is involved in escorting EF and LF to the cytoplasm. 

Toxicity is strictly dependent upon the delivery of the enzymatic subunits to the cytoplasm and thus much 

of our attention has been focused on understanding the molecular mechanisms that mediate toxin uptake 

and cytoplasmic delivery. These events are largely dependent on the anthrax toxin receptors (ATRs), of 

which there are two: capillary morphogenesis gene 2 (CMG2) and tumor endothelial marker 8 (TEM8). 

Very little is known about the structure and physiological functions of these proteins. Interestingly, 

mutations in CMG2 are associated with a severe autosomal recessive human disease called Systemic 

Hyalinosis. Interestingly, it has recently been proposed, and subsequently challenged by two groups, that 

ATRs require a partner protein called LRP6 (low-density lipoprotein receptor-related protein 6) is essential 

for the entry of the anthrax toxin. LRP6 is an essential component of the canonical Wnt signaling 

pathway. 

Response of macrophages and dendritic cells to the anthrax toxin 

One of our interests over the last years has ben to understand how cells respond to bacterial toxins and 

what the role of the cellular innate immune system is. For the anthrax toxin, we have focused on the lethal 

toxin (PA combined with LF) and its effects on macrophages and dendritic cells, since cells of the immune 

systems are the physiological targets of the toxin. Dietrich and co-workers (Boyden and Dietrich, 2006) 

found that, upon lethal toxin treatment, macrophages from certain inbred mice strains undergo rapid death 

mediated by caspase-1 through the activation of a Nalp1b containing inflammasome. Rapid lethal toxininduced 

death is however not observed in macrophages from humans and many mouse strains. We 

therefore studied the responses of various murine dendritic cells (DCs) and macrophages to lethal toxin. 

Using a variety of knock-out mice, we found that depending on the mouse strain, death of bone marrow 

derived DCs and macrophages was mediated either by a fast Nalp1b and caspase-1 dependent, or by a 

slow caspase-1 independent pathway (Reig et al., 2008). Caspase-1 independent death was observed in 

cells of different genetic backgrounds and interestingly occurred only in immature DCs. Interestingly 

maturation, triggered by different types of stimuli, led to full protection of these DCs (Reig et al., 2008). An 

interesting lesson derived from this work is that cells do not die from the direct damage inflicted by the 

toxin, but from the response of the cell to the toxin, this response depending on the genetic background, 

the type and the developmental stage of the cell. It is at present unclear which sensing event leads to the 

activation of the Nalp1b inflammasomes in response to lethal toxin, and this is the theme of current 

investgation in the lab.

Physical and functional interactions between the anthrax receptors and the Wnt signal protein 

LRP6 

As mentioned above, LRP6 was picked up in a screen searching for genes required for anthrax toxin 

endocytosis but the requirement for LRP6 was subsequently contradicted by two independent groups. Our 

work confirms that LRP6 interacts with ATRs. Although we find that LRP6 modulates anthrax toxin 

endocytosis, it is not absolutely required. More specifically, we found that anthrax toxin triggers 

LRP6 tyrosine phosphorylation –the role which remains to be determined–, redistribution of the protein to 

detergent resistant membranes, used as a biochemical readout for lipid rafts, LRP6 endocytosis and 

degradation in lysosomes. These findings show that LRP6 is part of the toxin-ATR complex. RNAi against 

LRP6 did not prevent toxin entry but strongly slowed down the kinetics, suggesting a modulatory role. 

More interestingly we found that the amount of LRP6 in cells was dependent on the expression levels of 

ATRs: RNAi against or overexpression of ATRs led to a drastic down regulation of LRP6, suggesting that 

optimal levels of LRP6 and ATRs need to be synthesized by cells to have optimal expression of both. We 

could show that down regulation of LRP6 occured in a post-translationnal manner, possibly in the 

endoplasmic reticulum (ER). This interaction also raised the possibility that ATRs play a role in Wnt 

signaling. We indeed found that RNAi against CMG2 leads to a strong decrease in Wnt signaling. Since 

the physiological role of ATRs is not act as a toxin receptor but to interact with the extracellular matrix, 

these findings raise the interesting possibility that, through the ATR-LRP6 interaction, adhesion to the 

extracellular matrix could locally control Wnt-signaling. This hypothesis will be tested in the future. 

Novel ubiquitin dependent ER quality control of transmembrane proteins 

Our studies on the palmitoylation of ATRs led us to the hypothesis that these receptors might interact with 

a palmitoylated partner protein (Abrami et al., 2006). We therefore investigated whether LRP6 underwent 

this lipid modification. We found that LRP6 is palmitoylated on juxtamembranous cysteines, soon after 

synthesis in the endoplasmic reticulum and that this modification is actually required for its exit from the 

ER (Abrami et al., 2008). Interestingly palmitoylation deficient LRP6 was monoubiquitinated and this 

modification of cytoplasmic cysteines was responsible for its retention in the ER, indicating that a ubiquitin 

dependent retention mechanism operates in the ER (Abrami et al., 2008). The failure in ER exit and the 

subsequent ubiquitin dependent retention is likely to be a consequence of the detection of palmitoylation 

deficient LRP6 by an ER quality control mechanism. Our work supports the following model: LRP6 has a 

very long transmembrane domain (23 residues vs. 21 in the vast majority of type I and II membrane 

proteins), on the other hand the ER is known to have a membrane that is thinner than that of other cellular 

membranes in particular the plasma membrane. Thus a hydrophobic mismatch would occur between the 

LRP6 transmembrane domain and the ER membrane, unless the transmembrane helix of LRP6 was 

tilted, which would decrease its effective length. Since LRP6 is palmitoylated on cysteines that are very 

close to the transmembrane domain, we proposed that palmitoylation serves to tilt the transmembrane 

helix. In agreement with this model we found that shortening of the transmembrane domain of 

palmitoylation deficient LRP6 releases the mutant LRP6 from the ER, and conversely, shortening the 

transmembrane domain of WT LRP6 leads to its ER retention (Abrami et al., 2008). This works thus 

shows the existence of a novel mechanism for regulating the configuration of single transmembrane 

helices. 

E3 

FS 

ER lumen 

ER Exit 

Cytosol 

E3 

Ub 

E3: E3 Ubiquitin ligase 

DUB: de-ubiquitinating enzyme 

FS: folding sensor 

Ub 

Ub binding 

protein 

DUB 

Model of a hypothetical Ubiquitin ER folding cycle for transmembrane proteins

On the basis of these findings we wish to propose a novel mechanism of ER quality control, that would be 

somewhat the cytosolic counter part of the calnexin/calreticulin cycle (see figure): upon co-translationnal 

insertion of a protein into the ER membrane, an ER ubiquitin ligase would ubiquitinate cytoplasmic 

domains on juxtamembranous lysines, this would allow the protein to bind to an ER ubiquitin binding 

protein, and retention would give the protein time to fold in a manner similar to the calnexin bound 

monoglucosylated protein that undergoes folding in the lumen of the ER. This interaction would be 

released by deubiqunating enzymes (DUB). DUBs would also ensure that the protein does not get polyubiquinated 

and targeted for retro-translocation and targeting to the proteasome. If after removal of the 

ubiquitin, the protein was properly folded, it would distribute to exit sites and leave the ER. If the protein 

was not yet properly folded, a folding sensor in association with an E3 ligase activity would reubiquitinated 

the protein and sends it through the cycle once more. The folding sensor does not 

necessarily have to be a protein but could involve physico-chemical properties that would lead to 

differential partitioning into ER membrane domains. Finally after a number of cycles of ubiquitinationdeubiquitination, 

a timer mechanism would allow poly-ubiquitination to occur, possibly by segregation from 

the DUBs, and thereby target the terminally misfolded protein to be targeted to the proteasome. Future 

studies are planned to test this model and identify its components. 

Characterization of human disease causing mutations in the anthrax toxin receptor CMG2 

Systemic hyalinosis is an autosomal recessive disease that encompasses two allelic syndromes, Infantile 

Systemic Hyalinosis and Juvenile Hyaline Fibromatosis, caused by mutations in the CMG2 gene. We 

have analyzed the cellular consequences of five patient-derived point mutations in the extracellular von 

Willebrand domain or the transmembrane domain of the CMG2 protein. We found that four of the 

mutations led to retention of the protein in the endoplasmic reticulum, albeit through different mechanisms. 

Analysis of recombinant CMG2 von Willebrand factor A domains, to which 3 of the mutations map, 

indicated that the mutations did not prevent proper folding and ligand binding, suggesting that, in vivo, 

slow folding, rather than misfolding, is responsible for ER retention. Our work shows that Systemic 

Hyalinosis can be qualified as a conformational disease at least for the mutations that have been mapped 

to the extracellular and transmembrane domains (Deuquet et al. 2008). The long ER half-life and the 

ligand binding ability of the mutated von Willebrand domains suggest that treatments based on chemical 

chaperones could be beneficial. 


Roduit, C., Van der Goot, G., De Los Rios, P., Yersin, A., Steiner, P., Dietler, G., Catsicas, S., Lafont, 

F. & Kasas, S. (2008) Elastic membrane heterogeneity of living cells revealed by stiff nanoscale 

membrane domains. Biophys J. (in press) 

Mirko Bischofberger, F. G. van der Goot. (2008) Exotoxin secretion: Getting out to find the way in. 

Cell : Host & Microbes 3 : 7-8 

I. Iacovache, F. G. van der Goot* and L. Pernot (2008) Pore formation: an ancient yet complex form 

of attack. Biochim. Biophys. Acta : Biomembranes (in press)* corresponding author 

N. Reig, A. Jiang, R. Couture, F. S. Sutterwala, Y. Ogura, R. A. Flavell, I. Mellman, and F. G. van der 

Goot (2008) Maturation Modulates Caspase-1 Independent Responses of Dendritic Cells to Anthrax 

Lethal Toxin. Cellular Microbiology 10(5):1190-207 

Abrami, L., Kunz, B., Iacovache, I., and van der Goot, F. G. (2008) Palmitoylation and ubiquitination 

regulate exit of the Wnt signaling protein LRP6 from the endoplasmic reticulum. Proc Natl Acad Sci 

U S A 105(14):5384-9 

Lafourcade C., K. Sobo, S. Kieffer-Jaquinod, J. Garin and van der Goot F.G. (2008) Regulation of the V- 

ATPase along the endocytic pathway occurs through reversible subunit association and membrane 

localization. PLOS One (in press) 

Deuquet J., Abrami L., Ramirez M.C.M., DiFeo A., Martignetti J. and van der Goot F.G. (2008) Systemic 

hyalinosis mutations in the CMG2 ectodomain leading to loss of function through retention in the 

endoplasmic reticulum. Human Mutations (in press) 

Small PL, van der Goot G. (2007) Editorial Overview. Curr Opin Microbiol. 10 : 1-3 

Aroian R, van der Goot FG.(2007) Pore-forming toxins and cellular non-immune defenses (CNIDs). Curr 

Opin Microbiol. 10 : 57-61

X. Li, D. Kaloyanova, M. van Eijk, Ruud Eerland, F.G. van der Goot, J. Klumperman, F. Lottspeich, V. 

Starkuviene, F. T. Wieland, and J. B. Helms. (2007) Involvement of a Golgi-resident GPI-anchored Protein 

in Maintenance of the Golgi Structure. Mol. Biol. Cell 18:1261-1271 

K. Sobo, J. Chevallier, R. G. Parton, J. Gruenberg and F. G. van der Goot. (2007) Diversity of raft-like 

domains in late endosomes. PlosONE Apr 25;2:e391 

Sobo, K., Le Blanc, I., Luyet, P. P., Fivaz, M., Ferguson, C., Parton, R. G., Gruenberg, J. & van der Goot, 

F. G. (2007) Late endosomal cholesterol accumulation leads to impaired intra-endosomal trafficking PLoS 

ONE 2, e851 

Freche, B., Reig, N. & van der Goot, F. G. (2007) The role of the inflammasome in cellular responses 

to toxins and bacterial effectors. Semin Immunopathol 29, 249-60 

M.R. Gonzalez, M. Bischofberger, L. Pernot, F.G. van der Goot and B. Freche, (2007) Bacterial poreforming 

toxins: The (w)hole story Cell Mol Life Sci 

L. Gurcel, L. Abrami, S. Girardin, J. Tschopp and F.G. van der Goot (2006) Caspase-1 dependent 

activation of SREBP promotes cell survival in response to bacterial pore-forming toxins. Cell 126: 

1135-1145 

Gruenberg, J. and van der Goot, F.G. (2006) Toxoplasma: guess who's coming to dinner. 

Cell 125, 226-8. (Comment) 

Iacovache, P. Paumard, H. Scheib, C. Lesieur, N. Sakai, S. Matile, M. W. Parker and F. G. van der Goot 

(2006) A rivet model for channel formation by aerolysin-like pore-forming toxins. EMBO J. 25 : 457-466 

Gruenberg, J. and van der Goot, F.G. (2006) Mechanisms of pathogen entry through the endosomal 

compartments. Nat Rev Mol Cell Biol. 7:495-504 

L. Abrami, S. H. Leppla and F. G. van der Goot. (2006) Receptor palmitoylation and ubiquitination 

regulate anthrax toxin endocytosis Journal of Cell Biology 172:309-320 

van der Goot, F.G. and Gruenberg, J. (2006) Intraendosomal Membrane traffick. Trends in Cell Biology 

16:514-21 

N. Reig and van der Goot, F.G . (2006) About toxins and lipids. FEBS Letters 580:5572-9 

Nohe A, Keating E, Fivaz M, van der Goot FG, Petersen NO. Dynamics of GPI-anchored proteins on the 

surface of living cells. Nanomedicine. 2006 Mar;2(1):1-7 


ISREC - THE SWISS INSTITUTE FOR EXPERIMENTAL CANCER RESEARCH 

The ISREC has, for over 40 years of its existence as an independent institute, been devoted to cancer 

related basic research, before being integrated as an institute into the EPFL School of Life Sciences. With 

the renewal of a substantial part of its scientific staff in the recent past, its research focus has shifted to 

areas including genome stability, cell proliferation and differentiation, and the role of developmental 

pathways in tumorigenesis and tumor progression. The ISREC Foundation (www.isrec.ch) continues to 

raise and provide resources that are primarily aimed at supporting projects with a potential for diagnostic 

or therapeutic innovation 

The ISREC is also leading house of a National Center of Competence in Research (NCCR) in molecular 

oncology, a network research program launched by the Swiss National Science Foundation. The program 

focuses on questions relating to the interaction of tumors with their microenvironment. Its explicit goal is to 

support projects at the interface to the clinic 


AGUET LAB 

TEAM MEMBERS 

Pascale Anderle, Postdoctoral Fellow 

Jennyfer Bultinck, Postdoctoral Fellow 

Juergen Deka, Staff Scientist & Scientific Manager NCCR 

Geneviève Rossier, Administrative Assistant 

Nathalie Vilain, Technician 

Norbert Wiedemann, PhD Student 

Michel Aguet 


Director ISREC 


http://aguet-lab.epfl.ch 

Director, NCCR “Molecular Oncology” 

INTRODUCTION 

Our group is focusing on two projects: A first project concentrates on characterizing an epithelial 

regeneration deficit observed in mouse null mutants of Bcl9/Bcl9l, which encode presumed transcriptional 

co-activators of Wnt target genes. The Wnt pathway is involved in a variety of developmental processes 

related to morphogenesis and organogenesis. Activation of this pathway is an early step in tumorigenesis, 

notably in colon cancer. 

In a second project, tissue from colon cancer patients was micro-dissected to compare profiles of genes 

expressed in non-invasive versus invasive tumor epithelium, as well as in underlying stromal tissue. 

Differentially expressed genes are assessed for their role in tumor progression using mouse xenograft 

models and whole animal imaging, and for their potential use as diagnostic tumor markers. 


1. Mouse mutants of the Wnt signaling components Pygo and Bcl9 

Bcl9 and Pygopus (Pygo) were discovered in Drosophila as essential components of the Wnt canonical 

signaling pathway. Bcl9 binds to β-Catenin and to Pygo and tethers Pygo to the ß-Catenin-Tcf activation 

complex (Kramps et al., Cell 109, 47-60, 2002). To elucidate the role of Bcl9 and Pygo during embryonic 

development and adult tissue homeostasis in the mouse, we generated loxP-flanked alleles of the four 

relevant genes (Bcl9, Bcl9l, Pygo1, Pygo2) and derived several conditionally mutant strains.

Role of Pygo1/2 in mouse embryonic development 

Ablating both Pygo orthologs in the mouse caused abnormalities including a striking defect in lens 

development, and a deficiency in cardiac neural crest cell expansion that resulted in lethal cardiac outflow 

tract and valve anomalies. Surprisingly, compound Pygo1/2 mutant embryos presented no anomalies in 

early Wnt mediated developmental processes. Accordingly, expression of known Wnt target genes was 

not significantly affected. 

Role of Bcl9/Bcl9l in homeostasis and regeneration of adult gastrointestinal epithelium 

In the gastrointestinal epithelium, locally confined Wnt signals regulate and compartmentalize cell 

proliferation and differentiation along the crypt villus axis. Surprisingly, ablation of Bcl9 and Bcl9l in the 

adult gastrointestinal epithelium did not result in any detectable anomaly and had no effect on cell 

proliferation and lineage determination. However, mutant mice proved highly susceptible to the irritant 

dextrane sulfate sodium (DSS) and displayed epithelial lesions that were markedly more extended as 

compared to wild-type mice (see Figure). Transcriptional profiles of epithelium micro-dissected at different 

time points of DSS treatment are currently compared. Preliminary results indicate that stress responses to 

DSS are indistinguishable, and that the anomaly is rather due to impaired epithelial regeneration during 

wound-healing. The comparison of genes differentially expressed during the regenerative phase is 

expected to provide hints regarding affected genes, and to clarify to what extend the anomaly can be 

attributed to altered Wnt-signaling. 

Role of Bcl9 and Pygo proteins in tumor development 

Constitutive activation of Wnt/β-catenin signaling is an initiating event in the development of colorectal 

carcinomas in humans. To assess the role of Pygo and Bcl9 proteins in colorectal tumorigenesis, colon 

tumors were induced in mice through exposure to the mutagen N,N'-dimethylhydrazine (DMH) and 

subsequent challenge with DSS. Unexpectedly, wild-type and Bcl9/Bcl9l or Pygo1/2 mutants developed 

tumors to the same extent and tumors had comparable morphology. Wnt signaling, as assessed by 

expression level of the Wnt target gene Axin2, was activated to a similar extent in wild-type and mutant 

tumors. 

While it cannot be ruled out that Pygo1/2 and Bcl9/Bcl9l may be required for discrete spatial and/or 

temporal activation of Wnt-regulated genes during embryonic development and adult tissue regeneration, 

their role as obligatory transcriptional co-activators of Wnt target genes in Drosophila does not appear to 

be conserved in the mouse. 

2. Exploring the microenvironment of human colon cancer 

There is increasing evidence that tumor cells actively recruit stromal cells, such as inflammatory cells, 

vascular cells, and fibroblasts, into the tumor. The resulting microenvironment seems to play an important 

role in tumor progression. Dissecting this intercellular cross-talk and the underlying molecular pathways 

might provide new rationales for inhibiting tumor progression through targeting the tumor 

microenvironment in addition to the tumor cell. 

The objectives of this project are to identify genes that are differentially expressed at the invasive tumor 

front and to use genetically engineered and/or xenograft mouse models to explore the functional 

relevance of candidate genes for promoting tumor growth, invasion and dissemination. Using laser 

capture micro-dissection of colon carcinoma tissue from freshly operated patients, we have established a 

database of genes differentially expressed in tumor versus normal epithelium, and in quiescent versus 

reactive tumor stroma. A mouse xenograft platform has been established to modulate expression of 

candidate genes in established tumors using lentivirus-based conditional shRNA or cDNA expression 

(Wiznerowicz and Trono, J. Virol. 77, 8957–8961, 2003) and to monitor tumor growth. Proof of concept 

has been obtained with colon carcinoma cell lines in which genes known to affect tumor proliferation have 

been attenuated (ß-catenin; HectH9, a regulator of Myc-mediated target gene expression). These models 

are currently adapted to focus more on monitoring tumor invasion and metastatic dissemination. 

Early diagnosis is likely to improve the outcome and prognosis of most solid tumors. While proteomic 

profiling for tumor marker discovery has hold particular promise, the use of biomarker screening has so far 

been limited to prostate cancer. A side project has emerged from our gene discovery effort at the invasive 

tumor front that aims at exploiting the activity of some genes as a means for detecting predictable 

degradation products as early potentially diagnostic markers of invasiveness. Our current work focuses 

increasingly on establishing proof for this concept.


Vilain, N., Bultinck, J., Anderle, P., Deka, J., Seiler, F., Zilian, O., Piccolo, S., Hengartner, D., Basler, K. 

and Aguet, M. Pygopus proteins mediate essential functions during development, but do not appear as 

major regulators of Wnt-signaling in the mouse. In revision 

van Bezooijen, R. L., Deruiter, M. C., Vilain, N., Monteiro, R. M., Visser, A., van der Wee-Pals, L., van 

Munsteren, C. J., Hogendoorn, P. C., Aguet, M., Mummery, C. L., Papapoulos, S. E., Ten Dijke, P. and 

Lowik, C. W. (2007). SOST expression is restricted to the great arteries during embryonic and neonatal 

cardiovascular development. Dev. Dyn. 236: 606-612 

Wilson A., Ardiet, D.-L., Saner, C., Vilain, N., Beermann, F., Aguet, M., MacDonald, H.R., and Zilian, O. 

(2007). Normal hematopoiesis and lymphopoiesis in the combined absence of Numb and Numblike.. J. 

