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Comprehensive Characterization of Dna Copy Number Alterations in Mouse and Human Breast Tumors

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COMPREHENSIVE CHARACTERIZATION OF DNA COPY NUMBER ALTERATIONS IN MOUSE AND HUMAN BREAST TUMORS Grace O. Silva A dissertation submitted to the faculty at the University of North Carolina at Chapel Hill in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Curriculum in Bioinformatics and Computational Biology Chapel Hill 2015 Approved by Charles M. Perou J.S. Marron Joel S. Parker Ivan Rusyn Andrew B. Nobel ! 2015 Grace O. Silva ALL RIGHTS RESERVED ! ""! ABSTRACT Grace O. Silva: Comprehensive Characterization of DNA Copy Number Alterations in Mouse and Human Breast Tumors (Under the direction of Charles M. Perou) Breast cancer is a heterogeneous disease as evident through the diversity observed between the molecularly identified “intrinsic subtypes”. These intrinsic subtypes are based upon patterns of gene expression, are predictive of relapse-free survival, overall survival, and responsiveness to treatment. Furthermore, these subtypes are in part driven by specific genomic DNA copy number alterations (CNAs), such that the identification of these intrinsic subtype- defining genetic events is of research and clinical value. To robustly identify breast cancer “driver” genes within frequently occurring DNA CNAs, we implemented multiple integrative strategies using genomic data from various human breast tumors and genetically engineered mouse (GEM) mammary models. One strategy, a cross- species conservation based method, identified “conserved genes” that are the subtype-specific DNA copy number altered genes found in both human breast tumors and GEM mammary tumors. Another strategy, incorporated gene expression signatures of oncogenic pathway activity to identify patterns of oncogenic signaling within each breast cancer subtype that correlated directly with DNA CNAs. In both strategies, additional functional data from genome-wide RNA- mediated interference screens and/or a molecular interaction network analysis were included highlighting multiple Basal-like-specific 1q21-23 amplified genes and also amplified genes unique in highly proliferative luminal breast tumors. ! """! In addition to using CNAs as a base for identifying therapeutic targets, we demonstrated that CNAs play other important roles in the advancement of “personalized medicine”. For example, when tumor DNA is used as the source DNA for genotyping, we demonstrate that CNAs should be taken into consideration as they can lead to erroneous classification of germline genotypes. We examined two separate breast cancer cohorts and observed frequent loss of heterozygosity at the CYP2D6 locus, which is a predictive marker of tamoxifen response. As result, when tumor tissue was used to determine germline CYP2D6 genotype, we observed departure from Hardy Weinberg equilibrium and misclassification of intermediate metabolizers (of tamoxifen) as either extensive or poor metabolizers. In summary, my work utilized multiple genomic data types to develop novel methods of analysis and data visualization to identify driver gene(s) within regions of DNA copy number change, which can and should be used to guide personalized treatment decisions. ! "#! To my loving parents and their many years of advice – “And this too shall pass” ! #! ACKNOWLEDGEMENTS I would like to thank: My advisor, Charles M. Perou The Perou Lab The Lineberger Bioinformatics Group Mouse Phase 1 Unit My committee members My Family: Lawrence, Moji, James, Emmanuel, Kristin, Daniel and Evan Silva Team Dynasty ! #"! PREFACE All scientific research is a team effort, and in that spirit I wish to acknowledge the contributions of others and give details concerning my specific contributions to the work discussed in each Chapter. Chapter 2 represents work that was recently accepted for publication in Breast Cancer Research and Treatment. I was the first author on this paper and was responsible for most aspects of this work. I performed the data analyses of gene expression and DNA copy number alterations, figure creation, and contributed to the writing of the manuscript. I would like to thank the following scientists for their collaborative help on this project: Conception and design: Joel S. Parker, Charles M. Perou Collection and assembly of data: Xiaping He, Lisa A. Carey, Jack P. Hou, Stacey L. Moulder, Paul K. Marcom, Jian Ma Provision of study materials or analytics tools: Victor Weigman, Andrey A. Shabalin, Joel S. Parker, Andrew Cherniack Analysis and interpretation of data: Jian Ma, Jack P. Hou, Charles M. Perou Manuscript writing: Michael L. Gatza, Jeffrey M. Rosen, Charles M. Perou Chapter 3 was previously published in Nature Genetics. I provided the analyses of the copy number data used to identify copy number alterations as a function of pathway activity and contributed to the writing of the manuscript. I would like to thank the following scientists for their collaborative help on this project: Conception and design: Michael L. Gatza, Joel S. Parker, Charles M. Perou ! #""! Conception and design: Michael L. Gatza, Joel S. Parker, Charles M. Perou Development of methodology: Michael L. Gatza, Joel S. Parker, Chris Fan, Charles M. Perou Acquisition of data: Michael L. Gatza Analysis of data: Michael L. Gatza, Chris Fan Manuscript writing: Michael L. Gatza, Charles M. Perou Chapter 4 was previously published in the Journal of National Cancer Institute. My role included data analyses of copy number alterations and loss of heterozygosity frequency for the gene of interest. I contributed to the writing of the manuscript and figure creation. I would like to thank the following scientists for their collaborative help on this project: Acquisition of data: Roman Yelensky, Mark J. Ratain Analysis and interpretation of data: Matthew P. Goetz, James X. Sun, Roman Yelensky, Charles M. Perou Manuscript writing: Matthew P. Goetz, James X. Sun, Vera J. Suman ! #"""! TABLE OF CONTENTS ! LIST OF TABLES...................................................................................................................... xii! LIST OF FIGURES................................................................................................................... xiii! LIST OF ABBREVIATIONS AND SYMBOLS..................................................................... xvi! INTRODUCTION .........................................................................................................................18! DNA Copy Number Alterations as Drivers of Carcinogenesis.................................................19! Molecular Intrinsic Subtypes of Breast Cancer.........................................................................22! Conservation Based Approach Using Genetically Engineered Mouse Models ...........................................................................................................................26! Research Introduction................................................................................................................29! FIGURES...................................................................................................................................31! REFERENCES ..........................................................................................................................32! CROSS-SPECIES DNA COPY NUMBER ANALYSES IDENTIFIES MULTIPLE 1q21–q23 SUBTYPE-SPECIFIC DRIVERS OF BREAST CANCER .......................................................................................................................................36! INTRODUCTION .....................................................................................................................38! MATERIALS AND METHODS ..............................................................................................39! RESULTS..................................................................................................................................40! Subtype-specific breast cancer copy number landscapes ......................................................40! Comparisons of copy number landscapes of mouse and human breast tumors..........................................................................................................................43! ! "$! Identification of Basal-like tumor chromosome 1 amplification driver genes............................................................................................................................44! Notch pathway features in 1q21-23 amplified Basal-like breast cancers ...................................................................................................................................46! DISCUSSION............................................................................................................................47! TABLES ....................................................................................................................................51! FIGURES...................................................................................................................................57! REFERENCES ..........................................................................................................................66! AN INTEGRATED GENOMICS APPROACH IDENTIFIES DRIVERS OF PROLIFERATION IN LUMINAL-SUBTYPE HUMAN BREAST CANCER.......................................................................................................................71! INTRODUCTION .....................................................................................................................72! MATERIALS AND METHODS ..............................................................................................73!
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