Research Summary

The Bandyopadhyay lab employs new cellular and molecular technologies to tackle the most urgent and clinically important problems in cancer therapy, including functional genomics, drug screens, proteomics and single cell approaches. Critically, these technologies often generate the scale and complexity of data that necessitate the development of new computational algorithms to maximize their impact and fully understand their relevance in the clinic. The lab is focused on identifying mechanisms of drug resistance and targetable synthetic lethal interactions in breast and lung cancers since these diseases are deadly in the metastatic setting and demonstrate suboptimal tumor responses even with out best, most targeted therapies. We are committed to the identification, mechanistic dissection and clinical translation of new targets and target combinations through broad collaborations with biotechnologists, chemists, clinicians and pharma.

Research Funding

  • February 20, 2020 - January 31, 2025 - Stress responses drive resistance and shape tumor evolution in EGFR mutant lung cancer , Principal Investigator . Sponsor: NIH, Sponsor Award ID: R01CA238236
  • August 10, 2017 - July 31, 2022 - The Cancer Target Discovery and Development Network at UCSF , Co-Principal Investigator . Sponsor: NIH, Sponsor Award ID: U01CA217882
  • September 1, 2014 - June 30, 2019 - Physical and Genetic Interaction Landscape of the Tyrosine Kinome , Principal Investigator . Sponsor: NIH, Sponsor Award ID: R01GM107671
  • June 26, 2013 - May 31, 2018 - Multiscale analysis of influenza host-pathogen interactions: Fluomics , Co-Investigator . Sponsor: NIH, Sponsor Award ID: U19AI106754


University of Wisconsin - Madison, BS, 5/02, Molecular Biology
University of Wisconsin - Madison, BS, 5/02, Computer Science
University of California, San Diego, PhD, 5/10, Bioinformatics and Systems Biology

Honors & Awards

  • 2009-2010
    Associate Member, Faculty of 1000
  • 2010-2012
    UCSF QB3/Cancer Center Faculty Fellow
  • 2011
    UCSF Breast SPORE Career Development Award

