Kunal Rai, Ph.D.
Department of Genomic Medicine, Division of Cancer Medicine
About Dr. Rai
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 Nature Communications ), melanoma progression ( Cell Reports 2017 and Cell Reports 2021 ), colon cancer progression ( Gut 2022) , head and neck cancer ( Frontiers in Cell and Developmental Biology 2022 ) and rare diseases including DSRCT ( Nature Communications, 2022 ), liposarcoma ( Journal of Clinical Investigation 2015 ), MPNST ( Acta Neuropathologica 2021) . We also identified major epigenetic drivers of in melanoma ( Cancer Discovery 2015), triple negative breast cancer (Nature Communications 2019); Cell Reports 2019 ) and stem cell differentiation ( Stem Cell Reports 2017) . Importantly, we have made significant contribution in the mechanistic biology and therapeutic opportunities in KMT2D-mutant cancers ( Cancer Cell, 2020, Cell Reports 2020, Nature Communications 2018 and biorxiv 2021). 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 am the leader of the Epigenetics SPORE for MDA.
Present Title & Affiliation
Primary Appointment
Adjunct Associate Professor, Department of Bioengineeering, Division of Cancer Medicine, Rice University, Houston, Texas
Scientific Director, Department of MDACC Epigenomics Therapy Initiative, The University of Texas MD Anderson Cancer Center, Houston, TX
Associate Professor, Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
Dual/Joint/Adjunct Appointment
Associate Professor, Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
Education & Training
Degree-Granting Education
| 2006 | University of Utah, Salt Lake City, Utah, US, Cancer Biology, Ph.D |
| 2002 | Indian Institute of Technology, Kharagpur, IN, Biotechnology and Biochemical Engineering, B.Tech |
Postgraduate Training
| 2010-2011 | Research Fellowship, Cancer Epigenetics, Harvard University, Boston, Massachusetts |
| 2007-2009 | Research Fellowship, Cancer Epigenetics, University of Utah, Salt Lake City, Utah |
Experience & Service
Academic Appointments
Assistant Professor, Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 2014 - 2020
Instructor, Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 2011 - 2014
Instructor, Harvard Medical School, Boston, MA, 2011 - 2011
Administrative Appointments/Responsibilities
Scientific Director, Department of MDACC Epigenomics Therapy Initiative, The University of Texas MD Anderson Cancer Center, Houston, TX, 2020 - Present
Other Appointments/Responsibilities
Founder, Koshika Therapeutics, 2024 - Present
Scientific Advisory Board member, Valemetostat US Academic Immunotherapy Advisory Board, Daiichi Sankyo, 2024 - Present
Founder and Consultant, Jivanu Therapeutics, Mumbai, Maharashthra, 2024 - Present
Institutional Committee Activities
Member, EMC Chair Search Committee, 2024 - 2024
Member, MCO Chair Search Committee, 2023 - 2024
Member, Graduate Education Committee, 2023 - Present
Ad hoc member, Research Integrity Committee, 2023 - Present
Departmental Representative, Faculty Senate, 2022 - Present
member, REACT, 2021 - Present
Departmental Representative, Faculty Senate, 2016 - 2018
Honors & Awards
| Summer Fellowship, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India | |
| Graduate Fellowship, University of Utah | |
| Potu N Rao Excellence in Basic Science, MD Anderson Cancer Center | |
| Young Alumni Achiever Award for the Year 2023, Indian Institute of Technology |
Professional Memberships
Selected Publications
Peer-Reviewed Articles
- Tomczak K, Patel MS, Bhalla AD, Peterson CB, Landers SM, Callahan SC, Zhang D, Wong J, Landry JP, Lazar AJ, Livingston JA, Guadagnolo BA, Lyu HG, Lillemoe H, Roland CL, Keung EZ, Scally CP, Hunt KK, McCutcheon IE, Slopis JM, Gu J, Scheet P, Wang L, Rai K, Torres KE. Plasma DNA Methylation-Based Biomarkers for MPNST Detection in Patients With Neurofibromatosis Type 1. Mol Carcinog 64(1):44-56, 2024. PMID: 39600120.
- Lee HM, Saw AK, Morris VK, Napolitano S, Bristow C, Srinivasan S, Peoples M, Sorokin A, Kanikarla Marie P, Schulz J, Singh AK, Terranova C, Coker O, Jain A, Kopetz S, Rai K. Epigenome Reprogramming Through H3K27 and H3K4 Trimethylation as a Resistance Mechanism to DNA Methylation Inhibition in BRAFV600E-Mutated Colorectal Cancer. Clin Cancer Res 30(22):5166-5179, 2024. PMID: 39269307.
- Citron F, Ho IL, Balestrieri C, Liu Z, Yen EY, Cecchetto L, Perelli L, Zhang L, Montanez LC, Blazanin N, Dyke CA, Shah R, Attanasio S, Srinivasan S, Chen KC, Chen Z, Scognamiglio I, Pham N, Khan H, Jiang S, Pan J, Vanderkruk B, Leung CS, Mattohti M, Rai K, Chu Y, Wang L, Gao S, Deem AK, Carugo A, Wang H, Yao W, Tonon G, Xiong Y, Lorenzi PL, Bonini C, Anna Zal M, Hoffman BG, Heffernan T, Giuliani V, Jeter CR, Lissanu Y, Genovese G, Pilato MD, Viale A, Draetta GF. WRAD core perturbation impairs DNA replication fidelity promoting immunoediting in pancreatic cancer. bioRxiv None(None):None, 2024. PMID: 39484624.
