Kunal Rai, Ph.D.
Department of Genomic Medicine, Division of Cancer Medicine
About Dr. Rai
I am a 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 the role of epigenome in cancer progression and identifying new venues for therapy and diagnostic tools. Our approach is as follows: 1) deploy cutting-edge epigenome mapping approaches to define chromatin state changes and higher-order chromatin structure in human tumors and genetically engineered mouse models, 2) utilize state-of-the-art machine and deep learning approaches to interpret the epigenome data, 3) employ epigenetic editing approaches to build novel cellular therapies and 4) build small molecule degraders for non-enzymatic core regulatory driver proteins. The highlights of our accomplishments include comprehensive understanding of chromatin state reprogramming during immunotherapy response (Under revision in Nature Comm), melanoma progression (Cell Reports 2017 and Cell Reports 2021), colon cancer progression (Gut 2021, Clinical Cancer Research 2024 and under revision in JCI), head and neck cancer (Frontiers in Cell and Developmental Biology 2022 and biorxiv 2021) skin cancer (under revision in Cell) and rare diseases including DSRCT (Nature Communications, 2022), liposarcoma (JCI 2015), MPNST (Acta Neuro 2021). We also identified major epigenetic drivers of in melanoma (Cancer Discovery 2015; Cell Reports 2019), triple negative breast cancer (Nature Comm 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 Comm 2018 and biorxiv). Importantly, we have collaborated with a number of clinical studies (current with 13 Phase I/II clinical trials) for epigenomic biomarker discovery, applying our expertise for clinical translation. Recently, our work had led to a ‘first in class’ epigenetically edited T cell product which is being ready for clinical trial. 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. On the technological advancement front, we have generated large amount of spatial transcriptomics data at single cell resolution (>1500 samples) and deployed spatial epigenomic methods in patient samples for the first time (under revision in Cell). My lab is funded by Department of Defense (5 active grants and 3 past), NCI (5 RO1s, two R21s, CEPs from 5 SPOREs), CPRIT (3 IIRAs), ACS (RSG), private foundations (Melanoma Research Alliance and Melanoma Research Foundation), and MDA Moonshot projects (Prostate, Colorectal).
Present Title & Affiliation
Primary Appointment
Professor, Genomic Medicine, Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
Adjunct Associate Professor, Department of Bioengineeering, Rice University, Houston, Texas
Scientific Director, MDACC Epigenomics Therapy Initiative, The University of Texas MD Anderson Cancer Center, Houston, TX
Associate Professor, Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
Dual/Joint/Adjunct Appointment
Professor, Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
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 |
Licenses & Certifications
| 2025 | Faculty Leadership Academy |
| 2023 | Management Development Program, Harvard Business School Alumni Club of Charlotte |
Experience & Service
Faculty Academic Appointments
Associate Professor, Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 2020 - 2025
Assistant Professor, Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 2014 - 2020
Instructor, 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, MDACC Epigenomics Therapy Initiative, The University of Texas MD Anderson Cancer Center, Houston, TX, 2020 - Present
Other Professional Positions
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
Intramural Institutional Committee Activities
Member, EMC Chair Search Committee, The University of Texas MD Anderson Cancer Center, 2024 - 2024
Member, MCO Chair Search Committee, The University of Texas MD Anderson Cancer Center, 2023 - 2024
Member, Graduate Education Committee, The University of Texas MD Anderson Cancer Center, 2023 - Present
Ad hoc member, Research Integrity Committee, The University of Texas MD Anderson Cancer Center, 2023 - Present
Departmental Representative, Faculty Senate, The University of Texas MD Anderson Cancer Center, 2022 - Present
member, REACT, The University of Texas MD Anderson Cancer Center, 2021 - Present
Departmental Representative, Faculty Senate, The University of Texas MD Anderson Cancer Center, 2016 - 2018
Extramural Institutional Committee Activities
Member, Promotion and Tenure Committee-Research (PTC-R), The University of Texas MD Anderson Cancer Center, 2025 - 2026
Editorial Activities
Editorial Board Member, Cancer research, 2025 - Present
Editorial Board Member, Cell reports, 2024 - Present
Editorial Board member, Molecular Oncology, 2020 - Present
Honors & Awards
| 2023 | Young Alumni Achiever Award for the Year 2023, Indian Institute of Technology |
| 2022 | Potu N Rao Excellence in Basic Science, MD Anderson Cancer Center |
| 2002 - 2006 | Graduate Fellowship, University of Utah |
| 2000 | Summer Fellowship, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India |
Professional Memberships
Selected Presentations & Talks
Local Presentations
- 2026. Cancer Epigenome: Mechanisms, Biomarkers and Therapeutics. Invited. Department of Systems Biology Spring Seminar Series. Houston, Texas, US.
- 2024. Spatial epigenomics of melanoma immunotherapy response. Invited. MD Anderson Special Symposium on Spatialomic Sequencing. Houston, TX, US.
- 2024. Functional epigenomics of Melanoma Progression and Response to Therapy. Invited. Melanoma Research Seminar. Houston, Texas, US.
- 2015. Epigenomics of Melanoma Progression. Invited. DoCM Grand Rounds. Houston, TX, US.
- 2015. Functional Epigenomics of Melanoma Metastasis. Invited. Seminar Series. Houston, TX, US.
- 2015. Functional Epigenomics of Melanoma Progression. Conference. Symposia on Cancer Epigenetics. Houston, TX, US.
- 2014. Functional Epigenomics of Melanoma Progression. Invited. Future of Cancer Science. Houston, TX, US.
- 2013. Chromatin States in Melanoma Progression. Invited. CCE Annual Retreat. Houston, TX, US.
- 2012. Role of RNF2 in melanoma metastasis. Conference. MD Anderson Cancer Center. Houston, TX, US.
Regional Presentations
- 2024. Functional epigenomics in cancer progression and therapy. Invited. Distinguished Lecture Series. Houston, Texas, US.
- 2024. METI as a platform for translation of epigenetic therapies. Invited. CCE Retreat. Houston, TX, US.
- 2023. Houston Translational Research Symposium & Xenium In Situ Showcase. Conference. 10X Genomics. Houston, TX, US.
- 2022. Epigenome aberrations underlying T cell differentiation during response to immunotherapy. Conference. 10X Genomics User Group Meeting. Houston, TX, US.
- 2020. Functional Epigenomics of Melanoma Progression. Invited. Texas A&M University. College Station, TX, US.
- 2019. Functional Epigenomics of Melanoma Progression. Invited. University of Texas Health Science Center. Houston, TX, US.
