Kunal Rai, Ph.D.

I am an Associate Professor of Genomic Medicine at MD Anderson Cancer Center. I also serve as Scientific Director of an epigenetics-focused translation research initiative at MDA, named MDACC Epigenomics Therapy Initiative (METI). My research is focused on understanding contribution of epigenome to cancer progression and identifying new venues for therapy and diagnostic tools. My lab utilizes cutting-edge epigenomic approaches to study chromatin state changes and higher order chromatin structure during evolution of tumor cells. Over last 20 years, I have developed expertise in studying epigenetic processes by identifying factors that perform epigenetic functions, identifying their roles in cellular events that regulate normal organ development and abnormal cell growth during tumorigenesis. The highlights of my current research include comprehensive understanding of chromatin state reprogramming during immunotherapy response (Under revision in Science Translation Medicine ), early stages of melanoma ( Cell Reports 2017 ), colon cancer progression ( Orouji et al, Gut 2021 ) and during metastasis ( Cell Reports 2021 ). We also identified major drivers of pre-malignant to malignant to metastatic transitions ( Cancer Discovery 2015; Nature Communications 2019; Cell Reports 2019 ). In addition, I co-led several studies with other investigators ( Cancer Cell, 2020; Acta Neuropathologica 2021; Nature Communications, 2019 & 2021; Journal of Clinical Investigation 2015; Stem Cell Reports 2017 ). Previously, as a trainee I defined a DNA-repair mediated DNA demethylation process ( Cell 2008 ), and discovered its role in colon cancer initiation ( Cell 2010 ). My PhD work deciphered roles of DNA and histone methyltransferases in early embryonic development ( MCB 2006, G&D 2007 and JBC 2010 ). We have systematically generated chromatin state maps into 9 other tumor types and have generated > 3000 ChIP-Seq datasets (usually undertaken by large consortium efforts) (Under revision in Nature Cell Biology ). These data have led to the discovery of several new concepts including a strategy to stratify patients based on their epigenomic content for specific therapies. We are also heavily invested in the single cell epigenomics ( PNAS, 2021 and Nature Communications 2021 ). Current research focus is on: 1) utilizing machine learning approaches to fully exploit cancer epigenomic data; 2) defining epigenetic aberrations at the single-cell resolution; 3) functionalizing ‘cancer-specific’ epigenetic elements using CRISPR-Cas9 based epigenetic editing approaches and 4) evaluating aberrations in higher-order chromatin structure. My lab is funded by NCI (three RO1s, two R21s, CEPs from 5 SPOREs), CPRIT (two IIRAs), ACS (RSG), private foundations (Melanoma Research Alliance and Melanoma Research Foundation), and MDA Moonshot (Prostate, Colorectal, Pancreatic). In addition, I have lead Epigenetics SPORE for MDA and Prostate Epigenetics PO1 applications.