- Folkert IW, Molina Arocho WA, To TKJ, Devalaraja S, Molina IS, Shoush J, Mohei H, Zhai L, Akhtar MN, Kochat V, Arslan E, Lazar AJ, Wani K, Israel WP, Zhang Z, Chaluvadi VS, Norgard RJ, Liu Y, Fuller AM, Dang MT, Roses RE, Karakousis GC, Miura JT, Fraker DL, Eisinger-Mathason TSK, Simon MC, Weber K, Tan K, Fan Y, Rai K, Haldar M. An iron-rich subset of macrophages promotes tumor growth through a Bach1-Ednrb axis. J Exp Med 221(10):None, 2024. PMID: 39347789.
- Kumar B, Singh A, Basar R, Uprety N, Li Y, Fan H, Cortes AKN, Kaplan M, Acharya S, Shaim H, Xu AC, Wu M, Ensley E, Fang D, Banerjee PP, Garcia LM, Tiberti S, Lin P, Rafei H, Munir MN, Moore M, Shanley M, Mendt M, Kerbauy LN, Liu B, Biederstadt A, Gokdemir E, Ghosh S, Kundu K, Reyes-Silva F, Jiang XR, Wan X, Gilbert AL, Dede M, Mohanty V, Dou J, Zhang P, Liu E, Muniz-Feliciano L, Deyter GM, Jain AK, Rodriguez-Sevilla JJ, Colla S, Garcia-Manero G, Shpall EJ, Chen K, Abbas HA, Rai K, Rezvani K, Daher M. BATF is a major driver of NK cell epigenetic reprogramming and dysfunction in AML. Sci Transl Med 16(764):eadp0004, 2024. PMID: 39259809.
- Jin Y, Miyama T, Brown A, Hayase T, Song X, Singh AK, Huang L, Flores II, McDaniel LK, Glover I, Halsey TM, Prasad R, Chapa V, Ahmed S, Zhang J, Rai K, Peterson CB, Lizee G, Karmouch J, Hayase E, Molldrem JJ, Chang CC, Tsai WB, Jenq RR. Tsyn-Seq: a T-cell Synapse-Based Antigen Identification Platform. Cancer Immunol Res 12(5):530-543, 2024. PMID: 38363296.
- Qin K, Wang K, Li S, Hong L, Padmakumar P, Waree R, Hubert SM, Le X, Vokes N, Rai K, Vaporciyan A, Gibbons DL, Heymach JV, Lee JJ, Woodman SE, Chung C, Jaffray DA, Altan M, Lou Y, Zhang J. Clinical Benefit from Docetaxel +/- Ramucirumab Is Not Associated with Mutation Status in Metastatic Non-Small-Cell Lung Cancer Patients Who Progressed on Platinum Doublets and Immunotherapy. Cancers (Basel) 16(5), 2024. e-Pub 2024. PMID: 38473297.
- Malgulwar PB, Danussi C, Dharmaiah S, Johnson W, Singh A, Rai K, Rao A, Huse JT. Sirtuin 2 inhibition modulates chromatin landscapes genome-wide to induce senescence in ATRX-deficient malignant glioma. Neuro Oncol 26(1):55-67, 2024. e-Pub 2023. PMID: 37625115.
- Fan H, Wang F, Zeng A, Murison A, Tomczak K, Hao D, Jelloul FZ, Wang B, Barrodia P, Liang S, Chen K, Wang L, Zhao Z, Rai K, Jain AK, Dick J, Daver N, Futreal A, Abbas HA. Single-cell chromatin accessibility profiling of acute myeloid leukemia reveals heterogeneous lineage composition upon therapy-resistance. Commun Biol 6(1):765, 2023. e-Pub 2023. PMID: 37479893.
- Osman AA, Arslan E, Bartels M, Michikawa C, Lindemann A, Tomczak K, Yu W, Sandulache V, Ma W, Shen L, Wang J, Singh AK, Frederick MJ, Spencer ND, Kovacs J, Heffernan T, Symmans WF, Rai K, Myers JN. Dysregulation and epigenetic reprogramming of NRF2 signaling axis promote acquisition of cisplatin resistance and metastasis in Head and Neck Squamous Cell Carcinoma. Clin Cancer Res 29(7):1344-1359, 2023. e-Pub 2023. PMID: 36689560.
- Jiang VC, Hao D, Jain P, Li Y, Cai Q, Yao Y, Nie L, Liu Y, Jin J, Wang W, Lee HH, Che Y, Dai E, Han G, Wang R, Rai K, Futreal A, Flowers C, Wang L, Wang M. TIGIT is the central player in T-cell suppression associated with CAR T-cell relapse in mantle cell lymphoma. Mol Cancer 21(1):185, 2022. e-Pub 2022. PMID: 36163179.
- Andrews MC, Oba J, Wu CJ, Zhu H, Karpinets T, Creasy CA, Forget MA, Yu X, Song X, Mao X, Robertson AG, Romano G, Li P, Burton EM, Lu Y, Sloane RS, Wani KM, Rai K, Lazar AJ, Haydu LE, Bustos MA, Shen J, Chen Y, Morgan MB, Wargo JA, Kwong LN, Haymaker CL, Grimm EA, Hwu P, Hoon DSB, Zhang J, Gershenwald JE, Davies MA, Futreal PA, Bernatchez C, Woodman SE. Multi-modal molecular programs regulate melanoma cell state. Nat Commun 13(1):4000, 2022. e-Pub 2022. PMID: 35810190.
- Lamhamedi-Cherradi SE, Maitituoheti M, Menegaz BA, Krishnan S, Vetter AM, Camacho P, Wu CC, Beird HC, Porter RW, Ingram DR, Ramamoorthy V, Mohiuddin S, McCall D, Truong DD, Cuglievan B, Futreal PA, Velasco AR, Anvar NE, Utama B, Titus M, Lazar AJ, Wang WL, Rodriguez-Aguayo C, Ratan R, Livingston JA, Rai K, MacLeod AR, Daw NC, Hayes-Jordan A, Ludwig JA. The androgen receptor is a therapeutic target in desmoplastic small round cell sarcoma. Nat Commun 13(1):3057, 2022. e-Pub 2022. PMID: 35650195.