- 2017. Functional Epigenomics of Melanoma Progression. Invited. Institute of Molecular Medicine. Houston, TX, US.
- 2017. Functional Epigenomics of Melanoma Progression. Invited. Baylor College of Medicine. Houston, TX, US.
- 2015. G&D and Epigenetics and Molecular Carcinogenesis Fall Retreat. Conference. University of Texas Graduate School of Biomedical Sciences at Houston (GSBS). Montgomery, TX, US.
National Presentations
- 2025. Epigenome Reprogramming During Response to Immunotherapy. Invited. The Cancer Molecular Therapeutics Research Association. Midway, Utah, US.
- 2025. Pan-cancer chromatin state profiling suggests enhancer-heterogeneity and precision medicine approach. Poster. American Association for Cancer Research (AACR). Chicago, Illinois, US.
- 2025. Functional epigenomics of colorectal cancer progression and response to therapy. Invited. AstraZeneca. Boston, MA, US.
- 2024. Cancer Epigenome: Junk or Gold. Invited. 8th Annual Research Symposium. Chicago, Illinois, US.
- 2024. Enhancers as targets for improvements in immunotherapy. Conference. The University of Texas MD Anderson Cancer Center. San Diego, US.
- 2023. Epigenome Reprogramming During Response to Immunotherapy and Cell Therapy. Invited. University of Pennsylvania. Philadelphia, PA, US.
- 2023. Epigenome Reprogramming During Response to Immunotherapy and Cell Therapy. Conference. Society for Melanoma Research. Philadelphia, PA, US.
- 2023. Epigenome Reprogramming During Response to Immunotherapy and Cell Therapy. Invited. Massachusetts Institute of Technology. Boston, MA, US.
- 2023. Epigenome Reprogramming During Response to Immunotherapy and Cell Therapy. Invited. Massachusetts General Hospital. Boston, MA, US.
- 2023. Epigenetic Basis of Immune Therapy in Melanoma. Invited. University of Utah Huntsman Cancer Institute. Salt Lake City, UT, US.
- 2022. Functional Cancer Epigenomics. Invited. Frontline Genomics, US.
- 2022. Exploiting Epigenome for Precision Medicine. Invited. University of Kansas Medical Center. Kansas City, KS, US.
- 2022. Single cell epigenomics of immunotherapy response. Invited. 10x Genomics. New Orleans, US.
- 2021. Functional Epigenomics of Cancer Progression. Invited. New England Biolabs, US.
- 2020. Functional Epigenomics of Melanoma Progression. Invited. Columbia University. New York, NY, US.
- 2020. Enhancer Reprogramming Contributes to anti-PD1 Resistance in Melanoma. Invited. Melanoma Research Alliance. Washington DC, US.
- 2019. Functional Epigenomics of Melanoma Progression. Invited. Huntsman Cancer Institute. Salt Lake City, UT, US.
- 2018. Functional epigenomics of melanoma progression. Invited. Jackson Institute for Genomic Medicine. Farmington, CT, US.
- 2018. Genotype-Specific Chromatin State Dynamics in Metastatic Melanoma Progression. Conference. Cancer Epigenetics: New Mechanisms, New Therapies. Breckenridge, CO, US.
- 2017. HDAC8 and higher order chromatin structure in melanoma metastasis. Invited. Epigenetic Mechanisms in Health Disease. Barcelona, US.
- 2016. Genotype-Specific Chromatin State Dynamics in Metastatic Melanoma Progression. Conference. Annual Meeting. New Orleans, LA, US.
- 2015. Chromatin State Dynamics During Pre-malignant to Malignant Transition in Melanoma. Conference. Neuroepigenetics. Santa Fe, NM, US.
- 2015. Chromatin State Dynamics During Pre-malignant to Malignant Transition in Melanoma. Conference. Epigenetics and Cancer. Keystone, CO, US.
- 2012. Role of RNF2 in Melanoma Metastasis. Invited. Model Organisms to Human Biology. Washington, DC, US.
- 2009. DNA Demethylation Involves Cooperative Action of AID, MBD4 and GADD45a and. Conference. Keystone Chromatin Meeting. Keystone, CO, US.
- 2008. Different tissue-specific roles for Dnmt1 and Dnmt3 in zebrafish organ development. Conference. American Association of Cancer Research. Keystone, CO, US.
- 2007. Dnmt2 functions in the cytoplasm to promote liver, brain and retina development in zebrafish. Conference. Keystone Meeting in Epigenetics. Keystone, CO, US.
- 2006. Zebrafish Dnmt1 and Suv39h1 regulate organ-specific terminal differentiation during development. Conference. Keystone. Keystone, CO, US.
International Presentations
- 2026. Gut Microbiome as an Epigenetic Rheostat During Fasting-Mediated Intestinal Regeneration. Invited. Gut Microbiome and Probiotics - Impact from Cradle to Centenarians. New Delhi, IN.
- 2026. Precision Epigenome Engineering to Improve T Cell Therapy. Poster. Keystone Symposia - Emerging Cell Therapies. Banff, CA.
- 2025. Precision Epigenetic Engineering to Improve T Cell Therapy. Invited. EpiCypher 2025: Biological and Clinical Frontiers in Epigenetics. Cancun, MX.
- 2025. Precision Epigenome Engineering to Improve T Cell Therapy. Poster. Keystone Symposia - Precision Genome Engineering: Translating the Human Genome to the Clinic. Killarney, IE.
- 2025. Cancer Epigenome: Evolution, Mechanisms and Therapies. Invited. External Seminar Series. Oxford, GB.
- 2023. Cancer Epigenetics to Personalized Medicine. Invited. Front Line Genomics Limited. Boston, US.
- 2023. Human Microbiome in Health and Disease. Invited. Translational Health Science and Technology Institute. Faridabad, IN.
- 2021. Precision Medicine through Cancer Epigenomics. Invited. University of Birmingham. Birmingham, GB.
- 2019. Reprogramming of Enhancer Patterns and Higher-order Chromatin Structure During Melanoma Progression. Invited. New York University. Abu Dhabi, AE.
- 2019. Enhancer Reprogramming Contributes to anti-PD1 Resistance in Melanoma. Conference. Cancer Genetics and Epigenetics Meeting. Lucca, IT.
- 2019. HDAC8 and Higher-order Chromatin Structure in Melanoma Metastasis. Conference. 3D genome: Gene Regulation and Disease. Banff, CA.
- 2018. Reprogramming of Enhancer Patterns and Higher-order Chromatin Structure During Melanoma Progression. Invited. Queen Mary University of London. London, US.
