Publications:
43. Hypoxia induces extensive protein and proteolytic remodeling of the cell surface in pancreatic adenocarcinoma (PDAC) cell lines. Lui I, Schaefer K, Kirkemo LL, Zhou J, Perera RM, Leung K, Wells JA. bioRxiv 2024 (link)
42. A multi-subunit autophagic capture complex facilitates degradation of ER stalled MHC-I in pancreatic cancer Berquez M*, Li AL*, Luy MA*, Venida AC, O’Loughlin T, Rademaker R, Barpanda A, Hu J, Yano J, Wiita A, Gilbert LA, Bruno PM, Perera RM. bioRxiv 2024. (link) (* co-first author)
41. Functional screen for mediators of onco-mRNA translation specificity. Kovalski JR, Sarioglu G, Subramanyam V, Hernandez G, Rademaker G, Oses-Prieto JA, Slota M, Mohan N, Yiakis K, Liu I, Wen KW, Kim GE, Miglani S, Burlingame AL, Goodarzi H, Perera RM, Ruggero D. bioRxiv. 2024 (link)
40. Lysosomes as coordinators of cellular catabolism, metabolic signalling and organ physiology. Settembre C¶, Perera RM¶. Nat Rev Mol Cell Biol. 2024 (link). (Review) (¶co-corresponding author).
39. Functional Characterization of Alzheimer’s disease genetic variants in microglia. Yang X, Wen J, Yang H, Jones IR, Zhu X, Liu W, Li B, Clelland CD, Luo W, Wong MY, Ren X, Cui X, Song M, Liu H, Chen C, Eng N, Ravichandran M, Sun Y, Lee D, Van Buren E, Jiang M, Chan CSY, Ye CJ, Perera RM, Gan L, Li Y, Shen Y. Nature Genetics, 2023, (link).
38. Emerging roles of the MiT/TFE factors in cancer. Zoncu R¶, Perera RM¶. Trends in Cancer, 2023 (link) (Review) (¶co-corresponding author).
37. Lysosomal GPCR-like Protein LYCHOS Signals Cholesterol Sufficiency to mTORC1. Shin HR, Citron YR, Goul CS, Wang L, Sugasawa Y, Tribouillard L, Samson N, Stipp R, Lim CY, Davis OB, Qian M, Nomura DK, Perera RM, Park E, Covey DF, Laplante M, Evers AS and Zoncu R. Science, 2022 (link)
36. Coordinated transcriptional and catabolic programs support iron dependent adaptation to Ras-MAPK pathway inhibition in pancreatic cancer. Ravichandran M, Hu J, Cai C, Ward NP, Venida A, Foakes, C, Kuljanin M, Yang A, Hennesey CJ, Desousa B, Rademaker G, Staes A, Cakir Z, Jain IH, Aguirre AJ, Mancias JD, Shen Y, DeNicola G, Perera RM. Cancer Discovery 2022 (link) (COVER ARTICLE)
Highlight: Cancer Discovery Commentary (link)
35. Autophagy in cancer cell remodeling and quality control. Hernandez G, Perera RM. Molecular Cell, 2022 (link) (Review for Special Issue)
34. Challenges and opportunities in 2021 Akkari L, Finley SD, Ho P-C, Jenkins M, Maier BB, McGranahan N, Mutebi M, Perera RM, Robles-Espinoza CD, Vardhana S, Wan L, Xu MM. Nature Cancer, 2021 (link) Essay
33. Zooming in on the cell biology of disease. Perera RM. Molecular Biol Cell 2021 (link) Essay
32. Autophagy in major human diseases. Klionsky, Petroni, Amaravadi, Baehrecke, Ballabio, Boya, Bravo-San Pedro, Cadwell, Cecconi, Choi, Choi, Chu, Codogno, Colombo, Cuervo, Deretic, Dikic, Elazar, Eskelinen, Fimia, Gewirtz, Green, Hansen, Jaatela, Johansen, Juhasz, Karantza, Kraft, Kroemer, Ktistakis, Kumar, Melendez, Mizushima, Munz, Penninger, Perera, Piacentini, Reggiori, Rubinsztein, Ryan, Sadoshima, Santambrogio, Scorrano, Simon, Simon, Simonsen, Stolz, Tavernarakis, Tooze, Yoshimori, Yuan, Yue, Zhong, Galluzzi, Pietrocola. EMBO J 2021 (link) (Review)
31. Lysosomal retargeting of Myoferlin mitigates membrane stress to enable pancreatic cancer growth. Gupta S, Yano J, Mercier V, Htwe HH, Shin HR, Rademaker G, Cakir Z, Ituarte T, Wen KW, Kim GE, Zoncu R, Roux A, Dawson DW, Perera RM. BioRxiv 2020 (link) Nature Cell Biology 2021 (link)