- Zamler DB, Shingu T, Kahn LM, Huntoon K, Kassab C, Ott M, Tomczak K, Liu J, Li Y, Lai I, Zorilla-Veloz R, Yee C, Rai K, Kim BY, Watowich SS, Heimberger AB, Draetta GF, Hu J. Immune landscape of a genetically engineered murine model of glioma compared with human glioma. JCI Insight 7(12), 2022. e-Pub 2022. PMID: 35653194.
- Bhalla AD, Landers SM, Singh AK, Landry JP, Yeagley MG, Myerson GSB, Delgado-Baez CB, Dunnand S, Nguyen T, Ma X, Bolshakov S, Menegaz BA, Lamhamedi-Cherradi SE, Mao X, Song X, Lazar AJ, McCutcheon IE, Slopis JM, Ludwig JA, Lev DC, Rai K, Torres KE. Experimental models of undifferentiated pleomorphic sarcoma and malignant peripheral nerve sheath tumor. Lab Invest 102(6):658-666, 2022. e-Pub 2022. PMID: 35228656.
- Orouji E, Raman AT, Singh AK, Sorokin A, Arslan E, Ghosh AK, Schulz J, Terranova C, Jiang S, Tang M, Maitituoheti M, Callahan SC, Barrodia P, Tomczak K, Jiang Y, Jiang Z, Davis JS, Ghosh S, Lee HM, Reyes-Uribe L, Chang K, Liu Y, Chen H, Azhdarinia A, Morris J, Vilar E, Carmon KS, Kopetz SE, Rai K. Chromatin State Dynamics Confers Specific Therapeutic Strategies in Enhancer Subtypes of Colorectal Cancer. Gut 71(5):938-949, 2022. e-Pub 2021. PMID: 34059508.
- Singh S, Roszik J, Saini N, Singh VK, Bavisi K, Wang Z, Vien LT, Yang Z, Kundu S, Davis RE, Bover L, Diab A, Neelapu SS, Overwijk WW, Rai K, Singh M. B Cells Are Required to Generate Optimal Anti-Melanoma Immunity in Response to Checkpoint Blockade. Front Immunol 13:794684, 2022. e-Pub 2022. PMID: 35720386.
- Callahan SC, Kochat V, Liu Z, Raman AT, Divenko M, Schulz J, Terranova CJ, Ghosh AK, Tang M, Johnson FM, Wang J, Skinner HD, Pickering CR, Myers JN, Rai K. High enhancer activity is an epigenetic feature of HPV negative atypical head and neck squamous cell carcinoma. Front Cell Dev Biol 10:936168, 2022. e-Pub 2022. PMID: 35927986.
- Terranova CJ, Stemler KM, Barrodia P, Jeter-Jones SL, Ge Z, de la Cruz Bonilla M, Raman A, Cheng CW, Allton KL, Arslan E, ÖH Y, Barton MC, Rai K, Piwnica-Worms H. Reprogramming of H3K9bhb at regulatory elements is a key feature of fasting in the small intestine. Cell Rep 37(8):110044, 2021. PMID: 34818540.
- Abbas HA, Hao D, Tomczak K, Barrodia P, Im JS, Reville PK, Alaniz Z, Wang W, Wang R, Wang F, Al-Atrash G, Takahashi K, Ning J, Ding M, Beird HC, Mathews JT, Little L, Zhang J, Basu S, Konopleva M, Marques-Piubelli ML, Solis LM, Parra ER, Lu W, Tamegnon A, Garcia-Manero G, Green MR, Sharma P, Allison JP, Kornblau SM, Rai K, Wang L, Daver N, Futreal A. Single cell T cell landscape and T cell receptor repertoire profiling of AML in context of PD-1 blockade therapy. Nat Commun 12(1):6071, 2021. e-Pub 2021. PMID: 34663807.
- Kochat V, Raman AT, Landers SM, Tang M, Schulz J, Terranova C, Landry JP, Bhalla AD, Beird HC, Wu CC, Jiang Y, Mao X, Lazcano R, Gite S, Ingram DR, Yi M, Zhang J, Keung EZ, Scally CP, Roland CL, Hunt KK, Feig BW, Futreal PA, Hwu P, Wang WL, Lazar AJ, Slopis JM, Wilson-Robles H, Wiener DJ, McCutcheon IE, Wustefeld-Janssens B, Rai K, Torres KE. Enhancer reprogramming in PRC2-deficient malignant peripheral nerve sheath tumors induces a targetable de-differentiated state. Acta Neuropathol 142(3):565-590, 2021. e-Pub 2021. PMID: 34283254.
- Terranova CJ, Tang M, Maitituoheti M, Raman AT, Ghosh AK, Schulz J, Amin SB, Orouji E, Tomczak K, Sarkar S, Oba J, Creasy C, Wu CJ, Khan S, Lazcano R, Wani K, Singh A, Barrodia P, Zhao D, Chen K, Haydu LE, Wang WL, Lazar AJ, Woodman SE, Bernatchez C, Rai K. Reprogramming of bivalent chromatin states in NRAS mutant melanoma suggests PRC2 inhibition as a therapeutic strategy. Cell Rep 36(3):109410, 2021. PMID: 34289358.
- Liu Y, Baggerly KA, Orouji E, Manyam G, Chen H, Lam M, Davis JS, Lee MS, Broom BM, Menter DG, Rai K, Kopetz S, Morris JS. Methylation-eQTL Analysis in Cancer Research. Bioinformatics. e-Pub 2021. PMID: 34117863.
