SAIKAT CHOWDHURY, PHD
Department of Gastrointestinal Medical Oncology, Division of Cancer Medicine
About Dr. SAIKAT CHOWDHURY
Dr. Saikat Chowdhury is a computational biologist whose research applies cancer genomics, multi-omics integration, and ML/AI models to precision oncology in gastrointestinal malignancies, with a focus on colorectal cancer (CRC) and appendiceal adenocarcinoma (AA).
Working within the laboratory of Dr. John Paul Shen, he combines large-scale molecular multi-omics profiling with clinically annotated real-world data to define tumor subtypes, identify biomarkers of therapeutic response and resistance, and improve patient stratification. His work has helped establish consensus molecular subtype (CMS) classification as a predictor of benefit from anti-EGFR therapy in metastatic CRC, introduced a single-cell approach to CMS assignment that resolves the contributions of tumor, immune, and stromal cells to bulk subtype calls, and characterized mechanisms of resistance to KRAS-targeted therapy in CRC and AA. He also contributes to molecular subtyping of appendiceal adenocarcinoma, a rare cancer for which disease-specific evidence remains limited, and to preclinical studies of KRAS and pan-RAS inhibition in appendiceal organoid and PDX models. He is also involved in the Foundational AI project at MD Anderson Cancer Center to develop computational models using large language models (LLMs) to predict response and molecular determinants to first-line and neoadjuvant chemotherapy in GI cancers.
Dr. Chowdhury received his Ph.D. in Biological Sciences from CSIR–National Chemical Laboratory, India, and joined MD Anderson in 2019. He has authored more than 35 peer-reviewed publications, with first-author work in the Journal of Hematology & Oncology, British Journal of Cancer, Molecular Cancer Research (Editors' Pick, April 2024), and JCO Precision Oncology. He is a three-time recipient of the AACR Scholar-in-Training Award and presented in a mini-symposium session at the AACR Annual Meeting 2024. He mentors trainees in computational cancer biology, and serves as a reviewer for leading journals in cancer and related topics.
Present Title & Affiliation
Primary Appointment
Instructor, Gastrointestinal and Medical Oncology - Research, Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
Selected Publications
Peer-Reviewed Articles
- Chowdhury S, Ito I, Pattalachinti VK, Yousef AMG, Yousef MMG, El Khoury S, Hornstein N, Seldomridge AN, Hong D, Overman MJ, Taggart MW, Foo WC, Helmink B, Fournier KF, Shen JP. KRAS inhibition is an effective therapy for appendiceal adenocarcinoma. J Hematol Oncol, 2026. e-Pub 2026. PMID: 42393724.
- 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. Clin Cancer Res, 2026. e-Pub 2026. PMID: 42101296.
- Maddalena G, Zeineddine FA, Chowdhury S, Zeineddine MA, Yousef AM, Bergamo F, Lonardi S, Yap TA, White MG, Overman MJ, Kopetz S, Shen JP. Prognosis and treatment response stratification according to loss of proofreading (LOP) POLE variants. J Immunother Cancer 13(11), 2025. e-Pub 2025. PMID: 41253491.
- Ciombor KK, Bae SW, Whisenant JG, Ayers GD, Sheng Q, Peterson TE, Smith GT, Lin K, Chowdhury S, Kanikarla Marie P, Sorokin A, Cohen AS, Goff LW, Cardin DB, Shen JP, Kopetz S, Eng C, Shyr Y, Berlin J, Manning HC. Results of the Phase I/II Study and Preliminary B-cell Gene Signature of Combined Inhibition of Glutamine Metabolism and EGFR in Colorectal Cancer. Clin Cancer Res 31(8):1437-1448, 2025. e-Pub 2025. PMID: 39927885.
- Ito I, Pattalachinti VK, Yousef AM, Chowdhury S, Fanaeian MM, Haque E, Gunes BB, Yousef M, Salle ER, Zeineddine MA, Ji S, Li R, Wang W, Helmink BA, Taggart MW, White MG, Fournier KF, Fowlkes NW, Shen JP. Development and characterization of orthotopic patient-derived xenograft models of peritoneal metastatic mucinous appendiceal adenocarcinoma. ESMO Gastrointest Oncol 7, 2025. e-Pub 2025. PMID: 41069644.
- Pattalachinti VK, Haque E, Yousef M, Yousef A, Chowdhury S, Overman M, Parseghian CM, Morris VK, Kee B, Huey RW, Raghav K, Court CM, Shen JP. BRAF mutant appendiceal adenocarcinoma differs from colorectal cancer but responds to BRAF-targeted therapy. NPJ Precis Oncol 9(1):38, 2025. e-Pub 2025. PMID: 39910160.
