Comprehensive Funtional Mapping of ADPRylation sites on Gene Regulatory Targets of PARP1 [RNA-Seq]

Breast cancer molecular subtypes are based on distinct gene expression patterns. Recently, we described how subtype-specific transcription factors and their cognate enhancers drive the distinct gene expression patterns observed across breast cancer subtypes. As an extension of these studies, we employed a mass spectrometry-based proteomic approach to screen gene regulatory proteins for ADP-ribosylation (ADPRylation) across six breast cancer cell lines representing the luminal and triple-negative subtypes. Using an analog-sensitive PARP1- coupled with mass spectrometry approach, we have identified and catalogued the PARP1 ADPRylated proteome. We find that ADPRylation varies dramatically across the different subtypes of breast cancers. We hypothesize that ADPRylation of subtype-specific gene regulatory proteins dictates their function and may influence the response of breast cancer cells to PARP inhibitors. Using RNA-seq (T-47D and MDA-MB-468) and ChIP-seq (T-47D) with or without PARP inhibitor (Olaparib) we sought to understand how the ADPRylated proteome drives gene regulation and gene expression in breast cancer. We find that Olaparib treatment modulates the binding activity of certain transcription factors in a subtype-specific manner, thereby regulating the downstream gene expression.