Photo of Dipanjan Chowdhury,  PhD

Dipanjan Chowdhury, PhD

Dana-Farber Cancer Institute

Dana-Farber Cancer Institute
Phone: (617) 582-8639
Fax: (617) 582-8213

Dipanjan Chowdhury, PhD

Dana-Farber Cancer Institute


  • Associate Professor, Radiation Oncology, Harvard Medical School
  • Assistant Professor, Radiation Oncology Department, Dana-Farber Cancer Institute


Research Abstract

Down regulating DNA repair- phosphatases and micro RNAs

Activation of DNA repair pathways have been well studied for decades with very limited research on down regulation. Most importantly, the physiological relevance of down modulating DNA repair is still unclear. We have focused on two aspects of down regulation, one is dephosphorylation of repair proteins via phosphatases, and second is decreased expression of repair factors via micro RNAs (miRNAs).

One of the earliest events in the double stranded DNA break (DSB) response is the phosphorylation of the histone H2A variant, H2AX. The phosphorylated form of H2AX (gamma-H2AX) has a role in repair, replication, recombination of DNA and regulating cell cycle. Although the formation of g-H2AX has been well studied very little is known about its down regulation. In two parallel studies – one in mammals, the other in S. cerevisiae – we identified roles for PP2A family phosphatases in g-H2AX dephosphorylation. We found that PP2AC specifically removes g-H2AX foci formed in mammalian cells in response to exogenous DNA damage. At the same time in a collaborative study we identified a Pph3 phosphatase-containing trimeric complex in yeast that regulates basal g-H2AX levels. Although both PP2AC and Pph3 efficiently dephosphorylate g-H2AX in vitro, their roles in cells appeared to be distinct leading to the speculation that more than one phosphatase might be involved in g-H2AX removal in mammalian cells. Investigating this question we found a trimeric PP4C-containing phosphatase complex in mammalian cells that controls basal levels ofg-H2AX in the absence of exogenous DNA damage. Although several putative PP4C-containing complexes have been identified, their biological function is not well defined. We are continuing to investigate the cellular roles of PP4.

MiRNAs are small non-coding RNAs that typically dampen gene expression and are mis-expressed in many cancer cells. DNA repair proteins represent a group of genes whose inappropriate downregulation leads to genomic instability, the underlying cause of cancer. We hypothesize that miRNAs downregulate the expression of DNA repair proteins. When do normal cells attenuate DNA repair? There are two scenarios, one in terminally differentiated cells where overall DSB repair is downregulated with decreased levels of repair factors and second, in different phases of the cell cycle where specific DSB pathways are selectively suppressed. Using microarrays we have identified miRNAs whose levels change radically during differentiation and/or in the course of the cell cycle, potentially influencing the choice of repair pathway. We use a combination of computational tools and a novel biochemical strategy to identify targets of these miRNAs. As proof of principle and method, we find that in blood cells miR-24 gets overexpressed with differentiation, downregulates H2AX, and significantly impacts DNA repair. In a complementary approach a miRNA expression library is being screened to identify miRNAs that affect the repair of a single DSB using a reporter system. A role for miRNAs in DNA repair is pertinent for understanding DNA replication and recombination.