- White MG, Zeineddine MA, Fallon EA, Zeineddine FA, Dansby J, Chowdhury S, Hornstein N, Yousef A, Yousef M, Bhutiani N, Gu Y, Kee B, Dasari A, Overman MJ, Raghav K, Kopetz S, Uppal A, Taggart M, Newhook T, Fournier K, Helmink B, Drusbosky LM, Shen JP. The Landscape of ctDNA in Appendiceal Adenocarcinoma. Clin Cancer Res 31(3):551-560, 2025. e-Pub 2025. PMID: 39679931.
- Gunes BB, Hornstein NJ, Wang M, Yousef M, Fanaeian MM, Yousef A, Chowdhury S, Zeineddine MA, Haymaker C, Helmink B, Fournier K, Shen JP. Single-cell RNA sequencing of appendiceal adenocarcinoma reveals a low proportion of epithelial cells and a fibroblast enriched tumor microenvironment. ESMO Gastrointest Oncol 6:100094, 2024. e-Pub 2024. PMID: 41646948.
- Yousef M, Yousef A, Chowdhury S, Fanaeian MM, Knafl M, Peterson J, Zeineddine M, Alfaro K, Zeineddine F, Goldstein D, Hornstein N, Dasari A, Huey R, Johnson B, Higbie V, Bent A, Kee B, Lee M, Morelli MP, Morris VK, Halperin D, Overman MJ, Parseghian C, Vilar E, Wolff R, Raghav KP, White MG, Uppal A, Sun R, Wang W, Kopetz S, Willis J, Shen JP. Molecular, Socioeconomic, and Clinical Factors Affecting Racial and Ethnic Disparities in Colorectal Cancer Survival. JAMA Oncol 10(11):1519-1529, 2024. e-Pub 2024. PMID: 39264607.
- Chowdhury S, Xiu J, Ribeiro JR, Nicolaides T, Zhang J, Korn WM, Poorman KA, Lenz HJ, Marshall JL, Oberley MJ, Sledge GW Jr, Spetzler D, Kopetz S, Shen JP. Consensus molecular subtyping of metastatic colorectal cancer expands biomarker-directed therapeutic benefit for patients with CMS1 and CMS2 tumors. Br J Cancer 131(8):1328-1339, 2024. e-Pub 2024. PMID: 39227409.
- Klomp JA, Klomp JE, Stalnecker CA, Bryant KL, Edwards AC, Drizyte-Miller K, Hibshman PS, Diehl JN, Lee YS, Morales AJ, Taylor KE, Peng S, Tran NL, Herring LE, Prevatte AW, Barker NK, Hover LD, Hallin J, Sorokin A, Kanikarla PM, Chowdhury S, Coker O, Lee HM, Goodwin CM, Gautam P, Olson P, Christensen JG, Shen JP, Kopetz S, Graves LM, Lim KH, Wang-Gillam A, Wennerberg K, Cox AD, Der CJ. Defining the KRAS- and ERK-dependent transcriptome in KRAS-mutant cancers. Science 384(6700):eadk0775, 2024. e-Pub 2024. PMID: 38843331.
- Lin K, Chowdhury S, Zeineddine MA, Zeineddine FA, Hornstein NJ, Villarreal OE, Maru DM, Haymaker CL, Vauthey JN, Chang GJ, Bogatenkova E, Menter D, Kopetz S, Shen JP. Identification of Colorectal Cancer Cell Stemness from Single-Cell RNA Sequencing. Mol Cancer Res 22(4):337-346, 2024. e-Pub 2024. PMID: 38156967.
- Pattalachinti VK, Ito I, Chowdhury S, Yousef A, Gu Y, Gunes BB, Salle ER, Taggart MW, Fournier K, Fowlkes NW, Shen JP. Peritoneal Microenvironment Promotes Appendiceal Adenocarcinoma Growth: A Multi-omics Approach Using Patient-Derived Xenografts. Mol Cancer Res 22(4):329-336, 2024. e-Pub 2024. PMID: 38226984.
- Yousef A, Yousef M, Zeineddine MA, More A, Fanaeian M, Chowdhury S, Knafl M, Edelkamp P, Ito I, Gu Y, Pattalachinti V, Naini ZA, Zeineddine FA, Peterson J, Alfaro K, Foo WC, Jin J, Bhutiani N, Higbie V, Scally CP, Kee B, Kopetz S, Goldstein D, Strach M, Williamson A, Aziz O, Barriuso J, Uppal A, White MG, Helmink B, Fournier KF, Raghav KP, Taggart MW, Overman MJ, Shen JP. Serum Tumor Markers and Outcomes in Patients With Appendiceal Adenocarcinoma. JAMA Netw Open 7(2):e240260, 2024. e-Pub 2024. PMID: 38416491.
