Chapter 2 - University of British Columbia

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Abstract Lung cancer has the highest mortality rate amongst all diagnosed malignancies with adenocarcinoma (AC) being the most commonly diagnosed subtype of this disease in North America. The dismal survival statistics of lung cancer patients are largely due to the detection of the disease at an advanced stage and to a lesser extent, the limited efficacy of current front line treatments. Genomic approaches, namely gene expression analysis, have provided tremendous insight into lung cancer. While many gene expression changes have been identified, most changes are likely reactive to changes which have a primary role in cancer development. Moreover, one feature which can discern primary from reactive changes is the presence of concordant DNA level alteration. Many well known genes involved in cancer such as TP53 and CDKN2A have been shown to be affected by multiple mechanisms of alteration such as somatic mutation in or loss of DNA sequence. For a given gene, one tumor may be affected by one mechanism while another tumor may be affected by a different mechanism. Although this level of multi-dimensional analysis has been performed for specific genes, such analysis has not been done at the genome-wide level. This thesis highlights the development and application of a multi-dimensional genetic and epigenetic approach to identify frequently aberrant genes and pathways in lung AC. I present, first, the design and implementation of the system for integrative genomic multi-dimensional analysis of cancer genomes, epigenomes and transcriptomes (SIGMA 2 ). Next, analyzing a multi-dimensional dataset generated from ten lung AC specimens with non-malignant controls, I identified novel genes and pathways that would have been missed if a non-integrative approach were used. Finally, examining genes involved with EGFR signaling, I identified a gene, signal receptor protein alpha (SIRPA), which had not been previously shown to be associated with lung cancer. Taken together, these findings demonstrate the power of a multi-dimensional approach to identify important genes and pathways in lung cancer. Moreover, identifying key genes using a multi-dimensional approach on a small sample set suggests the need of large datasets may be circumvented by using a more comprehensive approach on a smaller set of samples. ii
Table of Contents Abstract ......................................................................................................................................... ii Table of Contents ......................................................................................................................... iii List of Tables ............................................................................................................................... vii List of Figures ............................................................................................................................. viii List of Abbreviations ...................................................................................................................... x Acknowledgements ..................................................................................................................... xii Dedication ................................................................................................................................... xiii Co-Authorship Statement ........................................................................................................... xiv Chapter 1: Introduction ................................................................................................................. 1 1.1 Lung cancer ......................................................................................................................... 2 1.2 Genomic profiling of lung cancer ......................................................................................... 3 1.2.1 Gene expression analysis ............................................................................................. 3 1.2.2 DNA copy number analysis .......................................................................................... 4 1.2.3 Loss of heterozygosity (LOH) and allelic imbalance ..................................................... 5 1.3 Somatic mutations in lung cancer ....................................................................................... 5 1.4 Epigenetic alterations in lung cancer ................................................................................... 6 1.4.1 DNA methylation ........................................................................................................... 6 1.5 Current level of integrative analysis .................................................................................... 7 1.6 Need for an integrative approach to study lung cancer ....................................................... 7 1.7 Bioinformatic tools for genomic analysis ............................................................................. 8 1.8 Thesis theme ....................................................................................................................... 9 1.9 Objectives and hypothesis .................................................................................................. 9 1.10 Specific aims and outline of thesis .................................................................................. 10 1.11 Description of high throughput data in this thesis ............................................................ 13 1.12 Other relevant contributions not included as chapters in this thesis ............................... 13 1.12.1 Development of tools for genomic analysis .............................................................. 14 1.12.2 Baseline gene expression in non-malignant lung tissue ........................................... 14 1.12.3 Differential gene expression analysis in lung cancer ................................................ 15 1.12.4 Integration of gene dosage and gene expression in lung cancer ............................. 16 1.13 References ...................................................................................................................... 18 iii
Page 1: DEVELOPMENT AND APPLICATION OF AN I
Page 5 and 6: 3.3.2 Multi-dimensional analysis (M
Page 7 and 8: List of Tables Table 2.1. Features
Page 9 and 10: Figure 5.3. Overlay of chromosomal
Page 11 and 12: RB1 Retinoblastoma 1 RNA Ribonuclei
Page 13 and 14: Dedication To my family. xiii
Page 15 and 16: Chapter 5: Chari R, Thu KL, Wilson
Page 17 and 18: 1.1 Lung cancer Lung cancer has the
Page 19 and 20: expression changes are reactive to
Page 21 and 22: number of different cancer types. M
Page 23 and 24: large number of tumors, that a give
Page 25 and 26: (B) By using an integrative approac
Page 27 and 28: platforms, with one of the latest s
Page 29 and 30: 1.12.1 Development of tools for gen
Page 31 and 32: quantitative PCR experiments as wel
Page 33 and 34: 1.13 References 1. Jemal A, Siegel
Page 35 and 36: 33. Garber ME, Troyanskaya OG, Schl
Page 37 and 38: 71. Shivapurkar N, Gazdar AF: DNA M
Page 39 and 40: Chapter 2: SIGMA 2 : A system for t