- Deshmukh AP, Vasaikar SV, Tomczak K, Tripathi S, den Hollander P, Arslan E, Chakraborty P, Soundararajan R, Jolly MK, Rai K, Levine H, Mani SA. Identification of EMT signaling cross-talk and gene regulatory networks by single-cell RNA sequencing. Proc Natl Acad Sci U S A 118(19), 2021. PMID: 33941680.
- Maitituoheti M, Keung EZ, Tang M, Yan L, Alam H, Han G, Singh AK, Raman AT, Terranova C, Sarkar S, Orouji E, Amin SB, Sharma S, Williams M, Samant NS, Dhamdhere M, Zheng N, Shah T, Shah A, Axelrad JB, Anvar NE, Lin YH, Jiang S, Chang EQ, Ingram DR, Wang WL, Lazar A, Lee MG, Muller F, Wang L, Ying H, Rai K. Enhancer Reprogramming Confers Dependence on Glycolysis and IGF Signaling in KMT2D Mutant Melanoma. Cell Rep 33(3):108293, 2020. PMID: 33086062.
- Chakravarti D, Hu B, Mao X, Rashid A, Li J, Li J, Liao WT, Whitley EM, Dey P, Hou P, LaBella KA, Chang A, Wang G, Spring DJ, Deng P, Zhao D, Liang X, Lan Z, Lin Y, Sarkar S, Terranova C, Deribe YL, Blutt SE, Okhuysen P, Zhang J, Vilar E, Nielsen OH, Dupont A, Younes M, Patel KR, Shroyer NF, Rai K, Estes MK, Wang YA, Bertuch AA, DePinho RA. Telomere dysfunction activates YAP1 to drive tissue inflammation. Nat Commun 11(1):4766, 2020. e-Pub 2020. PMID: 32958778.
- Manzo T, Prentice BM, Anderson KG, Raman A, Schalck A, Codreanu GS, Nava Lauson CB, Tiberti S, Raimondi A, Jones MA, Reyzer M, Bates BM, Spraggins JM, Patterson NH, McLean JA, Rai K, Tacchetti C, Tucci S, Wargo JA, Rodighiero S, Clise-Dwyer K, Sherrod SD, Kim M, Navin NE, Caprioli RM, Greenberg PD, Draetta G, Nezi L. Accumulation of long-chain fatty acids in the tumor microenvironment drives dysfunction in intrapancreatic CD8+ T cells. J Exp Med 217(8), 2020. PMID: 32491160.
- Alam H, Tang M, Maitituoheti M, Dhar SS, Kumar M, Han CY, Ambati CR, Amin SB, Gu B, Chen TY, Lin YH, Chen J, Muller FL, Putluri N, Flores ER, DeMayo FJ, Baseler L, Rai K, Lee MG. KMT2D Deficiency Impairs Super-Enhancers to Confer a Glycolytic Vulnerability in Lung Cancer. Cancer Cell 37(4):599-617.e7, 2020. e-Pub 2020. PMID: 32243837.
- Cheng CW, Biton M, Haber AL, Gunduz N, Eng G, Gaynor LT, Tripathi S, Calibasi-Kocal G, Rickelt S, Butty VL, Moreno-Serrano M, Iqbal AM, Bauer-Rowe KE, Imada S, Ulutas MS, Mylonas C, Whary MT, Levine SS, Basbinar Y, Hynes RO, Mino-Kenudson M, Deshpande V, Boyer LA, Fox JG, Terranova C, Rai K, Piwnica-Worms H, Mihaylova MM, Regev A, ÖH Y. Ketone Body Signaling Mediates Intestinal Stem Cell Homeostasis and Adaptation to Diet. Cell 178(5):1115-1131.e15, 2019. PMID: 31442404.
- Adhikary S, Chakravarti D, Terranova C, Sengupta I, Maitituoheti M, Dasgupta A, Srivastava DK, Ma J, Raman AT, Tarco E, Sahin AA, Bassett R, Yang F, Tapia C, Roy S, Rai K, Das C. Atypical plant homeodomain of UBR7 functions as an H2BK120Ub ligase and breast tumor suppressor. Nat Commun 10(1):1398, 2019. e-Pub 2019. PMID: 30923315.
- Deribe YL, Sun Y, Terranova C, Khan F, Martinez-Ledesma J, Gay J, Gao G, Mullinax RA, Khor T, Feng N, Lin YH, Wu CC, Reyes C, Peng Q, Robinson F, Inoue A, Kochat V, Liu CG, Asara JM, Moran C, Muller F, Wang J, Fang B, Papadimitrakopoulou V, Wistuba II, Rai K, Marszalek J, Futreal PA. Author Correction: Mutations in the SWI/SNF complex induce a targetable dependence on oxidative phosphorylation in lung cancer. Nat Med 24(10):1627, 2018. PMID: 30104769.
- Ghosh K, Tang M, Kumari N, Nandy A, Basu S, Mall DP, Rai K, Biswas D. Positive Regulation of Transcription by Human ZMYND8 through Its Association with P-TEFb Complex. Cell Rep 24(8):2141-2154.e6, 2018. PMID: 30134174.
- Lissanu Deribe Y, Sun Y, Terranova C, Khan F, Martinez-Ledesma J, Gay J, Gao G, Mullinax RA, Khor T, Feng N, Lin YH, Wu CC, Reyes C, Peng Q, Robinson F, Inoue A, Kochat V, Liu CG, Asara JM, Moran C, Muller F, Wang J, Fang B, Papadimitrakopoulou V, Wistuba II, Rai K, Marszalek J, Futreal PA. Mutations in the SWI/SNF complex induce a targetable dependence on oxidative phosphorylation in lung cancer. Nat Med 24(7):1047-1057, 2018. e-Pub 2018. PMID: 29892061.
