Ovarian cancer is the most lethal gynecological malignancy. Although majority of the cancer cases are initially sensitive to platinum-based chemotherapy, most patients eventually develop recurrence and succumb to chemoresistant disease. Our lack of understanding of the key drivers that lead to the resistant state poses a critical roadblock that impedes therapeutic progress in the field. The long-term goal of our research is to understand the chromatin and transcriptional regulatory networks that allow cells to adapt to new environmental or developmental cues. The overall objective of this study, which is the next step toward attainment of our long-term goal, is to identify the major regulatory networks that allow ovarian cancer cells to survive chemotherapy. This knowledge will identify improved and effective therapeutics options. To achieve this, we started with epigenome mapping and transcriptome analysis of an in vitro system in which we employed chemonave, chemoresistant, and resensitized isogenic cells. Integrative analysis of expression profiles (RNA-Seq) and epigenomic features of promoter and enhancer elements (H3K27ac ChIP-Seq), identified large number of typical enhancers and a subset of ?super enhancers? that are specifically activated in resistant cells. Notably, pharmacological disruption of super enhancers by a small molecule epigenetic inhibitor confers cisplatin sensitivity to previously resistant cells in vitro and inhibits in vivo tumor growth in a xenograft model of resistant cells. Super enhancers tend to regulate the expression of master regulators of a given cellular state (1, 2). Among the top target genes of the resistant specific super enhancers (RSSE) were multiple transcription factors, whose depletion with CRISPR mediated knock significantly sensitized the resistant cells to chemotherapy. These preliminary data led to the central hypothesis that aberrant transcriptional program in chemoresistant cells is driven by a set of genes whose expression is regulated by distal enhancers that can be pharmacologically targeted. This proposal will determine the therapeutic efficacy of enhancer targeting to overcome chemoresistance (Aim 1), identify the in vivo dynamics of chemotherapy-induced aberrant enhancer activation (Aim 2), and delineate the core TFs that drives the chemoresistance process (Aim 3). The rationale is to identify and target the major drivers of chemoresistant cellular state genetically, epigenetically, and pharmacologically. The results will allow us to better understand the biology of chemoresistance, and enable development of new and innovative treatment approaches that are applicable to other cancers.
The overall goal of our research has focused on understanding the genetic and epigenetic basis of chemo-resistance in ovarian cancer. Ovarian cancer is associated with the worst survival of all gynecological cancers. Although the vast majority of ovarian cancers are initially chemo-sensitive, with a 70-80% response rate, the recurrence and progression due to chemo-resistance is nearly ubiquitous. Identifying the key drivers of chemo-resistance, which is the single major cause of high mortality rate of this disease, remains a major gap in our knowledge. Our in preliminary results support the hypothesis that aberrant regulation at distal regulatory sites in the genome called enhancers drive the expression of key genes that mediate chemo resistance in ovarian cancer. In this proposal, we will use clinically relevant in vivo models to assess a novel therapeutic approach to target and inhibit the acquired chemoresistance and get mechanistic understanding on the role of chemotherapy induced aberrant gene expression in driving chemoresistance in high grade serous ovarian cancer.
|Szlachta, Karol; Kuscu, Cem; Tufan, Turan et al. (2018) CRISPR knockout screening identifies combinatorial drug targets in pancreatic cancer and models cellular drug response. Nat Commun 9:4275|
|Adli, Mazhar (2018) The CRISPR tool kit for genome editing and beyond. Nat Commun 9:1911|
|Yang, Jiekun; Wei, Xiaolong; Tufan, Turan et al. (2018) Recurrent mutations at estrogen receptor binding sites alter chromatin topology and distal gene expression in breast cancer. Genome Biol 19:190|