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  • Drané P, Brault ME, Cui G, Meghani K, Chaubey S, Detappe A, Parnandi N, He Y, Zheng XF, Botuyan MV, Kalousi A, Yewdell WT, Münch C, Harper JW, Chaudhuri J, Soutoglou E, Mer G, Chowdhury D. TIRR regulates 53BP1 by masking its histone methyl-lysine binding function. Nature 2017; 543:211-216. PubMed
  • Fendler W, Malachowska B, Meghani K, Konstantinopoulos PA, Guha C, Singh VK, Chowdhury D. Evolutionarily conserved serum microRNAs predict radiation-induced fatality in nonhuman primates. Sci Transl Med 2017. PubMed
  • Howitt BE, Strickland KC, Sholl LM, Rodig S, Ritterhouse LL, Chowdhury D, D'Andrea AD, Matulonis UA, Konstantinopoulos PA. Clear cell ovarian cancers with microsatellite instability: A unique subset of ovarian cancers with increased tumor-infiltrating lymphocytes and PD-1/PD-L1 expression. Oncoimmunology 2017; 6:e1277308. PubMed
  • Chen CC, Moskwa P, Zinn PO, Hirshman BR, Choi YE, Shukla SA, Fendler W, Lu J, Golub TR, Hjelmeland A, Chowdhury D. 334 A Functional Screen Identifies miRNAs that Induce Radioresistance in Glioblastomas. Neurosurgery 2016; 63 Suppl 1:197-8. PubMed
  • Strickland KC, Howitt BE, Shukla SA, Rodig S, Ritterhouse LL, Liu JF, Garber JE, Chowdhury D, Wu CJ, D'Andrea AD, Matulonis UA, Konstantinopoulos PA. Association and prognostic significance of BRCA1/2-mutation status with neoantigen load, number of tumor-infiltrating lymphocytes and expression of PD-1/PD-L1 in high grade serous ovarian cancer. 2016. PubMed
  • Choi YE, Meghani K, Brault ME, Leclerc L, He YJ, Day TA, Elias KM, Drapkin R, Weinstock DM, Dao F, Shih KK, Matulonis U, Levine DA, Konstantinopoulos PA, Chowdhury D. Platinum and PARP Inhibitor Resistance Due to Overexpression of MicroRNA-622 in BRCA1-Mutant Ovarian Cancer. Cell Rep 2016; 14:429-39. PubMed
  • Dinh TK, Fendler W, Chałubińska-Fendler J, Acharya SS, O'Leary C, Deraska PV, D'Andrea AD, Chowdhury D, Kozono D. Circulating miR-29a and miR-150 correlate with delivered dose during thoracic radiation therapy for non-small cell lung cancer. Radiat Oncol 2016; 11:61. PubMed
  • Zheng XF, Kalev P, Chowdhury D. Emerging role of protein phosphatases changes the landscape of phospho-signaling in DNA damage response. DNA Repair (Amst) 2015. PubMed
  • Acharya SS, Fendler W, Watson J, Hamilton A, Pan Y, Gaudiano E, Moskwa P, Bhanja P, Saha S, Guha C, Parmar K, Chowdhury D. Serum microRNAs are early indicators of survival after radiation-induced hematopoietic injury. Sci Transl Med 2015; 7:287ra69. PubMed
  • Moskwa P, Zinn PO, Choi YE, Shukla SA, Fendler W, Chen CC, Lu J, Golub TR, Hjelmeland A, Chowdhury D. A functional screen identifies miRs that induce radioresistance in glioblastomas. Mol Cancer Res 2014. PubMed
  • Murphy AK, Fitzgerald M, Ro T, Kim JH, Rabinowitsch AI, Chowdhury D, Schildkraut CL, Borowiec JA. Phosphorylated RPA recruits PALB2 to stalled DNA replication forks to facilitate fork recovery. J Cell Biol 2014; 206:493-507. PubMed
  • Tubbs AT, Dorsett Y, Chan E, Helmink B, Lee BS, Hung P, George R, Bredemeyer AL, Mittal A, Pappu RV, Chowdhury D, Mosammaparast N, Krangel MS, Sleckman BP. KAP-1 promotes resection of broken DNA ends not protected by γ-H2AX and 53BP1 in G₁-phase lymphocytes. Mol Cell Biol 2014. PubMed
  • Kushwaha D, Ramakrishnan V, Ng K, Steed T, Nguyen T, Futalan D, Akers JC, Sarkaria J, Jiang T, Chowdhury D, Carter BS, Chen CC. A genome-wide miRNA screen revealed miR-603 as a MGMT-regulating miRNA in glioblastomas. 2014; 5:4026-39. PubMed
  • Shaltiel IA, Aprelia M, Saurin AT, Chowdhury D, Kops GJ, Voest EE, Medema RH. Distinct phosphatases antagonize the p53 response in different phases of the cell cycle. Proc Natl Acad Sci U S A 2014. PubMed
  • Choi YE, Battelli C, Watson J, Liu J, Curtis J, Morse AN, Matulonis UA, Chowdhury D, Konstantinopoulos PA. Sublethal concentrations of 17-AAG suppress homologous recombination DNA repair and enhance sensitivity to carboplatin and olaparib in HR proficient ovarian cancer cells. 2014; 5:2678-87. PubMed
  • Wang M, Kern AM, Hülskötter M, Greninger P, Singh A, Pan Y, Chowdhury D, Krause M, Baumann M, Benes CH, Efstathiou JA, Settleman J, Willers H. EGFR-mediated chromatin condensation protects KRAS-mutant cancer cells against ionizing radiation. Cancer Res 2014. PubMed
  • Lee DH, Acharya SS, Kwon M, Drane P, Guan Y, Adelmant G, Kalev P, Shah J, Pellman D, Marto JA, Chowdhury D. Dephosphorylation enables the recruitment of 53BP1 to double-strand DNA breaks. Mol Cell 2014. PubMed