- 2018. Functional Epigenomics of Melanoma Progression. Invited. SINP International Cancer Meeting, US.
- 2018. Functional Epigenomics of Melanoma Progression. Invited. Saha Institute. Kolkata, IN.
- 2018. HDAC8 and higher order chromatin structure in melanoma metastasis. Conference. Chromatin Architecture and Chromosome Organization. Whistler, CA.
- 2018. Functional Epigenomics of Melanoma Progression. Invited. 2nd International Conference on Genomic Medicine (GenMed-2018). Houston, US.
- 2017. Functional Epigenomics of Melanoma Progression. Invited. Indian Institute of Chemical Biology. Kolkata, IN.
- 2015. Young Investigator Workshop. Invited. Oslo University Hospital. Oslo, NO.
- 2014. Functional Epigenomics of Melanoma Progression. Invited. National Center for Biological Sciences. Bangalore, IN.
- 2014. Functional Epigenomics of Melanoma Progression. Invited. Indian Institute of Scientific Education and Research. Pune, IN.
- 2014. Functional Epigenomics of Melanoma Progression. Invited. National Cancer Center Singapore. Singapore, SG.
- 2014. Functional Epigenomics of Melanoma Progression. Invited. IFOM- FIRC Institute of Molecular Oncology. Milan, IT.
- 2013. Functional Epigenomics of Melanoma Progression. Invited. Center for Cellular and Molecular Biology. Hyderabad, IN.
- 2013. Functional Epigenomics of Melanoma Progression. Invited. Indian Institute of Scientific Education and Research. Mohali, IN.
- 2013. Functional Epigenomics of Melanoma Progression. Invited. Advanced Center for Treatment, Research and Education in Cancer. Mumbai, IN.
Grant & Contract Support
| Date: | 2025 - 2029 |
| Title: | Mechanisms of Age and Sex-Defendant Changes in Urinary Bladder Immunity (Subaward to MDA from BCM) |
| Funding Source: | NIH/NCI |
| Role: | Co-I |
| Date: | 2025 - 2028 |
| Title: | Enhancer editing to improve TIL therapy for melanoma |
| Funding Source: | Department of Defense |
| Role: | PI |
| ID: | HT9425-25-1-0808 |
| Date: | 2025 - 2028 |
| Title: | Building T-Cell Products in NF1-Associated MPNST Through Antigen Discovery and Epigenome Targeting |
| Funding Source: | Department of Defense |
| Role: | PI |
| ID: | HT9425-25-1-0851 |
| Date: | 2025 - 2030 |
| Title: | Chromatin structure in melanoma metastasis: Evolution, regulation and therapeutic targeting |
| Funding Source: | NIH/NCI |
| Role: | PI |
| ID: | FP00023109 |
| Date: | 2025 - 2028 |
| Title: | Epigenetic editing to improve melanoma TIL therapy |
| Funding Source: | Melanoma Research Alliance |
| Role: | PI |
| Date: | 2025 - 2030 |
| Title: | Functional characterization of the lineage plasticity landscape of cholangiocarcinoma |
| Funding Source: | NIH/NCI |
| Role: | Collaborator |
| ID: | Fp00022820 |
| Date: | 2025 - 2030 |
| Title: | Discovery of epigenomic drivers of HER2+ DCIS to enable precision prevention and therapeutic targeting |
| Funding Source: | NIH/NCI |
| Role: | PI |
| ID: | FP00023140 |
| Date: | 2025 - 2030 |
| Title: | MLL4-mediated temporal regulation of epigenomic and transcriptional programs in cerebellar neurons |
| Funding Source: | NIH/NCI |
| Role: | Co-I |
| ID: | FP00019435 |
| Date: | 2025 - 2030 |
| Title: | ADCK5 as a novel regulator of YAP-Hippo Pathway in Ovarian Cancer |
| Funding Source: | NIH/NCI |
| Role: | PI |
| ID: | FP00019708 |
| Date: | 2025 - 2029 |
| Title: | Discovery of epigenomic drivers of HER2+ DCIS to enable precision prevention and therapeutic targeting |
| Funding Source: | Department of Defense (DOD) |
| Role: | PI |
| ID: | FP00023102 |
| Date: | 2025 - 2027 |
| Title: | Identification of molecular and cellular targets for decoupling immune checkpoint blockade induced auto- and antitumor immunity |
| Funding Source: | NIH/NCI |
| Role: | Significant Contributor |
| ID: | FP00023303 |
| Date: | 2025 - 2029 |
| Title: | Leveraging synthetic and collateral lethality in MTAP loss tumors |
| Funding Source: | Cancer Prevention & Research Institute of Texas (CPRIT) |
| Role: | Co-I |
| ID: | FP00023170 |
| Date: | 2025 - 2028 |
| Title: | The epigenetic Modifier UTX, Breast Cancer, and Drug |
| Funding Source: | Cancer Prevention & Research Institute of Texas (CPRIT) |
| Role: | Co-I |
| ID: | FP00016839 |
| Date: | 2025 - 2028 |
| Title: | Functional characterization of the lineage plasticity landscape of cholangiocarcinoma |
| Funding Source: | Cancer Prevention & Research Institute of Texas (CPRIT) |
| Role: | Collaborator |
| ID: | FP00022821 |
| Date: | 2025 - 2027 |
| Title: | Disrupting Neuroimmune Interactions to Overcome |
| Funding Source: | Mark Foundation for Cancer Research |
| Role: | Other significant contributor |
| ID: | FP00018194 |
| Date: | 2024 - 2030 |
| Title: | ASCEND-CRC: Adaptive Strategies for Clinical Evolution and Novel |
| Funding Source: | Advanced Research Projects Agency for Health |
| Role: | Co-I |
| ID: | FP00022697 |
| Date: | 2024 - 2026 |
| Title: | Cell Plasticity and Epigenetic Reprogramming Underlying Well-Differentiated to De- Dedifferentiated Liposarcoma |
| Funding Source: | Department of Defense |
| Role: | PI |
| ID: | HT9425-24-1-0610 |