30. NPC1-mTORC1 signaling couples cholesterol sensing to organelle homeostatsis and is a targetable pathway in Neiman-Pick type C. Davis, OB, Shin HR, Lim CY, Wu EY, Kukurugya M, Maher C, Perera RM, Ordonez MP, Zoncu R. BioRxiv 2020 (link) Dev Cell 2021 (link)
29. Autophagy promotes immune evasion of pancreatic cancer by degrading MHC-I. 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¶. Nature, 2020 (*co-first author; ¶co-corresponding). (link)
Highlights:
Nature News and Views (link)
Cancer Discovery, 2020 June 1; 10(6):760-760
Cancer Cell, 2020, online May 28 (link)
Nat. Rev. Gastroenterol Hepatol, 2020, online May 20
Mol. Cell, 2020, July, 79(1):6-8 (link)
28. Oncogene regulated release of extracellular vesicles. Kilinc S, Paisner R, Camarda R, Gupta S, Momcilovic O, Kohnz RA, Avsaroglu B, L’Etoile N, Perera RM, Nomura DK, Goga A. BioRxiv, 2020. 04.04.025726. (link) Dev Cell 2021 Jun 8;S1534-5807(21)00443-3 (link)
27. Transcriptional control of subtype switching ensures adaptation and growth of pancreatic cancer. Adams CR, Htew HH, Marsh T, Wang AL, Montoya ML, Subbaraj L, Tward AD, Bardeesy N, Perera RM. eLife, 2019 8. pii: e45313. (pdf)
26. MiT/TFE family of transcription factors, lysosomes, and cancer. Perera RM¶, Di Malta C and Ballabio A¶. Ann Rev Cancer Biol, 2019; 3:203-22. (pdf) (¶co-corresponding) Review
25. Host control of tumor feeding: Autophagy holds the key. Venida A and Perera RM. Cell Metabolism, 2019 Feb 5; 29(2):236-238. (link)
24. Transcriptional activation of RagD GTPase controls mTORC1 and promotes cancer growth. Di Malta C, Siciliano D, Calcagni A, Monfregola J, Punzi S, Pastore N, Eastes AN, Davis O, De Cegli R, Zampelli A, Giovannantonio LG, Nusco E, Platt N, Guida A, Ogmundsdottir MH, Lanfrancone L, Perera RM, Zoncu R, Pelicci PG, Settembre C, Ballabio A. Science, 2017 June 16; 356:1188-1192. (pubmed)
23. Lysosomal cholesterol activates mTORC1 via an SLC38A9-Niemann-Pick C1 signaling complex. Castellano BM, Thelan 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. Science, 2017 Mar 24; 355:1306-1311. (pubmed)
22. The lysosome as a regulatory hub. Perera RM¶, Zoncu R¶. Ann Rev Cell Dev Biol, 2016 Oct 6; 32:223-253. (pubmed) (¶co-corresponding) Review
21. Beige adipocyte maintenance is regulated by autophagy-induced mitochondrial clearance. Atshuler-Keylin S, Shinoda K, Hasegawa Y, Ikeda K, Hong H, Kang Q, Yang Y, Perera RM, Debnath J, Kajimura S. Cell Metabolism, 2016 Sep 13;24(3):402-19. (pubmed)
20. Pancreatic cancer metabolism: Breaking it down to build it back up. Perera RM¶, Bardeesy, N¶. Cancer Discovery, 2015 Nov 3 (pubmed). (¶co-corresponding) Review
19. Transcriptional control of autophagy-lysosome function drives pancreatic cancer metabolism. Perera RM, Stoykova S, Nicolay BN, Ross K, 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. Nature, 2015 Aug 20; 524(7565):361-5.(pubmed)
Highlights:
Cancer Discovery (pubmed) Nature Rev Cancer (pubmed)
18. YAP inhibition restores hepatocyte differentiation in advanced HCC, leading to tumor regression. Fitamant J, Kottakis F, Benhamouche S, Tian H, Chuvin N, Parachoniak CA, Nagle JM, Perera RM, Lapouge M, Deshpande V, Zhu AX, Lai A, Min B, Hoshida Y, Avruch J, Sia D, Camprecios G, McClatchey AI, Llovet JM, Morrissey D, Raj L, Bardeesy N. Cell Reports, 2015 Mar 17; 10(10):1692-1707. (pubmed)
17. Stromal response to Hedgehog signaling restrains pancreatic cancer progression. Lee JJ*, Perera RM*, Wang, H, Wu, D, Lie XS, Han S, Fitamant J, Jones, PD, Ghanta KL, Kawano S, Nagle JM, Deshpande V, Boucher Y, Kato T, Chen JK, Willmann JK, Bardeesy N¶, Beachy PA¶. PNAS, 2014 Jul 29; 111(30):E3091-100. (pubmed) (*equal contributors ¶co-corresponding)
Highlights:
Sci Signal (link)