- Hillman RT, Celestino J, Terranova C, Beird HC, Gumbs C, Little L, Nguyen T, Thornton R, Tippen S, Zhang J, Lu KH, Gershenson DM, Rai K, Broaddus RR, Futreal PA. KMT2D/MLL2 inactivation is associated with recurrence in adult-type granulosa cell tumors of the ovary. Nat Commun 9(1):2496, 2018. e-Pub 2018. PMID: 29950560.
- Terranova C, Tang M, Orouji E, Maitituoheti M, Raman A, Amin S, Liu Z, Rai K. An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues. J Vis Exp(134), 2018. e-Pub 2018. PMID: 29683440.
- Oleksiewicz U, Gladych M, Raman AT, Heyn H, Mereu E, Chlebanowska P, Andrzejewska A, Sozanska B, Samant N, Fak K, Auguscik P, Kosinski M, Wróblewska JP, Tomczak K, Kulcenty K, Ploski R, Biecek P, Esteller M, Shah PK, Rai K, Wiznerowicz M. TRIM28 and Interacting KRAB-ZNFs Control Self-Renewal of Human Pluripotent Stem Cells through Epigenetic Repression of Pro-differentiation Genes. Stem Cell Reports 9(6):2065-2080, 2017. e-Pub 2017. PMID: 29198826.
- Sarkar S, Bristow CA, Dey P, Rai K, Perets R, Ramirez-Cardenas A, Malasi S, Huang-Hobbs E, Haemmerle M, Wu SY, McGuire M, Protopopov A, Jiang S, Liu JF, Hirsch MS, Chang Q, Lazar AJ, Sood AK, Drapkin R, DePinho R, Draetta G, Chin L. PRKCI promotes immune suppression in ovarian cancer. Genes Dev 31(11):1109-1121, 2017. e-Pub 2017. PMID: 28698296.
- Fiziev P, Akdemir KC, Miller JP, Keung EZ, Samant NS, Sharma S, Natale CA, Terranova CJ, Maitituoheti M, Amin SB, Martinez-Ledesma E, Dhamdhere M, Axelrad JB, Shah A, Cheng CS, Mahadeshwar H, Seth S, Barton MC, Protopopov A, Tsai KY, Davies MA, Garcia BA, Amit I, Chin L, Ernst J, Rai K. Systematic Epigenomic Analysis Reveals Chromatin States Associated with Melanoma Progression. Cell Rep 19(4):875-889, 2017. PMID: 28445736.
- Lissanu Deribe Y, Shi Y, Rai K, Nezi L, Amin SB, Wu CC, Akdemir KC, Mahdavi M, Peng Q, Chang QE, Hornigold K, Arold ST, Welch HC, Garraway LA, Chin L. Truncating PREX2 mutations activate its GEF activity and alter gene expression regulation in NRAS-mutant melanoma. Proceedings of National Academy of Sciences 113(9):E1296-305, 2016. e-Pub 2016. PMID: 26884185.
- Rai K, Akdemir KC, Kwong LN, Fiziev P, Wu CJ, Keung EZ, Sharma S, Samant NS, Williams M, Axelrad JB, Shah A, Yang D, Grimm EA, Barton MC, Milton DR, Heffernan TP, Horner JW, Ekmekcioglu S, Lazar AJ, Ernst J, Chin L. Dual roles for RNF2 during melanoma progression. Cancer Discov 5(12):1314-27, 2015. e-Pub 2015. PMID: 26450788.
- Keung EZ, Akdemir KC, Al Sannaa GA, Garnett J, Lev D, Torres KE, Lazar AJ, Rai K, Chin L. Increased H3K9me3 drives dedifferentiated phenotype via KLF6 repression in liposarcoma. J Clin Invest 10(8):1172, 2015. e-Pub 2015. PMID: 26193637.
- Rai K. Genomic Classification of Cutaneous Melanoma. Cell 7(161):1681-96. e-Pub 2015. PMID: 26091043.
- Cheng CS, Rai K, Garber M, Hollinger A, Robbins D, Anderson S, Macbeth A, Tzou A, Carneiro MO, Raychowdhury R, Russ C, Hacohen N, Gershenwald JE, Lennon N, Nusbaum C, Chin L, Regev A, Amit I. Semiconductor-based DNA sequencing of histone modification states. Nat Commun 4:2672, 2013. PMID: 24157732.
- Genovese G, Ergun A, Shukla SA, Campos B, Hanna J, Ghosh P, Quayle SN, Rai K, Colla S, Ying H, Wu CJ, Sarkar S, Xiao Y, Zhang J, Zhang H, Kwong L, Dunn K, Wiedemeyer WR, Brennan C, Zheng H, Rimm DL, Collins JJ, Chin L. microRNA Regulatory Network Inference Identifies miR-34a as a Novel Regulator of TGF-β Signaling in Glioblastoma. Cancer Discov 2(8):736-749, 2012. e-Pub 2012. PMID: 22750848.
- Rai K, Sarkar S, Broadbent TJ, Voas M, Grossmann KF, Nadauld LD, Dehghanizadeh S, Hagos FT, Li Y, Toth RK, Chidester S, Bahr TM, Johnson WE, Sklow B, Burt R, Cairns BR, Jones DA. DNA demethylase activity maintains intestinal cells in an undifferentiated state following loss of APC. Cell 142(6):930-42, 2010. PMID: 20850014.
- Rai K, Jafri IF, Chidester S, James SR, Karpf AR, Cairns BR, Jones DA. Dnmt3 and G9a cooperate for tissue-specific development in zebrafish. J Biol Chem 285(6):4110-21, 2010. e-Pub 2009. PMID: 19946145.