| Date: | 2024 - 2025 |
| Title: | Targeting of a novel enhancer hub to overcome T cell exhaustion |
| Funding Source: | American Cancer Society (ACS) |
| Role: | PI |
| ID: | FP00022861 |
| Date: | 2024 - 2028 |
| Title: | Microgravity and T Cell Therapy |
| Funding Source: | Center for the Advancement of Science in Space, Inc |
| Role: | Co-PI |
| ID: | FP00022170 |
| Date: | 2024 - 2029 |
| Title: | Histone lactylation(s) orchestrate epigenetic and transcriptional networks driving DCD8 T cell metabolism and function |
| Funding Source: | NIH/NCI |
| Role: | Co-I |
| ID: | FP00021803 |
| Date: | 2024 - 2029 |
| Title: | Targeting Perineural Invasion-Driven Inflammation to Overcome Skin cancer Resistance to Immunotherapy |
| Funding Source: | NIH/NCI |
| Role: | Co-I |
| ID: | FP00021481 |
| Date: | 2024 - 2026 |
| Title: | Spatial Interactions In the Microenvironment of Uterine Leiomyosarcomas |
| Funding Source: | American Association for Cancer Research (AACR) |
| Role: | Collaborator |
| ID: | FP00022851 |
| Date: | 2024 - 2029 |
| Title: | Lineage plasticity as a targetable vulerability for FGFR inhibition in bladder cancer |
| Funding Source: | NIH/NCI |
| Role: | Collaborator |
| ID: | FP00021232 |
| Date: | 2024 - 2028 |
| Title: | Epigenetic mechanism and targeting during response to BRAFi/anti-EGFR therapy in BRAF-mutant colorectal cancers |
| Funding Source: | Department of Defense |
| Role: | PI |
| ID: | HT9425-24-1-0807 |
| Date: | 2024 - 2027 |
| Title: | Small molecule degraders of YAP1 |
| Funding Source: | Welch Foundation |
| Role: | PI |
| ID: | FP00021905 |
| Date: | 2024 - 2029 |
| Title: | Bhlhe40 Regulation of T Cell Function During Cancer Immunotherapy |
| Funding Source: | NIH/NCI |
| Role: | Co-I |
| ID: | R01CA1282027 |
| Date: | 2024 - 2026 |
| Title: | Targeting RNA Surveillance Machinery in NF1-mutant MPNST |
| Funding Source: | Department of Defense |
| Role: | PI |
| ID: | HT9425-24-1-0986 |
| Date: | 2023 - 2026 |
| Title: | The Histone Modifier UTX, Breast Cancer, and Drug Resistance |
| Funding Source: | Department of Defense (DOD) |
| Role: | Co-I |
| ID: | BC220789 |
| Date: | 2023 - 2028 |
| 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 |
| ID: | RP230301 |
| Date: | 2023 - 2028 |
| Title: | The Histone Modifier UTX in Triple-Negative and HER2-Positive Breast Cancer |
| Funding Source: | NIH/NCI |
| Role: | Co-I |
| ID: | r01-ca285540 |
| Date: | 2023 - 2028 |
| Title: | BCL9 Induced Enhancer Activation Drives Cellular Stemness and DCIS Malignancy |
| Funding Source: | NIH/NCI |
| Role: | Subaward PI |
| ID: | R01-CA276832 |
| Date: | 2023 - 2028 |
| Title: | LOXL2 as a Mediator of Immunotherapy Response in Melanoma |
| Funding Source: | NIH/NCI |
| Role: | PI |
| ID: | R01-CA276530 |
| Date: | 2023 - 2028 |
| Title: | Chromatin Structure in Melanoma Metastasis: Evolution, Regulation and Therapeutic Targeting |
| Funding Source: | NIH/NCI |
| Role: | PI |
| ID: | R01-CA285584 |
| Date: | 2023 - 2028 |
| Title: | MD Anderson Cancer Immune Monitoring and Analysis Center MDA-CIMAC |
| Funding Source: | NIH/NCI |
| Role: | Co-I |
| ID: | 2U24CA224285 |
| Date: | 2023 - 2028 |
| Title: | HORMAD-Specific TGF-Beta Resistant Memory T Cells for Treatment of Patients with Gastroesophageal Cancer |
| Funding Source: | NIH/NCI |
| Role: | MPI |
| ID: | UG3CA283615 |
| Date: | 2023 - 2028 |
| Title: | MD Anderson Epigenetics SPORE |
| Funding Source: | NIH/NCI |
| Role: | PI |
| ID: | P50CA281766 |
| Date: | 2023 - 2028 |
| Title: | MD Anderson Cancer Immune Monitoring and Analysis Center MDA-CIMAC |
| Funding Source: | NIH/NCI |
| Role: | Co-I |
| ID: | 2U24CA224285 |
| Date: | 2023 - 2028 |
| 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 |
| ID: | GRANT13723182 |
| Date: | 2023 - 2028 |
| Title: | Enhancers as Targets for Improvements in Immunotherapy |
| Funding Source: | NIH/NCI |
| Role: | PI |
| ID: | R01-CA282313 |
| Date: | 2023 - 2028 |
| Title: | Epigenetic Mechanisms and Therapies in KMT2D-Mutant Melanoma |
| Funding Source: | NIH/NCI |
| Role: | PI |
| ID: | 2-R01-CA222214 |
| Date: | 2023 - 2028 |
| Title: | Mechanisms of Fasting-Induced Radioprotection of Small Intestinal Epithelial Cells |
| Funding Source: | NIH/NCI |
| Role: | MPI |
| ID: | R01-CA269495 |
| Date: | 2023 - 2028 |
| Title: | Mechanisms of Fasting-Induced Radioprotection of Small Intestinal Epithelial Cells |
| Funding Source: | NIH/NCI |
| Role: | MPI |
| ID: | R01-CA269495 |
| Date: | 2023 - 2028 |
| Title: | Targeting Epigenetic Machinery to Overcome Myeloid Cell-Mediated Resistance to Anti-PD-1 Therapy in GBM |
| Funding Source: | NIH/NCI |
| Role: | Co-I |
| ID: | R01-CA279192 |
| Date: | 2023 - 2028 |
| Title: | In Vivo Chemistry as a New Approach to Treat Solid Tumors |
| Funding Source: | NIH/NCI |
| Role: | Collaborator |
| ID: | FP00017207 |
| Date: | 2023 - 2026 |
| 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 |
| ID: | RP240272 |
| Date: | 2023 - 2026 |
| Title: | The Epigenetic Modifier UTX, Breast Cancer, and Drug Resistance |