16. CDK4/6 and IGF1R/IR inhibitors synergize to suppress growth of p16INK4A-deficient pancreatic cancers. Heilmann AM, Perera RM, Ecker V, Nicolay BN, Bardeesy N, Benes CH, and Dyson NJ. Cancer Research, 2014 Jul 15; 74(14):3947-58. (pubmed)
15. Glutamine supports pancreatic cancer growth through a KRAS-regulated metabolic pathway. Son J, Lyssiotis CA, Ying H, Wang X, Huan 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. Nature, 2013 Apr 4; 496(7443). (pubmed)
14. Ready, Set, Go: The EGF Receptor at the Pancreatic Cancer Starting Line. Perera RM and Bardeesy N. Cancer Cell, 2012 Sept 11; 22: 281-2. (pubmed)
13. On oncogenes and tumor suppressor genes in the mammary gland. Perera RM and Bardeesy N. Cold Spring Harb Perspect Biol. 2012 Jun 1;4(6). (pubmed) Review
12. Cancer: When antioxidants are bad. Perera RM and Bardeesy N. Nature, 2011 July 6; 475: 43-44. (pubmed)
11. The inositol 5-phophatase SHIP2 regulates endocytic clathrin-coated pit dynamics. Nakatsu F, Perera RM, Lucast L, Zoncu R, Domin J, Gertler F, Toomre D, De Camilli P. J Cell Biol, 2010 Aug 9; 190(3):307-15
10. A genome-wide screen for microdeletions reveals disruption of polarity gene components in diverse human cancers. 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. Cancer Research, 2010 Mar 15; 70(6):2158-64
9. A phosphoinositide switch controls the maturation and signaling properties of APPL endosomes. Zoncu R*, Perera RM*, Balkin D, Pirruccello M, Toomre D, De Camilli P. Cell 2009 Mar 20; 136(6):1110-21. (pubmed) (*equal contributors)
8. Structural basis of membrane tubule formation by F-BAR domains. Frost A, Perera R, Roux A, Spasov K, Destaing O, Egelman EH, De Camilli P and Unger VM. Cell 2008 Mar 7; 132(5):807-17.
7. The efficacy of EGFR specific antibodies against glioma xenografts is influenced by receptor levels, activation status and heterodimerization. Johns TG, Perera RM, Vernes SC, Vitali AA, Cao DX, Cavenee WK, Scott AM and Furnari FB. Clin Can Res, 2007 Mar 15; 13(6):1911-1925 (cover page)
6. Internalization, intracellular trafficking and biodistribution of monoclonal antibody 806: A novel anti-EGFR antibody. Perera RM, Zoncu R, Johns TG, Pypaert M, Lee FT, Mellman I, Old, LJ, Toomre DK and Scott AM. Neoplasia 2007 Dec 9;(12):1099-110
5. Loss of endocytic clathrin coated pits upon acute depletion of phosphatidylinositol 4,5 bisphosphate. Zoncu R, Perera RM, Sebastian R, Nakatsu F, Chen H, Balla T, Ayala G, Toomre D and De Camilli P. PNAS 2007 Mar; 104(10): 3793-8
4. Two isoforms of synaptojanin 1 are recruited to clathrin coated pits at different stages. Perera RM, Zoncu R, Lucast L, De Camilli P, Toomre D. PNAS 2006 Dec; 103(51):19332-7
3. Treatment of human tumour xenografts with monoclonal antibody 806 in combination with a prototypical epidermal growth factor receptor-specific antibody generates enhanced antitumor activity. Perera RM, Narita Y, Furnari FB, Gan HK, Murone C, Ahlkvist M, Luwor RB, Burgess AW, Stockert E, Jungbluth AA, Old LJ, Cavenee WK, Scott AM and Johns TG. Clin Can Res, 2005 Sept 1; 11(17):6390-9
2. The tumor specific de2-7 epidermal growth factor receptor (EGFR) promotes cell survival and heterodimerizes with the wild type EGFR. Luwor RB, Zhu H-J, Walker F, Vitali AA, Perera RM, Burgess AW, Scott AM and Johns TG. Oncogene, 2004 Aug 12;23(36):6095-104
1. Anti-tumor efficacy of cytotoxic drugs and the monoclonal antibody 806 is enhanced by the epidermal growth factor receptor (EGFR) inhibitor AG1478. Johns TG, Luwor RB, Murone C, Walker F, Weinstock J, Vitali AA, Perera RM, Jungbluth AA, Stockert E, Old LJ, Nice EC, Burgess AW and Scott AM. PNAS, 2003 Dec;100(26):15871-15876