Cancer is considered to be a genetic disease characterized by sequential accumulation of mutations. Recent studies have provided evidence that epigenetic changes and regulatory sequence mutations could also dysregulate oncogenes and tumor suppressors. As a transcription factor, P53 is activated in response to oncogenic stress and exerts distinct anti-proliferative functions based on the stressor and cell type. Though a number of ChIP-Seq studies have identified thousands of P53 binding sites in mammalian genomes, the functionality of these binding sites remains to be established. In addition, we know little about what controls stress and cell context specific binding profile of P53.

Traditionally, mutations in the coding regions of p53 have been extensively studied to gain insights on its role in cancer and to identify strategies to restore the functions of p53 in cancer cells. We hypothesize that mutations in or epigenetic silencing of functionally important P53 binding sites play an important role in tumorigenesis as well. Since functional regulatory regions tend to be more evolutionarily conserved, in this project we propose using a comparative genomics approach to identify functional P53 binding sites and determine if these regions are involved in tumorigenesis.

In order to study how P53 binding following DNA damage differs between cell types, we aim to perform comparison between P53 ChIP-Seq data generated in our lab from Drosophila embryos at different developmental stages and a cell line (Kc167) as well as published datasets from mammalian stem cells and differentiated cells. Differential expression analysis using RNA-Seq exhibited that at an early stem cell-like stage there is P53-dependent induction of pro-apoptotic genes in response to DNA damage but not in the differentiated stages. We are seeking to establish functionally significant P53 binding sites by combining ChIP-Seq data and gene expression data obtained using RNA-Seq. The importance of these binding sites will be verified by CRISPR-Cas9 -mediated genome editing. We will also perform comparison studies of DNA damage-induced P53 binding in human, mouse and Drosophila to identify analogous patterns.

Knowledge gained from this study will help us to understand the role of non-coding regulatory regions in tumorigenesis, and predict patient response to apoptosis inducing therapeutic agents. It may also lead to novel strategies to restore cellular sensitivity to chemotherapy or radiation.

Citation Format: Varsha Sundaresan, Ying Li, Benedetto DiCiaccio, Victor T. Lin, Lei Zhou. A comparative genomics approach to understanding the control of cell context dependent P53 binding [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 391. doi:10.1158/1538-7445.AM2017-391