| Funding Source: | Cancer Prevention & Research Institute of Texas (CPRIT) |
| Role: | Co-I |
| ID: | BC220789 |
| Date: | 2023 - 2026 |
| Title: | Nuclear and Non-Canonical Function of Phosphorylated Dicer1 in Cancer |
| Funding Source: | Cancer Prevention & Research Institute of Texas (CPRIT) |
| Role: | Collaborator |
| ID: | RP230008 |
| Date: | 2022 - 2027 |
| Title: | Heterozygous KMT2D Loss and Medulloblastoma |
| Funding Source: | NIH/NCI |
| Role: | Co-I |
| ID: | R01CA262324 |
| Date: | 2022 - 2027 |
| Title: | LOXL2 as a mediator of immunotherapy response in melanoma |
| Funding Source: | NIH/NCI |
| Role: | PI |
| ID: | 1-R01-CA276530 |
| Date: | 2022 - 2027 |
| Title: | KMT2D as modulator of epigenome and immune microenvironment in HNSCC |
| Funding Source: | NIH/NCI |
| Role: | MPI |
| ID: | 1-R01-CA270361 |
| Date: | 2022 - 2027 |
| Title: | Defining and targeting alterations of the epigenetic modifier KMT2D in non-small cell lung cancer |
| Funding Source: | NIH/NCI |
| Role: | Co-I |
| ID: | 1-R01-CA275958 |
| Date: | 2022 - 2025 |
| Title: | Contribution of tumor epigenome to immune response that influence metastatic spread |
| Funding Source: | Department of Defense (DOD) |
| Role: | PI |
| ID: | ME210296 |
| Date: | 2022 - 2024 |
| Title: | Fasting-induced microbiome changes and radioprotection |
| Funding Source: | Cancer Prevention & Research Institute of Texas (CPRIT) |
| Role: | Co-PI |
| ID: | RP-220567 |
| Date: | 2022 - 2026 |
| Title: | Mechanisms and therapies focused on epigenomic alterations in therapy-resistant prostate cancers |
| Funding Source: | Cancer Prevention & Research Institute of Texas (CPRIT) |
| Role: | PI |
| ID: | RP220410 |
| Date: | 2021 - 2023 |
| Title: | PRC2-Dependent Enhancer Reprogramming Promotes MPNST Pathogenesis |
| Funding Source: | DOD/Congressionally Directed Medical Research Programs (DOD/CDMRP) |
| Role: | Co-I |
| ID: | W81XWH2010098 |
| Date: | 2021 - 2023 |
| Title: | Contribution of Epigenome to PRKCI-Driven High-Grade Serous Ovarian Cancer |
| Funding Source: | NIH/NCI |
| Role: | PI |
| ID: | R21-CA256278 |
| Date: | 2020 - 2024 |
| Title: | Role of RNA exosome in NF-1 mutant MPNSTs |
| Funding Source: | DOD/Congressionally Directed Medical Research Programs (DOD/CDMRP) |
| Role: | PI |
| ID: | W81XWH2010646 |
| Date: | 2020 - 2026 |
| Title: | MD Anderson Epigenetic Therapy Initiative (METI) |
| Funding Source: | The University of Texas MD Anderson Cancer Center Internal Funding |
| Role: | PI |
| Date: | 2020 - 2026 |
| Title: | UCHL5 as a regulator and therapeutic target in metastatic melanoma |
| Funding Source: | NIH/NCI |
| Role: | PI |
| ID: | 1-R01-CA245395 |
| Date: | 2020 - 2026 |
| Title: | Role of UBR7, a novel H2BK120 E3 ubiquitin ligase, in suppression of breast cancer |
| Funding Source: | NIH/NCI |
| Role: | PI |
| ID: | 1-R01-CA226269 |
| Date: | 2020 - 2024 |
| Title: | Heterogeneity of Enhancer Patterns in Colorectal Cancers - Mechanisms and Therapy |
| Funding Source: | Cancer Prevention & Research Institute of Texas (CPRIT) |
| Role: | PI |
| ID: | RP-200390 |
| Date: | 2019 - 2024 |
| Title: | Role of Aberrant Enhancer Activation in Colorectal Cancer |
| Funding Source: | American Cancer Society (ACS) |
| Role: | PI |
| ID: | RSG-19-187-01-DMC |
| Date: | 2019 - 2021 |
| Title: | Stratification of colorectal cancers based on enhancer patterns for epigenetic therapy |
| Funding Source: | NIH/NCI |
| Role: | PI |
| Date: | 2019 - 2021 |
| Title: | LoxL2 and H3K4 methylation as effectors of anti-PD1 response in melanoma |
| Funding Source: | UT MD Anderson Cancer Center |
| Role: | PI |
| Date: | 2019 - 2020 |
| Title: | Flagship 4 - Lymphoma Moonshots |
| Funding Source: | UT MD Anderson Cancer Center |
| Role: | Co-Leader |
| Date: | 2019 - 2024 |
| Title: | Patient-Derived Models of Prostate Cancer for Personalized Medicine |
| Funding Source: | NIH/NCI |
| Role: | Co-I |
| ID: | 1-U01-CA224044 |
| Date: | 2019 - 2024 |
| Title: | Synthetic Lethal Targeting of CREBBP/EP300 in Head and Neck Squamous Cell Carcinoma |
| Funding Source: | NIH/NIDCR |
| Role: | Co-I |
| ID: | 1-R01-DE028061 |
| Date: | 2018 - 2024 |
| Title: | Role of KMT2D and aberrant enhancers in modulation of tumor microenvironment in melanoma |
| Funding Source: | NIH/NCI |
| Role: | PI |
| ID: | 1-R01-CA222214 |
| Date: | 2018 - 2020 |
| Title: | Co-operative Roles For YAP1 and UCHL5 in Cancer Progression and Therapy |
| Funding Source: | NIH/NCI |
| Role: | PI |
| ID: | 1R21CA231654 |
| Date: | 2017 - 2022 |
| Title: | Role of HDAC8 and higher-order chromatin structure in melanoma metastasis |
| Funding Source: | Cancer Prevention & Research Institute of Texas (CPRIT) |
| Role: | PI |
| Date: | 2017 - 2020 |
| 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 |
| Date: | 2017 - 2020 |
| Title: | Epigenetic effectors of responses to immune checkpoint blockade agents |
| Funding Source: | Melanoma Research Alliance |
| Role: | PI |
| Date: | 2017 - 2020 |
| Title: | Epigenetic effectors of tumor response to immune checkpoint blockade therapy |