Immunol. 178: 6746-6751 

Wang, X. D., Leow, C. C., Zha, J., Tang, Z., Modrusan, Z., Radtke, F., Aguet, M., de Sauvage, F. J. and 

Gao, W. Q. (2006). Notch signaling is required for normal prostatic epithelial cell proliferation and 

differentiation. Dev. Biol. 290 : 66-80 

Regeneration deficiency in Bcl9/Bcl9l mutant mice exposed to the gastrointestinal irritant DSS. HE stained 

sections of colon epithelium of A) wt and B) compound Bcl9/Bcl9l mutant mice 8 days after recovery from DSS 

treatment. 


BEARD LAB 

TEAM MEMBERS 

Nicole de Montmollin, Administrative Assistant 

Anika Ekrut, PhD Student 

Michalis Fragkos, Postdoctoral Fellow 

Carin Ingemarsdotter, PhD Student 

Debora Keller, PhD Student 

Florence Magnin, PhD Student 

Nicole Paduwat, Technician 

Peter Beard, Group Leader (2007-2008) 

Adjunct Professor since June 2008 


http://beard-lab.epfl.ch 

INTRODUCTION 

Several viruses of the parvovirus family infect cancer cells and have tumour suppressive activity. Our work 

is aimed at understanding how adeno-associated virus (AAV) interferes with cell division and induces cell 

killing of cancer cells that are defective in the p53- or certain other cellular signalling pathways. Part of the 

cell’s response to AAV is the triggering of DNA damage signalling originating from the viral DNA. The 

multi-functional viral replication protein, Rep, also can signal cell cycle arrest. AAV therefore provides a 

unique opportunity to study DNA damage response pathways without actually damaging the cellular DNA, 

as well as mechanisms of viral interference in cell cycle control. The information yielded by AAV adds a 

new dimension to our understanding of the behaviour of cancer cells and may have the potential to lead to 

novel approaches to cancer therapy. 


The DNA damage response to adeno-associated virus: centriole overduplication and induction of 

cell death through mitotic catastrophe. 

AAV2 provokes a DNA damage response in infected cells that leads to a cell cycle arrest at the G2/M 

border of the cell cycle. Since UV-inactivated AAV (UV-AAV2) is likewise effective, this arrest does not 

depend on virally coded proteins. Rather, the UV-AAV2 DNA mimics a stalled replication fork. Tumour 

cells lacking p53 cannot sustain the G2 arrest and enter a prolonged impaired mitosis, the outcome of 

which is cell death. Using U2OS osteosarcoma cells, we found that the virus is able to uncouple the 

centriole duplication cycle from the cell cycle, leading to amplified centrosome numbers. Chk1 colocalises 

with centrosomes in the infected cells and the centrosome overduplication is dependent on the presence 

of Chk1, as well as on the activities of ATR and CDK kinases and on the G2 arrest. The mitotic spindle 

checkpoint is activated in these cells, but interference with checkpoint components revealed that mitotic 

catastrophe occurs independently of spindle checkpoint function. Thus, in the p53-deficient cells, AAV2 

triggers mitotic catastrophe associated with a dramatic Chk1-dependent overduplication of centrioles and 

the consequent formation of multiple spindle poles in mitosis. As AAV2 acts through cellular damage 

response pathways, the results also provide new information on the role of Chk1 in mitotic catastrophe 

after DNA damage signalling in general (see figure). 

Recombinant adeno-associated viral vectors are deficient in provoking a DNA damage response 

AAV2 provokes a DNA damage response that mimics a stalled replication fork. This response is 

dependent on ATR kinase and involves recruitment of DNA repair proteins into foci associated with AAV2 

DNA. Since recombinant AAV2 (rAAV2) viral vectors are widely used, we tested if such vectors are able to 

produce a similar response. Surprisingly, our results show that both single-stranded and double-stranded 

GFP-expressing rAAV2 vectors are defective in producing such a response. DNA damage signaling 

initiated by AAV2 was not due to the virus-encoded Rep or viral capsid proteins, nor was it provoked by 

other DNA molecules, such as single-stranded bacteriophage M13 or plasmid DNAs. Rather, the results 

indicate that the ability of AAV2 to produce a DNA damage response can be attributed to the presence of 

cis-acting AAV2 DNA sequences, which are absent in rAAV2 vectors and could function as origins of 

replication creating stalled replication complexes. This hypothesis was tested by using a single-stranded 

rAAV2 vector containing the p5 AAV2 sequence that has previously been shown to enhance AAV2 

replication. This vector was indeed able to trigger DNA damage signaling. The findings support the 

conclusion that efficient formation of AAV2 replication complexes is required for this AAV2-induced DNA 

damage response and provide an explanation for the poor response in rAAV2-infected cells.

Interaction of adeno-associated virus with human papillomavirus episome-containing cervical keratinocytes 

AAV depends for growth on helper viruses. Gene products encoded by adenoviruses or herpesviruses 

provide an intracellular milieu that enables efficient replication of AAV. Several proteins encoded by 

human papillomaviruses (HPV) have also been shown to be able to provide a certain level of help. 

Moreover, the ability of genotoxic cellular stress to enhance AAV replication has been recognised, and 

AAV growth in organotypic skin cultures has been reported. Nevertheless, it is not known if there is a 

predominant host tissue for AAV replication or to what extent AAV can replicate in the absence of helper 

viral functions. Since an inverse correlation between AAV infection and cervical carcinoma has been 

reported, we have investigated the growth of AAV2 in keratinocytes (W12 cells) that were obtained from 

an HPV16-positve precancerous lesion. These cells contain HPV16 DNA as episomes and express viral 

genes, yet retain the capacity to differentiate in cell culture. AAV2 infects growing W12 cells but does not 

replicate, suggesting that the presence of episomal HPV in undifferentiated W12 cells is not sufficient to 

provide helper functions. On cultivation in the presence of calcium W12 cells start to differentiate as 

demonstrated by expression of differentiation markers. Nevertheless, we did not see AAV replication 

under these conditions. So differentiating W12 cells do not provide a helper milieu for AAV replication, 

either by way of HPV or differentiation itself. The cells are permissive since, in the presence of a low 

amount of helper adenovirus, we observed AAV replication concurrently with differentiation. We are 

currently testing whether AAV can replicate in keratinocytes under other differentiation conditions. 

How adeno-associated virus Rep78 arrests the cell cycle through its effect on Cdc25 proteins 

The AAV2 Rep78 protein has been shown to block the cell cycle at several stages. To be able to induce 

this arrest, Rep78 affects several proteins implicated in the regulation of the cell cycle, such as the family 

of the cell division cycle 25 (Cdc25) phosphatases. Rep78 has been shown to inactivate Cdc25A by 

interacting with it and thus preventing it to access to its substrates. Cdc25B shares conserved domains 

with Cdc25A and moreover has an important role in cell cycle regulation, especially to give the signal for 

entry into mitosis. Thus we examined Cdc25B in more detail and found that Rep78 also interacts with it. 

The interaction between Rep78 and Cdc25B alters the localisation of the latter protein. Cdc25B is most of 

the time nuclear, but has to migrate to the cytoplasm at the end of the G2 phase to activate proteins 

needed for entry into mitosis. The overexpressed Cdc25B, contrary to the endogenous protein, is 

predominantly cytoplasmic. The expression of AAV2 Rep78, which is nuclear, leads to the relocalisation of 

Cdc25B to the nucleus. Localisation studies show a close distribution pattern in the nucleus between 

Rep78 and the overexpressed Cdc25B. Our model is that Rep78 interacts with Cdc25B and thus retains it 

in the nucleus. This work thus establishes a novel mechanism in which sequestration of Cdc25B in the 

nucleus prevents it from activating the proteins in the cytoplasm needed to give the entry signal into 

mitosis, so contributing to the G2/M arrest induced by Rep78. 

Mitotic catastrophe and subsequent cell death in osteosarcoma cells infected 

by AAV due to the formation of multiple mitotic spindle poles. Tubulin – red, 

DNA – blue.


J. Jurvansuu, M. Fragkos, C. Ingemarsdotter and P. Beard. (2007). Chk1 instability is coupled to mitotic 

cell death of p53-deficient cells in response to virus-induced DNA damage signalling. J. Mol. Biol. 372: 

397-406 

E. Garner, F. Martinon, J. Tschopp, P. Beard and K. Raj. (2007). Cells with defective p53-p21-pRb 

pathway are susceptible to apoptosis induced by p84N5 via caspase-6. Cancer Res. 67: 7631-7637 

T. Oskarsson, N. Dubois, M. Essers, C. Dubey, C. Roger, D. Metzger, P. Chambon, E. Hummler, P. 

Beard, and A. Trumpp. (2006). Skin epidermis lacking the c-myc gene is resistant to Ras driven 

tumorigenesis but can re-acquire sensitivity upon additional loss of the p21 CIP1 gene. Genes and 

Development 20: 2024–2029 

R. Hoffmann, B. Hirt, V. Bechtold, P. Beard and K. Raj. (2006). Variable modes of human papillomavirus 

DNA replication during maintenance. J. Virol. 80: 4431-443 

P. Beard. (2006). Parvoviruses in Fundamentals of Molecular Virology, N. Acheson Ed., John Wiley and 

Sons 


BRISKEN LAB 

Cathrin Brisken 



http://brisken-lab.epfl.ch 

TEAM MEMBERS 

Ayyakkannu Ayyanan, Research Associate 

Manfred Beleut, PhD student 

Stephan Duss, PhD student 

Rosmarie Freymond, Laboratory Assistant 

Sandra Gass, PhD student 

Maria Gutierrez, Technician 

Sonia Mallepell , PhD student 

Nathalie Müller, Technician 

Renuga Devi Rajaram, PhD student 

Anne-Marie Rodel, Administrative Assistant 

Ozden Yalçin, PhD student 

Seda Yerlikaya, Trainee Student 

INTRODUCTION 

Breast cancer strikes one out of eight women in Switzerland. A woman's risk to get breast cancer is linked 

to her reproductive history. While early pregnancies have a protective effect, cancer risk increases with 

the number of menstrual cycles a woman undergoes prior to her first pregnancy. Although it is well 

established that the female sex hormones estrogen, progesterone and prolactin control breast 

development and have an important role in breast carcinogenesis, the mechanisms by which they exert 

their effects are poorly understood. 

Our goal is to understand how hormones interact with developmental signaling pathways in the breast to 

control growth and differentiation. 

Hormones exert control in the breast tissue by regulating interactions between different cells 

The effect of hormones is dependent on interactions between the different cell types that make up milk 

ducts and the surrounding stroma. Cells within milk ducts communicate with each other neighbours as 

well as with cells within the connective tissue. The highly complex interplay between hormones and the 

many different cell types of the breast cannot be mimicked by growing cells in plastic culture dishes but 

requires experiments within a living organism. The mouse is an excellent model because powerful 

techniques for genetic manipulation of the organism and of distinct tissues are available, and the 

mammary glands are readily accessible for experimentation(see scheme 1). 

Scheme 1: Scheme of mammary gland development. 

The use of mutant mice to study breast development 

The mouse mammary gland provides a unique experimental system to study in vivo how systemic 

hormones impinge on molecular determinants of development in the breast and how deregulation of these 

pathways leads to tumorigenesis. The mammary gland being the only organ to undergo most of its 

development after birth allows for extensive experimental manipulation. In young female mice, the part of 

the inguinal mammary glands that contains the epithelial tree can be surgically removed creating a 

"cleared fat pad". When epithelial tissue or primary cells are engrafted into a cleared fat pads, they will 

repopulate it and form a well-organized mammary gland, which responds to all hormonal stimuli (see 

scheme 2, next page).

Scheme 2: Mammary gland reconstitution: In the 3-week-old female mouse the ductal tree growing out from the 

nipple has only partially penetrated the mammary fat pad (left panel). It can be surgically removed leaving behind 

a cleared fat pad. Primary mammary epithelial cells injected into this fat pad can form new ducts that grow out to 

populate the fat pad (right panels). 

A rapidly increasing number of mice carrying transgenes or deletions of specific genes are available and 

the role of these genes in breast development and carcinogenesis can be evaluated. Since the mammary 

gland is a paired organ it is possible to compare genetically different cells engrafted within the same host, 

ensuring that both grafts are exposed to the same hormonal milieu. 

We have made extensive use of this model to define the influence of progesterone and prolactin signaling 

on the branching of the milk duct system and the formation of the secretory pouches and to study how 

these hormones control developmental signaling pathways in the breast. In particular, we have provided 

the first demonstration that, progesterone does not act directly on its target cells but affects intercellular 

communication to induce morphogenesis/proliferation. We identified wnt-4 as one of the molecules the 

cells use to talk to each other when they get organized to form new branches. Interestingly, wnt-4 is part 

of a signaling pathway that is frequently deregulated in various types of cancers (see scheme 3). 

Scheme 3: Schematic representation of mammary gland development (black) and our current working model of 

how various factors control different morphogenetic steps (color) based on our previous work. 

Normal development and breast cancer 

The dissection of the mechanisms underlying the actions of the female sex hormones in breast 

development will increase our understanding of the origins of breast cancer and provide the basis for 

developing new preventive and therapeutic strategies. To assess the relevance of our findings to the 

human situation more directly, we have established strong collaborative links with two clinical departments 

at the Centre Hospitalier Universitaire Vaudois, Lausanne (CHUV). We have established primary cultures 

of human breast cells that we obtain from reduction mammoplasties.


Amphiregulin is an essential mediator of ERα function in mammary gland development 

Most mammary gland development occurs after birth under the control of systemic hormones. Estrogens 

induce mammary epithelial cell proliferation during puberty via epithelial estrogen receptor α (ERα) by a 

paracrine mechanism. Epidermal growth factor receptor (EGFR) signaling has long been implicated 

downstream of ERα signaling and several EGFR ligands have been described as estrogen target genes in 

tumor cell lines. We have shown that amphiregulin is the unique EGF family member to be 

transcriptionally induced by estrogen, in the mammary glands of puberal mice at a time of exponential 

expansion of the ductal system. In fact, we have found that estrogens induce amphiregulin through the 

ERα and require amphiregulin to induce proliferation of the mammary epithelium. Like ERα amphiregulin 

is required in the epithelium of puberal mice for epithelial proliferation, terminal end buds (TEBs) formation 

and ductal elongation. Subsequent stages, such as sidebranching and alveologenesis are not affected. 

When amphiregulin -/- mammary epithelial cells are in close vicinity to wild type (WT) cells, they proliferate 

and contribute to all cell compartments of the ductal outgrowth. Thus, amphiregulin is an important 

paracrine mediator of estrogen function specifically required for puberty-induced ductal elongation but not 

any earlier nor later developmental stages. 


Duss, S., André S., Nicoulaz, A. L., Fiche, M., Bonnefoi, H., Brisken, C., Iggo, R. (2007). An estrogendependent 

model of breast cancer created by transformation of normal human mammary epithelial cells 

Breast Cancer Res. 9(3): R38 

Ciarloni, L., Mallepell, S., Brisken, C. (2007). Amphiregulin is an essential mediator of ERα function in 

mammary gland development. Proc. Natl. Acad. Sci. USA, 104(13): 5455-60 

Reviewed in: Lamarca HL, Rosen JM. Estrogen regulation of mammary gland development and breast 

cancer: amphiregulin takes center stage. 2007 Breast Cancer Res. Jul 20;9(4):304 

Brisken, C., Duss, S. (2007). Hormones and the stem cell niche in the breast: a developmental 

perspective. Stem Cell Reviews. 3 (2): 147-156 

Ayyanan, A., Civenni, G., Ciarloni, L., Morel, C., Lefort, K., Mandinova, A., Raffoul, W., Fiche, M., Dotto, 

G. P., Brisken, C. (2006). Increased Wnt signaling triggers oncogenic conversion of human mammary 

epithelial cells by a Notch-dependent mechanism mammary gland development. Proc. Natl. Acad. Sci. 

USA, 103 (10): 3799-3804 

Reviewed in: Collu GM, Brennan K. Cooperation between Wnt and Notch signaling in human breast 

cancer. 2007 Breast Cancer Res. Jul 20;9(3):105 

Mallepell, S., Krust, A., Chambon, P., Brisken, C. (2006). Paracrine signaling through the epithelial 

Estrogen Receptor α is required for proliferation and morphogenesis in the mammary gland. Proc. Natl. 

Acad. Sci. USA, 103 (7): 2196-2201 

Brisken, C., Rajaram, R. (2006). Alveolar and Lactogenic Differentiation. Journal of Mammary Gland 

Biol. and Neoplasia. 11: 239-248 


CONSTAM LAB 

Daniel Constam 



http://constam-lab.epfl.ch 

TEAM MEMBERS 

Stéphane Baflast, Technician 

Marie-Hélène Blanchet, PhD Student 

Sophie Cherpillod, Administative Assistant (2007) 

Anja Dietze, PhD Student 

Marie-France Divorne, Administrative Assistant (2008) 

Antonia Giugno, Laboratory Assistant 

Susanna Kallioinen, PhD Student 

Charlotte Maisonneuve, PhD Student 

Daniel Mesnard, Postdoctoral Fellow 

Marja Talikka, Postdoctoral Fellow 

Séverine Urfer-Beck, Technician 

INTRODUCTION 

Morphogenetic signaling in stem cells and early lineages of the mouse embryo 

Our laboratory investigates how pluripotent stem cells and their dynamic microenvironment communicate 

in vivo to balance self-renewal and differentiation during normal development of tissue-specific lineages, 

and how the signals involved can be skewed by cancer cells to promote tumor progression. Using 

transgenic mice, combined with biochemical analysis and cell-based assays, we currently study the role of 

secreted TGFß proteins such as Nodal and BMPs, and how they cooperate with Wnt and FGF pathways. 

We are also investigating how such morphogenetic activities and their movement across tissues are 

regulated by posttranslational processing, endocytic trafficking, and by monocilia. 

Pluripotent cells in the early embryo are allocated to distinct lineages by a Nodal activity gradient that is 

established by an intricate autoregulatory signaling network. Nodal also acts on the stem cell 

microenvironment, the so-called primitive endoderm, to differentiate anterior and posterior territories. 

Paradoxically, however, we and others observed that prior to stimulating germ layer differentiation; Nodal 

has the very opposite effect on pluripotent cells and initially is required to inhibit their premature 

differentiation. What determines whether Nodal acts as a stem cell factor or as a differentiation signal, and 

by what cellular and molecular mechanisms are these seemingly opposite activities kept in balance Does 

a shift in the balance promote oncogenic activities of Nodal, e.g. in invasive melanoma and possibly other 

malignant tumors Are differentiation and self-renewal distinguished by distinct Nodal signaling 

thresholds Or do cells respond differently to Nodal depending on dynamic changes induced in the stem 

cell microenvironment And what determines whether Nodal signals in an autocrine or paracrine fashion 


Role of the subtilisin-like proprotein convertase PC7 in the Nodal/BMP signaling network 

Different cell fates may be specified by distinct threshold concentrations of a Nodal morphogen gradient 

during gastrulation. However, Nodal is broadly expressed throughout the inner cell mass of the implanted 

blastocyst and its derivative, the epiblast (Mesnard et al. 2006), raising the question whether a Nodal 

morphogen gradient may be established posttranscriptionally. Moreover, to ensure that mesoderm and 

endoderm form at the right time, Nodal may specify distinct cell fates depending on the duration of 

signaling. 

Previous work from our lab has provided unexpected insights into how Nodal activity and germ layer 

formation are regulated. In particular, we have identified the two serine proteases Furin and PACE4, 

which are secreted by cells in the trophoblast and visceral endoderm lineages and necessary to remove 

an inhibitory N-terminal propeptide from the Nodal precursor (proNodal) in the epiblast (Fig. 1). Upon 

proteolytic maturation, Nodal signals through activin receptors and the accessory protein Cripto to activate 

Smad2,3 transcription factors, which stimulate Nodal/Cripto autoinduction and expression of the secreted 

feedback inhibitors Lefty-1 and Cerberus-like, thereby subdividing the microenvironment into embryonic 

(Fig. 1, bright green) and anterior visceral endoderm (AVE, yellow). Patterning of this microenvironment 

guides the positioning of the future body axis and defines on which side neighboring embryonic cells will 

activate Wnt3 and become mesoderm and endoderm. Does the establishment of such asymmetry depend 

on an asymmetric distribution of Nodal convertases

To detect potential asymmetries in the pattern of Nodal processing, we now developed new methods that 

will be suitable to visualize the distribution of Furin and PACE4 activities in vivo. Another important 

question was why Nodal only activates expression of the mesoderm-inducing factor Wnt3 after embryonic 

day E6.0, and not earlier. Computational modeling indicated that endoderm arises from cells in which 

Nodal expression is prolonged by sequential positive feedback of both mature Nodal and Wnt3, whereas 

signaling induced by Wnt3 alone is sufficient to specify mesoderm (BenHaim et al., 2006). Interestingly, 

this model also predicted that an unknown mechanism must delay the induction of Wnt3 to prevent 

precocious mesoderm and endoderm formation. 

So what delays the onset of Wnt3 expression Available evidence suggests that Nodal induces Wnt3 

indirectly through BMP4 (BenHaim et al., 2006). Possibly, the necessary threshold of Bmp activity is only 

reached after prolonged signaling, and/or relies on specific pathway agonists that are only active after 

E6.0. Among candidate activators of BMP pecursor proteins, we found that the proprotein convertase PC7 

is likely to be involved. Our analysis of Furin;PC7 double mutants showed that PC7 synergizes with Furin 

to activate BMP signaling at the onset of gastrulation (Fig. 1). 

Figure 1: Nodal activity regulated by positive and negative feedback signals coordinates 

stem cell proliferation and germ layer differentiation. Uncleaved Nodal maintains the source 

of proprotein convertases and Bmp4 in trophoblast stem cells, and thereby triggers Wnt3 

expression. Besides inducing mesoderm, Wnt3 together with processed Nodal also 

upregulates Cripto at the posterior pole (P), whereas this process is blocked anteriorly (A) 

by the AVE-derived feedback inhibitors Cerl, Lefty-1 and Dkk1. Integrated over time, the 

Nodal signal thus is highest at the posterior pole where it drives mesoderm and endoderm 

formation, but low in the vicinity of the AVE. Yet another feedback inhibitor, Lefty-2, induced 

in mesodermal cells has been show to limit endoderm formation. The factors which 

determine the timing of the onset of Wnt3 expression are not well defined, but include the 

protease PC7 which acts together with Furin to unleash the activity of BMP4. The mouse 

embryo and its amenability to genetic manipulation are crucial to define how these and 

other mediators of specific tissue interactions cooperate to determine the fate of pluripotent 

cells in mammals. 

