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MECHANISMS of TUMORIGENESIS in AFRICAN AMERICAN COLORECTAL CANCER by Gaius J. Augustus

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MECHANISMS of TUMORIGENESIS in AFRICAN AMERICAN COLORECTAL CANCER by Gaius J. Augustus Mechanisms of Tumorigenesis in African American Colorectal Cancer Item Type text; Electronic Dissertation Authors Augustus, Gaius Julian Publisher The University of Arizona. Rights Copyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction, presentation (such as public display or performance) of protected items is prohibited except with permission of the author. Download date 27/09/2021 11:20:21 Link to Item http://hdl.handle.net/10150/633006 MECHANISMS OF TUMORIGENESIS IN AFRICAN AMERICAN COLORECTAL CANCER by Gaius J. Augustus __________________________ Copyright © Gaius J. Augustus 2019 A Dissertation Submitted to the Faculty of the GRADUATE INTERDISCIPLINARY PROGRAM IN CANCER BIOLOGY In Partial Fulfillment of the Requirements For the Degree of DOCTOR OF PHILOSOPHY In the Graduate College THE UNIVERSITY OF ARIZONA 2019 Mechanisms of Tumorigenesis in African American CRC 2 Mechanisms of Tumorigenesis in African American CRC Acknowledgements This work was supported by grants from the National Cancer Institute (U01 CA153060 and P30 CA023074, NAE; RO1 CA204808, HRG, EM, LTH; RO1 CA141057, BJ) and the American Cancer Society Illinois Division (223187, XL). GJA was supported by a Cancer Biology Training Grant (T32CA009213). The funders had no role in the design of the study; the collection, analysis, or interpretation of the data; the writing of the manuscript; or the decision to submit the manuscript for publication. The author gratefully acknowledges the recruiters of the CCCC for their dedication and integrity, including Maggie Moran, Timothy Carroll, Katy Ceryes, Amy Disharoon, Archana Krishnan, Katie Morrissey, Maureen Regan, and Katya Seligman. Zarema Arbieva and the University of Illinois at Chicago Genomics Core in the Research Resources Core performed the hybridization and initial analysis of CytoScan HD arrays. The author additionally thanks Mary Yagle and Johnathan Blohm for their assistance in SNP genotyping. 3 Mechanisms of Tumorigenesis in African American CRC Dedication I dedicate this work to DiAngele Augustus, without whom none of my success would be possible. 4 Mechanisms of Tumorigenesis in African American CRC Table of Contents ABSTRACT 8 CHAPTER 1 - COLORECTAL CANCER DISPARITY IN AFRICAN AMERICANS: RISK FACTORS AND CARCINOGENIC MECHANISMS 9 ABSTRACT 10 INTRODUCTION 11 IMPACT OF RISK FACTORS ON CRC INCIDENCE 11 ENDOSCOPIC SCREENING REDUCES CANCER INCIDENCE 11 GENETIC RISK FACTORS AND CRC INCIDENCE 15 CAN VITAMIN D LEVELS EXPLAIN DIFFERENCES IN CRC INCIDENCE IN AFRICAN AMERICANS? 24 DIETARY INFLUENCES ON CRC AND THE GUT MICROBIOME 26 ARE CARCINOGENIC MECHANISMS DIFFERENT IN AFRICAN AMERICAN CRC? 29 SIMILAR FREQUENCIES OF MICROSATELLITE INSTABILITY 30 SOMATIC MUTATIONS IN AFRICAN AMERICAN CRC 31 EPIGENETIC CHANGES IN AFRICAN AMERICAN CRC 34 CRC-SPECIFIC GENE DYSREGULATION 38 THE CONTINUING PROBLEM OF CRC MORTALITY IN AFRICAN AMERICANS 39 CHAPTER 2 - IS INCREASED COLORECTAL SCREENING EFFECTIVE IN PREVENTING DISTANT DISEASE? 