University of California San Francisco
Helen Diller Family Comprehensive Cancer Center
Rushika Perera, PhD

Rushika Perera, PhD

Assistant Professor, Department of Anatomy, UCSF

Cancer Center Program Memberships

Cancer Immunology

Research Summary

I am an Assistant Professor in the Department of Anatomy, with appointments also in the Department of Pathology and the Helen Diller Family Comprehensive Cancer Center. My laboratory focuses on understanding how scavenging pathways such as autophagy and the lysosome - a degradative organelle - enables metabolic and cellular adaptation to stress and contributes to aggressive features of disease. Beyond mediating degradation of diverse macromolecules, the lysosome also plays an important role in signal transduction, cellular quality control, metabolism and detoxification.

My lab has a particular interest in how the lysosome contributes to cancer pathogenesis with a focus on studying pancreatic ductal adenocarcinoma (PDA). our work has identified novel mechanisms mediating constitutive activation of lysosome biogenesis via coordinated transcriptional upregulation of lysosome transcriptional signatures in PDA and in normal physiological contexts. We have also discovered a new role for autophagy and the lysosome in facilitating immune evasion of PDA cells through selective capture and degradation of Major Histocompatibility Complex Class I (MHC-I). Our ongoing research leverages our combined experience in cellular trafficking, autophagy and lysosome function combined with in vitro and in vivo model systems, organelle isolation and mass spectrometry based proteomics to determine critical roles of the lysosome in cancer progression and metastasis, tumor heterogeneity, stress adaptation and drug resistance.

Education

University of Melbourne, Australia, BSc, 1999, Pathology/ Biochemistry
University of Melbourne and Ludwig Institute for Cancer Research, BSc, 2000, Cancer Biology
University of Melbourne and Ludwig Institute for Cancer Research, PhD, 2007, Cancer Biology
Yale University, postdoctoral, 2008, Cell Biology
MGH Cancer Center, postdoctoral, 2013, Cancer Biology
MGH Cancer Center, Instructor, 2015, Cancer Biology

Honors & Awards

  • 2001
    John and Allan Gilmour Award, The University of Melbourne, Australia
  • 2001
    RJ Fletcher Award, The University of Melbourne, Australia
  • 2002-2004
    Melbourne Research Scholarship, The University of Melbourne, Australia
  • 2005
    Student commendation for outstanding achievement during PhD, (money prize)
  • 2010-2011
    ECOR Fund for Medical Discovery Fellowship, MGH Cancer Center
  • 2011-2012
    Dana Faber Cancer Institute/HCC GI SPORE Career Development Award
  • 2014
    Office for Research Career Development, MGH – Research Fellow Award
  • 2014-2015
    Andrew L. Warshaw Institute for Pancreatic Cancer Research Fellow Award
  • 2015
    American Association for Cancer Research NextGen STAR
  • 2014-2016
    Hirshberg Foundation for Pancreatic Cancer Seed Grant Recipient
  • 2016-2018
    AACR-Pancreatic Cancer Action Network Career Development Award
  • 2016-2021
    NIH Director’s New Innovator Award
  • 2016-2020
    Damon Runyon-Rachleff Innovation Award