New role for Cripto as a receptor of Nodal precursor and its convertases 

Nodal signal transduction is mediated by complexes of the Nodal/Activin reptors ActRII and Alk4 with the 

GPI-anchored coreceptor Cripto which are endocytosed to phosphorylate the transcription factors Smad2 

and-3 (Fig. 2). We now asked whether Cripto has an additional function during Nodal processing. We 

could show that Cripto captures Nodal already during exocytosis, in part by tethering its prosegment. 

Cripto thus promotes the localization or stability of Nodal precursor in lipid rafts and stimulates clathrinindependent, 

non-caveolar endocytosis in membrane carriers that can be labelled by GFP-Flotillin. 

Furthermore, coimmunoprecipitation assays revealed that Cripto also binds Furin and PACE4. To 

determine whether Nodal must mature in a complex with Cripto to efficiently ativate signaling receptors, 

we first mapped a Cripto-interacting region (CIR) in the prosegement of the Nodal precursor.

Using a luciferase reporter assay for Smad2 activation, we then could show that mutation of this motif in 

the Nodal precursor markedly inhibited signaling. These results suggest a new role for Cripto as a 

protease receptor that localizes Nodal processing to specific membrane microdomains to promote 

Smad2, 3 signaling (Blanchet et al., in press). 

Role of Smad-independent Cripto signaling 

Cripto can also signal independently of Nodal and trigger cellular transformation by stimulating MAPK and 

other pathways e.g. in cultured fibroblasts and mammary epithelial cells. Therefore, we wondered whether 

in addition to its known functions, Cripto also mediates Smad-independent signals even in its physiological 

context in the mouse embryo. 

To address this question, we analyzed a point mutant form of Cripto which failed to stimulate Nodal 

signaling via Smad2,3 in embryoid bodies and in tissue culture cells, yet retained the ability to activate 

MAPK. In the collaborating laboratory of Dr. Minchiotti (Naples), this mutation was also introduced in mice 

at the Cripto locus using homologous recombination in embryonic stem cells. Interestingly, this point 

mutant Cripto F78A was still able to mediate a subset of known Cripto activities that drive gastrulation 

movements, even though the expression of known Smad2,3-dependent Nodal target genes was absent or 

severely reduced (D’Andrea et al. 2008). These results suggest a novel function for Smad2-independent 

Cripto signaling in vivo. Our ongoing work seeks to elucidate new roles for Cripto and related GPIanchored 

receptors in signal transduction during development and cancer (Fig. 2). 

Figure 2: Role of the GPI-anchored receptor Cripto at the 

crossroads of TGFß and Wnt signaling pathways. 

Cripto localizes Nodal processing and Smad2,3 activation by 

capturing the Nodal precursor, its convertases Furin and PACE4, as 

well as ALK4. While Cripto primarily functions in the 

Nodal/Alk4/Smad2,3 pathway, its interactions with other signaling 

molecules contribute to germ layer formation and elicit oncogenic 

effects, notably in human breast cancer. Point mutations which we 

found to selectively inhibit Smad2,3 signaling without affecting 

Nodal-independent activities can now be used to dissect the roles of 

individual pathways. 

2006 2007 PUBLICATIONS 

Blanchet, M.-H., Le Good, J.A., Mesnard, D., Baflast, S., Minchiotti, G., Klumperman, J., Constam, D.B. 

(2008) Cripto recruits Furin and PACE4 and controls Nodal trafficking during proteolytic maturation. 

EMBO J. (in press) 

Szumska, D., Pieles, G., Essalmani, R., Bilski, M., Mesnard, D., Kaur, K., Franklyn, A., El Omari, K., 

Jefferis, J., Bentham, J., Taylor, J., Schneider, J., Arnold, S., Johnson, P., Tymowska-Lalanne, Z., 

Stammers, D., Clarke, K., Neubauer, S., Morris, A., Brown, S., Shaw-Smith, C., Cama, A., Capra, V., 

Ragoussis-J., Constam, D., Seidah, N.G., Prat, A., Bhattacharya, S. (2008). VACTERL / Caudal 

Rregression / Currarino Syndrome-like malformations in mice with mutation in the proprotein convertase 

Pcsk5. Genes Dev. 22 :1465-1477 

D’Andrea, D., Liguori, G.L., Le Good, J.A., Lonardo, E., Andersson, O., Constam, D.B., Persico, M.G., 

Minchiotti, G. (2008). Cripto promotes A-P axis specification independently of its stimulatory effect on 

Nodal autoinduction. J. Cell Biol. 180:597-605 

Ben-Haim, N., Lu., C., Guzman-Ayala, M., Pescatore, L., Mesnard, D., Bischofberger, M., Naef, F., 

Robertson, E.J. and Constam, D.B. (2006). The Nodal precursor acting via activin receptors induces 

mesoderm by maintaining a source of its convertases and BMP4. Dev. Cell 11:313-323 

Mesnard, D., Guzman-Ayala, M. and Constam, D.B. (2006). Nodal specifies embryonic visceral endoderm 

and sustains pluripotent cells in the epiblast before overt axial patterning. Development 133: 2497-2505 


DUBOULE LAB 

TEAM MEMBERS 

Guillaume Andrey, PhD Student 

Caroline Guinchard, Administrative Assistant 

Istvan Gyurjan, Postdoctoral Fellow 

Elisabeth Joye, Laboratory Technician 

Thomas Montavon, Postdoctoral Fellow 

Denis Duboule 


Joint Chair 

UNIGE / EPFL, School of Life Sciences 

since January 2007 


http://duboule-lab.epfl.ch 

INTRODUCTION 

This laboratory has started operating during 2007. Its major aim is to study principles of mammalian 

embryological development by using the recent tools of functional genomics. A special focus is given to 

those similarities and differences that exist between the embryological development of vertebrates (to 

whom mammals belong) and those of other animals (invertebrates), from whom vertebrates derive. To 

achieve this task, we use the developing mouse embryo in vivo as an experimental system, and try and 

apply the methodology developed following the sequencing of complex genomes. Our major, though not 

exclusive, target is the understanding of the regulation of a critical family of transcription factors during the 

construction of the animal body plan, referred to as architect genes (the Hox gene family). These genes 

have a special interest in the study of both our ontogenesis (our development as individuals) and our 

phylogeny (our origin as a group of individuals) and the detailed understanding of their regulations and 

functions will be a important step in our understanding of our own histories. 


2007 has seen the start of this new laboratory (developmental genomics), which is now fully operational. 

We have imported some of the approaches required to manipulate the mammalian embryo and started 

projects aimed at understanding the global genomic regulation at work during the development of our 

limbs. To do this, we have used a large allelic series of mice mutant in their architect (Hox) genes to 

precisely quantify the transcriptional reallocations, in the presumptive digit domain, which were observed 

following either the deletion or the duplication of Hoxd gene loci. Micro-dissected samples obtained from 

several mutant strains were thus quantified by real-time PCR analyses and used to elaborate a 

mathematical model of large-scale gene regulation at this locus. In collaboration with Drs J.-F. Le Garrec 

and M. Kerzsberg, from the university Paris VI, we developed a model, through several rounds of 

predictions/validations, i.e. using alleles to verify the predictions of the model. This model (Montavon et 

al., 2008) is the first mathematical model proposed to account for any kind of collinear regulatory 

mechanism. It gives an explanation as to how tetrapods generally display very different morphologies 

between the thumb (the most anterior digit) and other digits, through an obligatory unequal dosage effect. 


J. Zakany and D. Duboule, The role of Hox genes during vertebrate limb development, Current Opinion 

in Genetics & Development, 2007, 359-366 

J. Zakany, G. Zacchetti and D. Duboule, Interactions between HOXD and Gli3 genes control the limb 

apical ectodermal ridge via Fgf10, Dev Biol, 2007, 306, 883-93 

G. Zacchetti, D. Duboule and J. Zakany, Hox gene function in vertebrate gut morphogenesis: the case of 

the caecum, Development, 2007, 134, 3967-73 

F.G. Grosveld and D. Duboule, Differentiation and gene regulation, Curr Opin Genet Dev, 2007, 17, 369- 

72

F. Gonzalez, D. Duboule and F. Spitz, Transgenic analysis of Hoxd gene regulation during digit 

development, Dev Biol, 2007, 306, 847-59 

N. Di-Poi, J. Zakany and D. Duboule, Distinct Roles and Regulations for Hoxd Genes in Metanephric 

Kidney Development, PLoS Genet, 2007, 3, e232 

Expression of the architect gene Hoxd13 during mouse 

embryonic development (E11.5) 


GÖNCZY LAB 

Pierre Gönczy 



http://gonczy-lab.epfl.ch 

TEAM MEMBERS 

Katayoun Afshar, Research Associate 

Alexandra Bezler, PhD Student 

Yemima Budirahardja, PhD Student 

Coralie Canard, Technician 


Virginie Hamel Hachet, Postdoctoral Fellow 

Daiju Kitagawa, Postdoctoral Fellow 

Gregor Kohlmaier, PhD Student 

Tamara Mikeladze-Dvali, Postdoctoral Fellow 

Tu Nguyen Ngoc, PhD Student 

Petr Strnad, PhD Student 

Kalyani Thyagarajan, PhD Student 

INTRODUCTION 

We are interested in understanding fundamental cell division processes, notably in the context of a 

developing organism. We focus in particular on three processes that are crucial for genome integrity: 

centrosome duplication, cell division timing and asymmetric cell division. To this end, we use a unique 

combination of genetic, functional genomic, cell biological and live imaging approaches, primarily in the 

early embryo of the nematode Caenorhabiditis elegans, as well as in human cells in culture when 

appropriate. 


Centrosome duplication 

The centrosome is the principal microtubule-organizing center of animal cells and comprises two 

centrioles surrounded by pericentriolar material. Just like the genetic material, the centrosome must 

duplicate once per cell cycle to ensure genome integrity. Formation of a single centriole next to each 

mother centriole marks the onset of centrosome duplication. We and others identified five proteins 

required for centriole formation in C. elegans: the kinase ZYG-1, as well as the coiled-coil proteins SAS-4, 

SAS-5, SAS-6 and SPD-2. We established that centriole formation is an orderly assembly process in 

which these proteins are recruited in a step-wise fashion. Relatives of these proteins are crucial for 

centriole formation also in other organisms. Thus, we found that HsSAS-6 is necessary for centriole 

formation in human cells and that excess HsSAS-6 results in supernumerary centrioles, indicating that 

regulated HsSAS-6 levels ensure formation of a single centriole per mother centriole during the 

centrosome duplication cycle. We also established that CPAP, a distant relative of C. elegans SAS-4, is 

required for centriole formation in human cells (see Fig. 1), further illustrating that the function of this set of 

proteins has been evolutionarily conserved. 

Figure 1: Human cell in mitosis treated with siRNAs 

directed against the SAS-4-related centriolar protein 

CPAP and stained with antibodies against α -tubulin 

(red), the centriolar protein centrin (green, visible in 

yellow at the spindle pole), as well as counterstained 

with a DNA dye (blue). Note that a monopolar spindle 

assembles upon CPAP depletion.

Cell division timing 

Cell division timing is important for faithful partition of the genetic material. We developed a sensitive 

assay for mitotic entry in C. elegans embryos, which uncovered that centrosomes orchestrate the proper 

execution of mitosis in time and space. Furthermore, we found that the centrosomal Aurora-A kinase AIR- 

1 is crucial for timing mitotic entry. We initiated a functional genomic RNAi-based visual screen that relies 

on this assay to identify novel spatial and temporal regulators of mitosis, which we expect to shed light on 

the general mechanisms that ensure faithful chromosome segregation. In a related line of work, we 

discovered that the Polo-like kinase PLK-1 plays a crucial role in coupling anterior-posterior (A-P) 

embryonic polarity and cell division timing during early C. elegans development. There is more PLK-1 

protein in the anterior blastomere of two-cell stage embryos, and our findings indicate that this is 

responsible in part for ensuring that entry into mitosis occurs earlier in that cell than in the posterior one. 

Asymmetric cell division 

Asymmetric cell division is crucial for generating diversity during development. In animal cells, including in 

the one-cell stage C. elegans embryo, the mitotic spindle must be eccentrically positioned for unequal cell 

division to occur. Together with the work of other laboratories, our previous findings indicate a model in 

which two Gα proteins recruit the GoLoco protein GPR-1/2 and the coiled-coil protein LIN-5 to the cell 

cortex to generate force on the plus-end of astral microtubules. We found recently that the ternary 

complex comprised of LIN-5/GPR-1/2/Gα serves to recruit the minus-end directed microtubule motor 

dynein to the cell cortex. Together with microtubule depolymerization, dynein activity allows pulling forces 

to be exerted along astral microtubules, which ensures proper spindle positioning. Since the central role of 

the Gα proteins and their associated partners in asymmetric cell division is evolutionarily conserved, we 

expect this mechanism to be of broad significance. 

Figure 2: One-cell stage C. elegans embryo in 

mitosis stained with antibodies against α-tubulin, 

which highlights microtubules (green), the 

centrosomal protein TAC-1 (red, visible in yellow at 

spindle poles) and counterstained with a DNA dye 

(blue). Note astral microtubules extending from the 

spindle poles to the cell membrane. 


Nguyen-Ngoc T., Afshar K. and Gönczy P. Cortical dynein couples force generation and Gα proteins 

during spindle positioning in C. elegans. Nat. Cell Biol. 9: 294-302 (2007) 

Strnad P., Leidel S., Vinogradova,T., Euteneur,U., Khodjakov A. and Gönczy P. Regulated HsSAS-6 

levels ensure formation of a single procentriole per centriole during the centrosome duplication cycle. Dev. 

Cell 13: 203-213 (2007) 

Bellanger J.-M., Carter J. C., Phillips, J.B., Canard C., Bowerman, B. and Gönczy P. ZYG-9, TAC-1 and 

ZYG-8 together ensure proper microtubule function throughout the cell cycle of C. elegans embryos. J. 

Cell Sci. 120: 2963-2973 (2007) 

Hachet V., Canard, C. and Gönczy P. Centrosomes promote timely mitotic entry in C. elegans embryos. 

Dev. Cell 12: 531-541 (2007) 

Delattre, M., Canard, C. and Gönczy, P. (2006). Sequential protein recruitment in C. elegans centriole 

formation. Curr. Biol. 19: 1844-1849 


GRAPIN-BOTTON LAB 

Anne Grapin-Botton 



http://grapinbotton-lab.epfl.ch 

TEAM MEMBERS 

Elke Bayha, PhD Student 

Rosemarie Freymond, Laboratory Assistant 

Emilie Gésina, Postdoctoral Fellow 

Joan Goulley, Postdoctoral Fellow 

Mathieu Gouzi, PhD Student 

Chiara Greggio, PhD Student 

Yvan Pfister, Technician 

Julie Piccand, Master Student 

Marine Rentler Courdier, PhD Student 

Anne-Marie Rodel, Administrative Assistant 

Nancy Thompson, Research Associate 

INTRODUCTION 

The definitive endoderm gives rise to the epithelium of the digestive tract, the respiratory system, and 

several endocrine and exocrine glands. Our experiments in mouse and chick embryos are designed to: 

- identify the signals that induce different organs at different positions in the digestive tract 

- determine the pancreas-specific transcription factors induced and how their network controls 

organogenesis and 

- determine how these signals lead to cancer or diabetes when inaccurately controlled. 


Organizing endoderm organs along the body axis 

Appropriate and reproducible organ layout is generally established at an early stage of development by 

the expression of patterning genes. These genes are expressed in restricted areas of the embryo and 

control differentiation and morphogenesis. Our experiments demonstrated that the mesoderm at different 

locations sends signals that instruct the endoderm of its identity along the antero-posterior (A-P, mouth to 

anus) axis (Kumar et al., 2003) (Fig. 1). We recently demonstrated that the most anterior endoderm forms 

in the absence of FGF4 and that more posterior endoderm is progressively induced as the amount of 

FGF4 received increases (Dessimoz et al., 2006). FGF signaling from endoderm formation to gut tube 

closure is absolutely essential to form mid- and hindgut and accurately maintain the boundaries between 

different digestive tract organs. Our ongoing experiments suggest that accurate levels of retinoic 

acid (Fig. 1) and Wnt signalling are also required in addition to FGFs. Taken together these observations 

show that the mesoderm sends similar signals to define regions in the nervous system and digestive tract. 

Figure 1: Graded activity of Fgf4 (orange) and 

retinoic acid (blue) integrated over time induce 

specific transcription factors at specific positions 

along the antero-posterior axis in endoderm in the 

early embryo. These patterning factors then induce 

the formation of specific endoderm-derived organs 

and segments of the digestive tract.

Regulation of pancreas organogenesis: role of the bHLH transcription factor Ptf1a in pancreas 

progenitor maintenance 

Signaling activity from the mesoderm induces pancreatic genes at a given position along the A-P axis. 

The transcription factors Pdx1 and Ptf1a maintain pancreas progenitors (Fig. 2). At a later stage Ptf1a 

becomes restricted to exocrine cells (Fig. 2). We compared the transcriptome of early pancreas 

progenitors lacking Ptf1a to that of wild type progenitors. Our experiments identified the molecular 

mechanisms by which Ptf1a maintains pancreas progenitors. Ptf1a blocks the expression of intestinal 

genes while activating a network of transcription factors of known importance in pancreas progenitors. In 

addition, we identified new targets of Ptf1a that we are studying functionally. 

Regulation of pancreas organogenesis: role of the bHLH transcription factor Neurogenin 3 (Ngn3) 

in endocrine cell differentiation 

In addition to exocrine cells, the pancreas gives rise to multiple endocrine cells whose main function is the 

regulation of glucose homeostasis. The transcription factor Ngn3 is absolutely necessary to generate 

endocrine cells. All pancreatic endocrine cells, producing glucagon, insulin, somatostatin or PP, 

differentiate from Pdx1 + progenitors that transiently express Neurogenin3 (Fig. 2). To understand whether 

the competence of pancreatic progenitors changes over time, we generated transgenic mice expressing a 

tamoxifen-inducible Ngn3 fusion protein under the control of the Pdx1 promoter and backcrossed the 

transgene into the Ngn3 -/- background, devoid of endogenous endocrine cells (Johansson et al., 2007). 

We showed that pancreas progenitors, similar to retinal or cortical progenitors, go through competence 

states that each allow the generation of a subset of endocrine cell types (Fig. 2). We further showed that 

the progenitors acquire the competence to generate late-born cells in a mechanism that is intrinsic to the 

epithelium. Ongoing experiments aim at understanding whether the change in competence is cell 

autonomous and what its molecular basis is. 

This transgenic line was also used to identify targets of Ngn3 that may unravel the molecular mechanisms 

by which Ngn3 promotes endocrine cell migration and aggregation, a process relevant to the formation of 

islets of Langerhans. 

Figure 2: Immunocytochemistry showing Ptf1a (green) and Ngn3 (red) expression at 

different developmental stages. Endocrine progenitors and exocrine cells differentiate 

from pancreas progenitors. Ngn3 expression triggers the differentiation of different 

proportions of endocrine cell types at different stages, as represented on the time line of 

the bottom scheme.

Regulation of pancreas organogenesis: role of the Wnt pathway 

Cell to cell signaling is important not only to initially induce the pancreas but also to generate specific cell 

types. We previously found that the Wnt pathway is active in endocrine cells during development 

(Dessimoz et al., 2005) (Fig. 3). Inactivation of β-catenin in the pancreas epithelium invalidates this 

pathway and results in reduced numbers of endocrine cells. Our ongoing efforts are aimed at 

understanding the mechanisms leading to this effect and the interactions between the canonical and 

planar cell polarity pathways. In addition to its role in the Wnt pathway, β-catenin is important for cell-cell 

adhesion. This may explain why exocrine cells in which Wnt pathway activity is not detected are also 

affected by β-catenin inactivation. Activating β-catenin mutations and Adenomatous Polyposis Coli (APC) 

loss of function lead to acinar cell carcinoma and pancreatoblastoma. Ongoing experiments are aimed at 

understanding how β-catenin functions in adhesion and Wnt pathway activity lead to pancreatic cancer. 

Figure 3: Wnt Pathway activity (black dots) in a pancreas section of a BAT-gal 

mouse at 14.5 dpc . Endocrine cells are in red. Blue cells are exocrine cells 

and pancreas progenitors. 

Significance of this work for diabetes and pancreatic cancer 

Although the function of the pancreas in controlling glucose homeostasis is compensated by insulin 

injection in diabetic patients, the physiological effects are inexact and too variable. Among approaches 

that are currently being explored to find a cure for diabetes are the isolation and propagation of embryonic 

or adult stem cells that can be engineered to produce endocrine hormones and then transplanted to 

patients. Our experiments are aimed at identifying the critical cellular transcription factors and signaling 

molecules that are sufficient to transform cells into pancreas and β cells. Collaborations within the context 

of the European 6 th framework project BetaCellTherapy allow us to test these ideas by introducing 

transcription factors in stem cells or exposing these cells to signalling molecules in vivo or in vitro to force 

their differentiation into β cells. 

In addition, pre-cancerous and cancerous cells often reactivate the expression of developmental genes. In 

pancreatic carcinoma many developmental genes are reactivated. Further work on developmental genes 

may give a better understanding of pancreas cancer development and may point to new therapeutic 

targets. 


