Integrative Analysis of Epigenomics and Transcriptomics: Identifying Genes Necessary for Chemoresistance

Given the increasing longevity of the average individual, cancer is becoming more ubiquitous as the cause of death in the aging world. Due to the combinations of advances in cancer awareness, early detection, and treatment options, the relative rates of new cancer cases and deaths are steadily decreasing(1). Despite this steady decrease, ovarian cancers are still the deadliest gynecological malignancies for women. This is largely due to tumors becoming therapy resistant, allowing the tumors to metastasize and eventually overcome the body. Therefore, it is necessary to find approaches towards discovering mechanisms for chemoresistance in an effort to find different ways to specifically target these chemoresistant cells against proliferation. Towards this end, much research has been performed to identify the mechanisms in which cells are surviving against the common therapy agents, such as cisplatin.

Cisplatin is one of the first chemotherapeutic agents discovered to have effectiveness against cancers, and is a platinum-based drug that utilizes intrastrand crosslinks, among others, to kill tumor cells. Despite many advances in developing novel chemotherapy agents, currently most high-grade ovarian cancer patients receive a combination treatment involving a platinum-based drug. Without total clearance of the tumors, which is rare, the tumors will inevitably stop responding to chemotherapy, and develop platinum resistance. In an effort to develop new therapies to overcome this resistance, a plethora of research has elucidated many platinum resistance mechanisms. Nevertheless, platinum resistance remains a problem and continues to kill many women today.

In our study, we have attempted to address this issue by performing the first integrative analysis of transcriptomics and enhancer epigenomics over multiple ovarian cancer models. By repeatedly treating many different ovarian cancer cell lines with progressively increasing doses of cisplatin, we have generated multiple resistant counterpart cell lines, resulting in at least 5 naïve-resistant cell line pairs. By analyzing the sequencing of chromatin immunoprecipitation (ChIP) experiments against H3K27ac, a chemical histone modification enriched at active enhancers and promoters, we identified unique sets of enhancers and superenhancers (SEs) for these models. We integrated this data with RNA-seq to identify a unique set of consensus superenhancer-associated gene targets that are upregulated during chemoresistance. Small molecule epigenetic inhibitors targeting enhancers inhibited the expression of these gene targets, restoring cisplatin sensitivity in vitro and in vivo. Through Cas9-mediated deletion, we have also validated the consensus gene target SOX9 as being a master regulator of chemoresistance necessary for the maintenance of chemoresistance, suggesting that proper maintenance of resistance associated SEs (RSSEs), and their associated targets may be necessary for the maintenance chemoresistance. This thesis will attempt to outline the many strategies and considerations used to identify mechanisms of chemoresistance, focusing on integrative analysis approaches.

The evidences and conclusions presented here represent the products of the insights and information gathered by Stephen Shang on or before Sept 19, 2019. I thank the University of Virginia, my friends, family, and colleagues for the production of this work. I hope that this document may mark the beginning of a prolific career geared towards the benefit of all humankind.