Single cell chromatin profiling to study epigenetic alterations of ovarian tumors
An understanding of how epigenetic changes rewire the regulatory network of cancer cells would facilitate the development of new therapeutic strategies. However, tumor heterogeneity hinders the study of epigenetic landscapes in cancer. I propose to leverage a new single-cell genome profiling technology I recently developed to map epigenetic changes in single cells, allowing me to characterize different cell populations within ovarian tumors, including cancer stem cells (CSCs) and more differentiated cell types. These studies will uncover how the epigenome is re-wired upon inhibition of epigenetic enzymes implicated in multiple cancers. EZH2 is a histone methyltransferase that is often overexpressed in different types of cancer, including ovarian cancer, and inhibition of EZH2 has been shown to strongly reduce the aggressiveness of tumors by impairing metastasis, reducing invasiveness, and promoting differentiation. Yet, how EZH2 overexpression alters the repressive histone mark, H3K27me3 in each tumor cell type remains unknown. I propose three Aims, the first of which will use a combination of single cell Multi-CUT&Tag—a single cell profiling technology I recently developed—and scRNA-seq to characterize the epigenomic landscapes in each ovarian cancer cell type. In Aim 2, I will examine how perturbation of EZH2 alters the epigenetic architecture of tumor sub-populations, including CSCs, and identify how EZH2 promotes CSC self-renewal and tumor progression. Finally, in Aim 3, I will uncover the roles of genes and pathways subjected to epigenomic remodeling, in order to identify potential weaknesses that can be exploited therapeutically. Successful completion of these studies will provide considerable insight into the epigenetic regulation of CSCs in ovarian cancers and candidates for new therapies for ovarian cancer treatment. In addition, these studies will provide extensive training in tumor biology and single cell bioinformatics, which will be essential for my goal of running an independent group focused on tumor epigenetics.
