Graduation Year

2018

Document Type

Dissertation

Degree

Ph.D.

Degree Name

Doctor of Philosophy (Ph.D.)

Degree Granting Department

Biology (Cell Biology, Microbiology, Molecular Biology)

Major Professor

Alvaro N.A. Monteiro, Ph.D.

Committee Member

W. Douglas Cress, Ph.D.

Committee Member

Jiandong Chen, Ph.D.

Committee Member

Kathleen M. Egan, Ph.D.

Committee Member

Kevin Brown, Ph.D.

Keywords

8q24 locus, GWAS, ovarian cancer, SNPs

Abstract

Ovarian cancer is a leading cause of death among women diagnosed with cancer. Mortality rate is high because an overwhelming majority of new cases are diagnosed with late-stage disease when the survival statistics are very poor with an overall 5-year survival rate of less than 40%. Despite the large burden of disease, the etiology of ovarian cancer is not well understood. In addition to linkage studies that have identified highly penetrant cancer susceptibility genes such as BRCA1 and BRCA2, the emergence of Genome Wide Association Studies (GWAS) in the last decade has facilitated the identification of common genetic variants with low to moderate penetrance, termed single nucleotide polymorphisms (SNPs). However, the vast majority of risk-associated SNPs are found in non-coding regions and their mechanistic basis underlying susceptibility to cancer remains widely unknown.

Functional analyses are critical in providing insight into the mechanism of action of these variants. In this study we have implemented bioinformatics methods, in silico tools, and cell culture models to interrogate functional effects of SNPs that predispose to cancer. Importantly, we have developed and adopted new techniques that have been instrumental in our functional studies.

GWAS have identified forty chromosomal loci associated with susceptibility to ovarian cancer. In this study we present a comprehensive fine mapping and functional analysis of the 8q24.21 ovarian cancer susceptibility locus to establish biological mechanisms underlying disease susceptibility. This locus was initially identified in a previous study, which discovered this region to be association with ovarian cancer. This follow-up work serves to replicate and confirm the initial findings and, most importantly, to investigate the biological mechanisms underpinning the association with ovarian cancer at the 8q24.21 chromosomal region.

The 8q24.21 locus is characterized as a gene desert, which interestingly is also associated with various cancer types including prostate, colorectal, breast and urinary bladder cancer. Following the signal of association with fine mapping and functional assays, we identify eight putative causal SNPs, which reside within two distinct enhancer elements, displaying allele-specific activity in ovarian cells. Long-range physical interactions with the promoter region of the MYC oncogene, and to a lesser extent, the non-coding RNA, PVT1, establish these two genes as the targets of the enhancer elements containing the putative causal SNPs. We present evidence that the ATF1 transcription factor binds exclusively to the minor allele of variant rs2165806. Additionally, we report a comparative analysis testing the cell-type specific activity of different enhancer regions in breast, prostate, colorectal and ovarian cell lines. In summary, this work highlights the regulatory landscape at the 8q24.21 locus and provides a mechanistic basis to understand susceptibility to ovarian cancer in this region.

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