- Phelps RA, Chidester S, Dehghanizadeh S, Phelps J, Sandoval IT, Rai K, Broadbent T, Sarkar S, Burt RW, Jones DA. A two-step model for colon adenoma initiation and progression caused by APC loss. Cell 137(4):623-34, 2009. PMID: 19450512.
- Rai K, Huggins IJ, James SR, Karpf AR, Jones DA, Cairns BR. DNA demethylation in zebrafish involves the coupling of a deaminase, a glycosylase, and gadd45. Cell 135(7):1201-12, 2008. PMID: 19109892.
- Rai K, Chidester S, Zavala CV, Manos EJ, James SR, Karpf AR, Jones DA, Cairns BR. Dnmt2 functions in the cytoplasm to promote liver, brain, and retina development in zebrafish. Genes Dev 21(3):261-6, 2007. PMID: 17289917.
- Rai K, Nadauld LD, Chidester S, Manos EJ, James SR, Karpf AR, Cairns BR, Jones DA. Zebra fish Dnmt1 and Suv39h1 regulate organ-specific terminal differentiation during development. Mol Cell Biol 26(19):7077-85, 2006. PMID: 16980612.
- Nadauld LD, Chidester S, Shelton DN, Rai K, Broadbent T, Sandoval IT, Peterson PW, Manos EJ, Ireland CM, Yost HJ, Jones DA. Dual roles for adenomatous polyposis coli in regulating retinoic acid biosynthesis and Wnt during ocular development. Proc Natl Acad Sci U S A 103(36):13409-14, 2006. e-Pub 2006. PMID: 16938888.
Invited Articles
- Rai K. Personalized Cancer Therapy: YES1 Is the New Kid on the Block. Cancer Res 79(22):5702-5703, 2019. PMID: 31772072.
- Raman AT, Rai K. Loss of histone acetylation and H3K4 methylation promotes melanocytic malignant transformation. Mol Cell Oncol 5(3):e1359229, 2018. e-Pub 2018. PMID: 30250885.
- Keung EZ, Rai K. H3K9me3 Mediated Repression of KLF6: Discovering a Novel Tumor Suppressor in Liposarcoma Using a Systematic Epigenomic Approach. Mol Cell Oncol 3(3):e1093691, 2016. e-Pub 2015. PMID: 27314083.
Other Articles
- Chaudhri A, Lizee G, Hwu P, Rai K Chromatin Remodelers Are Regulators of the Tumor Immune Microenvironment. Cancer Res 84(7):965-976, 2024. PMID: 38266066.
- Wu M, Rai K Demystifying extrachromosomal DNA circles: Categories, biogenesis, and cancer therapeutics. Comput Struct Biotechnol J 20:6011-6022, 2022. PMID: 36382182.
- Arslan E, Schulz J, Rai K Machine Learning in Epigenomics: Insights into Cancer Biology and Medicine. Biochim Biophys Acta Rev Cancer 1876(2):188588, 2021. PMID: 34245839.
Book Chapters
- Tang M, Rai K. Chapter 20 - Computational Analysis of Epigenetic Modifications in Melanoma. In: Computational Epigenetics and Diseases. None. Academic Press, 327-342, 2019.
Grant & Contract Support
| Title: | ASCEND-CRC: Adaptive Strategies for Clinical Evolution and Novel |
| Funding Source: | Advanced Research Projects Agency for Health |
| Role: | Co-I |
| Title: | Microgravity and T Cell Therapy |
| Funding Source: | Center for the Advancement of Science in Space, Inc |
| Role: | Co-PI |
| Title: | HORMAD-specific TGF-beta resistant |
| Funding Source: | NIH/NCI |
| Role: | Co-PI |
| Title: | HORMAD-Specific TGF-Beta Resistant Memory T Cells for Treatment of Patients with Gastroesophageal Cancer |
| Funding Source: | NIH/NCI |
| Role: | MPI |
| Title: | Mechanisms of Fasting-Induced Radioprotection of Small Intestinal Epithelial Cells |
| Funding Source: | NIH/NCI |
| Role: | MPI |
| Title: | The Epigenetic Impact and Therapeutic Opportunity of AR-Directed Therapy for DSRCT |
| Funding Source: | Cancer Prevention & Research Institute of Texas (CPRIT) |
| Role: | Co-I |
| Title: | Mechanisms and therapies focused on epigenomic alterations in therapy-resistant prostate cancers |
| Funding Source: | Cancer Prevention & Research Institute of Texas (CPRIT) |
| Role: | PI |
| Title: | UCHL5 as a regulator and therapeutic target in metastatic melanoma |
| Funding Source: | NIH/NCI |
| Role: | PI |
| Title: | MD Anderson Epigenetic Therapy Initiative (METI) |
| Funding Source: | The University of Texas MD Anderson Cancer Center Internal Funding |
| Role: | PI |
| Title: | Role of UBR7, a novel H2BK120 E3 ubiquitin ligase, in suppression of breast cancer |
| Funding Source: | NIH/NCI |
| Role: | PI |
| Title: | Role of Aberrant Enhancer Activation in Colorectal Cancer |
| Funding Source: | American Cancer Society (ACS) |
| Role: | PI |
| Title: | PRC2-Dependent Enhancer Reprogramming Promotes MPNST Pathogenesis |
| Funding Source: | DOD/Congressionally Directed Medical Research Programs (DOD/CDMRP) |
| Role: | Co-I |
| Title: | Contribution of Epigenome to PRKCI-Driven High-Grade Serous Ovarian Cancer |
| Funding Source: | NIH/NCI |
| Role: | PI |
| Title: | Role of RNA exosome in NF-1 mutant MPNSTs |
| Funding Source: | DOD/Congressionally Directed Medical Research Programs (DOD/CDMRP) |
| Role: | PI |
| Title: | Flagship 4 - Lymphoma Moonshots |
| Funding Source: | UT MD Anderson Cancer Center |