Selected Publications

  1. Yamamoto K, Venida A, Perera RM, Kimmelman AC. Selective autophagy of MHC-I promotes immune evasion of pancreatic cancer. Autophagy. 2020 Aug; 16(8):1524-1525.
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  2. Yamamoto K, Venida A, Yano J, Biancur DE, Kakiuchi M, Gupta S, Sohn ASW, Mukhopadhyay S, Lin EY, Parker SJ, Banh RS, Paulo JA, Wen KW, Debnath J, Kim GE, Mancias JD, Fearon DT, Perera RM, Kimmelman AC. Autophagy promotes immune evasion of pancreatic cancer by degrading MHC-I. Nature. 2020 05; 581(7806):100-105.
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  3. Adams CR, Htwe HH, Marsh T, Wang AL, Montoya ML, Subbaraj L, Tward AD, Bardeesy N, Perera RM. Transcriptional control of subtype switching ensures adaptation and growth of pancreatic cancer. Elife. 2019 05 28; 8.
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  4. Venida A, Perera RM. Host Control of Tumor Feeding: Autophagy Holds the Key. Cell Metab. 2019 02 05; 29(2):236-238.
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  5. Perera RM, Di Malta C, Ballabio A. MiT/TFE Family of Transcription Factors, Lysosomes, and Cancer. Annu Rev Cancer Biol. 2019 03; 3:203-222.
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  6. Di Malta C, Siciliano D, Calcagni A, Monfregola J, Punzi S, Pastore N, Eastes AN, Davis O, De Cegli R, Zampelli A, Di Giovannantonio LG, Nusco E, Platt N, Guida A, Ogmundsdottir MH, Lanfrancone L, Perera RM, Zoncu R, Pelicci PG, Settembre C, Ballabio A. Transcriptional activation of RagD GTPase controls mTORC1 and promotes cancer growth. Science. 2017 06 16; 356(6343):1188-1192.
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  7. Castellano BM, Thelen AM, Moldavski O, Feltes M, van der Welle RE, Mydock-McGrane L, Jiang X, van Eijkeren RJ, Davis OB, Louie SM, Perera RM, Covey DF, Nomura DK, Ory DS, Zoncu R. Lysosomal cholesterol activates mTORC1 via an SLC38A9-Niemann-Pick C1 signaling complex. Science. 2017 03 24; 355(6331):1306-1311.
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  8. Altshuler-Keylin S, Shinoda K, Hasegawa Y, Ikeda K, Hong H, Kang Q, Yang Y, Perera RM, Debnath J, Kajimura S. Beige Adipocyte Maintenance Is Regulated by Autophagy-Induced Mitochondrial Clearance. Cell Metab. 2016 09 13; 24(3):402-419.
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  9. Perera RM, Zoncu R. The Lysosome as a Regulatory Hub. Annu Rev Cell Dev Biol. 2016 10 06; 32:223-253.
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  10. Perera RM, Bardeesy N. Pancreatic Cancer Metabolism: Breaking It Down to Build It Back Up. Cancer Discov. 2015 Dec; 5(12):1247-61.
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  11. Perera RM, Stoykova S, Nicolay BN, Ross KN, Fitamant J, Boukhali M, Lengrand J, Deshpande V, Selig MK, Ferrone CR, Settleman J, Stephanopoulos G, Dyson NJ, Zoncu R, Ramaswamy S, Haas W, Bardeesy N. Transcriptional control of autophagy-lysosome function drives pancreatic cancer metabolism. Nature. 2015 Aug 20; 524(7565):361-5.
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  12. Fitamant J, Kottakis F, Benhamouche S, Tian HS, Chuvin N, Parachoniak CA, Nagle JM, Perera RM, Lapouge M, Deshpande V, Zhu AX, Lai A, Min B, Hoshida Y, Avruch J, Sia D, Campreciós G, McClatchey AI, Llovet JM, Morrissey D, Raj L, Bardeesy N. YAP Inhibition Restores Hepatocyte Differentiation in Advanced HCC, Leading to Tumor Regression. Cell Rep. 2015 Mar 17; 10(10):1692-1707.
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  13. Lee JJ, Perera RM, Wang H, Wu DC, Liu XS, Han S, Fitamant J, Jones PD, Ghanta KS, Kawano S, Nagle JM, Deshpande V, Boucher Y, Kato T, Chen JK, Willmann JK, Bardeesy N, Beachy PA. Stromal response to Hedgehog signaling restrains pancreatic cancer progression. Proc Natl Acad Sci U S A. 2014 Jul 29; 111(30):E3091-100.
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  14. Heilmann AM, Perera RM, Ecker V, Nicolay BN, Bardeesy N, Benes CH, Dyson NJ. CDK4/6 and IGF1 receptor inhibitors synergize to suppress the growth of p16INK4A-deficient pancreatic cancers. Cancer Res. 2014 Jul 15; 74(14):3947-58.
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  15. Son J, Lyssiotis CA, Ying H, Wang X, Hua S, Ligorio M, Perera RM, Ferrone CR, Mullarky E, Shyh-Chang N, Kang Y, Fleming JB, Bardeesy N, Asara JM, Haigis MC, DePinho RA, Cantley LC, Kimmelman AC. Glutamine supports pancreatic cancer growth through a KRAS-regulated metabolic pathway. Nature. 2013 Apr 04; 496(7443):101-5.
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  16. Perera RM, Bardeesy N. Ready, set, go: the EGF receptor at the pancreatic cancer starting line. Cancer Cell. 2012 Sep 11; 22(3):281-2.
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  17. Perera RM, Bardeesy N. On oncogenes and tumor suppressor genes in the mammary gland. Cold Spring Harb Perspect Biol. 2012 Jun 01; 4(6).
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  18. Perera RM, Bardeesy N. Cancer: when antioxidants are bad. Nature. 2011 Jul 06; 475(7354):43-4.
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  19. Nakatsu F, Perera RM, Lucast L, Zoncu R, Domin J, Gertler FB, Toomre D, De Camilli P. The inositol 5-phosphatase SHIP2 regulates endocytic clathrin-coated pit dynamics. J Cell Biol. 2010 Aug 09; 190(3):307-15.
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  20. Rothenberg SM, Mohapatra G, Rivera MN, Winokur D, Greninger P, Nitta M, Sadow PM, Sooriyakumar G, Brannigan BW, Ulman MJ, Perera RM, Wang R, Tam A, Ma XJ, Erlander M, Sgroi DC, Rocco JW, Lingen MW, Cohen EE, Louis DN, Settleman J, Haber DA. A genome-wide screen for microdeletions reveals disruption of polarity complex genes in diverse human cancers. Cancer Res. 2010 Mar 15; 70(6):2158-64.
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