Kerstin Johansson, Umut Dursun, Nathalie Jordan, Friedrich Beermann, Guoqiang Gu, Gérard Gradwohl, 

and Anne Grapin-Botton (2007). Temporal control of Neurogenin3 activity in pancreas progenitors reveals 

competence windows for the generation of different endocrine cells. Developmental Cell, In press 

Dessimoz, J.,Opoka, R., Kordich, J.J., Grapin-Botton, A. and Wells, J.M. (2006) FGF signaling is 

necessary for establishing gut tube domains along the anterior-posterior axis in vivo. Mechanisms of 

Development, 123, 42-45 

Dessimoz, J. and Grapin-Botton, A. (2006) Pancreas development and cancer: Wnt/beta-catenin at 

issue…Cell Cycle. 5:7-10 


HUELSKEN LAB 

Joerg Huelsken 



http://huelsken-lab.epfl.ch 

TEAM MEMBERS 

Stephane Duboux, Technician 

Wan-Hung Fan, PhD Student 

Tea Fevr, PhD Student 

Thomas Hussenet, Postdoctoral Fellow 

Fabien Kuttler, Postdoctoral Fellow 

Deepika Kassen, Postdoctoral Fellow 

Ilaria Malanchi, Postdoctoral Fellow 

Catherine Pache, Administrative Assistant 

Hong Peng, Visiting Scientist 

INTRODUCTION 

Our long term goal is to identify signaling pathways which control the biology of tissue-specific and cancer 

stem cells. By comparing between these two cell entities we want to make out differences which could be 

utilized for therapeutic intervention. It is expected that many properties of tissue stem cells are conserved 

in cancer stem cells, which are currently being identified in a multitude of carcinomas. Stem cells possess 

the ability to self-renew for the life span of an organ giving rise to cycling (transit-amplifying) cells which in 

turn generate terminally differentiated cells. Similar functions are attributed to cancer stem cells which are 

believed to drive tumor formation and maintenance and to be derived from tissue stem cells or from early 

progeny which regain essential stem cell properties. Very recently, it has been shown that cancer stem 

cells also contribute to metastasis formation. While these similarities have stimulated our thinking about 

the nature of the oncogenic process, a potential application of this new concept requires recognizing 

differences between tissue and cancer stem cells that can be utilized for effective and save therapy. 


Using marker expression, marker-mediated cell enrichment and tumorigenesis assays in vivo, we have 

identified cancer stem cells in skin tumors (Malanchi et al., 2008). Recently, several markers of normal 

skin stem cells including CD34 have been identified. These normal stem cells are located in the bulge 

area of the hair follicle and can contribute to all keratinocyte lineages. We asked whether a similar 

population of cells exist in early (papillomas) and advanced (squamous cell carcinomas) skin tumors. We 

employed FACS and MACS to isolate skin stem cells based on expression of CD34 with the concurrent 

exclusion of endothelial (CD31 + ) and immune cells (CD45 + ) which represent non-keratinocytes cells 

expressing CD34 in skin or skin tumors. Skin stem cells isolated from wild type, C57Bl6 adult back skin 

(CD34 + CD31 - CD45 - ) account for approximately 2% of total cells. In contrast, in skin tumors induced by 

chemical carcinogenesis (DMBA/TPA) a dramatic increase of CD34 positive cells was observed. Based 

on FACS analysis, these cells account for around 15% of tumor cells. Additional, established skin stem 

cell markers were found to be expressed in the same subpopulation of tumor cells. Together, these data 

identify a cell population in murine skin tumors which derives from and closely resembles skin stem cells 

of the bulge. 

We next assessed the in vivo tumorigenic capacity of CD34 + positive cells in an orthotopic transplantation 

model. Using unsorted tumor cells in this system, we routinely obtain tumor formation from 5x10 5 cells, 

while lower amounts rarely produce tumors. Importantly, CD34 positive tumor cells reproducibly give rise 

to secondary tumors using only 1000 cells. This corresponds to an enrichment of tumor initiating cells by a 

factor of more then 200 fold, which is comparable to cancer stem cell populations identified in other solid 

tumors. In contrast, CD34 negative cells do not produce tumors. Together, these data establish the 

population of CD34 + cells as the main source of tumorigenesis in skin tumors. Tumors derived from 

CD34 + tumor cells closely resemble the architecture of the parental tumor. Moreover, these secondary 

tumors maintain a small population of CD34 + cells similar to the parental tumors and mainly consist of 

cells expressing early differentiation markers. Serial transplantation assays confirm that the stemness of 

these cells is maintained over several generations. In addition, a CD34 + population of cancer stem cells is 

also detected in advanced squamous cell carcinomas. Importantly, expression of CD34 correlates with 

individual, invasive tumor cells, which supports the notion that cancer stem cells might be also responsible 

for tumor spreading and metastasis formation.

We and others had recently established that β-catenin/Wnt signaling is essential in the control of lineage 

decisions of skin stem cells. We now assessed the involvement of β-catenin in skin stem cell derived 

tumor formation. We employed our mice with a floxed β-catenin allele in combination with a tamoxifen 

inducible variant of cre expressed under control of the keratin14 promoter (keratin14-creERT). DMBA was 

applied to groups of inducible mutant mice (K14-creERT:β-catenin lox/lox ) and control littermates (K14- 

creERT:β-catenin +/lox ), followed by continuous TPA treatment for 8 weeks. After tumors had formed in both 

groups, deletion of β-catenin was induced by tamoxifen injection. Remarkably, lack of β-catenin resulted in 

complete tumor regression within 6 weeks. This indicates an essential role for β-catenin signaling in tumor 

maintenance, further substantiated by expression analysis of the general Wnt target gene 

conductin/axin2. Conductin was strongly upregulated throughout the cancer stem cell population, which 

demonstrates continuous activation of β-catenin signaling in skin tumors. Regression of β-catenin deficient 

tumors is characterized by enhanced terminal differentiation, which ultimately produces structures largely 

consisting of keratinized layers. The first difference we have been able to detect in β-catenin deleted 

tumors is a strong reduction of tumor cells with stem cell-like characteristics. This was analyzed by LTR 

BrdU incorporation assays and FACS analysis of CD34 + cells. The number of cancer stem cells was 

reduced by at least one order of magnitude in β-catenin deficient tumors. Nevertheless, within the first two 

weeks subsequent to deletion of β-catenin signs of reduced cell cycling, as assessed by BrdU 

incorporation and Ki67 immunostaining, were undetectable. In addition, we did not observe an increased 

incidence of cell death in β-catenin deficient tumors. Importantly, mutant tumor cells concomitantly lost the 

ability to form new tumors. Even transplantation of large numbers of β-catenin deficient tumor cells (up to 

1x10 6 ) failed to propagate skin tumors. We therefore conclude that β-catenin signaling is essential in 

maintaining cancer stem cells in skin tumors. In the absence of β-catenin, cells fail to propagate the stem 

cell phenotype and undergo terminal differentiation. Importantly, β-catenin is not required for normal tissue 

homeostasis in the skin. We therefore aim to use this difference for future therapy of skin tumor patients. 

In the hematopoietic system, several reports have implicated Wnt signaling in hematopoietic stem cell 

(HSC) expansion and demonstrated responsiveness of HSCs to Wnt signals. Conversely, deletion of Wnt 

genes or the Wnt receptor Fzd9 affects T- and/or B-cell development and transgenic or retroviral 

expression of inhibitors of canonical Wnt signaling such as axin or dkk1 further indicated an important 

function of this pathway in hematopoiesis and thymopoiesis. Individual gene ablations of LEF-1 and 

TCF-1 transcription factors displayed phenotypes in B, T and NK cell development and a combination of 

alleles aggravated these phenotypes, demonstrating that the two factors play to some degree redundant 

functions during T cell development. Conversely, deregulation of canonical Wnt signaling by aberrant 

stabilization of β-catenin is linked to a range of diseases including various cancers while ectopic 

expression of β-catenin has been linked to acute myeloid leukemias. Similarly, experimental evidence 

demonstrates that cells from acute and chronic myelogenous leukemia patients display activated Wnt 

signaling. We now show that hematopoiesis including thymopoiesis is normal in the combined absence of 

β- and γ-catenin (Jeannet et al., 2008), the only known signal transmitters of canonical Wnt signaling. 

Hematopoietic stem cells (HSCs) lacking both genes maintain long-term repopulation capacity and multi 

lineage differentiation potential. Surprisingly, ex vivo reporter gene assays show that β/γ-catenin doubledeficient 

HSCs and thymocytes retain the ability to transmit Wnt signals. In contrast, reporter gene activity 

is strongly reduced in TCF-1-deficient immature thymocytes. These data provide the first evidence that 

canonical Wnt signals can be transduced in the combined absence of β- and γ-catenin. Given that the 

downstream transcription factors LEF-1 and TCF-1 are known to be essential for thymopoiesis, we 

postulate a thus far unidentified mechanism of Wnt signaling in thymic development. Consistent with such 

a scenario, a novel Wnt signaling transducer has recently been identified in C. elegans, which however 

lacks a vertebrate orthologue. Our results support the feasibility of targeting β- and/or γ-catenin in 

leukemia patients as novel therapeutic strategy. Based on our results in the double mutant animals, we 

expect that such a therapy will exhibit no major side effects on normal hematopoiesis. We are currently 

testing this hypothesis in mouse models of leukemia and in human leukemia xenotransplants. 


Malanchi, I., H. Peinado, D. Kassen, T. Hussenet, D. Metzger, P. Chambon, M. Huber, D. Hohl, A. Cano, 

W. Birchmeier and J. Huelsken (2008). Cutaneous cancer stem cell maintenance is dependent 

on β-catenin signaling. Nature, in print 

Jeannet, G., M. Scheller, L. Scarpellino, S. Duboux, N. Gardiol, J. Back, F. Kuttler, I. Malanchi, W. 

Birchmeier, A. Leutz, J. Huelsken* and W. Held* (2008). Long-term, multilineage hematopoiesis occurs in 

the combined absence of β-catenin and γ-catenin. Blood 111, 142-9. *these two authors contributed 

equally

Schaeper, U., R. Vogel, J. Chmielowiec, J. Huelsken, M. Rosario, & W. Birchmeier (2007). Distinct 

requirements for Gab1 in Met and EGF receptor signaling in vivo. Proc.Natl.Acad.Sci U. S. A. 104, 

15376-81 

Fevr, T., S. Robine, D. Louvard, & J. Huelsken (2007). Wnt/γ-catenin is essential for intestinal 

homeostasis and maintenance of intestinal stem cells. Mol.Cell Biol. 27, 7551-9 

Baurand, A., L. Zelarayan, R. Betney, C. Gehrke, S. Dunger, C. Noack, A. Busjahn, J. Huelsken, M.M. 

Taketo, W. Birchmeier, R. Dietz, & M.W. Bergmann (2007). Beta-catenin downregulation is required for 

adaptive cardiac remodeling. Circ.Res. 100, 1353-62 

Faraldo, M.M., J. Teuliere, M.A. Deugnier, W. Birchmeier, J. Huelsken, J.P. Thiery, A. Cano and M.A. 

Glukhova (2007). beta-Catenin regulates P-cadherin expression in mammary basal epithelial cells. FEBS 

Lett. 581, 831-6 

Scheller, M., J. Huelsken, F. Rosenbauer, M. M. Taketo, W. Birchmeier, D. G. Tenen and A. Leutz (2006). 

Hematopoietic stem cell and multi lineage defects by β-catenin activation. Nat. Immun. 7, 1037-47 

Isolation of CDB4* cancer stem cell by MACS 


KÜHN LAB 

TEAM MEMBERS 

Sophie Cherpillod, Administrative Assistant 

Afzal Dogar, PhD Student 

Barbara Grisoni-Neupert, Scientific Collaborator 

Larry Richman, Senior Technician 

Liviu Vanoaica, PhD Student 

Lukas Kühn, Group Leader (2007-2008) 

Adjunct Professor since June 2008 


http://kuhn-lab.epfl.ch 

INTRODUCTION 

The laboratory works on two different topics: the mechanisms of rapid mRNA degradation and the 

physiology of iron in mice with a conditional ferritin H deletion. About 5 percent of all human genes 

produce mRNA that is unstable. We study how specific sequences in unstable mRNAs are recognized by 

nuclear and cytoplasmic proteins and how this initiates rapid mRNA degradation. We have notably studied 

IL-6 and c-myc mRNA. We also have constructed a mouse strain to learn about physiological 

consequences of a conditional deletion of the ferritin H gene. Ferritin stores iron and protects cells from 

the formation of hydroxyl radicals, potentially oncogenic compounds that modify nucleotides in DNA. Our 

studies are relevant to the understanding of the hereditary disease of iron overload and anemia. 


1. Mechanisms of rapid mRNA degradation 

Rapid mRNA degradation is a way to limit protein translation in time or space. It may have evolved in 

order to contain the level of proteins that cause cell transformation when over-expressed. There exists 

evidence of prolonged mRNA half-life in tumor cells. For this reason we study mechanisms of rapid mRNA 

decay. A prominent group of unstable mRNAs comprises AU-rich sequences in the non-coding 

3'-untranslated regions. This is notably the case for mRNA of numerous cytokines and growth factors. 

They all decay with half-lives of 30 to 60 min. We have identified RNA sequences required for instability of 

IL-6 and c-myc mRNA. To study mRNA decay we have constructed retroviral vectors for the tet-off system 

which permit to turn off rapidly transcription of green fluorescent protein (GFP) cDNA reporter constructs 

without affecting general cellular transcription. With this method mRNA decay can be accurately 

measured by RT-PCR. We graft cis-acting elements from 3'-untranslated or coding regions of unstable 

mRNAs into stable GFP mRNA and study their effect. 

Instability elements in IL-6 mRNA and the role of AUF1 in rapid mRNA decay 

We have applied the tet-off decay measurements to human IL-6 mRNA and have identified two instability 

elements in the 5'-half of the 3'-untranslated region. The first one corresponds to an AU-rich sequence. 

The second one, 80 nucleotides further 5', comprises a sequence predicted to form a stem-loop structure. 

Neither element alone was sufficient to confer strong instability suggesting that they might cooperate. We 

then could show that the p37 and p42 isoforms of the RNA-binding protein AUF1 bind in vivo to the same 

specific AU-rich sequence which makes IL-6 mRNA unstable. Furthermore, suppression of endogenous 

AUF1 by RNA interference stabilized IL-6 mRNA indicating a functional role for AUF1 in IL-6 mRNA 

degradation. 

We now have extended the study to a genome-wide search for mRNAs which bind AUF1. We have 

analyzed the in vivo binding of myc-epitope tagged AUF1 p42 to target mRNAs in mouse 3T3 cells by coimmunoprecipitation 

of RNA-protein complexes (RNP-IP) combined with Affymetrix microarray analysis. 

We have identified 507 potential targets of AUF1 that were more than 3-fold enriched on the chips. 23.6% 

of these mRNAs are present in the ARED 3.0 database, which shows that AUF1-bound mRNAs show a 

2.8-fold higher frequency of classical AUUUA sequences than random mRNAs. AUF1 seems also to bind 

to many mRNAs without classical AUUUA sequences. Limited experimental data available for AUF1 

binding preferences does thus far not allow a prediction of the consensus AUF1 binding sequence. A 

survey with a subset of 21 sequences revealed 10 unstable mRNAs, a number significantly above random 

expectation. It suggests that AUF1 binds frequently to unstable mRNAs. 

Instability elements in c-myc mRNA 

Endogenous c-myc mRNA is rapidly degraded with a 26-min half-life. We have identified instability 

elements of mouse c-myc mRNA by testing green fluorescence protein reporter constructs in mouse 3T3 

fibroblasts using tet-off degradation assays.

The c-myc coding region was sufficient to induce a 33-min half-life, whereas the 3’-untranslated region 

conferred only partial instability. The dominant effect of c-myc coding sequences was abolished when 

translation was blocked by a stop codon. With stop codons at different positions, instability increased the 

further translation advanced and was complete at the first half of exon 3. A previously identified coding 

region determinant in the second half of exon 3 did not need to be translated. Frame shift mutations in the 

c-myc coding region indicated that the mRNA sequence rather than the protein sequence is essential for 

instability. Shorter constructs indicated that elements of both exons 2 and 3 are required. They may 

cooperate or act sequentially to destabilize c-myc mRNA. Translation of the c-myc coding sequence 

triggered rapid deadenylation which may precede the decay of the RNA body. The proteasome inhibitor 

MG132 stabilized constructs with the c-myc 3’-untranslated region, but failed to show a pronounced effect 

with the coding sequence alone. RNA interference against UPF1 had no effect on c-myc mRNA 

degradation, suggesting that the pathway of c-myc mRNA degradation does not converge with the one of 

nonsense-mediated mRNA decay. 

2. Analysis of ferritin H knock-out mice 

Iron is an essential metal for life and at the same time a hazard since, in its free form, it catalyzes the 

formation of hydroxyl radicals, which are thought to be a natural cause of mutations in DNA. Therefore, 

free iron must be delicately controlled to avoid deprivation or excess. The protein complex of ferritin, 

composed of ferritin H and L chains, stores excess free iron and is thought to play a central role in the 

protection against radical formation. To test this hypothesis and to understand the role of ferritin in 

general, we have constructed a mouse strain with a conditional ferritin H gene knock-out. We use the 

Cre-Lox strategy to delete the ferritin H gene with inducible Cre and/or tissue-specific Cre. We initially 

confirmed that deletion of ferritin H in the germ-line provokes lethality of embryos. However, when ferritin 

H is deleted to 95% in the liver, spleen and bone marrow of mice at 10 weeks of age, they survive without 

major disadvantage for two years. Notably, we find no changes in the hematocrit and formation of red 

blood cells indicating that ferritin H is not required for heme biosynthesis in erythroid precursor cells. On 

the other hand we find a diminished number of B and T cells. Mice which are fed for 2 weeks with a high iron 

regimen prior to ferritin H deletion show an acute and strong liver damage with signs of apoptosis (Figure below). 

In order to test the effects of the loss of ferritin H in tissue culture cells we have derived cell lines from 

primary embryonal fibroblasts. We notably find a 30-fold increased toxicity of iron salts in cells that lack 

the ferritin H gene. This could be reversed by re-expression of functional ferritin H but not by mutant 

ferritin H lacking the ferroxidase activity needed for iron storage. It indicates that ferritin H is necessary to 

protect cells by storing free iron. The fibroblast cell lines with a ferritin H deletion show a rapid and strong 

increase in reactive oxygen species when exposed to iron. Even very low concentrations of iron in the 

medium provoke cell death by a mechanism resembling apoptosis, and high concentrations of iron lead to 

rapid depolarization of mitochondria. Compounds that prevent the formation of reactive oxygen species 

prevent iron toxicity partially. 

We have started to make tissue-specific ferritin H deletions in liver, intestine, B cell precursors, and heart. 

Deletion of ferritin H in the heart provokes fibrosis, a condition seen in certain patients with hereditary 

hemochromatosis. In collaboration, we have started to measure heart physiology parameters. Deletion of 

ferritin H by CD19-Cre provokes a diminished number of mature B cells. The precise cause for this 

decrease needs to be investigated further. 

Liver tissue sections of iron-loaded control Fth lox/lox 

(a) and Fth −/− 

mice (b to d) analyzed 5 days after 

ferritin H deletion. The sections of Fth −/− mice show 

extensive regions of macrosteatosis (b), 

hemorrhage (c) and polymorphonuclear cell 

infiltration (d). Scale bar 100 μm. The insert in (d) 

shows a neutrophil (scale bar 5 μm). 

2006 PUBLICATION 

Paschoud, S., Dogar, A.M., Kuntz, C., Grisoni-Neupert, B., Richman, L. and Kühn, L.C. (2006). 

Destabilization of interleukin-6 mRNA requires a putative RNA stem-loop structure, an AU-rich element 

and the RNA-binding protein AUF1. Mol. Cell. Biol. 26: 8228-8241 


LINGNER LAB 

Joachim Lingner 



http://lingner-lab.epfl.ch 

TEAM MEMBERS 

Elena Aratinovska, PhD Student 

Claus Azzalin, Postdoctoral Fellow 

Michael Chang, Postdoctoral Fellow 

Gaël Cristofari, Postdoctoral Fellow 

Romain Groux, Technician Apprentice 

Nele Hug, PhD Student, Postdoctoral Fellow 

Brian Luke, Postdoctoral Fellow 

Vered Machluf, PhD Student 


Andrea Panza, PhD Student 

Sophie Redon, Scientific Collaborator 

Patrick Reichenbach, Senior Technician 

Katarzyna Sikora, PhD Student 

INTRODUCTION 

The ends of eukaryotic chromosomes, known as telomeres, play crucial roles as guardians of genome 

stability and tumor suppressors. Telomere dysfunction also causes dyskeratosis congenita, a bone 

marrow failure syndrome leading to premature death due to aplastic anemia and telomere dysfunction has 

been recently linked to the pathogenesis of idiopathic pulmonary fibrosis. Telomeric DNA is maintained by 

the ribonucleoprotein enzyme telomerase. Most normal human somatic cells express only very low levels 

of telomerase and telomeres shorten with continuous cell division cycles. Ultimately, short telomeres 

activate a DNA damage response that leads to a permanent cell cycle arrest or apoptosis. Reactivation of 

telomerase leads to stabilization of telomere length and is a key requisite for human cancer cells to attain 

unlimited proliferation potential. Our laboratory combines in vitro biochemistry and molecular genetics to 

study telomere function and replication in human cells and in the yeast Saccharomyces cerevisiae. A 

thorough understanding of this process may allow manipulation of telomere function in tumors and other 

diseased tissues. 


1. Regulation of telomerase at chromosome ends 

Telomerase is a cellular reverse that counteracts telomere shortening that occurs due to incomplete DNA 

end replication and nucleolytic processing. Telomerase extends chromosome 3’ ends by iterative reverse 

transcription of a small region of its tightly associated telomerase RNA moiety. To study the mechanisms 

that control telomerase access at chromosome ends and telomere extension efficiency we previously 

developed for S. cerevisiae a system to measure telomerase activity at nucleotide resolution at single 

chromosome end molecules. We demonstrated that telomerase exhibits an increasing preference for 

telomeres as their lengths decline. We now identified two pathways that activate telomerase at short 

telomeres. First, the DNA checkpoint kinase Tel1 (human ATM) mediates preferential elongation of short 

telomeres by telomerase. Second, Tbf1p, a poorly understood protein that binds subtelomeric sequences, 

may function in parallel to Tel1p for activation of telomerase at short telomeres (Figure 1). 