| Role: | Co-Leader |
| Title: | Stratification of colorectal cancers based on enhancer patterns for epigenetic therapy |
| Funding Source: | NIH/NCI |
| Role: | PI |
| Title: | LoxL2 and H3K4 methylation as effectors of anti-PD1 response in melanoma |
| Funding Source: | UT MD Anderson Cancer Center |
| Role: | PI |
| Title: | Patient-Derived Models of Prostate Cancer for Personalized Medicine |
| Funding Source: | NIH/NCI |
| Role: | Co-I |
| Title: | Role of KMT2D and aberrant enhancers in modulation of tumor microenvironment in melanoma |
| Funding Source: | NIH/NCI |
| Role: | PI |
| Title: | Co-operative Roles For YAP1 and UCHL5 in Cancer Progression and Therapy |
| Funding Source: | NIH/NCI |
| Role: | PI |
| Title: | Role of HDAC8 and higher-order chromatin structure in melanoma metastasis |
| Funding Source: | Cancer Prevention & Research Institute of Texas (CPRIT) |
| Role: | PI |
| Title: | Epigenetic effectors of tumor response to immune checkpoint blockade therapy |
| Funding Source: | DOD/Congressionally Directed Medical Research Programs (DOD/CDMRP) |
| Role: | PI |
| Title: | Epigenetic effectors of responses to immune checkpoint blockade agents |
| Funding Source: | Melanoma Research Alliance |
| Role: | PI |
| Title: | Characterization of EZH2s Pro-Oncogenic Activity as a Transcriptional Modulator in NF1-Associated MPNST |
| Funding Source: | DOD/Congressionally Directed Medical Research Programs (DOD/CDMRP) |
| Role: | Co-I |
| Title: | Fasting Protects Small Intestinal Stem Cells from Lethal DNA Damage: Mechanistic Insight and Preclinical Translation |
| Funding Source: | NIH/NCI |
| Role: | Collaborator |
| Title: | Melanoma Research Foundation |
| Funding Source: | Melanoma Research Foundation |
| Role: | PI |
| Title: | Contribution of Epigenome to Head and Neck Cancer |
| Funding Source: | NIH/NCI |
| Role: | PI |
| Title: | UTMDACC Lung SPORE: Career Enhancement Program Award |
| Funding Source: | NIH/NCI |
| Role: | Investigator |
| Title: | UTMDACC Brain SPORE - Career Enhancement Project |
| Funding Source: | NIH/NCI |
| Role: | PI |
| Title: | CRC Moonshot project #9 |
| Funding Source: | UTMDACC |
| Role: | Investigator |
| Title: | Characterization of epigenome in cancer cell lines |
| Funding Source: | UTMDACC |
| Role: | PI |
| Title: | Epigenetic of Melanoma Metastasis |
| Funding Source: | NIH/NCI |
| Role: | PI |
| Title: | UT MD Anderson Cancer Center Melanoma SPORE- Project 4 |
| Funding Source: | NIH/NCI |
| Role: | Co-I |
| Title: | Epigenetic regulators of metastasis in bladder cancer |
| Funding Source: | MDACC BLADDER CANCER SPORE |
| Role: | PI |
| Title: | Defining metastasis-specific higher-order chromatin structure in melanoma |
| Funding Source: | UTMDACC Center for Cancer Epigenetics |
| Role: | Co-PI |
| Title: | Epigenome changes during melanoma progression |
| Funding Source: | Center for Cancer Epigenetics |
| Role: | PI |
| Title: | Epigenetic of Melanoma Metastasis |
| Funding Source: | NIH/NCI |
| Role: | PI |
| Title: | Investigating the Mechanism of Action of Epigenetic Modifications and Factors during Metastatic Progression of Melanoma |
| Funding Source: | Charles A King Trust Post-doctoral Fellowship |
| Role: | PI |
| Title: | Targeting of a novel enhancer hub to overcome T cell exhaustian |
| Funding Source: | American Cancer Society (ACS) |
| Role: | PI |
| Title: | Small molecule degraders of YAP1 |
| Funding Source: | Welch Foundation |
| Role: | PI |
| Title: | The Histone Modifier UTX, Breast Cancer, and Drug Resistance |
| Funding Source: | Department of Defense (DOD) |
| Role: | Co-I |
| Title: | LOXL2 as a Mediator of Immunotherapy Response in Melanoma |
| Funding Source: | NIH/NCI |
| Role: | PI |
| Title: | The Histone Modifier UTX in Triple-Negative and HER2-Positive Breast Cancer |
| Funding Source: | NIH/NCI |
| Role: | Co-I |
| Title: | Assessment of Mechanism and Anti-Tumor Activity of Small Molecule Degraders of YAP1 |
| Funding Source: | Cancer Prevention & Research Institute of Texas (CPRIT) |
| Role: | PI |
| Title: | Chromatin Structure in Melanoma Metastasis: Evolution, Regulation and Therapeutic Targeting |
| Funding Source: | NIH/NCI |
| Role: | PI |
| Title: | BCL9 Induced Enhancer Activation Drives Cellular Stemness and DCIS Malignancy |
| Funding Source: | NIH/NCI |
| Role: | Subaward PI |
| Title: | Epigenetic Mechanisms and Therapies in KMT2D-Mutant Melanoma |
| Funding Source: | NIH/NCI |
| Role: | PI |
| Title: | Deciphering How the Ewing Sarcoma Fusion Protein Dysregulates Cell Fate, Differentiation, and Plasticity by Single-Cell CRISPR-seq |
| Funding Source: | NIH/NCI |
| Role: | Co-I |
| Title: | MD Anderson Cancer Immune Monitoring and Analysis Center MDA-CIMAC |