42 ABSTRACT 43 INTRODUCTION 45 MATERIALS AND METHODS 46 DATA ACQUISITION 46 STATISTICAL ANALYSES 48 AVAILABILITY OF DATA AND MATERIAL 48 RESULTS 49 DECREASE IN INCIDENCE RATE OF DISTANT CRC IS SLOWER THAN THE DECREASE IN INCIDENCE RATES OF LOCALIZED AND REGIONAL CRC 49 DECREASE IN INCIDENCE RATE OF DISTANT CRC IS SLOWER IN PATIENTS DIAGNOSED WITH CRC AT 50 OR MORE YEARS OF AGE 54 DECREASE IN INCIDENCE RATE OF DISTANT CRC IS SLOWER FOR BOTH PROXIMAL AND DISTAL CRCS 56 DECREASE IN INCIDENCE RATE OF DISTANT CRC IS SLOWER FOR MOST ETHNIC GROUPS 57 DECREASE IN INCIDENCE RATE OF DISTANT CRC IS SLOWER IN BOTH MALES AND FEMALES 57 DISCUSSION 58 INADEQUATE SCREENING DOES NOT EXPLAIN THE SLOW DECREASE IN INCIDENCE OF DISTANT CRC 60 MORE RAPIDLY ADVANCING CANCERS OF THE SERRATED ADENOMA PATHWAY CAN ONLY EXPLAIN PART OF THE SLOW DECREASE IN INCIDENCE OF DISTANT CRC 61 HYPOTHESIS OF NONMSI CRC THAT ADVANCES RAPIDLY 62 LIMITATIONS AND ALTERNATIVE THEORIES 64 5 Mechanisms of Tumorigenesis in African American CRC CHAPTER 3 - RACE-DEPENDENT ASSOCIATION OF SULFIDOGENIC BACTERIA WITH COLORECTAL CANCER 66 ABSTRACT 67 ABBREVIATIONS 69 INTRODUCTION 70 MATERIALS AND METHODS 71 HUMAN SUBJECTS 71 QUANTITATIVE POLYMERASE CHAIN REACTION (QPCR) ANALYSIS 72 STATISTICAL ANALYSIS 75 ANALYSIS OF DIETARY INTAKE 75 RESULTS 76 RACE-SPECIFIC DIFFERENCES IN MUCOSAL SULFIDOGENIC BACTERIA 76 ASSOCIATIONS BETWEEN DIET AND SULFIDOGENIC BACTERIA 81 DISCUSSION 92 CHAPTER 4 - LACK OF APC SOMATIC MUTATION IS ASSOCIATED WITH EARLY-ONSET COLORECTAL CANCER IN AFRICAN AMERICANS 96 ABSTRACT 97 INTRODUCTION 99 MATERIALS AND METHODS 100 ASCERTAINMENT, RECRUITMENT, AND BIOSPECIMEN COLLECTION 100 DNA SEQUENCE ANALYSIS 101 COPY NUMBER ANALYSIS 102 METHYLATION ANALYSIS 103 STATISTICAL ANALYSIS 103 RESULTS 104 APC MUTATION-NEGATIVE TUMORS ARE ASSOCIATED WITH EARLY-ONSET CRC 115 UNDER-REPRESENTATION OF KNOWN DRIVER GENES IN AFRICAN AMERICAN CRCS 119 COPY NUMBER VARIATION IN AFRICAN AMERICAN CRCS 123 METHYLATION PATTERNS IN APC MUTATION-NEGATIVE VS. MUTATION-POSITIVE TUMORS 127 DISCUSSION 134 CHAPTER 5 - DECREASED COPY-NEUTRAL LOSS OF HETEROZYGOSITY IN AFRICAN AMERICAN COLORECTAL CANCERS 139 ABSTRACT 140 INTRODUCTION 142 METHODS 146 DATA ACQUISITION 146 DATA PROCESSING 147 SMALL INTERSTITIAL CNLOH ANALYSIS 149 STATISTICAL ANALYSES 151 RESULTS 153 AFRICAN AMERICANS AND WHITES HAVE SIMILAR FREQUENCIES OF COPY NUMBER GAINS AND LOSSES 153 6 Mechanisms of Tumorigenesis in African American CRC WHITE CRCS HAVE A HIGHER FREQUENCY OF CNLOH THAN AFRICAN AMERICAN CRCS FOR MOST CHROMOSOME ARMS 153 WHITE CRCS HAVE MORE CHROMOSOME ARMS AFFECTED BY CNLOH THAN AFRICAN AMERICAN CRCS AFTER ADJUSTMENT FOR COVARIATES 162 SMALL INTERSTITIAL COPY-NEUTRAL LOSS OF HETEROZYGOSITY (SI-CNLOH) 166 DISCUSSION 180 CONCLUSIONS 186 CHAPTER 6 - IMPLICATIONS AND FUTURE DIRECTIONS FOR AFRICAN AMERICAN COLORECTAL CANCER 187 INTRODUCTION 188 SUSCEPTIBILITY 189 TUMORIGENESIS 190 LIMITATIONS AND FUTURE DIRECTIONS 191 APPENDIX A 192 APPENDIX B 193 APPENDIX C 194 APPENDIX D 202 REFERENCES 207 7 Mechanisms of Tumorigenesis in African American CRC Abstract While colorectal cancer (CRC) incidence has decreased over the past 20 years, the reduction in incidence has not been uniform across all stages of disease. The reduction