| Funding Source: | DOD/Congressionally Directed Medical Research Programs (DOD/CDMRP) |
| Role: | PI |
| Date: | 2017 - 2022 |
| Title: | Fasting Protects Small Intestinal Stem Cells from Lethal DNA Damage: Mechanistic Insight and Preclinical Translation |
| Funding Source: | NIH/NCI |
| Role: | Collaborator |
| Date: | 2016 - 2018 |
| Title: | Melanoma Research Foundation |
| Funding Source: | Melanoma Research Foundation |
| Role: | PI |
| Date: | 2016 - 2017 |
| Title: | Contribution of Epigenome to Head and Neck Cancer |
| Funding Source: | NIH/NCI |
| Role: | PI |
| ID: | Head and Neck SPORE |
| Date: | 2015 - 2017 |
| Title: | CRC Moonshot project #9 |
| Funding Source: | UTMDACC |
| Role: | Investigator |
| Date: | 2015 - 2016 |
| Title: | UTMDACC Lung SPORE: Career Enhancement Program Award |
| Funding Source: | NIH/NCI |
| Role: | Investigator |
| ID: | 5 P50 CA070907 17 |
| Date: | 2015 - 2016 |
| Title: | UTMDACC Brain SPORE - Career Enhancement Project |
| Funding Source: | NIH/NCI |
| Role: | PI |
| Date: | 2015 - 2016 |
| Title: | Characterization of epigenome in cancer cell lines |
| Funding Source: | UTMDACC |
| Role: | PI |
| Date: | 2015 - 2018 |
| Title: | Epigenetic of Melanoma Metastasis |
| Funding Source: | NIH/NCI |
| Role: | PI |
| ID: | 4R00CA160578-03 |
| Date: | 2014 - 2015 |
| Title: | UT MD Anderson Cancer Center Melanoma SPORE- Project 4 |
| Funding Source: | NIH/NCI |
| Role: | Co-I |
| ID: | CA093459 10 |
| Date: | 2014 - 2016 |
| Title: | Epigenetic regulators of metastasis in bladder cancer |
| Funding Source: | MDACC BLADDER CANCER SPORE |
| Role: | PI |
| Date: | 2013 - 2014 |
| Title: | Defining metastasis-specific higher-order chromatin structure in melanoma |
| Funding Source: | UTMDACC Center for Cancer Epigenetics |
| Role: | Co-PI |
| Date: | 2013 - 2015 |
| Title: | Epigenome changes during melanoma progression |
| Funding Source: | Center for Cancer Epigenetics |
| Role: | PI |
| Date: | 2011 - 2015 |
| Title: | Epigenetic of Melanoma Metastasis |
| Funding Source: | NIH/NCI |
| Role: | PI |
| Date: | 2010 - 2011 |
| 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 |
Selected Publications
Peer-Reviewed Articles
- Naara S, Kochat V, Rao X, Arslan E, Saddawi-Konefka R, Satpati S, Garbarino J, Anderson JL, Gleber-Netto FO, Nagarajan P, Kerr TD, Akhter S, Li S, Fodor R, Koyfman SA, Yaniv D, Xie T, Glaun M, Bobian M, Padron WI, Ng C, Gunaratne PH, Thevasagayampillai S, Migden MR, Abbas HA, Reville PK, Tsai KY, McGrail DJ, Wang J, Myers JN, Gross ND, Rai K, Amit M. Spatial biology reveals altered macrophage states in immunosuppressed non-melanoma skin cancer. Cell, 2026. e-Pub 2026. PMID: 42556334.
- Lee HM, Zheng Z, Sorokin A, Wong CW, Napolitano S, Chowdhury S, Kanikarla Marie P, Singh AK, Kochat V, Bristow CA, Srinivasan S, Peoples M, Arslan E, Alshenaifi JY, Villarreal OE, Morris VK, Shen JP, Meric-Bernstam F, Jain AK, Fowlkes NW, Anderson A, Menter DG, Saw AK, Rai K, Kopetz S. Reprogramming of Cellular Plasticity via ETS and MYC Core-Regulatory Circuits during Response to MAPK Inhibition in BRAF-Mutant Colorectal Cancer. Clin Cancer Res 32(15):3309-3324, 2026. e-Pub 2026. PMID: 42101296.
- Carter BZ, Mak PY, Satpati S, Ayoub E, Boettcher S, Ostermann LB, Wei Y, Garcia-Manero G, Haferlach T, Rai K, Andreeff M. The novel hypomethylating agent NTX-301 reprograms epigenetic and Hippo signaling pathways and exhibits pre-clinical activity in venetoclax-resistant and TP53-mutant AML. Clin Cancer Res, 2026. e-Pub 2026. PMID: 42439804.
- Audia A, Mattohti M, Ravikumar V, Garofano L, Emam A, Tang T, Huie EZ, Oizumi T, Villanueva DST, Esmaeili Anvar N, Garces AA, Vaillant BD, Rao A, Iavarone A, Katayama H, Rai K, Bhat KP. TAZ mediates enhancer reprogramming blocks neuronal differentiation in glioma stem-like cells. Sci Rep, 2026. e-Pub 2026. PMID: 42432169.
- Barrodia P, Saw AK, Jeter-Jones SL, Chang CC, Shao J, Arslan E, Singh AK, Satpati S, Jenq RR, Rai K, Piwnica-Worms H. Fasting primes small intestinal regeneration after damage via a microbiome-metabolite-chromatin axis. Proc Natl Acad Sci U S A 123(26):e2529215123, 2026. e-Pub 2026. PMID: 42335240.
- Mahmud MI, Kochat V, Anzum H, Satpati S, Dwarampudi JMR, Rai K, Banerjee T. NanoCellAnnotator: Formalizing Expert Cell Type Annotation with Large Language Models. bioRxiv, 2026. e-Pub 2026. PMID: 42395456.
- Mahmud MI, Kochat V, Anzum H, Satpati S, Dwarampudi JMR, Rai K, Banerjee T. Ambiguity-Aware Multi-Stage Cell-Type Annotation for Spatial Transcriptomics. bioRxiv, 2026. e-Pub 2026. PMID: 42395369.
- Malgulwar PB, Singh A, Saw AK, Danussi C, Dharmaiah S, Johnson WE, Machado AA, Barathi BB, Raman A, Satpati S, Rai K, Huse JT. ATRX inactivation disrupts global chromatin state and topology to dysregulate neurodevelopmental pathways in glioma pathogenesis. Nucleic Acids Res 54(12), 2026. e-Pub 2026. PMID: 42339622.
- Bae SS, Ling HH, Zhang J, Chen Y, Chen H, Kumar D, Saw AK, Rai K, Viny AD, DePinho RA, Giancotti FG. Mediator subunit MED4 enforces metastatic dormancy in breast cancer. Nat Cell Biol, 2026. e-Pub 2026. PMID: 42332201.