- Yousef A, Yousef M, Chowdhury S, Abdilleh K, Knafl M, Edelkamp P, Alfaro-Munoz K, Chacko R, Peterson J, Smaglo BG, Wolff RA, Pant S, Lee MS, Willis J, Overman M, Doss S, Matrisian L, Hurd MW, Snyder R, Katz MHG, Wang H, Maitra A, Shen JP, Zhao D. Impact of KRAS mutations and co-mutations on clinical outcomes in pancreatic ductal adenocarcinoma. NPJ Precis Oncol 8(1):27, 2024. e-Pub 2024. PMID: 38310130.
- Ito I, Yousef AMG, Chowdhury S, Dickson PN, Naini ZA, White MG, Fleten KG, Flatmark K, Fournier KF, Fowlkes NW, Shen JP. Intraperitoneal Paclitaxel Is a Safe and Effective Therapeutic Strategy for Treating Mucinous Appendiceal Adenocarcinoma. Cancer Res 83(19):3184-3191, 2023. e-Pub 2023. PMID: 37433032.
- Yousef A, Yousef M, Zeineddine M, More A, Chowdhury S, Knafl M, Edelkamp P, Ito I, Gu Y, Pattalachinti V, Naini ZA, Zeineddine F, Peterson J, Alfaro K, Foo WC, Jin J, Bhutiani N, Higbie V, Scally C, Kee B, Kopetz S, Goldstein D, Uppal A, White MG, Helmink B, Fournier K, Raghav K, Taggart M, Overman MJ, Shen JP. The Clinical Significance of CEA, CA19-9, and CA125 in Management of Appendiceal Adenocarcinoma. medRxiv, 2023. e-Pub 2023. PMID: 37745596.
- Chowdhury S, Gupta R, Millstein J, Lin K, Haridas V, Zeineddine MA, Parseghian C, Lenz HJ, Kopetz S, Shen JP. Transcriptional Profiling and Consensus Molecular Subtype Assignment to Understand Response and Resistance to Anti-Epidermal Growth Factor Receptor Therapy in Colorectal Cancer. JCO Precis Oncol 7:e2200422, 2023. e-Pub 2023. PMID: 37487150.
- Zeineddine FA, Zeineddine MA, Yousef A, Gu Y, Chowdhury S, Dasari A, Huey RW, Johnson B, Kee B, Lee MS, Morelli MP, Morris VK, Overman MJ, Parseghian C, Raghav K, Willis J, Wolff RA, Kawaguchi Y, Vauthey JN, Sun R, Kopetz S, Shen JP. Survival improvement for patients with metastatic colorectal cancer over twenty years. NPJ Precis Oncol 7(1):16, 2023. e-Pub 2023. PMID: 36781990.
- More A, Ito I, Haridas V, Chowdhury S, Gu Y, Dickson P, Fowlkes N, Shen JP. Oncogene addiction to GNAS in GNAS(R201) mutant tumors. Oncogene 41(35):4159-4168, 2022. e-Pub 2022. PMID: 35879396.
- Chowdhury S, Hofree M, Lin K, Maru D, Kopetz S, Shen JP. Implications of Intratumor Heterogeneity on Consensus Molecular Subtype (CMS) in Colorectal Cancer. Cancers (Basel) 13(19), 2021. e-Pub 2021. PMID: 34638407.
- Henry JT, Coker O, Chowdhury S, Shen JP, Morris VK, Dasari A, Raghav K, Nusrat M, Kee B, Parseghian C, Pant S, Jeyakumar N, Zhu L, Nishioka Y, Fogelman D, Wolff RA, Hong D, Overman MJ, Vauthey J, Kopetz S, Johnson B. Comprehensive Clinical and Molecular Characterization of KRAS (G12C)-Mutant Colorectal Cancer. JCO Precis Oncol 5, 2021. e-Pub 2021. PMID: 34250391.
Letters to the Editor
- Yousef M, Yousef A, Hurd MW, Pillai A, Chowdhury S, Snyder R, Knafl M, Lewis RL, Roy PM, Fanaeian M, Albarouki S, Castelnovo LF, Peterson J, Smaglo BG, Wolff RA, Pant S, Willis J, Huey R, Overman M, Tzeng CW, Kim MP, Ikoma N, Maxwell JE, Katz MHG, Wang H, Maitra A, Koay E, Ludmir EB, Chen A, Lopez C, Ying H, Shen JP, Zhao D. KRAS mutation detection by liquid biopsy for pancreatic ductal adenocarcinoma. J Hematol Oncol 18: 44, 2025.
- Maddalena G, Zeineddine FA, Rivero-Hinojosa S, Aushev VN, Chowdhury S, Zeineddine MA, Yousef AM, Yap TA, EINaggar AC, Liu MC, White M, Overman MJ, Kopetz S, Shen JP. Defining the subset of mutations in polymerase epsilon (POLE) associated with loss-of-proofreading (LOP) functionality. Ann Oncol 35: 678-680, 2024.
Patient Reviews
CV information above last modified September 17, 2026