Target Discovery and Validation Reviews and Protocols

Target Discovery and Validation 7
information obtained through transcript analysis needs complementation with
information on the cellular protein level. Proteomics, the study of the proteins and
protein pathways, is a promising technique for the rational identification of novel
therapeutic targets (23). Two-dimensional (2D) polyacrylamide gel electrophoresis,
multidimensional liquid chromatography, mass spectrometry, and protein
microarray are among the proteomics techniques available for target discovery.
Usually, protein extracts from cells or tissues are analyzed by 2D gel electrophoresis
to identify differentially expressed or modified proteins. This technique
is followed by mass spectrometry to determine the identity of individual
protein spots of interest from the silver-stained gels. Also, several subcellular proteins
fractions can be separately analyzed by proteomics, thereby reducing the
complexity of the proteome. Regarding target and biomarker discovery, recent
studies stress the power of combining several approaches to identity informative
drug targets. For example, the combination of DNA microarray, SAGE, and proteomics
led to an unbiased elucidation of new cancer biomarkers (see Chapter 4,
Volume 1). Additionally, proteomics approaches can identify posttranslational
modifications that can be important in the discovery of tumor antigens. Analysis
of protein extract from cancer cells by immunoproteomics has resulted in the
identification of novel tumor antigens (see Chapter 16, Volume 1).
Several other techniques such as the yeast two-hybrid system, protein chips,
and phage display have joined proteomics strategies now available for profiling
immune response in patients and identification of tumor antigens. During the
past decade, several tumor antigens were discovered using SEREX (22,24,25),
a method that screens the antibody response of cancer patients against a library
containing autologous or allogeneic tumor cDNA libraries (see Chapter 29). In
contrast to SEREX, the selectivity and specificity are expected to be higher
when iterative methods are used. By biopanning peptides or cDNA phage-display
libraries, we have identified peptides and antigenic proteins to which patients
developed humoral immune responses (26,27). The technique, known as phage
display, should substantially accelerate the pace of tumor antigen discovery
and could provide a molecular signature for immune responses in different
types of cancer. Chapter 14, Volume 1, provides an excellent overview of the
immune system and technical advances in tumour antigen discovery. It also
highlights the problem of immune tolerance and tumor editing, particularly to
cancer vaccine development.
Whereas the principal goal of gene or serum profiling is to identify novel therapeutic
targets, or serological markers, predictive screening strategies primary
attempt to characterize treatment responses, coupled with the secondary aim of
identifying novel therapeutic molecules. By contrast to the analysis of single
serum biomarkers, protein arrays can be used to detect group of proteins that, in
the aggregate, contain significantly more predictive information than do individual