in late stage (distant) CRC was significantly less than that of than earlier stage CRC, a trend enriched for early-onset CRCs. African Americans have the highest incidence and mortality rates of CRC of any ethnic group in the United States and are more likely to present before recommended guidelines for screening (i.e., age of 50 years). Despite this ongoing health disparity, relatively few studies have sought to address risk factors and etiological signatures unique to African American CRC. We hypothesized that molecular characteristics in the gut microenvironment and tumor mutation profiles of African American CRCs are unique. The studies presented here sought to address this hypothesis through molecular studies in a low-income cohort from urban Chicago, the Chicago Colorectal Cancer Consortium, as well as a publicly available cohort, The Cancer Genome Atlas. We found that African Americans have higher abundances of the sulfidogenic bacterium Bilophila wadsworthia, a trend that remained after adjusting for covariates including diet. African American cases had significantly higher abundances than African American controls, a trend that did not exist in non-Hispanic Whites. We found that African American CRCs had molecular features that were distinct from non- Hispanic Whites. CCCC African American CRCs had significantly fewer mutations than expected in APC, a gene typically mutated in 80% of CRCs, and that the lack of APC mutation was associated with younger age, chromosome stability, and a non-CIMP DNA methylation profile. Together, the findings presented here suggest that unknown risk factors and unique tumorigenic processes drive CRC in African Americans. 8 Mechanisms of Tumorigenesis in African American CRC Chapter 1 Colorectal Cancer Disparity in African Americans: Risk Factors and Carcinogenic Mechanisms Originally published in the American Journal of Pathology (Permissions can be found in Appendix A) Augustus GJ, Ellis NA. Colorectal Cancer Disparity in African Americans: Risk Factors and Carcinogenic Mechanisms. Am J Pathol. 2018;188(2):291-303. doi:10.1016/J.AJPATH.2017.07.023 9 Mechanisms of Tumorigenesis in African American CRC Chapter 1 Abstract African Americans have the highest incidence and mortality rates of colorectal cancer (CRC) of any ethnic group in the United States. Although some of these disparities can be explained by differences in access to care, cancer screening, and other socioeconomic factors, disparities remain after adjustment for these factors. Consequently, an examination of recent advances in the understanding of ethnicity-specific factors, including genetic and environmental factors relating to risk of CRC, the biology of CRC progression, and the changes in screening and mortality, is important for evaluating our progress toward eliminating the disparities. An overarching limitation in this field is the number and sample size of studies performed to characterize the etiological bases of CRC incidence and mortality in African Americans. Despite this limitation, significant differences in etiology are manifest in many studies. These differences need validation, and their impacts on disparities need more detailed investigation.
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