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/NCI, Sponsor Award ID: R01CA238236
  • August 10, 2017 - July 31, 2022 - The Cancer Target Discovery and Development Network at UCSF, Co-Principal Investigator. Sponsor: NIH/NCI, Sponsor Award ID: U01CA217882
  • September 1, 2014 - June 30, 2018 - Physical and Genetic Interaction Landscape of the Tyrosine Kinome, Principal Investigator. Sponsor: NIH/NIGMS, 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

Education

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. 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 Aug 03; 118(31).  View on PubMed
  2. 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
  3. 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
  4. Kim D, Bandyopadhyay S. Aurora kinases shed light on resistance to EGFR inhibition in head and neck cancer. EBioMedicine. 2021 Mar; 65:103257.  View on PubMed
  5. 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 Nov; 19(11):2382-2395.  View on PubMed
  6. 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
  7. 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 PI3Ka/d and HDAC. J Invest Dermatol. 2021 02; 141(2):364-373.  View on PubMed
  8. 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
  9. 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
  10. 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
  11. Shah KN, Bandyopadhyay S. Targeting the evolution of drug resistance in lung cancer. Mol Cell Oncol. 2019; 6(5):e1603092.  View on PubMed
  12. Shah KN, Bhatt R, Rotow J, Rohrberg J, Olivas V, Wang VE, Hemmati G, Martins MM, Maynard A, Kuhn J, Galeas J, Donnella HJ, Kaushik S, Ku A, Dumont S, Krings G, Haringsma HJ, Robillard L, Simmons AD, Harding TC, McCormick F, Goga A, Blakely CM, Bivona TG, Bandyopadhyay S. Aurora kinase A drives the evolution of resistance to third-generation EGFR inhibitors in lung cancer. Nat Med. 2019 01; 25(1):111-118.  View on PubMed
  13. Webber JT, Kaushik S, Bandyopadhyay S. Integration of Tumor Genomic Data with Cell Lines Using Multi-dimensional Network Modules Improves Cancer Pharmacogenomics. Cell Syst. 2018 11 28; 7(5):526-536.e6.  View on PubMed
  14. K. Shah, C. Blakely, T. Bivona, S. Bandyopadhyay. P1.13-10 Aurora Kinase A Drives the Evolution of Resistance to Third Generation EGFR Inhibitors in Lung Cancer. Journal of Thoracic Oncology. 2018 Oct 1; 13(10):s585-s586.  View on PubMed
  15. Donnella HJ, Webber JT, Levin RS, Camarda R, Momcilovic O, Bayani N, Shah KN, Korkola JE, Shokat KM, Goga A, Gordan JD, Bandyopadhyay S. Kinome rewiring reveals AURKA limits PI3K-pathway inhibitor efficacy in breast cancer. Nat Chem Biol. 2018 08; 14(8):768-777.  View on PubMed
  16. Hu HM, Zhao X, Kaushik S, Robillard L, Barthelet A, Lin KK, Shah KN, Simmons AD, Raponi M, Harding TC, Bandyopadhyay S. A Quantitative Chemotherapy Genetic Interaction Map Reveals Factors Associated with PARP Inhibitor Resistance. Cell Rep. 2018 Apr 17; 23(3):918-929.  View on PubMed
  17. 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. Cross-talk Signaling between HER3 and HPV16 E6 and E7 Mediates Resistance to PI3K Inhibitors in Head and Neck Cancer. Cancer Res. 2018 05 01; 78(9):2383-2395.  View on PubMed
  18. Martinko AJ, Truillet C, Julien O, Diaz JE, Horlbeck MA, Whiteley G, Blonder J, Weissman JS, Bandyopadhyay S, Evans MJ, Wells JA. Targeting RAS-driven human cancer cells with antibodies to upregulated and essential cell-surface proteins. Elife. 2018 01 23; 7.  View on PubMed
  19. Brand TM, Hartmann S, Bhola NE, Peyser ND, Li H, Zeng Y, Isaacson Wechsler E, Ranall MV, Bandyopadhyay S, Duvvuri U, LaVallee TM, Jordan RCK, Johnson DE, Grandis JR. Human Papillomavirus Regulates HER3 Expression in Head and Neck Cancer: Implications for Targeted HER3 Therapy in HPV+ Patients. Clin Cancer Res. 2017 Jun 15; 23(12):3072-3083.  View on PubMed
  20. Webber JT, Ranall MV, Kaushik S, Bandyopadhyay S.. Connecting tumor genomics with therapeutics through multi-dimensional network modules. BioArxiv. 2016.  View on PubMed

Go to UCSF Profiles, powered by CTSI