- Denu RA, Zheng Z, Jiang Y, Satpati S, Kochat V, Anand K, Truong DD, Lynch AR, Padron W, Ingram DR, Wani KM, Shamsutdinova D, Bhalla AD, Landers SM, Ratan R, Somaiah N, Roland CL, Torres KE, Van Loo P, Soliman PT, Meyer LA, Lazar AJ, Keung EZ, Haddad EFN, Rai K. Spatially-Resolved Multiomic Atlas of Leiomyosarcoma Identifies Two Clinically Relevant Epigenetically-Driven Cell States. bioRxiv, 2026. e-Pub 2026. PMID: 42244620.
- Schueddig E, Kochat V, Arslan E, Dallas Y, Yang P, Padron W, Li Z, Henry R, Lin J, Mattohti M, Madan R, Fields T, Golem S, Khan SA, Wagner JL, Larson KE, Balanoff C, Aripoli A, Huppe A, Winblad O, Peterson J, Hill M, Smith C, Jeffers EJ, Kilgore LJ, Zang C, Wei P, Navin N, Fabian C, Lewis MT, Zhu Q, Thompson A, Godwin AK, Koestler DC, Rai K, Behbod F. Cellular stemness identifies high-risk ductal carcinoma in situ and offers a therapeutic interception opportunity. bioRxiv, 2026. e-Pub 2026. PMID: 42182462.
- Bentebibel SE, McGrail DJ, Kochat V, Arslan E, Abdel-Wahab R, Pazdrak B, Murthy R, Tahon NHM, Cho SN, Duose DY, Wani K, Liu J, Haymaker C, Gomez JA, Sonnemann H, Katailiha AS, Nassif-Rausseo B, Rahim M, Li I, Mayer AT, Yang X, Hsu FJ, Zhang J, Johnson DH, Amaria RN, Glitza Oliva IC, Patel SP, Hwu P, Elsayes KM, Tawbi HA, Burks JK, Bernatchez C, Davies MA, Rai K, Lizee G, Ekmekcioglu S, Diab A. Intratumoral sotigalimab with pembrolizumab induces rapid activation of antigen presenting cells and drives anti-tumor responses in non-injected tumors in metastatic melanoma: A phase I/II study. Cancer Discov, 2026. e-Pub 2026. PMID: 42013310.
- Huang C, Moorthy S, Li Q, Ahmed KM, Saab K, Deng D, Wang J, Rao X, Zhang J, Xi Y, Wang J, Liu Z, Tanaka N, Wheeler DA, Shinbrot E, Saade R, Pickering CR, Xie TX, El-Naggar AK, Osman AA, Rai K, Zweidler-McKay PA, Heymach JV, Byers LA, Johnson FM, Sandulache VC, Myers JN, Yadollahi P, Frederick MJ. NOTCH1 acts as a tumor suppressor that induces early differentiation in head and neck cancer. JCI Insight, 2026. e-Pub 2026. PMID: 41989846.
- Anzum H, Kochat V, Satpati S, Mahmud MI, Dwarampudi JMR, Shukla P, Javle M, Kwong L, Rai K, Banerjee T. A Counterfactual Framework for Directional Cell-Cell Interaction Analysis in Spatial Transcriptomics. bioRxiv, 2026. e-Pub 2026. PMID: 42005861.
- Dwarampudi JMR, Kochat V, Satpati S, Mahmud MI, Anzum H, Wani K, Lazar A, Saw AK, Malke J, Nguyen HV, Rai K, Banerjee T. Spatially Anchored Regulatory State Inference in Melanoma. bioRxiv, 2026. e-Pub 2026. PMID: 41993479.
- Denu RA, Kochat V, Zheng Z, Satpati S, Truong DD, Arslan E, Weistuch C, Divenko M, Wu M, Padron W, Ingram DR, Wani KM, Wang WL, Landers SM, Beird HC, McCuisto JL, Simmons A, Albertorio-Saez LM, Maryanski DN, Szany CC, Venters BJ, Windham CL, Keogh MC, Torres KE, Roland CL, Keung EZ, Haddad EFN, Lazar AJ, Ludwig JA, Somaiah N, Rai K. Spatially-resolved single cell atlas of liposarcoma reveals lineage hierarchies, immune niches, and regulatory circuits. bioRxiv, 2026. e-Pub 2026. PMID: 41929055.
- Barrodia P, Saw AK, Jeter-Jones SL, Chang CC, Shao J, Arslan E, Singh AK, Satpati S, Jenq RR, Rai K, Piwnica-Worms H. Fasting primes small intestinal regeneration after damage via a microbiome-metabolite-chromatin axis. bioRxiv, 2026. e-Pub 2026. PMID: 41867705.
- Mahmud MI, Kochat V, Satpati S, Dwarampudi JMR, Anzum H, Rai K, Banerjee T. hSNMF: Hybrid Spatially Regularized NMF for Image-Derived Spatial Transcriptomics. ArXiv, 2026. e-Pub 2026. PMID: 41675352.
- Le NB, Sona S, Santo B, Zhang Y, Ou R, Schweickart RA, Kochat V, Padron WI, Rai K, Lee SH, Yi JM, Wessely O, Lee BH, Ting AH. Differentiation in the human urothelia is defined by distinct alternative polyadenylation. Cell Rep 45(1):116839, 2026. e-Pub 2026. PMID: 41533515.
- Alonso S, Raghav K, Morris VK, Alfaro-Munoz K, Bekaii-Saab T, Cannon TL, Corcoran RB, Duesbery N, George M, Hsu D, Lieu C, Maitra A, Maru D, McQuerry JA, Menter D, Mizrahi J, Ng K, Parikh A, Rai K, Sangar MC, Shaw KR, Shen JP, Strickler JH, Feehan AD, Tam AL, Vetere G, Yaeger R, Yuan Y, Shen X, Bild AH, Kopetz S. Framework for cancer evolution profiling and interception in colorectal cancer: ASCEND-CRC program. Cancer Cell, 2026. e-Pub 2026. PMID: 41512869.
- Santo BA, Fink EE, Desprez PE, Lin YC, Eltemamy M, Wee A, Le NB, Krylova A, Tran U, Kochat V, Rai K, Strand DW, Wessely O, Lee BH, Ting AH. A poly(A) isoform-aware single-cell and spatial atlas defines fibroblast niches in the human bladder. bioRxiv, 2025. e-Pub 2025. PMID: 41473332.
- Garg V, Mathew R, Rai K, Shin J, Ghosh SK. Interplay of tail length and confinement in the formation of interior loops in flexible chains. J Chem Phys 163(13), 2025. e-Pub 2025. PMID: 41055199.
