Nir Hacohen, PhD

Massachusetts General Hospital

Massachusetts General Hospital
Phone: (617) 724-3768
Fax: (617) 726-5651

nhacohen@partners.org

Massachusetts General Hospital
Phone: (617) 724-3768
Fax: (617) 726-5651

nhacohen@partners.org

Nir Hacohen, PhD

Massachusetts General Hospital

EDUCATIONAL TITLES

Professor, Medicine, Harvard Medical School
Director, Cancer for Cancer Immunology, Massachusetts General Hospital

HCC PROGRAM AFFILIATION

Cancer Immunology, Member

Research Abstract

Dr. Hacohen is an immunologist, geneticist and systems biologist focused on dissecting the basic mechanisms of immunity, developing and applying genetic technologies that accelerate the study of the immune system, and deciphering and treating human diseases -- including cancer and immune disorders -- based on genomic approaches. He is the Director of the Center for Cancer Immunology at MGH. Dr. Hacohen is also a founding member of the Broad Institute's RNAi Consortium -- a public-private partnership that has built genome-wide RNA interference libraries to silence every gene in mice and humans -- and the Immune Circuits Initiative. He is also co-director of the Broad Cell Circuits Program and NHGRI Center for Cell Circuits. These efforts have put genetic perturbation technologies in the hands of the community to address numerous biological and immunological questions.

Projects in the laboratory focus on innate immunity and dendritic cells, as well as technology development, and include: (I) developing methods for network reconstruction of pathogen-sensing pathways in mice and humans, with a focus on viral and bacterial sensing pathways; (II) dissecting how DNA is sensed by the immune system, including the role of nucleases in clearance of self DNA; (III) analyzing mechanisms underlying autoimmunity in lupus patients; (IV) uncovering interactions between tumors and the immune system; (V) testing a new generation of personalized tumor vaccines (together with Dr. Catherine Wu, DFCI).