| Funding Source: | NIH/NCI |
| Role: | Co-I |
| Title: | MD Anderson Epigenetics SPORE |
| Funding Source: | NIH/NCI |
| Role: | PI |
| Title: | Enhancers as Targets for Improvements in Immunotherapy |
| Funding Source: | NIH/NCI |
| Role: | PI |
| Title: | In Vivo Chemistry as a New Approach to Treat Solid Tumors |
| Funding Source: | NIH/NCI |
| Role: | Collaborator |
| Title: | The Epigenetic Modifier UTX, Breast Cancer, and Drug Resistance |
| Funding Source: | Cancer Prevention & Research Institute of Texas (CPRIT) |
| Role: | Co-I |
| Title: | Nuclear and Non-Canonical Function of Phosphorylated Dicer1 in Cancer |
| Funding Source: | Cancer Prevention & Research Institute of Texas (CPRIT) |
| Role: | Collaborator |
| Title: | LOXL2 as a mediator of immunotherapy response in melanoma |
| Funding Source: | NIH/NCI |
| Role: | PI |
| Title: | Defining and targeting alterations of the epigenetic modifier KMT2D in non-small cell lung cancer |
| Funding Source: | NIH/NCI |
| Role: | Co-I |
| Title: | Contribution of tumor epigenome to immune response that influence metastatic spread |
| Funding Source: | Department of Defense (DOD) |
| Role: | PI |
| Title: | KMT2D as modulator of epigenome and immune microenvironment in HNSCC |
| Funding Source: | NIH/NCI |
| Role: | MPI |
| Title: | Fasting-induced microbiome changes and radioprotection |
| Funding Source: | Cancer Prevention & Research Institute of Texas (CPRIT) |
| Role: | Co-PI |
| Title: | Heterogeneity of Enhancer Patterns in Colorectal Cancers - Mechanisms and Therapy |
| Funding Source: | Cancer Prevention & Research Institute of Texas (CPRIT) |
| Role: | PI |
| Title: | Synthetic Lethal Targeting of CREBBP/EP300 in Head and Neck Squamous Cell Carcinoma |
| Funding Source: | NIH/NIDCR |
| Role: | Co-I |
| Title: | Chromatin structure in melanoma metastasis: Evolution, regulation and therapeutic targeting |
| Funding Source: | NIH/NCI |
| Role: | PI |
| Title: | Discovery of epigenomic drivers of HER2+ DCIS to enable precision prevention and therapeutic targeting |
| Funding Source: | Department of Defense (DOD) |
| Role: | PI |
| Title: | MLL4-mediated temporal regulation of epigenomic and transcriptional programs in cerebellar neurons |
| Funding Source: | NIH/NCI |
| Role: | Co-I |
| Title: | ADCK5 as a novel regulator of YAP-Hippo Pathway in Ovarian Cancer |
| Funding Source: | NIH/NCI |
| Role: | PI |
| Title: | Functional characterization of the lineage plasticity landscape of cholangiocarcinoma |
| Funding Source: | NIH/NCI |
| Role: | Collaborator |
| Title: | Discovery of epigenomic drivers of HER2+ DCIS to enable precision prevention and therapeutic targeting |
| Funding Source: | NIH/NCI |
| Role: | PI |
| Title: | Identification of molecular and cellular targets for decoupling immune checkpoint blockade induced auto- and antitumor immunity |
| Funding Source: | NIH/NCI |
| Role: | Significant Contributor |
| Title: | Leveraging synthetic and collateral lethality in MTAP loss tumors |
| Funding Source: | Cancer Prevention & Research Institute of Texas (CPRIT) |
| Role: | Co-I |
| Title: | Functional characterization of the lineage plasticity landscape of cholangiocarcinoma |
| Funding Source: | Cancer Prevention & Research Institute of Texas (CPRIT) |
| Role: | Collaborator |
| Title: | The epigenetic Modifier UTX, Breast Cancer, and Drug |
| Funding Source: | Cancer Prevention & Research Institute of Texas (CPRIT) |
| Role: | Co-I |
| Title: | Disrupting Neuroimmune Interactions to Overcome |
| Funding Source: | Mark Foundation for Cancer Research |
| Role: | Other significant contributor |
| Title: | Spatial Interactions In the Microenvironment of Uterine Leiomyosarcomas |
| Funding Source: | American Association for Cancer Research (AACR) |
| Role: | Collaborator |
| Title: | Lineage plasticity as a targetable vulerability for FGFR inhibition in bladder cancer |
| Funding Source: | NIH/NCI |
| Role: | Collaborator |
| Title: | Targeting Perineural Invasion-Driven Inflammation to Overcome Skin cancer Resistance to Immunotherapy |
| Funding Source: | NIH/NCI |
| Role: | Co-I |
| Title: | Histone lactylation(s) orchestrate epigenetic and transcriptional networks driving DCD8 T cell metabolism and function |
| Funding Source: | NIH/NCI |
| Role: | Co-I |
| Title: | Targeting Epigenetic Machinery to Overcome Myeloid Cell-Mediated Resistance to Anti-PD-1 Therapy in GBM |
| Funding Source: | NIH/NCI |
| Role: | Co-I |
| Title: | Mechanisms of Fasting-Induced Radioprotection of Small Intestinal Epithelial Cells |
| Funding Source: | NIH/NCI |
| Role: | MPI |
Patient Reviews
CV information above last modified December 31, 2024