Figure 1: Model for telomerase regulation 

at chromosome ends. Telomeres switch 

between telomerase extendible and nonextendible 

states in a length-dependent 

manner. Tel1 and Tbf1 mediate 

preferential elongation of short telomeres 

by telomerase. Telomerase is nonprocessive 

in vivo except at very short 

telomeres at which Tel1 kinase enhances 

its processivity by unknown mechanisms.

To determine how telomerase functions in vivo we assessed whether telomerase turns over at single 

chromosome ends or whether it extends telomeres in a processive manner, without dissociation. This was 

achieved by co-expressing two different telomerase RNA subunits that specified different telomeric repeat 

sequences and examining the telomere extensions after one cell cycle. Thus, we determined 

that S. cerevisiae telomerase can dissociate and re-associate from a given telomere during one cell cycle 

and that telomerase is non-processive in terms of telomeric repeat addition. However, repeat addition 

processivity significantly increased at extremely short telomeres, a process which is dependent upon Tel1. 

We proposed that this enhancement of telomerase processivity at short telomeres serves to rapidly 

elongate critically short telomeres. 

Recruitment and activation of telomerase at chromosome ends is not well understood in complex 

eukaryotes including humans. We have developed assays to measure association of human telomerase 

with chromosome ends by chromatin immunoprecipitation, and our collaborators from the Terns-lab 

(University of Georgia) could for the first time detect human telomerase at chromosome ends by 

immunofluorescence. We have used these assays to determine the importance of accumulation of the 

telomerase RNA moiety (hTR) in Cajal bodies (CBs), subnuclear structures implicated in RNP assembly 

and maturation. We demonstrated that a mutant hTR which fails to accumulate in CBs is fully capable of 

forming catalytically active telomerase in vivo, but is nonetheless strongly impaired in telomere extension. 

The functional deficiency is accompanied by a decreased association of telomerase with telomeres. 

These data identify subnuclear localization as an important regulatory mechanism for telomere length 

homeostasis in human cells. 

2. Discovery of telomeric repeat containing RNA (TERRA) 

The heterochromatic state of telomeres, their gene-less nature and their ability to silence transcription of 

experimentally inserted subtelomeric reporter genes, known as Telomere Position Effect (TPE), supported 

the idea that telomeres are transcriptionally silent. However, we now demonstrated that mammalian 

telomeres possess gene-like properties in that they are transcribed into telomeric repeat containing RNA 

(TERRA) at several chromosome ends (Fig. 2). TERRA molecules are heterogeneous in length from ~100 

to > 10’000 nucleotides and localize to telomeres. We also showed that proteins involved in RNA 

surveillance pathways are enriched at telomeres in vivo, where they negatively regulate TERRA 

association with chromatin and protect chromosome ends from telomere loss. Some of the RNA 

surveillance factors, including EST1A, physically interact with telomerase and we have characterized this 

interaction biochemically. We speculate that TERRA may be a key regulator of the enzymatic activities 

that assure telomere replication and length homeostasis. In addition TERRA may play roles in telomeric 

heterochromatin by mechanisms similar to the X chromosome inactivation in females, which is mediated 

by the long noncoding Xist RNA. 

Figure 2:. Mammalian telomeres are transcribed into 

telomeric repeat containing RNA (TERRA). TERRA 

which is detected by RNA-FISH (red signals) at 

chromosome ends in human fibrosarcoma (HeLa) and 

osteosarcoma (U2OS) cells stays associated with 

telomeric heterochromatin. Telomeres are detected by 

indirect immunofluorescence with an antibody against 

the telomeric Rap1 protein (green dots). Signal overlap 

of TERRA and Rap1 is in yellow. DAPI stained nuclei 

are shown in grey. See Azzalin et al., Science 318: 798- 

801 (2007) for further details.

3. Telospot : high scale analysis of telomerase modulators 

Because of its upregulation in cancer cells, telomerase has been considered to be an effective target to 

specifically inhibit the growth of a wide range of tumors. One major obstacle for the discovery of 

telomerase drugs and cellular modulators may stem from the limitations of the currently available 

telomerase activity assays. In collaboration with the team of Gerrardo Turcatti from the EPFL biomolecular 

screening facility, we designed a method termed Telospot to discover and characterize telomerase 

modulators as anticancer drugs and chemical biology tools. Telospot is based on a highly efficient human 

telomerase expression system and the detection of telomerase DNA reaction products in macroarray 

format. Telospot offers a highly scalable, cost- and time-effective alternative to present telomerase 

detection assays, which are limited by the need of PCR, telomerase purification, or technologies not 

amenable to high-throughput. 


Arneric, M., and Lingner, J. (2007). Tel1 kinase and subtelomere-bound Tbf1 mediate preferential 

elongation of short telomeres by telomerase in yeast. Embo Rep. 8: 1080-1085 

Azzalin, C. M., and Lingner, J. (2007). Molecular biology: damage control. Nature 448: 1001-1002 

Azzalin, C.M., Reichenbach, P., Khoriauli, L., Guilotto, E., and Lingner, J. (2007). Telomeric repeatcontaining 

RNA and RNA surveillance factors at mammalian chromosome ends. Science 318: 798-801 

Chang, M., Arneric, M. and Lingner, J. (2007). Telomerase repeat addition processivity is increased at 

critically short telomeres in a Tel1-dependent manner in Saccharomyces cerevisiae. Genes & Dev. 21: 

2485-2494 

Cristofari, G., and Lingner, J. (2007). Telomerase unplugged. ACS Chem Biol. 2: 155-158. 

Cristofari, G., Adolf, E., Reichenbach, P., Sikora, K., Terns, R. M., Terns, M. P., and Lingner, J. (2007). 

Human telomerase RNA accumulation in Cajal Bodies facilitates telomerase recruitment to telomeres and 

telomere elongation. Mol. Cell 27: 882-889 

Cristofari, G., Reichenbach, P., Regamey, P.-O., Banfi, D., Chambon, M., Turcatti, G., and Lingner, J. 

(2007). Low- to high-throughput analysis of telomerase modulators with Telospot. Nature Meth. 

4: 851-853 

De Cian, A., Cristofari, G., Reichenbach, P., Delemos, P., Monchaud, D., Teulade-Fichou, M.-P., Shin-ya, 

K., Lacroix, L., Lingner, J., and Mergny, J.-L. (2007). Re-evaluation of telomerase inhibition by quadruplex 

ligands and their mechanisms of action. Proc. Natl. Acad. Sci. USA. 104: 17347-17352 

Luke, B., Azzalin, C. M., Hug N., Deplazes, A., Peter, M., and Lingner, J. (2007). Saccharomyces 

cerevisiae Ebs1p is a putative ortholog of human Smg7 and promotes nonsense mediated mRNA decay. 

Nucleic Acids Res. 35: 7688-7697 

Redon, S., Reichenbach. P., and Lingner, J. (2007). Protein-RNA and protein-protein interactions mediate 

association of human EST1A/SMG6 with telomerase. Nucleic Acids Res. 35: 7011-7022 

Amiard S., Doudeau M., Pinte S., Poulet A., Lenain C., Faivre-Moskalenko C., Angelov D., Hug N., 

Vindigni A, Bouvet P, Paoletti J, Gilson E, Giraud-Panis MJ. (2007). A topological mechanism for 

TRF2-enhanced strand invasion. Nature Struct. Mol. Biol. 14: 147-154 

Azzalin, C. M., and Lingner, (2006) J. The double life of UPF1 in RNA and DNA stability pathways. 

Cell Cycle 5: 1496-1498 

Azzalin, C. M., and Lingner, J. (2006). The human RNA surveillance factor UPF1 is essential for S-phase 

progression and genome stability. Current Biology 16: 433-439 

Cristofari, G., and Lingner, J. (2006). Telomere length homeostasis requires that telomerase levels are 

limiting. EMBO J. 25: 565-574 

Cristofari, G., and Lingner, J. (2006) The telomerase RNP. In Telomeres, second edition, edited by Titia 

de Lange, Vicki Lundblad and Elizabeth Blackburn (Cold Spring Harbor Laboratory Press) : 21-47 

Eugster, A., Lanzulo, C., Bonneton, M., Luciano, P., Pollice, A., Pulitzer, J. F., Stegberg, E., Berthiau., 

A.-S., Förstemann, K., Corda, Y., Lingner, J., Géli, V., and Gilson, E. (2006). The finger subdomain of 

yeast telomerase cooperates with Pif1p to limit telomere elongation. Nature Struct. Mol. Biol. 

13: 734-739 

Hug, N., and Lingner, J. (2006). Telomere length homeostasis. Chromosoma 115: 413-425 


NAEF LAB 

Felix Naef 



http://naef-lab.epfl.ch 

TEAM MEMBERS 

Arnaud Amzallag, Postdoctoral Fellow 

Mirko Bischofberger, PhD Student 

Thomas d’Eysmond, PhD Student 

Nicolas Musolino, Postdoctoral Fellow 


Fabio Parisi, PhD Student 

Guillaume Rey, PhD Student 

Bernhard Sonderegger, Postdoctoral Fellow 

INTRODUCTION 

We use theoretical and computational approaches to study regulatory and cellular networks involved in 

cell-cycle regulation, oncogenic signaling and molecular oscillators. We combine functional data sources 

such as microarrays, chromatin-immunoprecipitation (ChIP) and genomes to infer regulatory 

dependencies between genes and regulatory proteins involved in cell proliferation. Well-characterized 

networks such as the cell cycle in yeast offer opportunities to study how information propagates through 

these systems and to identify links that are crucial in mediating function, or alternatively that confer 

robustness properties. One thematic focus is the study of biomolecular oscillators, in particular the 

circadian clock which drives periodic behavior and physiology in most living organisms. Recently we 

studied how collective properties in populations of cellular oscillators, such as the emergence of 

synchronization, affect circadian outputs measured as bioluminescence recordings. 


We focus on the modeling of genome-wide functional data, notably through the study of circadian 

oscillators. The circadian clock drives periodic behavior and physiology in most living organisms, through 

a complex network of feedback control mechanisms acting at the transcriptional and post-transcriptional 

levels. Transcription regulation in these clocks uses a collection of cis-elements that are active at different 

phases in the cycle. Through a combination of expression array analyses and comparative genomics, we 

have recently proposed a Hidden Markov Model describing a so-called E1-E2 enhancer which is 

conserved from insects to mammals. Currently we are testing in vitro the binding specificity of this 

sequence element, and are planning functional assays in vivo. We are also pursuing our work on the 

desynchronization dynamics in a population of noisy circadian cells where we study the phase diffusion 

characteristics of common circadian oscillator models. We expect that these analyses will shed new light 

on the molecular processes affecting dephasing properties in circadian tissues. As part of our activities in 

functional genomics, we are studying the relationships between promoter configuration, as measured e.g. 

in ChIP experiments, and gene expression for the estrogen receptor ER1alpha. 

Functional Genomics Projects 

Identifying promoter states that predict gene induction by estrogen receptor ER1alpha. 

To understand cancer-related modifications to transcriptional programs requires detailed knowledge of the 

activation of signal-transduction pathways in gene expression programs. We combine location and 

expression data with genomic sequence analysis to build prediction functions to explain the influence of 

DNA occupancy by human estrogen receptor alpha (hERα) on expression phenotypes. To identify genes 

that respond to hERalpha signals, we compiled a compendium of expression data sets measuring 

transcription responses to ER signaling. We use data from chromatin immuno-precipitation in conjunction 

with DNA tiling arrays (ChIP-chip) experiments to quantify protein-DNA interactions and analyze genomic 

sequence to study matches to the estrogen receptor PWMs (EREs) and partner cis-elements. Finally we 

apply machine-learning techniques and multi-linear regression models to assess the relationships 

between the various promoter features and expression phenotypes of the target genes. Overall, binding 

strength and density of sites along the entire transcript provide the best discriminators of estrogenmediated 

induction.

Circadian biology 

1. Populations of circadian phase oscillators. 

Circadian Clocks (CCs) are cell-autonomous molecular oscillators with an approximate 24h period that 

control a number of important physiological processes such as metabolism in humans.In the absence of 

entrainment signals or coupling to other cells, one expects that intrinsic and extrinsic noise at the cellular 

level perturbs the clock phase and hence will drive cell populations to desynchronization. To study the 

dephasing kinetics, it is necessary to understand how noise perturbs a particular clock network. It is 

expected that the stability properties of the limit cycle orbit will affect its response to noise and ultimately 

influence the dephasing rate. 

Here we study how the dephasing rate depends on model parameters, and whether the most important 

dependencies are shared across a library of mathematical models describing the cell-autonomous clocks. 

Our preliminary analysis shows that while the stability of the cycle does indeed contribute significantly, the 

complete dependency involves other geometric properties of the cyclic orbits. Through this in silico 

analysis we expect to identify principles that allow circadian timing systems to tick accurately in the 

presence of molecular and environmental fluctuations. 

2. Modeling and validating a conserved circadian cis-elements in flies and mammals. 

Several experimental and computational studies show that partner elements around circadian E-boxes in 

insects and mammals influence such enhancers. Here we build a probabilistic sequence model for a 25bp 

sequence located in the center of the 69bp period enhancer reported in Hao et al., and also in the majority 

of known CLK/CYC targets in flies. The model is trained on multiple alignments of fly core clock genes 

and reveals a motif composed of a canonical E-box (E1) separated by 6 or 7 base pairs from a more 

degenerate version thereof (E2). We tested our model with functional genomics datasets and we found 

that CLOCK-induced genes were enriched in high scoring cis-elements. Surprisingly the fly model also 

predicts many known CLOCK/BMAL1 targets in mouse. This finding is supported by a phylogenetic 

analysis showing the evolutionary conservation of the E1-E2 structure in core circadian and output genes 

in vertebrates, fishes and insects. To study the importance of E2 in mediating protein-DNA interactions, 

we tested our consensus sequence by EMSA. We observe significantly different patterns of shifted 

proteins for the original and the mutated version of the consensus. Our data show that both E1 and E2 

bind proteins, but with different affinities. Moreover a cooperative binding of the two complexes is likely, as 

indicated by the affinity for doubly occupied sequences compared to single ones. Supershift assays 

confirmed that shifted bands contained CLOCK/BMAL1. This suggests that E1-E2 can be bound by one or 

two CLOCK/BMAL1 heterodimers, but does not fully exclude the involvement of other binding proteins. 

Experiments to test the functional role of these enhancer elements are under way. 

Evolutionary conserved E1-E2 elements in promoters of PAR bZip (Tef) genes. Sites in the human paralogues 

Dbp and Hlf are shown in the first two lines. Two sites are shown for the mammals and three for the fish. Right 

(top): The 5’ end of the Tef mRNA is shown with two conserved E1-E2 sites located at -200 (a) and -600 (b) bp. 

Right (middle): Two closely spaced E1-E2 sites in the Tef promoter at -500 bp of the putative start site. Right 

(bottom): The enhancer in the Pdp1 gene at -2.2 kbp of the Pdp1-RD transcript. Adapted from Paquet, Rey and 

Naef, PLoS Computational Biology, 2008.


Fabio Parisi, Pratyaksha Wirapati and Felix Naef, Identifying synergistic regulation involving c-Myc and 

sp1 in human tissues, Nucleic Acids Res. 2007;35(4):1098-107 

Rougemont, J., and Naef, F. Dynamical signatures of cellular fluctuations and oscillator stability in 

peripheral circadian clocks. Mol Syst Biol 3, 93 (2007) 

Catharine Boothroyd, Herman Wijnen, Felix Naef, Lino Saez, and Michael Young. Integration of Light and 

Temperature in the Regulation of Circadian Gene, PLoS Genetics, 2007 Apr 6;3(4):e54 

Stoll, G., Rougemont, J., and Naef, F. (2007). Representing perturbed dynamics in biological network 

models. Phys Rev E Stat Nonlin Soft Matter Phys 76, 011917 

J. Rougemont, F. Naef, Stochastic Phase Oscillators and Circadian Bioluminescence Recordings, Cold 

Spring Harbor Symposia on Quantitative Biology, ahead of print, posted online on 15 Nov 2007 

Ben-Haim N, Lu C, Guzman-Ayala M, Pescatore L, Mesnard D, Bischofberger M, Naef F, Robertson EJ, 

Constam DB., The nodal precursor acting via activin receptors induces mesoderm by maintaining a 

source of its convertases and BMP4. Dev Cell. 2006 Sep;11(3):313-23 

Stoll G, Rougemont J, Naef F. Few crucial links assure checkpoint efficiency in the yeast cell-cycle 

network. Bioinformatics. 2006 Oct 15;22(20):2539-46 

Jacques Rougemont and Felix Naef, Collective synchronization in populations of globally coupled phase 

oscillators with drifting frequencies, Phys. Rev. E73, 011104 (2006) 

Dorota Retelska, Christian Iseli, Philipp Bucher, C.Victor Jongeneel and Felix Naef, Similarities and 

differences of polyadenylation signals in human and fly, BMC Genomics. 2006 Jul 12;7:176 

Wijnen H, Naef F, Boothroyd C, Claridge-Chang A, Young MW. Control of daily transcript oscillations in 

Drosophila by light and the circadian clock. PLoS Genet. 2006 Mar;2(3):e39. Epub 2006 Mar 24 


RADTKE LAB 

Freddy Radtke 



http://radtke-lab.epfl.ch 

TEAM MEMBERS 

April Bezdek, PhD Student 

Sylvie Dufresne, Laboratory Assistant 

Alexis Dumortier, Postdoctoral Fellow 

Andre-Dante Durham, MD-PhD Student 

Doris Lorini. Masters Student 

Ute Koch, PhD Scientist 

Véronique Lahaye, Technician 


Luca Pellegrinet, PhD Student 

Caroline Poisson, PhD Student 

Orbicia Riccio, PhD Student 

Emma Smith, Postdoctoral Fellow 

Agnieszka Wendorff, PhD Student 

Introduction 

Our group is interested in the molecular mechanisms controlling stem cell maintenance, lineage 

commitment and differentiation in self-renewing systems such as the hematopoietic system, the skin and 

the gut. The basic principle of self-renewing tissues is that they constantly produce cells from a stem cell 

reservoir that gives rise to proliferating transient amplifying cells, which subsequently differentiate and 

migrate to the correct compartment. These processes have to be under stringent control to ensure lifelong 

homeostasis. In recent years a substantial body of evidence has accumulated to support the notion 

that signaling pathways known to be important during embryonic development (such as e.g. Shh, Wnt and 

Notch) play important roles in regulating self-renewing tissues. Moreover, the same pathways are often 

deregulated during tumorigenesis due to mutations of key elements of these pathways. The general 

concept is that a better understanding of the mechanisms controlling stem maintenance versus 

differentiation may lead to the identification of novel therapeutic targets, as well as improving strategies for 

influencing these players during tumorigenesis. Currently, attention is being focused on the evolutionarily 

conserved Notch signaling pathway, which plays pleiotropic roles in different self-renewing tissues and 

cancer. 


Notch signaling in hematopoiesis and T cell leukemias 

Using conditional gene targeting strategies we have established an essential role for Notch1 in specifying 

the T cell lineage. Inducible inactivation of Notch1 in BM progenitors results in a block in T cell 

development and ectopic B cell development in the thymus suggesting that Notch1 instructs an early 

lymphoid progenitor to adopt a T cell fate. In the absence of a Notch1 signal an early lymphoid progenitor 

chooses the B cell fate by default. In addition, we uncovered a function for Notch1 at a later stage of T cell 

development where it is involved in the control of VDJ rearrangement at the T cell receptor (TCR) beta 

locus. 

More recently, we explored the ability of the Notch ligands Delta1 (DL1) and Delta4 (DL4) to induce T cell 

lineage commitment and/or maturation in vitro and in vivo from BM progenitors. Collectively our results 

establish a hierarchy of Notch:Delta interactions in which Notch1:DL4 exhibits the greatest capacity to 

induce and support T cell development suggesting that DL4 might be the physiological ligand within the 

thymus. Furthermore we have generated conditional gene targeted mice for DL4 which are currently being 

analyzed in order to determine the specific role of DL4 within the thymic epithelium for T cell development. 

Another aspect of our work focuses on the role of Notch in T cell leukemia. Aberrant Notch1 signaling 

within the hematopoietic system results in the development of acute lymphoblastic T cell leukemia in mice 

and humans. Thus Notch1 functions as oncogene in the hematopoietic system. We are currently 

investigating the molecular mechanisms by which uncontrolled Notch1 signaling exerts its oncogenic 

functions. 

Notch signaling in the skin 

In contrast to the previously established role of Notch1 as an oncogene and lineage specifier in the 

hematopoietic system, we unexpectedly identified novel roles for Notch1 in the cornea and the skin. 

Inducible ablation of Notch1 in the skin results in hair loss and epidermal hyperplasia within four weeks of 

deletion. By 3 months post deletion, corneas of Notch1 deficient mice also become hyperplastic. The 

corneal hyperplasia is characterized by the expression of epidermis specific markers such as keratin1 and 

loricrin, suggesting a cell fate change of the cornea into skin-like epidermis. This cell fate switch leads to 

corneal blindness and involves cell non-autonomous processes, characterized by secretion of FGF-2 

through Notch1 -/- epithelium followed by vascularisation and remodelling of the underlying stroma. Vitamin 

A deficiency is known to induce a similar corneal defect in humans (severe xerophthalmia).

Accordingly, we found that Notch1 signaling is linked to vitamin A metabolism by regulating the expression 

of CRBP1, required to generate a pool of intracellular retinol. 