- Yang J, Wang C, Fu D, Ho LL, Galani K, Chen L, Gonzalez J, Fu J, Huang AY, Frederick DT, He L, Asnani M, Tacke R, Robitschek EJ, Yadav SK, Deng W, Burke KP, Sharova T, Sullivan RJ, Weiss S, Rai K, Liu D, Boland GM, Kellis M. Mature and migratory dendritic cells promote immune infiltration and response to anti-PD-1 checkpoint blockade in metastatic melanoma. Nat Commun 16(1):8151, 2025. e-Pub 2025. PMID: 40890106.
- Baruch EN, Gleber-Netto FO, Nagarajan P, Rao X, Akhter S, Eichwald T, Xie T, Balood M, Adewale A, Naara S, Sathishkumar HN, Islam S, McCarthy W, Mattson BJ, Ferrarotto R, Wong MK, Davies MA, Jindal S, Basu S, Roversi K, Nikpoor AR, Ahmadi M, Ahmadi A, Harwood C, Leigh I, Gong D, Tallon de Lara P, Tao DL, Davidson TM, Ajami NJ, Futreal A, Rai K, Kochat V, Castillo M, Gunaratne P, Goepfert RP, Hernandez SD, Khushalani NI, Wang J, Watowich SS, Calin GA, Migden MR, Yuan M, Liu N, Ye Y, Hwang WL, Vermeer PD, D'Silva NJ, Bunimovich YL, Yaniv D, Burks JK, Gomez J, Dougherty PM, Tsai KY, Allison JP, Sharma P, Wargo JA, Myers JN, Talbot S, Gross ND, Amit M. Cancer-induced nerve injury promotes resistance to anti-PD-1 therapy. Nature, 2025. e-Pub 2025. PMID: 40836096.
- Lee HM, Zheng Z, Sorokin A, Wong CW, Napolitano S, Chowdhury S, Kanikarla PM, Singh AK, Kochat V, Bristow CA, Srinivasan S, Peoples M, Arslan E, Alshenaifi JY, Villarreal OE, Morris VK, Shen JP, Meric-Bernstam F, Jain AK, Fowlkes NW, Anderson A, Menter DG, Saw AK, Rai K, Kopetz S. Reprogramming of Cellular Plasticity via ETS and MYC Core-regulatory Circuits During Response to MAPK Inhibition in BRAF-mutant Colorectal Cancer. bioRxiv, 2025. e-Pub 2025. PMID: 40611889.
- Zhu B, Chen P, Aminu M, Li JR, Fujimoto J, Tian Y, Hong L, Chen H, Hu X, Li C, Vokes N, Moreira AL, Gibbons DL, Solis Soto LM, Parra Cuentas ER, Shi O, Diao S, Ye J, Rojas FR, Vilar E, Maitra A, Chen K, Navin N, Nilsson M, Huang B, Heeke S, Zhang J, Haymaker CL, Velcheti V, Sterman DH, Kochat V, Padron WI, Alexandrov LB, Wei Z, Le X, Wang L, Fukuoka J, Lee JJ, Wistuba II, Pass HI, Davis M, Hanash S, Cheng C, Dubinett S, Spira A, Rai K, Lippman SM, Futreal PA, Heymach JV, Reuben A, Wu J, Zhang J. Spatial and multiomics analysis of human and mouse lung adenocarcinoma precursors reveals TIM-3 as a putative target for precancer interception. Cancer Cell 43(6):1125-1140.e10, 2025. e-Pub 2025. PMID: 40345189.
- Jammihal T, Saliby RM, Labaki C, Soulati H, Gallegos J, Peris A, McCurry D, Yu C, Shah V, Poduval D, El Zarif T, El Ahmar N, Laimon YN, Eid M, Sheshdeh AB, Krajewski KM, Buttner FA, Schwab M, Heng D, Casellas RC, Rai K, Zacharias Millward NM, Msaouel P, Karam J, Signoretti S, Van Allen E, Choueiri TK, Braun DA, Shukla SA. Immunogenomic determinants of exceptional response to immune checkpoint inhibition in renal cell carcinoma. Nat Cancer 6(2):372-384, 2025. e-Pub 2025. PMID: 39789182.
- 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. e-Pub 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. e-Pub 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, 2024. e-Pub 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), 2024. e-Pub 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. e-Pub 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. e-Pub 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 2024. 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 2022. PMID: 34059508.
- 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.
- 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.
- 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. e-Pub 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. e-Pub 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. e-Pub 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. e-Pub 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. e-Pub 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. e-Pub 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. e-Pub 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. e-Pub 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. e-Pub 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. e-Pub 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. e-Pub 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 2010. 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. e-Pub 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. e-Pub 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. e-Pub 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. e-Pub 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. e-Pub 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 2016. PMID: 27314083.
Review 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. e-Pub 2024. PMID: 38266066.
- Wu M, Rai K. Demystifying extrachromosomal DNA circles: Categories, biogenesis, and cancer therapeutics. Comput Struct Biotechnol J 20:6011-6022, 2022. e-Pub 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. e-Pub 2021. PMID: 34245839.
Other Articles
- Bild, AH, Sangar, MC, McQuerry, JA, Ideker, T, Kopetz, S, Carey, L, Nath, A, Marcus, D, Regier, AA, Rashid, N, Barzilay, R, Winer, EP, Salgia, R, Malhotra, J, Gentles, A, Buetow, K, Mahmood, F, Markman, DW, Eddy, J, Afkhami, M, Alfaro-Munoz, KD, Alonso Martinez, S, Alpert, K, Anampa, J, Bafna, V, Balic, M, Balko, JM, Barzilay, R, Bates, S, Bekaii-Saab, T, Bernard-Pagan, V, Bild, A, Boland, GM, Borad, MJ, Buetow, K, Buhle, L, Burns, R, Cannon, TL, Carey, LA, Castelnovo, LF, Chen, R, Cianfrocca, M, Clark, A, Hamilton, SR, Kopetz, S, Maru, DM, Menter, DG, Raghav, KS, Rai, K, Tayob, N The ADAPT learning cancer treatment system. Cancer cell 44(3):449-454, 2026. PMID: 41512871.
Book Chapters
- Tang M, Rai K. Chapter 20 - Computational Analysis of Epigenetic Modifications in Melanoma. In: Computational Epigenetics and Diseases. Academic Press, 327-342, 2019.
Patents
- Chin L, Scott KL, Ghosh P, Rai K, Min C. Method of predicting prognosis in cancer. Patent Number: US20140302042 A1.
- Jones DA, Cairns BR, Rai K. Identification and regulation of a novel DNA demethylase system. Patent Number: US2011/0318738 A1.
Patient Reviews
CV information above last modified September 14, 2026