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. Kim D, Bandyopadhyay S Aurora kinases shed light on resistance to EGFR inhibition in head and neck cancer.  View on PubMed
  2. 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.  View on PubMed
  3. 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.  View on PubMed
  4. 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.  View on PubMed
  5. 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.  View on PubMed
  6. 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.  View on PubMed
  7. 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.  View on PubMed
  8. Shah KN, Bandyopadhyay S Targeting the evolution of drug resistance in lung cancer.  View on PubMed
  9. 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.  View on PubMed
  10. Webber JT, Kaushik S, Bandyopadhyay S Integration of Tumor Genomic Data with Cell Lines Using Multi-dimensional Network Modules Improves Cancer Pharmacogenomics.  View on PubMed
  11. 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.  View on PubMed
  12. 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.  View on PubMed
  13. 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.  View on PubMed
  14. 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.  View on PubMed
  15. 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.  View on PubMed
  16. 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.  View on PubMed
  17. Webber JT, Ranall MV, Kaushik S, Bandyopadhyay S. Connecting tumor genomics with therapeutics through multi-dimensional network modules  View on PubMed
  18. Kohnz RA, Roberts LS, DeTomaso D, Bideyan L, Yan P, Bandyopadhyay S, Goga A, Yosef N, Nomura DK Protein Sialylation Regulates a Gene Expression Signature that Promotes Breast Cancer Cell Pathogenicity.  View on PubMed
  19. Hofree M, Carter H, Kreisberg JF, Bandyopadhyay S, Mischel PS, Friend S, Ideker T Challenges in identifying cancer genes by analysis of exome sequencing data.  View on PubMed
  20. Miller RE, Brough R, Bajrami I, Williamson CT, McDade S, Campbell J, Kigozi A, Rafiq R, Pemberton H, Natrajan R, Joel J, Astley H, Mahoney C, Moore JD, Torrance C, Gordan JD, Webber JT, Levin RS, Shokat KM, Bandyopadhyay S, Lord CJ, Ashworth A Synthetic Lethal Targeting of ARID1A-Mutant Ovarian Clear Cell Tumors with Dasatinib.  View on PubMed

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