Moreover Notch1 deficiency in the skin results in derepressed β-catenin and shh signaling which 

cumulates in the development of basal cell carcinoma like tumors and facilitated chemical induced skin 

carcinogenesis. Thus Notch1 functions as a tumor suppressor gene in mammalian skin. 

We are currently investigating the roles of additional Notch receptor and ligand family members within the 

epidermis and skin appendages under normal and cancer promoting situations. 

Notch signaling in the intestine 

Aberrant Wnt signaling in the intestine is one of the most frequent events during the development of 

colorectal cancer. The inhibitory interaction between Notch and wnt signaling in our skin studies prompted 

us to investigate Notch function in the gastrointestinal tract. If Notch signaling plays a similar role in the 

gut as in the skin, then mice in which Notch signaling is inhibited are expected to develop tumors as a 

consequence of increased β -catenin mediated wnt signaling. Surprisingly, conditional inactivation of the 

CSL (which mediates Notch signaling of all receptors) within the crypt compartment results in the 

complete loss of transient amplifying cells followed by their conversion into mucus secreting goblet cells. 

Thus in the intestine Notch functions as progenitor gate-keeper, and seems to cooperate with wnt 

signaling in order to maintain the undifferentiated proliferative crypt compartment. 

More recently we assessed the crucial role of individual Notch receptors and the mechanism by which 

they maintain intestinal crypt progenitor cells by using a series of inducible gut-specific Notch mutant 

mice. We found that Notch1 and Notch2 receptors function redundantly in the gut, as only simultaneous 

loss of both receptors results in complete conversion of proliferating crypt progenitors into post-mitotic 

goblet cells. This conversion correlates with the loss of Hes1 expression and derepression of the cyclin 

dependent kinase (CDK) inhibitors p27Kip1 and p57Kip2. We also found that the Notch effector Hes1 in 

wild-type crypt progenitor cells occupies the promoter of both CDK inhibitor genes. Thus, our results 

indicate that Notch-mediated Hes1 expression contributes to the maintenance of the proliferative crypt 

compartment of the small intestine by transcriptionally repressing two CDK inhibitors (Figure 1). 

Figure 1 : Redundant function of Notch1 and Notch2 in the small intestine maintains proliferating crypt 

progenitor cells. A. In situ hybridization for Notch1 and Notch2 shows expression of both receptors in 

crypts of the small intestine. Scale bars, 50 mm. B. Model indicating a mechanism by which the Notch 

signaling pathway promotes the cycling of progenitor cells. Signaling through Notch1 (N1) and Notch2 

(N2) in crypt progenitor cells represses the two cyclin dependent kinase inhibitors p27Kip1 and p57Kip2.

Therefore, the question arises; how can the Notch signaling pathway, which is not only evolutionarily but 

also mechanistically conserved, lead to so many different and sometimes opposing outcomes (Figure 2). 

One of the major goals in the future will be to gain further insights into Notch target genes, and cross talk 

between Notch and other signaling pathways. This will lead to a better understanding on how one and the 

same pathway can function context dependent either as an oncogene or a tumor suppressor. 

Figure 2. The four major roles of the Notch cascade that are relevant within self-renewing tissues or 

during tumorigenesis are schematically illustrated. A. Gate-keeper function: Notch maintains stem 

and/or transient amplifying cells (TA) in an undifferentiated state. In the intestine for example, Notch 

prevents crypt progenitor cells (TA) from differentiating. B. Binary cell fate decisions: In the lymphoid 

system Notch specifies the T cell lineage at the expense of the B cell lineage from an (at least) bi-potent 

early thymocyte progenitor. C. Induction of differentiation: In the skin, Notch induces terminal 

differentiation events of TA cells, and during thymocyte differentiation Notch1 promotes differentiation of 

pro-T-cells into pre-T cells. D. Tumorigenesis: Overexpression of Notch within hematopoietic bone 

marrow cells or in T cell progenitors results in T cell leukemias, and as such, Notch functions as an 

oncogene. However in the skin, Notch functions as a tumor suppressor since loss of Notch signaling 

results in the development of basal cell carcinoma-like tumors. 

2006-2007 Publications 

Komine, O., Nagaoka M, Watase K, Gutmann DH, Tanigaki K, Honjo T, Radtke F., Saito T, Chiba S, 

Tanaka K. (2007). The monolayer formation of Bergmann glial cells is regulated by Notch/RBP-J 

signaling. Dev Biol. Nov 1;311(1):238-250. Epub 2007 Aug 31 

Koch U, and Radtke F. (2007) Notch and cancer: a double-edged sword. Cell Mol Life Sci. Nov. 64, 

(21):2746-62 

Vauclair S, Majo F, Durham AD, Ghyselinck NB, Barrandon Y, and Radtke F., (2007) Corneal epithelial 

cell fate is maintained during repair by Notch1 signaling via the regulation of vitamin A metabolism. Dev 

Cell. Aug;13(2):242-53 

Koch U, and Radtke F. (2007). Haematopoietic stem cell niche in Drosophila. (2007). Bioessays. 

Aug;29(8):713-6

Amsen D, Antov A, Jankovic D, Sher A, Radtke F, Souabni A, Busslinger M, McCright B, Gridley T, and 

Flavell RA. (2007). Direct regulation of gata3 expression determines the T helper differentiation potential 

of notch. Immunity. Jul;27(1):89-99. Epub 2007 Jul 19 

Kelly AP, Finlay DK, Hinton HJ, Clarke RG, Fiorini E, Radtke F, and Cantrell DA. (2007). Notch-induced 

T cell development requires phosphoinositide-dependent kinase 1. EMBO J. Jul 25;26(14):3441-50. Epub 

2007 Jun 28 

Schouwey K, Delmas V, Larue L, Zimber-Strobl U, Strobl LJ, Radtke F, and Beermann F. (2007) 

Notch1 and Notch2 receptors influence progressive hair graying in a dose-dependent manner. Dev. Dyn., 

January 236 (1): 282-9 

Takeshita K, Satoh M, Ii M, Silver M, Limbourg FP, Mukai Y, Rikitake Y, Radtke F, Gridley T, Losordo 

DW, and Liao JK. (2007). Critical Role of Endothelial Notch1 Signaling in Postnatal Angiogenesis. 

Circulation Research 5; 100 (1) 70-78) 

Besseyrias, V., Fiorini, E., Strobl, L.J., Zimber-Strobl, U., Dumortier, Al., Koch, U., Ancrangeli, ML., Ezine, 

S., MacDonald HR., and Radtke, F. (2007). Hierarchy of Notch:Delta interactions promoting T cell lineage 

commitment and maturation. J. Exp. Med. Feb 19;204(2):331-43 

Wang, X., Leow, C., Zha, J., Tang, Z., Modrusan, Z., Radtke, F., Aguet, M., de Sauvage, FJ., and Gao, 

WQ. (2006). Notch signaling is required for normal prostatic epithelial cell proliferation and differentiation. 

Developmental Biology. Feb. 1;290(1):66-80 (Epub 2005 Dec.15) 

Wilson A. and Radtke, F. (2006). Notch signaling in self-renewing tissues and cancer. FEBS Letters, 

(Epub March 20), May 22;580(12):2860-2868 

Radtke, F., Clevers, H., and Riccio, O. (2006). From Gut Homeostasis to Cancer (2006). Curr. Mol. Med., 

May; 6(3):275-289 

Nemir, M., Croquelois, A., Pedrazzini, T., and Radtke, F. (2006). Induction of cardiogenesis in embryonic 

stem cells via downregulation of Notch1 signaling. Circulation Research. (Epub May 11), June 23; 

98(12):1471-1478 


SIMANIS LAB 

TEAM MEMBERS 

Elena Cano del Rosario,Technician 

Philippe Collin, PhD Student 

Sandra Dischinger, PhD Student 

Olivier Hachet, Postdoctoral Fellow 

Andrea Krapp, Research Associate 


Viesturs Simanis 



http://simanis-lab.epfl.ch 

Introduction 

Proper coordination of cell cycle events is crucial for successful cell division. Failure to coordinate mitosis 

and cytokinesis may lead to imprecise segregation of chromosomes, which may lead to cell death or alter 

the cell’s behaviour. We use the fission yeast Schizosaccharomyces pombe as a model to study the 

regulation of cytokinesis and its coordination with chromosome segregation. Fission yeast cells are rodshaped, 

and grow mainly by elongation at their tips. The spatial cue which defines the position of the 

division site is provided in part by the protein mid1p/dmf1p, which leaves the nucleus at the onset of 

mitosis. An actomyosin based contractile ring (CAR) assembles at the cell cortex from the onset of 

mitosis, with components being added throughout metaphase and anaphase. At the end of mitosis, the 

CAR contracts and is thought to guide synthesis of a dividing cell wall and deposition of new membranes. 

The initiation of CAR contraction and cytokinesis is regulated by a signal transduction pathway called the 

septation initiation network, or SIN. The SIN consists of three protein kinases (cdc7p, sid1p, sid2p) and 

their regulatory subunits (spg1p, cdc14p and mob1p, respectively). SIN signalling is thought to originate 

from the poles of the mitotic spindle, where SIN proteins are located during mitosis. They assemble at the 

spindle pole bodies (SPBs) on a scaffold composed of sid4p and cdc11p. Signalling is modulated by the 

nucleotide status of the GTPase spg1p, which is controlled by a two-component GAP byr4p - cdc16p. SIN 

signalling is also regulated by the master cell cycle regulator cdc2p and the mitotic regulator plo1p. The 

mob1p-sid2p protein kinase is also observed at the contractile ring late in mitosis. This is thought to be the 

trigger for ring contraction. If the SIN does not function, cells become elongated and multinucleated, as 

growth, DNA synthesis and mitosis continue in the absence of cytokinesis. In contrast, ectopic activation 

of the SIN can uncouple contractile ring formation and septation from other cell cycle events. Regulation 

of the SIN is therefore important for proper co-ordination of mitosis with cytokinesis. 

We also collaborate with the group of Philippe Hauser at the Institute of Microbiology, Centre Hospitalier 

Universitaire Vaudois, using S. pombe as a model to understand the biology of the pathogenic fungus 

Pneumocystis sp, which is an opportunistic pathogen infecting immunocompromised patients. 


The S. pombe septation initiation network 

Our work on the SIN has focussed upon the role of the mitotic cyclin dependent protein kinase cdc2pcdc13p 

in regulating the SIN during mitosis. We have used a chemical-genetics approach to study 

whether inactivation of cdc2p is sufficient to activate the SIN. We have also studied the regulation of the 

byr4p-cdc16p GAP that controls the nucleotide status of the GTPase spg1p. The data we obtained lead 

us to propose a homoeostatic mechanism to assure the steady state level of the GAP and the GTPase it 

regulates are matched. 

Chemical genetic analysis of the role of cdc2p in regulating the S.pombe septation initiation network 

(Collaboration with Linfeng Xie and James R. Paulson of the Department of Chemistry, University of 

Wisconsin-Oshkosh, WI, USA) 

The protein kinase cdc2p is the master regulator of cell cycle progression in the fission yeast 

Schizosaccharomyces pombe. It is required both for entry into mitosis and onset of DNA replication. 

Cdc2p must be inactivated to permit exit from mitosis, licensing of replication origins and cytokinesis. To 

study the role of cdc2p in greater detail, we have generated a cdc2 allele sensitive to an inhibitory ATP 

analogue.

We demonstrate that the inhibitor-induced cell cycle arrest is reversible and examine the effect of 

inhibiting cdc2p on the regulation of the septation initiation network (SIN), which controls the initiation of 

cytokinesis in S. pombe. We find that specific inactivation of cdc2p in a mitotically arrested cell promotes 

both the asymmetric recruitment of SIN proteins to the spindle poles and the recruitment of the most 

downstream SIN components and beta-(1,3) glucan synthase to the contractile ring. Thus, we conclude 

that inactivation of cdc2p is sufficient to activate the SIN and promote cytokinesis. 

Homoeostasis between the GTPase spg1p and its GAP in the regulation of cytokinesis in S. pombe 

Cytokinesis in S. pombe begins at mitotic entry, when the site of division is defined by formation of the 

acto-myosin ring (CAR) at the cell cortex. Contraction of the CAR and formation of the division septum is 

triggered at the end of mitosis by the spindle pole body (SPB) associated septation initiation network (SIN) 

proteins. SIN signalling requires activation of the GTPase spg1p, which is regulated by the bipartite GAP 

byr4p-cdc16p. We show that for spg1p to associate with the SPB, it must be bound to its GAP, or its 

mitotic effector, the protein kinase cdc7p. Analysis of the GAP proteins reveals that the steady state level 

of byr4p reflects that of spg1p. Furthermore, if the interaction of byr4p with spg1p is compromised, the 

level of byr4p decreases dramatically. The adaptation of the level of byr4p to that of spg1p requires the 

presence of cdc16p and is mediated by proteasome-dependent destruction. It does not require 

association with the SPB, or an active SIN. We propose a mechanism that limits the amount of the byr4pcdc16p 

GAP to the amount required to inhibit spg1p signalling. We are attempting to define the domains 

and trigger events that are required for degradation of byr4p. 

Functional characterization of pneumocystis carinii brl1 by transspecies complementation analysis 

Pneumocystis jirovecii is a fungus which causes severe opportunistic infections in immunocompromised 

humans. The brl1 gene of P. carinii, which infects rats, was identified and characterized by using 

bioinformatics in conjunction with functional complementation in Saccharomyces cerevisiae and 

Schizosaccharomyces pombe. The ectopic expression of this gene rescues null alleles of essential 

nuclear membrane proteins of the Brr6/Brl1 family in both yeasts. We also demonstrated that the null 

allele of S. pombe brl1 produces a phenotype characteristic of cell cycle arrest. The nature of the arrest is 

under investigation. 


Bedhomme M, Jouannic S, Champion A, Simanis V, and Henry Y. Plants, MEN and SIN (2007). Review, 

Plant Physiology and Biochemistry. 46, 1-10 

Lo Presti L, Cockell M, Cerutti L, Simanis V, and Hauser PM. Functional Characterization of Pneumocystis 

carinii brl1 by Transspecies Complementation Analysis. (2007) Eukaryotic Cell. 6, 2448-2452 

Krapp, A., Collin, P., Cokoja, A., Dischinger, S., Cano, E. and Simanis, V. (2006). The 

Schizosaccharomyces pombe septation initiation network (SIN) is required for spore formation in meiosis. 

J. Cell Sci. 119, 2882-2891 

Chen, C. T., Peli-Gulli, M. P., Simanis, V. and McCollum, D. (2006). S. pombe FEAR protein orthologs are 

not required for release of Clp1/Flp1 phosphatase from the nucleolus during mitosis. J. Cell Sci. 119, 

4462-4466 

This image shows a fission yeast cell in the late stages 

of anaphase. The nuclei are shown in blue, the mitotic 

spindle in green and the contractile ring in red 


TRUMPP LAB 

Andreas Trumpp 



http://trumpp-lab.epfl.ch 

TEAM MEMBERS 

Irène Baccelli, PhD Student 


Nicole Dubois, PhD Student (UNIL) 

Armin Ehninger, PhD Student 

Maike Jaworski, PhD Student 

Yulia Kirpicheva, Master’s Student 

Elisa Laurenti, PhD Student (UNIL) 

Gabriela Oser, PhD Student (UNIL) 

Konstantin Shakhbazov, PhD Student 

NEXT INSTITUTION 

University of Heidelberg, since July 1, 2008 

INTRODUCTION 

Cancer genes and stem cells 

In the last decade, it has become evident that specific signaling pathways that control crucial steps during 

embryonic development are often inappropriately reactivated during tumorigenesis. In addition cancer 

cells seem to take advantage of cellular principles inherent to normal stem cells which are crucial for 

maintenance, repair and regenerative processes of most adult tissues such as the intestinal epithelium or 

the hematopoietic system. Like immortal cancer cells normal stem cells have the capacity of life-long selfrenewal. 

Stem cell self-renewal is a physiological mechanism that maintains a small pool of (stem) cells 

that are able to proliferate indefinitely (immortal), but at the same time produce a variety of differentiated 

cells that fulfill and maintain the function of the body. Our research takes advantage of various mouse models 

in which we have altered the expression of a number of oncogenes and tumor suppressor genes. We use those 

model systems to study the molecular and cellular basis of stem cell self-renewal, the interaction of stem cells with 

their specialized microenvironment (stem cell niche) and the relationship between stem cells and tumorigenesis. 

Self-renewing (or highly regenarative) tissues and the function of adult stem cells 

Many adult tissues such as the skin epidermis, the gastrointestinal epithelia or the hematopoietic system 

are regenerative. In such tissues mature cells such as the stratum corneum of the skin, differentiated 

enterocytes at the tip of the intestinal villi or blood erythrocytes have rather short half-lives and must be 

continuously produced to replenish the large number of cells steadily lost by shedding or apoptosis. Lifelong 

production of differentiated progeny relies on the activity of rare long lived adult tissue stem cells, 

which have the ability to both perpetuate themselves through self-renewal and to generate all mature cell 

types of a particular tissue through differentiation. Stem cells are thought to be located in a special 

microenvironment called the stem cell niche, which prevents differentiation and maintains stem cell activity 

by poorly understood mechanisms (Fig. 1) (Wilson and Trumpp, 2006). Upon division two daughter cells are 

generated one of which, on average, stays in the niche maintaining its stem cell identity. In contrast, the other 

daughter cell eventually leaves the niche consequently losing the capacity to self-renew and acquiring the fate of a 

transit amplifying cell (TA-cell). The function of these cells is to rapidly expand through proliferation while 

simultaneously differentiating along one of the lineages present in the given tissue. Continuous differentiation 

correlates with progressive loss of multipotency. This ends by exit from the cell cycle allowing maturation into 

terminally differentiated cell types such as enterocytes, erythrocytes or terminally differentiated skin keratinocytes. 

In case of injury quiescent stem cells are activated and recruited to the site of injury and ensure rapid tissue repair 

for example after blood loss or skin damage. In striking contrast, non-self renewing tissues such as brain, lung, 

heart or kidney respond to injury with extensive scaring, remodeling and often loss of tissue function. 

Figure 1: Bone marrow HSC niche. Right: Hematopoietic stem 

cells (HSCs) are mainly located in the trabecular part of the long 

bones. The endosteum lines the inner bone surfaces and is 

comprised of stromal cells, osteoclasts (white) and spindle 

shaped osteoblasts (brown). The latter are thought to serve as 

niche cells to maintain quiescence and prevent differentiation of 

attached HSCs. In response to injury HSCs can be mobilized 

resulting in the migration of HSCs to peripheral hematopoietic 

organs such as the spleen and the liver. HSCs in the circulation 

can home back to the endosteal niche a process called lodging. 

Left: Purified and fluorescently (CFSE) labeled stem/progenitor 

cells can be detected at the endosteum 15hrs after 

transplantation (Wilson et al., 2004). An HSC (green) is in direct 

contact with an osteopontin secreting (OPN-red, nuclei-blue) 

osteoblast at the endosteum comprising a stem cell niche (see 

also Wilson and Trumpp, Nature Reviews Immunology 2006)


The cancer genes c-myc and pten play crucial roles in adult stem cells 

Adult stem cells likely represent a major target for tumor initiation and gene therapy. Therefore, 

understanding the regulation of normal stem cell self-renewal is also fundamental to understand the 

regulation of cancer cell proliferation, because cancer can be considered to be a disease of unregulated 

self-renewal. Our research focuses on the elucidation of the molecular basis of stem cell self-renewal and 

differentiation as well as the identification of cancer stem cells in vivo. For this we take advantage of a 

number of mouse models which are mutant for two of the most frequently affected genes in human 

cancers, c-myc and Pten. 

Both cancer genes seem to play non-overlapping roles in stem cell function. We have recently shown that 

loss of Pten in the brain leads to an increase in neuronal stem cell number due to increased survival, 

proliferation and growth (Groszer et al., 2001). In contrast loss of c-Myc in the bone marrow (BM) does not 

affect proliferation of hematopoietic stem cells (HSC), but blocks stem cell differentiation and appears to 

have a direct role in controlling the balance between self-renewal and differentiation. This leads to an 

increase of the HSC pool while differentiating cell types are lost providing the mechanism for the severe 

anemia observed in those mutants (Wilson et al., 2004). The increased number of stem cells is apparently 

due to a change in the interaction between the mutant HSCs and their niche. 

Identification and characterization of “cancer stem cells” in primary tumors 

Despite major advances in basic cancer research, and especially in understanding the molecular and 

biochemical pathways that are involved in tumorigenesis and malignant transformation, there hasn’t really 

been much significant progress in cancer therapy since years. Could this suggest that conventional 

strategies for confronting cancer have been exhausted A tumor can be viewed as an aberrant organ 

initiated by a tumorigenic cancer cell that has acquired the capacity for indefinite proliferation through 

accumulated mutations. In searching for the cancer originating cell type apparent analogies between 

tumorigenic cells and normal stem cells have long been recognized even before the discovery of 

oncogenes and tumor suppressor genes twenty-five years ago (reviewed in Reya et al., 2001 and Dean et 

al., 2005). The aim of this program which we have recently initiated is to obtain evidence whether solid 

tumors are driven by a small number of genetically altered stem cells called “Cancer Stem Cells” (CSC) 

(Fig. 2). We have recently started to develop techniques for the identification, isolation and 

characterization of CSC from primary murine and human cancer. Using technologies related to stem cell 

enrichment methods using sophisticated cell sorting (FACS) technologies (e.g. “side population”) in 

combination with specialized stem cell maintaining culture conditions allowed us to enrich tumor initiating 

cells, putative CSC. As the most stringent functional test for the tumor initiating potential we use orthotopic 

grafts of enriched CSC cells into NOD/SCID or RAG2 -/- ; γC -/- mice. Comparison of the transcriptome of 

purified CSC and tumor cells that have no tumor initiating activity will in the future allow the isolation of 

specific pathways engaged in CSC. This may enable us to specifically target and destroy CSCs, thus 

preventing tumor relapse after chemotherapy (Fig. 2). 

