University of California San Francisco
Helen Diller Family Comprehensive Cancer Center
Sourav Bandyopadhyay, PhD

Sourav Bandyopadhyay, PhD

Associate Professor, Bioengineering and Therapeutic Sciences, UCSF

Cancer Center Program Memberships

Experimental Therapeutics

Research Summary

Our lab focuses on methods to map pathway rewiring in cancer. Our major goal is to understand at the systems level how the biological networks within cancer cells are fundamentally different from that in normal cells. Using our technologies, we intend to develop platforms for the rational application of personalized medicine and design of combination cancer therapies.

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

Professional Experience

  • 2002 - 2003
    Informatics Programmer, Eragen Biosciences, Madison, WI
  • 2003 - 2004
    Research Staff, National Institute on Aging / NIH
  • 2004 - 2010
    Doctoral Dissertation, Advisor Trey Ideker, UCSD
  • 2010 - 2013
    Assistant Professional Researcher/Faculty Fellow, Helen Diller Family Comprehensive Cancer Center, UCSF
  • 2013 - present
    Assistant Professor, Bioengineering and Therapeutic Sciences, UCSF
  • Research Interests
    The Bandyopadhyay Lab is focused on systems-wide functional analysis of pathways that are deregulated and mutated in different types of cancers. While a number of large-scale efforts are underway to catalog the genetic aberrations in a variety of cancers, there is a lack of systematic efforts to understand which of these aberrations mediate the transformation from a normal to malignant cancer cell. The lab focuses on adapting existing technologies into a high-throughput network-mapping framework and then developing novel computational techniques to generate biologically meaningful hypotheses that can be subsequently tested using more traditional biochemical techniques.

    The lab focuses on the role of RAS-activated signal transduction pathways, which are mutated in 25 percent of all human cancers with a much higher prevalence in skin, pancreatic, and lung cancer. Through a combination of RNAi screening and immuno-precipitation coupled with mass spectrometry, the lab is focused on elucidating mechanisms by which members of the RAS-RAF-MEK-ERK signaling cascade alters cell growth and survival in cancer cells.

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. Shah KN, Bandyopadhyay S. Targeting the evolution of drug resistance in lung cancer. Mol Cell Oncol. 2019; 6(5):e1603092.
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  2. 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.
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  3. 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.
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  4. 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.
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  5. 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.
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  6. 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.
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  7. 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.
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  8. 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.
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  9. Webber JT, Ranall MV, Kaushik S, Bandyopadhyay S.. Connecting tumor genomics with therapeutics through multi-dimensional network modules. BioArxiv. 2016.
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  10. 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. ACS Chem Biol. 2016 08 19; 11(8):2131-9.
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  11. 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. Nat Commun. 2016 07 15; 7:12096.
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  12. 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. Mol Cancer Ther. 2016 07; 15(7):1472-84.
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  13. Fujita-Sato S, Galeas J, Truitt M, Pitt C, Urisman A, Bandyopadhyay S, Ruggero D, McCormick F. Enhanced MET Translation and Signaling Sustains K-Ras-Driven Proliferation under Anchorage-Independent Growth Conditions. Cancer Res. 2015 Jul 15; 75(14):2851-62.
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  14. Kohnz RA, Mulvihill MM, Chang JW, Hsu KL, Sorrentino A, Cravatt BF, Bandyopadhyay S, Goga A, Nomura DK. Activity-Based Protein Profiling of Oncogene-Driven Changes in Metabolism Reveals Broad Dysregulation of PAFAH1B2 and 1B3 in Cancer. ACS Chem Biol. 2015 Jul 17; 10(7):1624-30.
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  15. Blakely CM, Pazarentzos E, Olivas V, Asthana S, Yan JJ, Tan I, Hrustanovic G, Chan E, Lin L, Neel DS, Newton W, Bobb KL, Fouts TR, Meshulam J, Gubens MA, Jablons DM, Johnson JR, Bandyopadhyay S, Krogan NJ, Bivona TG. NF-?B-activating complex engaged in response to EGFR oncogene inhibition drives tumor cell survival and residual disease in lung cancer. Cell Rep. 2015 Apr 07; 11(1):98-110.
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  16. Martins MM, Zhou AY, Corella A, Horiuchi D, Yau C, Rakhshandehroo T, Gordan JD, Levin RS, Johnson J, Jascur J, Shales M, Sorrentino A, Cheah J, Clemons PA, Shamji AF, Schreiber SL, Krogan NJ, Shokat KM, McCormick F, Goga A, Bandyopadhyay S. Linking tumor mutations to drug responses via a quantitative chemical-genetic interaction map. Cancer Discov. 2015 02; 5(2):154-67.
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  17. Sos ML, Levin RS, Gordan JD, Oses-Prieto JA, Webber JT, Salt M, Hann B, Burlingame AL, McCormick F, Bandyopadhyay S, Shokat KM. Oncogene mimicry as a mechanism of primary resistance to BRAF inhibitors. Cell Rep. 2014 Aug 21; 8(4):1037-48.
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  18. Benjamin DI, Louie SM, Mulvihill MM, Kohnz RA, Li DS, Chan LG, Sorrentino A, Bandyopadhyay S, Cozzo A, Ohiri A, Goga A, Ng SW, Nomura DK. Inositol phosphate recycling regulates glycolytic and lipid metabolism that drives cancer aggressiveness. ACS Chem Biol. 2014 Jun 20; 9(6):1340-50.
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  19. Lin L, Asthana S, Chan E, Bandyopadhyay S, Martins MM, Olivas V, Yan JJ, Pham L, Wang MM, Bollag G, Solit DB, Collisson EA, Rudin CM, Taylor BS, Bivona TG. Mapping the molecular determinants of BRAF oncogene dependence in human lung cancer. Proc Natl Acad Sci U S A. 2014 Feb 18; 111(7):E748-57.
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  20. Salt MB, Bandyopadhyay S, McCormick F. Epithelial-to-mesenchymal transition rewires the molecular path to PI3K-dependent proliferation. Cancer Discov. 2014 Feb; 4(2):186-99.
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