  • Kolacinska A, Morawiec J, Fendler W, Malachowska B, Morawiec Z, Szemraj J, Pawlowska Z, Chowdhury D, Choi YE, Kubiak R, Pakula L, Zawlik I. Association of microRNAs and pathologic response to preoperative chemotherapy in triple negative breast cancer: preliminary report. Mol Biol Rep 2014. PubMed
  • Li XL, Hara T, Choi Y, Subramanian M, Francis P, Bilke S, Walker RL, Pineda M, Zhu Y, Yang Y, Luo J, Wakefield LM, Brabletz T, Park BH, Sharma S, Chowdhury D, Meltzer PS, Lal A. A p21-ZEB1 complex inhibits epithelial-mesenchymal transition through the microRNA 183-96-182 cluster. Mol Cell Biol 2014; 34:533-50. PubMed
  • Choi YE, Pan Y, Park E, Konstantinopoulos P, De S, D'Andrea A, Chowdhury D. MicroRNAs down-regulate homologous recombination in the G1 phase of cycling cells to maintain genomic stability. Elife 2014; 3:e02445. PubMed
  • Johnson N, Johnson SF, Yao W, Li YC, Choi YE, Bernhardy AJ, Wang Y, Capelletti M, Sarosiek KA, Moreau LA, Chowdhury D, Wickramanayake A, Harrell MI, Liu JF, D'Andrea AD, Miron A, Swisher EM, Shapiro GI. Stabilization of mutant BRCA1 protein confers PARP inhibitor and platinum resistance. Proc Natl Acad Sci U S A 2013; 110:17041-6. PubMed
  • Li YH, Wang X, Pan Y, Lee DH, Chowdhury D, Kimmelman AC. Inhibition of non-homologous end joining repair impairs pancreatic cancer growth and enhances radiation response. PLoS ONE 2012; 7:e39588. PubMed
  • Moskwa P, Buffa FM, Pan Y, Panchakshari R, Gottipati P, Muschel RJ, Beech J, Kulshrestha R, Abdelmohsen K, Weinstock DM, Gorospe M, Harris AL, Helleday T, Chowdhury D. miR-182-mediated downregulation of BRCA1 impacts DNA repair and sensitivity to PARP inhibitors. Mol Cell 2011; 41:210-20. PubMed
  • Lee DH, Pan Y, Kanner S, Sung P, Borowiec JA, Chowdhury D. A PP4 phosphatase complex dephosphorylates RPA2 to facilitate DNA repair via homologous recombination. Nat Struct Mol Biol 2010; 17:365-72. PubMed
  • Wang B, Li S, Qi HH, Chowdhury D, Shi Y, Novina CD. Distinct passenger strand and mRNA cleavage activities of human Argonaute proteins. Nat Struct Mol Biol 2009; 16:1259-66. PubMed
  • Lal A, Navarro F, Maher CA, Maliszewski LE, Yan N, O'Day E, Chowdhury D, Dykxhoorn DM, Tsai P, Hofmann O, Becker KG, Gorospe M, Hide W, Lieberman J. miR-24 Inhibits cell proliferation by targeting E2F2, MYC, and other cell-cycle genes via binding to "seedless" 3'UTR microRNA recognition elements. Mol Cell 2009; 35:610-25. PubMed
  • Zhu P, Martinvalet D, Chowdhury D, Zhang D, Schlesinger A, Lieberman J. The cytotoxic T lymphocyte protease granzyme A cleaves and inactivates poly(adenosine 5'-diphosphate-ribose) polymerase-1. Blood 2009; 114:1205-16. PubMed
  • Wang H,Zhao A,Chen L,Zhong X,Liao J,Gao M,Cai M,Lee DH,Li J,Chowdhury D,Yang YG,Pfeifer GP,Yen Y,Xu X. Human RIF1 encodes an anti-apoptotic factor required for DNA repair. Carcinogenesis 2009; 30:1314-9. PubMed
  • Lal A,Pan Y,Navarro F,Dykxhoorn DM,Moreau L,Meire E,Bentwich Z,Lieberman J,Chowdhury D. miR-24-mediated downregulation of H2AX suppresses DNA repair in terminally differentiated blood cells. Nat Struct Mol Biol 2009; 16:492-8. PubMed
  • Wang B,Zhao A,Sun L,Zhong X,Zhong J,Wang H,Cai M,Li J,Xu Y,Liao J,Sang J,Chowdhury D,Pfeifer GP,Yen Y,Xu X. Protein phosphatase PP4 is overexpressed in human breast and lung tumors. Cell Res 2009; 18:974-7. PubMed
  • Wang B, Zhao A, Sun L, Zhong X, Zhong J, Wang H, Cai M, Li J, Xu Y, Liao J, Sang J, Chowdhury D, Pfeifer GP, Yen Y, Xu X. Protein phosphatase PP4 is overexpressed in human breast and lung tumors. Cell Res 2008. PubMed
  • Chowdhury D, Xu X, Zhong X, Ahmed F, Zhong J, Liao J, Dykxhoorn DM, Weinstock DM, Pfeifer GP, Lieberman J. A PP4-phosphatase complex dephosphorylates gamma-H2AX generated during DNA replication. Mol Cell 2008; 31:33-46. PubMed
  • Chowdhury D, Lieberman J. Death by a thousand cuts: granzyme pathways of programmed cell death. Annu Rev Immunol 2008; 26:389-420. PubMed
  • Dykxhoorn DM, Chowdhury D, Lieberman J. RNA interference and cancer: endogenous pathways and therapeutic approaches. Adv Exp Med Biol 2008; 615:299-329. PubMed
  • Martinvalet D, Thiery J, Chowdhury D. Granzymes and cell death. Methods Enzymol 2008; 442:213-30. PubMed
  • Chowdhury D, Beresford PJ, Zhu P, Zhang D, Sung JS, Demple B, Perrino FW, Lieberman J. The exonuclease TREX1 is in the SET complex and acts in concert with NM23-H1 to degrade DNA during granzyme A-mediated cell death. Mol Cell 2006; 23:133-42. PubMed