Figure 2: Conventional therapies may shrink 

tumor mass, but spare cancer stem cells (CSC). 

CSC are resistant and remain viable and after 

some time re-establish the tumor. 

By contrast if therapies can be targeted aginst 

CSC, then they might render tumors unable to 

maintain themselves to grow. Thus, therapies 

that target CSC should not shrink the tumor 

immediately but may eventually lead to tumor 

degeneration. Combination of conventional 

therapies with drugs that specifically target CSC 

should lead to fast and long lasting cures.

Future studies will further extend the use of mouse models to study stem cell self-renewal in various adult 

tissues such as skin and intestine as well as in the hematopoietic system. Furthermore we have begun to 

visualize self-renewal divisions of highly purified normal and mutant HSCs by time lapse video microscopy 

and are using normal and mutant stem cells for genome wide Affymetrix microarray analysis to identify 

novel genes involved in stem cell self-renewal. Our aim is to use these insights to develop strategies that 

would allow expansion of adult stem cells in vitro and obtain insights into the pathological events that lead 

to the generation of cancer stem cells. 

Our goal is to use mouse molecular genetics to understand: 

- the molecular mechanism that controls the balance between stem cell 

- self-renewal and differentiation 

- the molecular and cellular nature of a “stem cell niche” 

- the role of c-Myc and Pten in stem cells, differentiating cells, organs and tumors 

- the molecular and cellular difference between “cancer stem cells” and normal stem cells. 


Dubois N., Adolphe C., Ehninger A., Robertson E., Wang R. and Trumpp A. (2008). Placental rescue 

reveals a sole requirement for c-Myc in erythroblast survival and hematopoietic stem cell function. 

Development, 135; 2455-2465 

Chen He, Huiqing Hu, Shun-Yin Fong, Trumpp A., Timothy R. Carlson, Rickmer Braren, and Rong Wang 

(2008). Lineage-specific deletions of c-myc reveal its essential function in hematopoiesis and placentation 

but not vasculogenesis. Development, 135; 2467-2477 

Trumpp A. and Otmar D. Wiestler, (2008). Targeting the evil Twin. NATURE Clinical Practice Oncology, 

Jun; 5(6):337-47 

Wilson A. and Trumpp A. (2008). Hematopoietic Stem Cell Niches in “Molecular Mechanisms of 

Hematopoiesis” edited by Amittha Wickrema and Barbara Kee. Springer publishing. In press 

Blanco-Bose W.E. * , Murphy M.J. * , Ehninger A., Offner S., Dubey C., Huang W., Moore D.D. and Trumpp 

A. (2008). c-Myc and its target FoxM1 are critical downstream effectors of TCPOBOP-CAR induced direct 

liver hyperplasia. Hepatology, in press 

Wilson A., Oser G.M., Jaworski M., Blanco, W., Laurenti E., Adolphe C., Essers M.A., MacDonald H.R. 

and Trumpp A. (2007). Dormant and self-renewing hematopoietic stem cells and their niches. Ann N Y 

Acad Sci. 1106:64-75. Epub Apr 18 2007 

Ju Z., H. Jiang, Jaworski M., A. Gompf, C. Rathinam, C. Klein, Trumpp A. and K. L. Rudolph (2007). 

Telomere dysfunction induces environmental alterations limiting hematopoietic stem cell function and 

engraftment. Nat Med. 13(6):742-747 

Strom A, Bonal C, Ashery-Padan R, Hashimoto N, Campos ML, Trumpp A, Noda T, Kido Y, Real FX, 

Thorel F, and Herrera PL. Unique mechanisms of growth regulation and tumor suppression upon Apc 

inactivation in the pancreas.(2007). Development 134:2719-2725 

Beermann, F., Kaloulis, K., Hofmann, D., Murisier, F., Bucher, P. and Trumpp, A. (2006). Identification of 

evolutionarily conserved regulatory elements in the mouse Fgf8 locus. Genesis 44(1):1-6 

Prathapam, T., Tegen, S., Oskarsson, T., Trumpp, A. and Martin G.S. (2006). Activated Src abrogates the 

Myc requirement for the G0/G1 transition but not for the G1/S transition. Proc. Natl Acad. Sci. USA. 103 

(8):2695-2700 

Bianchi, T., Gasser, S., Trumpp, A. and MacDonald, H.R. (2006). c-Myc acts downstream of IL-15 in the 

regulation of memory CD8 T cell homeostasis. Blood 107: 3992-3999 

Oskarsson, T., Essers, M., Dubois, D., Dubey, C., Roger, C., Metzger, D., Chambon, P., Hummler, E., 

Beard, P. and Trumpp, A. . (2006). Skin epidermis lacking the c-myc gene is resistant to Ras driven 

tumorigenesis but can re-acquire sensitivity upon additional loss of the p21 CIP1 gene. Genes Dev. 20: 

2024-2029. This article was picked and evaluated by one “Faculty of 1000” member and has received a 

F1000 Score of 3.0

Sclafani, A.M., Skidmore, J.M., Ramaprakash, H., Trumpp, A., Gage, P.J. and Martin, D. (2006). Genesis, 

44: 336-344 

Dubois, N., Hofmann, D., Kaloulis, K., Bishop, J.M. and Trumpp, A. (2006). The Nestin-Cre transgenic 

mouse line Nes-Cre1 mediates highly efficient Cre/loxP mediated recombination in the nervous system, 

kidney and somite derived tissues. Genesis 44: 355-360 

Wilson, A. and Trumpp, A. (2006). Bone marrow hematopoietic stem cell niches. Na. Rev. Immunol. 

6 :93-106 

Trumpp A. (2007). c-Myc and Activated Ras during Skin Tumorigenesis: Cooperation at the Cancer Stem 

Cell Level In: Wiestler/Mumberg (eds) Cancer Stem Cells. (Ernst Schering Foundation Symposium ) 

Springer, Berlin Heidelberg 2006/5 


BEERMANN GROUP 

TEAM MEMBERS 

Iraz T. Aydin, PhD Student 

Sandra Brunschwiler, Technician 


Sabrina Guichard, Technician 

Irina Pshenichnaya, PhD Student 

Karine Schouwey, PhD Student 

Friedrich Beermann 

Group Leader 

http://isrec.epfl.ch/Beermann 

INTRODUCTION 

The incidence of melanoma is increasing worldwide. We are interested in pigment cells which are neural 

crest-derived melanocytes and cells of the retinal pigment epithelium (RPE) to study gene regulation, 

development and interplay between stem cells and differentiating cells. Changes in pigment cell regulation 

can result in hair graying, albinism, and vitiligo but also in cutaneous melanoma, one of the most 

devastating types of cancer. 

Transgenic mice are essential tools for the study of gene function in developmental biology, immunology 

and cancer research. The transgenic facility provides support for producing genetically modified mice for 

basic research. This includes pronuclear injections, as well as expertise and assistance in the 

development and production of genetically engineered mice. 


Melanocyte biology 

Melanocytes differentiate from pluripotent neural crest cells at about E8.5 in mice, migrate along the 

dorsolateral pathway and subsequently proliferate through the dermis horizontally to the ventral region. By 

E14.5, melanocytes exit from the dermis and invade into the epidermis to finally be located in the skin and 

the hair follicles. Many genes are implicated in specific aspects of melanocyte/melanoblast differentiation 

and more than 130 loci were identified in the mouse affecting pigmentation. Many of the factors involved 

in proliferation and differentiation of the melanocyte lineage act synergistically, but also at specific stages 

of embryonic development. The Notch signaling pathway affects melanocyte homeostasis, leading to a 

distinct hair graying phenotype in gene-targeted mice. In Notch knockout mice, the results indicate a loss 

of stem cells in the bulge. We are actually interested to understand the cause of this stem cell loss, and to 

identify downstream effectors of Notch signaling in melanocytes and melanoblasts. 

ß-catenin and its role in melanoma 

Activation of N-Ras is one of the most frequent oncogenic alterations found in human melanoma. To 

mimic this disease in mice, we had targeted expression of a dominant-active human N-Ras (N-Ras Q61K ) 

gene to melanocytes. Upon additional activation of the INK4a locus, encoding the tumor suppressors 

p16 INKA and p19 ARF , hyperpigmented N-ras mice develop cutaneous melanoma. In collaboration with the 

group of L. Larue (France), we have analyzed the importance of ß-catenin in melanoma. Stabilized 

ß-catenin bypasses the requirement for p16 INK4A mutations, and together with the activated N-ras 

oncogene, leads to melanoma with high penetrance and short latency. These results reveal that synergy 

between the Wnt and mitogen-activated protein (MAP) kinase pathways may represent an important 

mechanism underpinning the genesis of melanoma. 

Gene regulation in pigment cells 

Gene expression in pigment cells is differentially regulated in melanocytes and the retinal pigment 

epithelium (RPE). Conserved noncoding sequences are present in the vicinity of pigmentation genes, and 

some of them represent enhancers/distal regulatory elements. Previous experiments revealed the 

importance of distal regulatory elements at -15 kb of the tyrosinase and the Tyrp1 gene in melanocytespecific 

gene expression. Bioinformatics and use of genetic modifications of bacterial artificial 

chromosomes (BACs) in transgenic mice have now revealed a novel RPE-specific distal regulatory 

element at -47kb of the mouse tyrosinase gene.

Transgenic and mutant mice 

The introduction of genetic material into the germ line of mammals is one of the major experimental 

achievements developed in the last three decades, and genetically-engineered mice represent a powerful 

tool in today's biomedical research. To cope with the increasing demand for mouse studies and transgenic 

experiments, a transgenic facility was set up already in 1992. Pronuclear microinjection of DNA into 

fertilized mouse oocytes was the service most extensively used. DNA constructs were provided by the 

scientist and injected into fertilized oocytes derived mainly from FVB/N inbred or B6D2F1 hybrid mice. At 

weaning of offspring, further analysis is performed by the scientist. If desired, the facility collaborates and 

provides expertise in designing the construct and performing the analysis of the mice. We have injected 

column-purified fragments isolated from plasmid vectors, but have also successfully generated mice 

following injection of supercoiled BAC DNA. 

Melanocytes are visualized by lacZ staining (Dct::lacZ; left) or by immunofluorescence (in bulb and 

bulge of hair follicles; right). 


Delmas, V., Beermann, F., Martinozzi, S., Carreira, S., Ackermann, J., Kumasaka, M., Denat, L., Goodall, 

J., Luciani, F., Viros, A., Demirkan, N., Bastian, B.C., Goding, C.R. and Larue, L. (2007). beta-catenin 

induces immortalization of melanocytes by suppressing p16INK4a expression and cooperates with N-Ras 

in melanoma development. Genes & Development 21: 2923-2935. 

Larue, L. and Beermann, F. (2007). Cutaneous melanoma in genetically modified animals. Pigment Cell 

Research 20: 485-497. 

Wiznerowicz, M., Jakobsson, J., Szulc, J., Liao, S., Quazzola, A., Beermann, F., Aebischer, P. and 

Trono, D. (2007). The Krab repressor domain can trigger de novo promoter methylation during mouse 

early embryogenesis. Journal of Biological Chemistry 282; 34535-34541. 

Kianizad, K., Marshall, L.A., Grinshtein, N., Bernard, D., Margl, R., Cheng, S., Beermann, F., Wan, Y. and 

Bramson, J. (2007) Elevated frequencies of self-reactive CD8+ T cells following immunization with a 

xenoantigen are due to the presence of a heteroclitic CD4+ T cell helper epitope. Cancer Research 67: 

6459-6467. 

Murisier, F., Guichard, S. and Beermann, F. (2007) The tyrosinase enhancer is activated by Sox10 and 

Mitf in mouse melanocytes. Pigment Cell Research 20: 173-184. 

Stecca, B., Mas, C., Clement, V., Zbinden, M., Correa, R., Piguet, V., Beermann, F. and Ruiz i Altaba, A. 

(2007) Melanomas require HEDGEHOG signaling regulated by interactions between GLI1 and the RAS- 

MEK/AKT pathways. Proceedings of the National Academy of Sciences (USA) 104: 5895-5900. 

Wilson, A., Ardiet, D.L., Saner, C., Vilain, N., Beermann, F., Aguet, M., MacDonald, H.R. and Zilian, O. 

(2007) Normal hematopoiesis and lymphopoiesis in the combined absence of Numb and Numblike. 

Journal of Immunology 178: 6746-6751. 

Johansson, K.A., Dursun, U., Jordan, N., Gu, G., Beermann, F., Gradwohl, G., Grapin-Botton, A. (2007). 

Temporal control of Neurogenin 3 activity in pancreas progenitors reveals competence windows for 

generation of different endocrine cell types. Developmental Cell 12: 457-465. 

Murisier, F., Guichard, S. and Beermann, F. (2007) Distinct distal regulatory elements control tyrosinase 

expression in melanocytes and the retinal pigment epithelium. Developmental Biology 303: 838-847.

Schouwey, K., Delmas, V., Larue, L., Zimber-Strobl, U., Strobl, L., Radtke, F. and Beermann, F. (2007. 

Notch1 and Notch2 receptors influence progressive hair graying in a dose-dependent manner. 

Developmental Dynamics 236: 282-289. 

Frau, E., Magnon, C., Opolon, P., Connault, E., Opolon, D., Beermann, F., Abitbol, M., Perricaudet, M. 

and Bouquet, C. (2007) A gene transfer comparative study of HSA-conjugated antiangiogenic factors in a 

transgenic mouse model of metastatic ocular cancer. Cancer Gene Therapy 14: 251-261. 

Wong, C.E., Paratore, C., Dours-Zimmermann, M.T., Rochat, A., Pietri, T., Suter, U., Zimmermann, D.R., 

Dufour, S., Thiery, J.P., Meijer, D., Beermann, F., Barrandon, Y. and Sommer, L. (2006). Neural crestderived 

cells with stem cell features can be traced back to multiple lineages in the adult skin. Journal of 

Cell Biology 175: 1005-1015. 

Zou, J., Beermann, F., Wang, J., Kawakami, K. and Wei, X. (2006). The Fugu tyrp1 promoter directs 

specific GFP expression in zebrafish: tools to study the RPE and the neural crest-derived melanophores. 

Pigment Cell Research 19: 615-627. 

Beermann, F. (2006) Modeling melanoma. Drug Discovery Today: Disease Models 3. 129-135. 

Murisier, F. and Beermann, F. (2006) Genetics of pigmentation: lessons from the tyrosinase gene family. 

Histology and Histopathology 21: 567-578 

Murisier, F., Guichard, S. and Beermann, F. (2006). A conserved transcriptional enhancer that specifies 

Tyrp1 expression to melanocytes. Developmental Biology 298: 644-655. 

Membrez, M., Hummler, E., Beermann, F., Haefliger, J.A., Savioz, R., Pedrazzini, T. and Thorens, B. 

(2006). Glut8 is dispensable for embryonic development but influences hippocampal neurogenesis and 

heart function. Molecular & Cellular Biology 26: 4268-4276. 

Moriyama, M., Osawa, M., Mak, S.S., Ohtsuka, T., Yamamoto, N., Han, H., Delmas, V., Kageyama, R., 

Beermann, F., Larue, L., and Nishikawa, S.I. (2006). Notch signaling via Hes1 transcription factor 

maintains survival of melanoblasts and melanocyte stem cells. Journal of Cell Biology 173: 333-339. 

Beermann, F., Kaloulis, K., Hofmann, D., Murisier, F., Bucher, P. and Trumpp, A. (2006). Identification of 

evolutionarily conserved regulatory elements in the mouse Fgf8 locus. Genesis 44: 1-6. 

Preynat-Seauve, O., Schuler, P., Contassot, E., Beermann, F., Huard, B. and French, L.E. (2006.) Tumorinfiltrating 

dendritic cells are potent antigen-presenting cells able to activate T cells and mediate tumor 

rejection. Journal of Immunology 176: 61-67. 

Porret, A., Mérillat, A.M., Guichard, S., Beermann, F. and Hummler, E. (2006). Tissue-specific transgenic 

and knockout mice. Methods in Molecular Biology 337: 185-205. 


BUCHER GROUP 

TEAM MEMBERS 

Giovanna Ambrosini, Scientist 


Viviane Praz, Scientist 

Dorota Retelska, Postdoctoral Fellow 

Christoph Schmid, Scientist 

Peter Sperisen, Scientist 

Haleh Yasrebi, PhD student 

Philipp Bucher 

Group Leader 

http://isrec.epfl.ch/Bucher 

INTRODUCTION 

Genome sequencing projects and new high-throughput technologies are producing large amounts of 

biological data that are potentially relevant to cancer. Our group contributes to the analysis of these data 

by developing new methods and database resources related to genome structure and gene regulation. In 

addition, we use our methods to carry out question-driven bioinformatics research focusing on 

transcriptional control mechanisms distorted in cancer cells. 


Biological data and cancer 

Computers have become indispensable tools for accessing, visualizing, analyzing, managing, and 

publishing biological data. Recently, high-throughput sequencing and functional genomics projects have 

generated unprecedented quantities of biological data which cannot anymore be processed manually or 

interpreted visually. The emergence of the new field of bioinformatics is a response to this development. It 

comprises all research and development activities that help to make sense out of biological data with the 

aid of computers. Specifically, these activities include mathematical modeling of biological processes, the 

conception of new algorithms to fit models to data, as well as the development of software and databases 

as community resources. 

Characterization of transcription factor binding sites 

Transcriptional control mechanisms in higher organisms are poorly understood. We are, for instance, still 

not able to predict the effects of genetic variations and somatic mutations in gene regulatory regions, 

which nowadays are readily detectable by comprehensive genotyping assays. What seems to hamper 

progress is the lack of accurate tools for predicting transcription factor binding sites, the elementary 

building blocks of regulatory regions. Fortunately, novel technologies are emerging that allow for detailed 

characterization of transcription factor binding specificity. However, the generation of accurate predictive 

binding site models from the large data sets produced by the new technologies remains a challenge to 

computational biologists. 

Over the years, our group has devised several bioinformatics-inspired strategies to produce accurate 

binding site models for transcription factor binding sites, including the SAGE/SELEX technique developed 

in collaboration with Nicolas Mermod at the University of Lausanne. Recent research has focused on 

computational methods for interpreting data from protein-binding microarrays (PBM), a technique we used 

to analyze the sequence specificity of transcription factor AP-2. On the more technical side, we 

implemented a fast computational pipeline for genome-wide mapping of transcription factor binding site 

matrices, relying on new software jointly developed with Christian Iseli at the Ludwig Institute for Cancer 

Research in Lausanne (Iseli et al., 2007). 

Studying gene regulatory mechanisms by comparative genomics 

The possibility to assess evolutionary conservation of gene regulatory regions by cross-genome 

comparison helps to discriminate functional elements from the large excess of function-less DNA. With 

more complete genomes becoming available every year, our group is increasingly solicited for 

collaborations in this area. A recent example is the identification of evolutionarily conserved regulatory 

elements in the mouse Fgf8 locus. These regions were subsequently analyzed in mouse embryos by the 

group of Andreas Trumpp (Beerman et al. 2006).

The comparative genomics approach is also applied for de novo discovery of gene regulatory regions 

located far away from known genes. Both the most conserved and the fastest evolving DNA sequences 

are interest. The former are supposed to contain instructions for the conserved parts of the vertebrate 

body plan. The latter may encode lineage-specific morphological features and pathways. We made a 

theoretical contribution to this field, by proposing a quantitative measure for estimating the amount of 

conserved sequence information contained in whole-genome alignments (Retelska et al. 2008). Using this 

metric, we were able to demonstrate that the ratio of non-coding versus coding sequence information is 

higher in vertebrates than in insects. This suggests that the apparently higher morphological complexity of 

vertebrates is mainly due to non-coding sequences. 

Analysis of breast cancer gene expression data sets 

Gene expression profiling has become a standard technique for molecular characterization of cancer 

tissues. By comparing large numbers of expression profiles together with corresponding clinical data, one 

hopes to improve tumor classification, which in turn could help choosing the optimal treatment for a 

patient. However, the relatively small number of samples from a single study has so far limited the 

success of this approach. One could possibly overcome this limitation by merging data from different 

studies. However, the currently available data sets differ in many respects, including technical biases, 

patient selection criteria, and follow-up treatment, raising doubts about the potential benefits from data 

merging. 

Our group has considerable experience with merging gene expression data thanks to the development of 

the CleanEx database, an early integration effort in this field. We recently carried out a systematic 

evaluation of data integration and class prediction methods, focusing on the problem of breast cancer 

survival prediction. The results indicate that prediction algorithms based on merged data sets are more 

robust, even if the patient cohorts enrolled in different studies differed significantly from each other in 

terms of clinical parameters. Moreover, a systematic investigation of the performance limiting factors led 

to the discovery of at least one new prominent survival gene. 

First insights from ChIP-chip and ChIP-seq data analysis 

The recent advent of high-resolution, genome-wide chromatin immunoprecipitation protocols (ChIP-chip 

and ChIP-seq) is likely to revolutionize research on gene regulation. Data published last year allowed for 

the first time a detailed view of the chromatin conformation of a whole genome (see Figure 1A). The large 

data sets generated with this new technology present a new challenge to computational biologists. To 

gain first experience in this field, we have adjusted and tested on Chip-chip data a peak recognition 

algorithm, which was originally developed by Mauro Delorenzi for transcription start sites inference 

(Schmid et al. 2007). When analyzing public ChIP-seq data for histone variants in CD4+ T-cell, we made 

the surprising discovery that human promoters had a distinct chromatin conformation (Figure 1B) 

characterized by a remarkably conserved distance between the transcription start site and the first 

downstream nucleosome (Schmid and Bucher, 2007). We are also engaged in several collaborations with 

wet lab researcher using ChIP assays. For instance, with Walter Reith from the University of Geneva we 

characterized the complete set of target loci of the regulatory protein CIITA using ChIP-chip data 

(Krawczyk et al. 2008). 