Selected Publications

  1. Yu K, Basu A, Yau C, Wolf DM, Goodarzi H, Bandyopadhyay S, Korkola JE, Hirst GL, Asare S, DeMichele A, Hylton N, Yee D, Esserman L, van 't Veer L, Sirota M. Computational drug repositioning for the identification of new agents to sensitize drug-resistant breast tumors across treatments and receptor subtypes. Front Oncol. 2023; 13:1192208.  View on PubMed
  2. Meng D, Zhao X, Yang YC, Navickas A, Helland C, Goodarzi H, Singh M, Bandyopadhyay S. A bi-steric mTORC1-selective inhibitor overcomes drug resistance in breast cancer. Oncogene. 2023 Jul; 42(28):2207-2217.  View on PubMed
  3. Brand TM, Hartmann S, Bhola NE, Li H, Zeng Y, O'Keefe RA, Ranall MV, Bandyopadhyay S, Soucheray M, Krogan NJ, Kemp C, Duvvuri U, LaVallee T, Johnson DE, Ozbun MA, Bauman JE, Grandis JR. Correction: Cross-talk Signaling between HER3 and HPV16 E6 and E7 Mediates Resistance to PI3K Inhibitors in Head and Neck Cancer. Cancer Res. 2022 Sep 02; 82(17):3187.  View on PubMed
  4. Brand TM, Hartmann S, Bhola NE, Li H, Zeng Y, O'Keefe RA, Ranall MV, Bandyopadhyay S, Soucheray M, Krogan NJ, Kemp C, Duvvuri U, LaVallee T, Johnson DE, Ozbun MA, Bauman JE, Grandis JR. Editor's Note: Cross-talk Signaling between HER3 and HPV16 E6 and E7 Mediates Resistance to PI3K Inhibitors in Head and Neck Cancer. Cancer Res. 2022 Sep 02; 82(17):3188.  View on PubMed
  5. Kim SH, Song JH, Kim MJ, Song MG, Ku AA, Bandyopadhyay S, McCormick F, Kim SE. Novel Regulators of Macropinocytosis-Dependent Growth Revealed by Informer Set Library Screening in Pancreatic Cancer Cells. Metabolites. 2022 Sep 02; 12(9).  View on PubMed
  6. John Gordan, Adriana Pitea, Rigney E Turnham, Manon Eckhardt, Gwendolyn M Jang, Huat Lim, Alex L Choi, Sourav Bandyopadhyay, Danielle Swaney, Kevan Shokat, Trey Ideker, Nevan Krogan. Abstract PO017: HBV alters YAP regulation in liver cancer by remodeling PP2A complexes. Clinical Cancer Research. 2022 Sep 1; 28(17_Supplement):po017-po017.  View on PubMed
  7. Wong DR, Conrad J, Johnson N, Ayers J, Laeremans A, Lee JC, Lee J, Prusiner SB, Bandyopadhyay S, Butte AJ, Paras NA, Keiser MJ. Trans-channel fluorescence learning improves high-content screening for Alzheimer's disease therapeutics. Nat Mach Intell. 2022 Jun; 4(6):583-595.  View on PubMed
  8. Wolfe AL, Zhou Q, Toska E, Galeas J, Ku AA, Koche RP, Bandyopadhyay S, Scaltriti M, Lebrilla CB, McCormick F, Kim SE. UDP-glucose pyrophosphorylase 2, a regulator of glycogen synthesis and glycosylation, is critical for pancreatic cancer growth. Proc Natl Acad Sci U S A. 2021 08 03; 118(31).  View on PubMed
  9. Brand TM, Hartmann S, Bhola NE, Peyser ND, Li H, Zeng Y, Wechsler EI, Ranall MV, Bandyopadhyay S, Duvvuri U, LaVallee TM, Jordan RCK, Johnson DE, Grandis JR. Correction: Human Papillomavirus Regulates HER3 Expression in Head and Neck Cancer: Implications for Targeted HER3 Therapy in HPV+ Patients. Clin Cancer Res. 2021 Jul 15; 27(14):4129.  View on PubMed
  10. Collin M. Blakely, Matthew A. Gubens, Gregory M. Allen, Shrusti Shah, Matthew Jereza, Bianca Bacaltos, Sourav Bandyopadhyay. Phase I study of the aurora kinase A inhibitor alisertib in combination with osimertinib in EGFR-mutant lung cancer. Journal of Clinical Oncology. 2021 May 20; 39(15_suppl):9074-9074.  View on PubMed
  11. Kim D, Bandyopadhyay S. Aurora kinases shed light on resistance to EGFR inhibition in head and neck cancer. EBioMedicine. 2021 03; 65:103257.  View on PubMed
  12. Pucciarelli D, Angus SP, Huang B, Zhang C, Nakaoka HJ, Krishnamurthi G, Bandyopadhyay S, Clapp DW, Shannon K, Johnson GL, Nakamura JL. Nf1-Mutant Tumors Undergo Transcriptome and Kinome Remodeling after Inhibition of either mTOR or MEK. Mol Cancer Ther. 2020 11; 19(11):2382-2395.  View on PubMed
  13. Maynard A, McCoach CE, Rotow JK, Harris L, Haderk F, Kerr DL, Yu EA, Schenk EL, Tan W, Zee A, Tan M, Gui P, Lea T, Wu W, Urisman A, Jones K, Sit R, Kolli PK, Seeley E, Gesthalter Y, Le DD, Yamauchi KA, Naeger DM, Bandyopadhyay S, Shah K, Cech L, Thomas NJ, Gupta A, Gonzalez M, Do H, Tan L, Bacaltos B, Gomez-Sjoberg R, Gubens M, Jahan T, Kratz JR, Jablons D, Neff N, Doebele RC, Weissman J, Blakely CM, Darmanis S, Bivona TG. Therapy-Induced Evolution of Human Lung Cancer Revealed by Single-Cell RNA Sequencing. Cell. 2020 09 03; 182(5):1232-1251.e22.  View on PubMed
  14. Andrew L. Wolfe, Jacqueline Galeas, Eneda Toska, Qing Zhou, Angel Ku, Richard P. Koche, Sourav Bandyopadhyay, Carlito B. Lebrilla, Maurizio Scaltriti, Frank McCormick, Sung Eun Kim. Abstract 1470: UGP2 is a critical regulator of protein glycosylation in pancreatic cancer. Cancer Research. 2020 Aug 15; 80(16_Supplement):1470-1470.  View on PubMed
  15. Wu CH, Yang CY, Wang L, Gao HX, Rakhshandehroo T, Afghani S, Pincus L, Balassanian R, Rubenstein J, Gill R, Bandyopadhyay S, McCormick F, Moasser M, Ai WZ. Cutaneous T-Cell Lymphoma PDX Drug Screening Platform Identifies Cooperation between Inhibitions of PI3Kα/δ and HDAC. J Invest Dermatol. 2021 02; 141(2):364-373.  View on PubMed
  16. Ku AA, Hu HM, Zhao X, Shah KN, Kongara S, Wu D, McCormick F, Balmain A, Bandyopadhyay S. Integration of multiple biological contexts reveals principles of synthetic lethality that affect reproducibility. Nat Commun. 2020 05 12; 11(1):2375.  View on PubMed
  17. F. Haderk, C. Fernández-Méndez, K.N. Shah, W. Wu, J. Guan, J. Rotow, D. Allegakoen, V. Olivas, S. Bandyopadhyay, C. Kuo, T. Bivona. B01 Active YAP as a Functional Marker of Drug-Tolerant Persister Cells in EGFR-Mutant and ALK Fusion-Positive NSCLC. Journal of Thoracic Oncology. 2020 Feb 1; 15(2):s27.  View on PubMed
  18. CHI-HENG WU, Chen-Yen Yang, Linlin Wang, Hua-Xin Gao, Rakhshandehroo Taha, Shervin Afghani, Laura Pincus, Ronald Balassanian, James Rubenstein, Ryan Gill, Sourav Bandyopadhyay, Frank McCormick, Mark Moasser, Weiyun Z. Ai. Development of a Pathway-Directed Drug Screen Platform for Cutaneous T Cell Lymphoma Using Patient-Derived Xenograft Models. Blood. 2019 Nov 13; 134(Supplement_1):1578-1578.  View on PubMed
  19. Khyati N. Shah, Roma Bhatt, Julia Rotow, Julia Rohrberg, Victor Olivas, Victoria E. Wang, Jonathan Kuhn, Sophie Dumont, Frank Mccormick, Andrei Goga, Collin M. Blakely, Trever G. Bivona, Sourav Bandyopadhyay. Abstract 2902: Non-genetic TPX2/AURKA signaling facilitates tumor evolution in EGFR-TKI resistance in NSCLC. Tumor Biology. 2019 Jul 1; 2902-2902.  View on PubMed
  20. Shah KN, Bandyopadhyay S. Targeting the evolution of drug resistance in lung cancer. Mol Cell Oncol. 2019; 6(5):e1603092.  View on PubMed

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