Page 41 and 42: Here, we present SIGMA 2 , a novel
Page 43 and 44: datasets. To utilize this, the user
Page 45 and 46: 2.3.7 Analysis of data from multipl
Page 47 and 48: expression (Figure 2.8). ERBB2 has
Page 49 and 50: Figure 2.1 R -Segmentation -Statist
Page 51 and 52: Figure 2.3 numSamples
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Figure 2.5. Consensus calling and h
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Figure 2.6 HCC2218 HCC2218 HCC2218B
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Figure 2.8. Multi-dimensional persp
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Table 2.1. Features required for in
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2.6 References 1. Garnis C, Buys TP
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Chapter 3: An integrative multi-dim
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observed gene expression deregulati
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Raw gene expression profiles from a
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screening approach to gene amplific
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many regions of frequent LOH/AI do
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approach to examining the whole gen
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PTEN expression [44]. Using this pa
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mechanisms at the DNA and RNA level
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In this study, three DNA dimensions
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Figure 3.2. Quantitative and qualit
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Figure 3.3 a Proportion of genes in
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70 Figure 3.5 -log(pvalue) 5.0 4.0
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72 Figure 3.7 Sample: HCC1008 Copy
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Figure 3.8 a b Proportion of random
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16. Chari R, Lockwood WW, Coe BP, C
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50. Giovane A, Pintzas A, Maira SM,
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4.1 Introduction Genetic alteration
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4.2.3 Determining frequent regions
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etween loss and UPD (Figure 4.3). S
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obtained, profiled and used as the
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Figure 4.1. Detection of UPD using
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Figure 4.2. Comparison of frequent
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Figure 4.3 Gain Loss 642 441 7 Figu
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94 Figure 4.4 1 2 3 4 5 6 7 8 9 10
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Figure 4.6 a b c Percent of cases A
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Figure 4.7 a b 6p25.3 Log2 fold cha
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Chr BPStart BPEnd # of Chr BPStart
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Table 4.3. Overlap of oncogenes in
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Table 4.5. Cell lines and oncogene
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Table 4.7. RefSeq genes in focal re
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4.6 References 1. Bell DW: Our chan
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33. Garnis C, Coe BP, Lam SL, MacAu
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5.1 Introduction In the past decade
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polymorphism (SNP) arrays with over
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substitutions) and UV exposure (C t
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developed antibodies and methylated
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Histone modification states. While
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metastasis [226]. High throughput a
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Implications on sample size require
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analyzed using the "minet" package
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expression. The next challenge is t
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Figure 5.2 # of copies Total copy n
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Figure 5.4. Integration of copy num
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Figure 5.5. Integration of copy num
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Figure 5.6 SHC1 GRB2 SOS2 RRAS ER R
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Figure 5.8 a Log2 Fold Change (T vs
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Figure 5.10 (a) (b) Figure 5.10. Au
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Table 5.2. List of genomic resource
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5.5 References 1. Pinkel D, Segrave
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37. Oliphant A, Barker DL, Stuelpna
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75. Selzer RR, Richmond TA, Pofahl
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111. Melcher R, Al-Taie O, Kudlich
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145. Takai D, Yagi Y, Wakazono K, O
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179. Kondo M, Suzuki H, Ueda R, Osa
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alterations in human prostate cance
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248. Xi L, Feber A, Gupta V, Wu M,
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281. Fernandez-Ranvier GG, Weng J,
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Chapter 6: Conclusions 162
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can identify nearly three times as
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was identified in a small set of sa
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will be done at the pathway level a
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previously described genetic and ep
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16. Zhang K, Li JB, Gao Y, Egli D,
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APPENDIX I: List of publications Th
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This publication is described in se
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This chapter details the technologi
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epigenetic alteration. This led to
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This manuscript describes the curre
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APPENDIX III: Sources of data Sampl
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APPENDIX V: Kaplan-Meier and Oncomi
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APPENDIX VI: Summary of Kaplan-Meie
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University of British Columbia - Br
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Chapter 2 - University of British Columbia

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