Development of Bioinformatics Resources 

We always adhered to the principle that data sets and software tools developed for specific research 

projects should be made freely available to the scientific community, and that a reasonable level of 

support should be offered to potential users. As a consequence of this policy, our group is today 

maintaining and updating a number of bioinformatics resources. Funds for such activities are provided by 

the Swiss Institute of Bioinformatics (SIB). The Eukaryotic Promoter Database (EPD) is a compilation of 

experimentally characterized eukaryotic promoters, which has been maintained for more than 20 years 

(Schmid et al. 2007). The already mentioned CleanEx database provides access to public gene 

expression data via unique gene names. Its second objective is to represent heterogeneous expression 

data from different technologies in a way that facilitates joint analysis and cross-data set comparisons. 

The gene-mapping tables of CleanEx are now also used by Splicy, a new web-based tool for the 

prediction of possible alternative splicing events, developed by the group of Alessandro Guffanti at CNR- 

ITP in Milano (Rambaldi et al. 2007). The HTPSELEX database (Jagannathan et al. 2007) contains large 

sets of in vitro selected transcription factor binding site sequences useful for building accurate 

computational models for their binding specificity. The Signal Search Analysis (SSA) server offers 

software tools for the discovery and characterization sequence motifs in gene regulatory regions. The four 

web-accessible resources are hyperlinked to each other and can be used jointly to carry out complex data 

analysis tasks addressing a wide variety of biological questions.

A 

Chromatin conformation at promoter regions in CD4+ T-cells. 

This figure is based on public data described in (Barski et al., Cell 129, 823-837, 2007). 

A. Location of histone variants and RNA Pol II in the MGMT promoter region. Custom tracks for ChIP-Seq data 

were generated with software developed by our group and displayed in a UCSC genome browser window. The 

peaks indicate the center positions of protein-DNA complexes (nucleosomes in the case of histone modifications). 

Also shown are the 5’ ends of two alternative transcripts and a CpG island. Clearly visible are four nucleosomes 

marked by histone variant H2AZ at distinct positions upstream of the two putative transcription start sites (TSS). 

The H3K4me3 profile suggests two alternative positions for the first downstream nucleosome. The enrichment in 

PolII signal near the TSS suggests that the gene is active. Note that the MGMT gene is epigenetically silenced in 

certain tumors and is currently evaluated as a predictive marker for therapy choice (Hegi et al., N. Engl. J. Med. 

352, 997-1003, 2005). Its epigenetic status, as visualized here, may predict a tumor’s response to alkylating 

agents 

B 

B. Relative abundance of histone variants and RNA Pol II in the vicinity of 

human TSS from ENSEMBL. These profiles suggest fixed positions and 

dense packaging of downstream nucleosomes. Moreover, there appears to 

be a nucleosome-free region around the TSS of at least 150 bp

2006-2007 PUBLICATION 

Schmid, C.D. and Bucher, P. (2007). ChIP-Seq Data Reveal Nucleosome Architecture of Human 

Promoters. Cell 131, 831-832 

Krawczyk, M., Seguín-Estévez, Q., Leimgruber, E., Sperisen, P., Schmid, C., Bucher, P. and Reith W. 

(2008). Identification of CIITA regulated genetic module dedicated for antigen presentation. PLoS Genet. 

4:e1000058 

Retelska, D., Beaudoing, E., Notredame, C., Jongeneel, C.V. and Bucher, P. (2007). Vertebrate 

conserved non coding DNA regions have a high persistence length and a short persistence time. BMC 

Genomics 8:398 

Girod, P.A., Nguyen, D.Q., Calabrese, D., Puttini, S., Grandjean, M., Martinet, D., Regamey, A., Saugy, 

D., Beckmann, J.S., Bucher, P. and Mermod, N. (2007). Genome-wide prediction of matrix attachment 

regions that increase gene expression in mammalian cells. Nat. Methods 4, 747-753 

Iseli, C., Ambrosini, G., Bucher, P. and Jongeneel, C.V. (2007). Indexing strategies for rapid searches of 

short words in genome sequences. PLoS ONE 2, e579 

Schmid, C.D., Sengstag, T., Bucher, P. and Delorenzi M. (2007). MADAP, a flexible clustering tool for the 

interpretation of one-dimensional genome annotation data. Nucleic Acids Res. 35, W201-W205 

Rambaldi, D., Felice, B., Praz, V., Bucher, P., Cittaro, D. and Guffanti A. (2007). Splicy: a web-based tool 

for the prediction of possible alternative splicing events from Affymetrix probeset data. 

BMC Bioinformatics, 8 Suppl 1:S17 

Armougom, F., Poirot, O., Moretti, S., Higgins, D.G., Bucher, P., Keduas, V. and Notredame C. (2006). 

APDB: a web server to evaluate the accuracy of sequence alignments using structural information. 

Bioinformatics 22, 2439-2440 

Retelska, D., Iseli, C., Bucher, P., Jongeneel, C.V. and Naef F. (2006). Similarities and differences of 

polyadenylation signals in human and fly. BMC Genomics 7:167 

Beermann, F., Kaloulis, K., Hofmann, D., Murisier, F., Bucher, P. and Trumpp A (2006). Identification of 

evolutionarily conserved regulatory elements in the mouse Fgf8 locus. Genesis 44, 1-6 

. 

Jagannathan, V., Roulet, E., Delorenzi, M. and Bucher, P. (2006). HTPSELEX--a database of highthroughput 

SELEX libraries for transcription factor binding sites. Nucleic Acids Res. 34, D90-D94 

Schmid, C.D., Perier, R., Praz, V. and Bucher, P. (2006). EPD in its twentieth year: towards complete 

promoter coverage of selected model organisms. Nucleic Acids Res. 34, D82-D85 


EXTERNAL ADJUNCT PROFESSOR 

Daniel F. Schorderet 

External Adjunct Professor 

Joint Chair EPFL / UNIL 

Director IRO 

Institute for Research in Opthtalmology, Sion 

http://www.irovision.ch 

TEAM MEMBERS 

Sandra Cottet, PhD, Senior Scientist 

Pascal Escher, PhD, senior Postdoctoral Fellow 

Raphaël Roduit, PhD, senior Postdoctoral Fellow 

Mauro Bustamante, PhD, Postdoctoral Fellow 

Bozena Polok, PhD, Postdoctoral Fellow 

Nathalie Produit, PhD, Postdoctoral Fellow 

Margaret Shaw, PhD, Postdoctoral Fellow 

Leila Tiab, Biologist 

Olivia Nichini, PhD Student (UNIL) 

Gaëlle Boisset, PhD Student (UNIL) 

INTRODUCTION 

Our Institute is devoted to identify the genes implicated in the development of the eye and the 

maintenance of vision from embryo until late in life. This program has two main lines of research: 

Identification of new loci and genes 

We have developed in collaboration with many clinical groups a program of gene identification based on 

linkage and associations studies. In this program, families with blinding conditions are identified, clinically 

evaluated and blood is drawn for linkage analysis based on microsatellite markers or Affymetrix SNP 

technology. Once a new locus is established, potential candidate genes are evaluated by bio-informatics 

and the most promising ones are sequenced. Using this approach, we have been successful in 

discovering the implication of many genes: Bietti Crystalline Corneoretinal Dystrophy (2004), François- 

Neetens mouchetée fleck corneal dystrophy (2005), epithelial basement membrane corneal dystrophy 

(2006), autosomal recessive night blindness (2006). 

Neurodegenerative disorders of the retina and therapy 

Most blinding conditions are the result of the ultimate death of photoreceptors. As human retina is difficult 

to obtain, we use animal models that we develop ourselves or obtain from collaborators. Diseases are 

studied in mouse or rat models while development is best studied in zebrafish. We recently focused our 

attention on the various cellular pathways that trigger apoptosis in the photoreceptors. Discovering the 

detailed molecular interactions that govern the development of diseases has also clinical implication as 

new molecular or gene therapies will be developed. 


Identifying genes in blinding diseases (Leila Tiab, Olivia Nichini) 

Band-shaped spheroidal dystrophy of the cornea, first described in 1939 by Fuchs, a Swiss 

ophthalmologist, is a rare disease affecting the cornea. It is transmitted as an autosomal or a dominant 

trait and is responsible for blindness. The identification of a consanguineous family with this disorder 

allowed us to use homozygosity mapping to identify the M1S1 gene as responsible for this disease in an 

Algerian family. Also this gene was already implicated in other corneal dystrophy, it was not known that it 

was also mutated in disease. 

Cell signaling in the retina of Leber’s congenital amaurosis (LCA) murine model (Sandra Cottet) 

Retinal degeneration leads to irreversible loss of vision. Grouped under the term of retinitis pigmentosa, 

these diseases affect 1 in 4’000 individuals worldwide and currently no cure is available. As a way to 

better understand the various pathways implicated in these diseases, we study the role of proteins of the 

Bcl-2 family, a major player in modulating survival and apoptosis. This family comprises pro- and antiapoptotic 

molecules. We observed a strong disequilibrium between the anti-apoptotic Bcl-2 and 

proapoptotic Bax proteins in the Rpe65 knock-out mouse model of LCA. During the development of the 

disease, Bax increases and is specifically activated, while Bcl-2 decreases. The combination of 

suppression of protection and activation of death signals is responsible for the death of the 

photoreceptors.

Evaluation of the transcription factor NR2E3 in autosomal and recessive retinal degenerations 

(Pascal Escher). 

NR2E3 is a transcription factor implicated in the development of rod photoreceptors by inactivating in the 

rods, the genes specific to cone photoreceptors. When mutated, NR2E3 is no more capable to maintain 

correct rod structure and aberrant rods with cone expressing proteins are made. In collaboration with 

doctors from the Jules-Gonin Eye Hospital in Lausanne, we identified a new mutation in NR2E3 that 

causes a severe form of dominantly inherited retinitis pigmentosa, which is usually not the case with 

mutations in this gene. The NR2E3 transcription factor has many domains but two are of great importance 

in order to understand the situation in these families. A ligand binding domain (LBD) is used to activate the 

protein through a yet undefined molecule. The activated factor interacts then through its DNA binding 

domain (DBD) with specific genes and modulates their expression. We have shown that mutations in the 

DBD induce a dominant-negative effect and abolish the natural inhibition of cone genes which results in 

death of the photoreceptors. Interestingly, this situation can arise in a same family where inheritance of a 

second mutation elsewhere in the gene will dramatically reduce the severity of the disease. This brings an 

interesting concept in gene therapy whereby introducing a second mutation in patients may be done easily 

than removing the first mutation. 

Evaluation of the kinases in retina (Raphaël Roduit) 

Kinases belong to a family of proteins implicated in cell signaling and act with or are responsible of the 

activation, localization or affinity of more than 30% of all the proteins of a cell. We are investigating the 

role of these kinases in normal and diseased retinas. The model we are using is the response of the retina 

to UV radiations and we have shown that the MAP kinases are strongly induced in this model. Activation 

of such kinases is a general retinal response to stress as we have seen a similar reaction in the Rpe65 

KO LCA mouse model. Further work is undergoing in order to clarify the role of each MAPK member and 

to identify protective peptides. 

Zebrafish and eye diseases (Bozena Polok, Gaëlle Boisset) 

Zebrafish, a small aquarium animal originating from India, and although it has already been studied for a 

long time, has gained in importance as its genome is almost fully sequenced. In addition, the development 

of many organs, in particular the eye correlates well with the development of similar organs in 

mammalians and in humans. We have setup a screening program aiming at identifying new genes 

involved in eye development. We recently identified a novel gene called iro-x which, when knock-down, 

leads to the formation of a coloboma in zebrafish. In wild-type animal the closure of the optic fissure takes 

place around 35 hours post fertilization. In morphant animals (morphant is a wild-type animal injected with 

morpholino, a molecule that prevents mRNA translation), this closure doen’t take place and severe renoproctodeum 

defects develop leading to the death of the embryo in later stages of development (figure). 

The phenotype is reminiscent of a human disorder called Townes-Brocks Syndrome which is the 

consequence of a mutation in the gene SALL1. IRO-X is upstream of SALL1 and may represent a key 

element in understanding the development of coloboma and physiological closure of the optic fissure. 


Canola K, Angénieux B, M Tekaya, A Quiambao, MI Naash, Munier FL, Schorderet DF, and Arsenijevic Y. 

Retinal stem cells transplanted into models of late stages of retinitis pigmentosa preferentially adopt a glial 

or a retinal ganglion cell fate. Invest Ophthalmol Vis Sci 48:446-454,2007 

Schorderet DF, Cottet S, Lobrinus JA, Borruat FX, Balmer A, Munier FL. Retinopathy in Danon disease. 

Arch Ophthalmol, 125:231-236,2007 

Marchant D, Yu K, Bigot K, Roche O, Germain A, Bonneau D, Drouin-Garraud V, Schorderet DF, Schmidt 

D, Le Neindre P, Marsac C, Menasche M, Dufier JL, Fischmeister R, Hartzell HC, Abitbol M. New VMD2 

gene mutations identified in patients affected by Best Vitelliform macular dystrophy. 

J Med Genet, 44(3):e70,2007 

Dansault A, David G, Schwartz C, Jaliffa C, Vieira V, de la Houssaye G, Bigot K, Cattin F, Tattu L, Halimi 

P, Roche O, Van Regemorter N, Munier F, Schorderet D, Dufier JL, Marsac C, Ricquier D, Menasche M, 

Penfornis A, Abitbol M. Three new PAX6 mutations including one causing an unusual ophthalmic 

phenotype associated with neuro-developmental abnormalities. Molec Vision 13:511-523, 2007 

Pitchon EM, Cachat F, Jacquemont S, Hinard C, Schorderet DF, Morris MA, Munier F. Patient with 

Fanconi syndrome (FS) and retinitis pigmentosa (RP) caused by a deletion and duplication of 

mitochondrial DNA (mtDNA). Klin Monatsbl Augenheilkd, 224(4):340-342, 2007 

Schorderet DF, Tiab L, Gaillard MC, Lorenz B, Klainguti G, Kerrison JB, Traboulsi EI, Munier FL. Novel 

mutations in FRMD7 in X-linked congenital nystagmus. Human Mutatation, 28(5):525,2007

Shaw MM, Gurr WK, McCrimmon RJ, Schorderet DF, Sherwin RS. 5’ AMP-activated protein kinase a 

deficiency enhances stress-induced apoptosis in BHK and PC12 cells. J Cell Mol Med, 

11(2);286-298,2007 

Hilton EN, Manson FDC, Black GCM, Schorderet DF, Munier FL. De novo mutation in the BIGH3 gene 

causing granular corneal dystrophy. Br J Ophthalmol. 91(8):1083-1084, 2007 

Kolokotronis A, Markopoulos A, Voutas S, Mataftsi A, Ikinomidis P, Antoniades D, Schorderet DF, PFAPA 

syndrome : conjuctivitis as sign of the syndrome. Ophthalmology, 114;1584,2007 

Abouzeid H, Munier FL, Thonney F, Schorderet DF. Ten novel RB1 mutations in patients with 

retinoblastoma. Molecular Vision, 13:1740-1745,2007 

Mataftsi A, Schorderet DF, Chachoua L, Boussalah M, Nouri MT, Barthelmes D, Borruat FX, Munier FL. 

Novel TULP1 mutation causing Leber congenital amaurosis or early onset retinal degeneration. 

Invest Ophthalmol Vis Sci 48(11):5160-5167,2007 

Wild-type zebrafish eye at 35 hpf. Optic fissure is 

clearly visible and on its way to close 

Eye of zebrafish treated with morpholino against 

IRO-X. Picture is taken at the same time and shows 

reduction of the size of the retina and colobma 

(non closure of the optic fissure) 


EXTERNAL ADJUNCT PROFESSOR 

RESEARCH KEYWORDS 

Epidemiology, Public Health, Vaccines 

and Drug Resistance 

Prof. Tanner’s research activities are linked to the Swiss 

Tropical Institute (STI) 

Marcel Tanner 

External Adjunct Professor 

Since July 2007 

Director 

Swiss Tropical Institute, Basel 

http://www.sti.ch 

The STI is hosting two EPFL Master Students for their 

final Master thesis 

New joint research projects between STI and the EPFL 

School of Life Sciences are developped and will be 

operational from 2009 onwards 


WELCOME TO OUR NEW RESEARCH GROUPS! 

IBI – Institute of Bioengineering 


Louis Pasteur University in Strasbourg (France) 

EPFL School of Life Sciences since September 2008 

Johan Auwerx 



Signaling pathways of cellular nuclear receptors, lipid 

metabolism and the pathogenesis of complex metabolic 

disorders 

IBI – CO-AFFILIATED FACULTY FROM THE SCHOOL OF ENGINEERING 

FORMER HOME INSTITUTIONS 

California Institute of Technology & Stanford University 

EPFL School of Engineering since January 2008 

Sebastian J. Maerkl 



Microfluidic Large-Scale Integration applied to Systems 

Biology; specific foci include the analysis of single cell protein 

expression dynamics, promoter architecture, and protein 

interaction networks 


University of California at Berkeley 

EPFL School of Engineering since July 2008 

Aleksandra Radenovic 



Single molecule, nanopore, nanotechnology, laser tweezers, 

microfluidics design, optical microscopy, protein synthesis, 

fluorescence, RNAP, DNA-protein interaction 

Formerly at the EPFL School of Architecture, Civil 

and Environmental Engineering (ENAC) 

Since September 2008 at the EPFL School of 

Engineering and co-affiliated with the IBI Institute 

Hubert Van Den Bergh 


RESEARCH DOMAIN 

Photomedicine 


4 th edition 2007/2008 

Produced and edited by the EPFL School of Life Sciences 

Printed at the EPFL ‘Atelier de Reprographie’ 

Editor : Michèle Bonnard Giacobino 

With warm thanks to 

Claudine Ravussin, Gabi Grenningloh and Dietrich Reinhard 

for their help and support 

Available online: “http://sv.epfl.ch”

Who's Who 

BMI — Brain Mind Institute 

Aebischer Lab 

Blanke Lab 

Fraering Lab 

Gerstner Lab 

Hadjikhani Lab 

Herzog Lab 

Lashuel Lab 

Luthi-Carter Lab 

Magistretti Lab 

Markram Lab & Blue Brain Project 

Petersen Lab 

Sandi Lab 

Schneggenburger Lab 

Hirling Group 

Study of Neurodegenerative Diseases 

Cognitive Neuroscience 

Molecular and Cellular Biology of Alzheimer’s Disease 

Computational Neuroscience 

Social Cognitive Neuroscience 

Psychophysics 

Molecular Neurobiology and Functional Neuroproteomics 

Functional Neurogenomics 

Neuroenergetics and Cellular Dynamics 

Neural Microcircuitry 

Sensory Processing 

Behavioral Genetics 

Synaptic Mechanisms 

Cellular Neurobiology 

IBI — Institute of Bioengineering 

Barrandon Lab 

Stem Cell Dynamics 

Dal Peraro Lab 

Biomolecular Modeling 

Deplancke lab 

Systems Biology and Genetics 

Hubbell Lab 

Regenerative Medicine and Pharmacobiology 

Lutolf lab 

Stem Cell Bioengineering 

Stergiopulos Lab 

Hemodynamics and Cardiovascular Disease 

Swartz Lab 

Mechanobiology and Morphogenesis 

Wurm Lab 

Cellular Biotechnology 

IBI — Co-affiliated EPFL Faculty 

Aminian Lab 

Hatzimanikatis Lab 

Johnsson Lab 

Pioletti Lab 

Psaltis Lab 

GHI — Global Health Institute 

Cole Lab 

Lemaître Lab 

McKinney Lab 

Trono Lab 

Van der Goot 

Movement Analysis and Measurement 

Computational Systems Biotechnology 

Protein Engineering 

Biomechanical Orthopedics 

Optics 

Microbial Pathogenesis 

Mechanisms of Microbial Infection 

Persistent Mechanisms in Mycobacteria Tuberculosis 

Virology and Genetics 

Cell Biology of Bacterial Toxins 

ISREC — Swiss Institute for Experimental Cancer Research 

Aguet Lab 

Cellular Differentiation and Cancer 

Beard Lab 

Anti-Oncogenic Functions of Viruses 

Brisken Lab 

Genetic Dissection of Signaling Pathways in Breast Cancer 

Constam Lab 

Molecular Mechanisms of Morphogenesis and Tissue Homeostasis 

Duboule Lab 

Developmental Genetics and Genomics 

Gönczy Lab 

Mechanisms of Centrosome Duplication & Asymmetric Cell Division 

Grapin-Botton Lab 

Pancreas Development and Cancer 

Huelsken Lab 

Role of Wnt Signals in Tissue Homeostasis and Cancer Stem Cells 

Kühn Lab 

Molecular Analysis of the Cellular Metabolism of Iron 

Lingner Lab 

Telomerase and Chromosome end Replication 

Naef Lab 

Computational Systems Biology 

Radtke Lab 

Molecular Mechanisms 

Simanis Lab 

Regulation of Cell Division 

Trumpp Lab 

Cancer Genes and Stem Cells 

Beermann Group 

Melanocytes and transgenic mice 

Bucher Group 

Computational cancer genomics 

Adjunct Professors 

Brigitte Jolles-Haeberli 

Pierre-François Leyvraz 

William Pralong 

Daniel-Francis Schorderet 

Marcel Tanner 

Director, Center of Translational Biomechanics (EPFL-CHUV-HOSR) 

Director, Lausanne University Hospital (CHUV) 

Director, Life Sciences and Technology Bachelor/Master Programs 

Director, Institute for Research in Ophtalmology (Sion) 

Director, Swiss Tropical Institute (Basel) 

Core facilities & Technology platforms 

Bioimaging & Optics 

Flow Cytometry 

Bio-Electron Microscopy 

Histology 

Biomolecular Screening 

Protein Expression 

Bioinformatics & Biostatistics 

Proteomics 

Center for the Study of Living Systems Transgenic Technologies 

couverture: www.oxyde.ch

Annual Report EPFL School of Life Sciences

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