Wright SJ, Zamora I, Parikh M, Yeramosu D, Rucevic M, Sade-Feldman M, LaSalle TJ, Blaum EM, Liu B, Bi L, Kang S, Blum SM, Nguyen N, Guess J, Kar A, Schneider AM, Lieb D, Woods E, Michaud W, Lawless AR, Sharova T, Cohen S, Kasumova G, Kim MS, Cheng LC, Villani AC, Park RJ, Jenkins RW, Klempner SJ, Sullivan RJ, Flaherty KT, Hacohen N, Mehta A, Boland GM. Multimodal blood based proteomic profiling reveals insights into mechanisms of immunotherapy resistance. Nat Commun 2026. PubMed
Tsingas K, Thomas M, Reale M, Xiao M, Wickramasinghe J, Chen Y, Duong B, Lucas A, Thacker G, Li H, Mou H, Ramirez-Salazar E, Elbasir A, Villanueva J, Xu X, Flowers A, Karakousis GC, Miura JT, Mitchell TC, Amaravadi RK, Schuchter LM, Liu S, Long Q, Hoon DSB, Ramos RI, Catbagan JJ, Bustos MA, Gershenwald JE, Simon JM, Wargo JA, Davies MA, Lu Y, Mills GB, Cohen S, Lawless A, Sharova T, Frederick DT, Flaherty KT, Hacohen N, Boland GM, Auslander N, Herlyn M. Melanoma-patient-derived xenograft multi-omics resource melPDomiX maps gain- and loss-of-function alterations. Cell Rep 2026; 45:117455. PubMed
Holden B, Mutaher M, Raychowdhury R, Bakalar M, Lopez A, Schwartz MA, Olajide E, Santos M, Hacohen N. An affinity reagent-conjugated biotin ligase for amplified cell surface labelling in vitro and in vivo. Sci Rep 2026. PubMed
Manakongtreecheep K, Ctortecka C, Correa-Medero LO, Zhu T, Lippincott I, Lawrence GM, Howard A, Hernandez GM, Forman C, Duggan EC, Wilbrink MA, Verzani EK, Afeyan AB, Li J, Nesvizhskii AI, Oliveira G, Keskin DB, Ott PA, Clauser KR, Bakalar M, Sarkizova S, Hacohen N, Carr SA, Abelin JG, Wu CJ. Sensitive detection of cancer antigens enabled by user-defined peptide libraries. Nat Biotechnol 2026. PubMed
Tan Y, Kim BJ, Mujal AM, Chen ACY, Weis AM, Bergaggio E, Micevic G, Xie H, Park JS, Hor JL, Papanicolaou M, Shobaki N, Domizi P, Delconte RB, Vendramin R, Hegde S, Han S, Su Y, Hacohen N. Training Tomorrow's Leaders in Cancer Immunology. Cancer Immunol Res 2026; 14:186-193. PubMed
Tiago M, Purwin TJ, Stefanski CD, da Silva RO, Fane ME, Chhabra Y, Haj JI, Teh JL, Kadamb R, Cai W, Rosenbaum SR, Chua V, Hacohen N, Davies MA, Villanueva J, Chervoneva I, Weeraratna AT, Erkes DA, Capparelli C, Aguirre-Ghiso JA, Aplin AE. Elevated NR2F1 underlies the persistence of invasive disease after treatment of BRAF-mutant melanoma. J Clin Invest 2025. PubMed
Babu S, Chen J, Baron CS, Sun K, Robitschek E, McConnell AM, Wu C, Dedeilia A, Sade-Feldman M, Modhurima R, Manos MP, Chen KY, Cox AM, Ludwig CG, Kellis M, Buchbinder EI, Hacohen N, Yang J, Boland GM, Abraham BJ, Liu D, Zon LI, Insco ML. Specific oncogene activation of the cell of origin in mucosal melanoma. Nat Commun 2025; 16:6750. PubMed
Blass E, Keskin DB, Tu CR, Forman C, Vanasse A, Sax HE, Shim B, Chea V, Kim N, Carulli I, Southard J, Lyu H, Lu W, Rickles-Young M, Afeyan AB, Olive O, Mehndiratta A, Greenslade H, Shetty K, Baginska J, Gomez Diaz I, Nau A, Pfaff KL, Gans A, Ranasinghe S, Buchbinder EI, Sussman TA, Insco ML, Yoon CH, Rodig SJ, Shukla SA, Li S, Aster JC, Braun DA, Cibulskis C, Hacohen N, Neuberg DS, Giobbie-Hurder A, Livak KJ, Fritsch EF, Oliveira G, Simon JM, Wu CJ, Ott PA. A multi-adjuvant personal neoantigen vaccine generates potent immunity in melanoma. Cell 2025. PubMed
Revach OY, Cicerchia AM, Shorer O, Palin CA, Petrova B, Anderson S, Liu B, Park J, Chen L, Mehta A, Wright SJ, McNamee N, Tal-Mason A, Cattaneo G, Tiwari P, Xie H, Sweere JM, Cheng LC, Sigal N, Enrico E, Miljkovic M, Evans SA, Nguyen N, Whidden ME, Srinivasan R, Spitzer MH, Sun Y, Sharova T, Lawless AR, Michaud WA, Rasmussen MQ, Fang J, Brook JR, Chen F, Wang X, Ferrone CR, Lawrence DP, Sullivan RJ, Liu D, Sachdeva UM, Sen DR, Flaherty KT, Manguso RT, Bod L, Kellis M, Boland GM, Yizhak K, Yang J, Kanarek N, Sade-Feldman M, Hacohen N, Jenkins RW. Overcoming resistance to immunotherapy by targeting CD38 in human tumor explants. Cell Rep Med 2025. PubMed
Zisman E, Stern O, Lewis R, Tzaban S, Eisenhaure T, Henrickson SE, Sade-Feldman M, Silberman-Klein S, Eisenberg G, Hacohen N, Yizhak K, Lotem M. Unveiling alternative splicing dynamics in activated T lymphocytes and their implications for immune checkpoint blockade efficacy. iScience 2025; 28:112434. PubMed
Monette A, Aguilar-Mahecha A, Altinmakas E, Angelos MG, Assad N, Batist G, Bommareddy PK, Bonilla DL, Borchers CH, Church SE, Ciliberto G, Cogdill AP, Fattore L, Hacohen N, Haris M, Lacasse V, Lie WR, Mehta A, Ruella M, Sater S, Spatz A, Taouli B, Tarhoni I, Gonzalez-Kozlova E, Tirosh I, Wang X, Gnjatic S. The Society for Immunotherapy of Cancer Perspective on Liquid Biopsy and Radiomics Based Technologies for Immuno-Oncology Biomarker Discovery and Application. Clin Cancer Res 2025. PubMed

Millard N, Chen JH, Palshikar MG, Pelka K, Spurrell M, Price C, He J, Hacohen N, Raychaudhuri S, Korsunsky I. Batch correcting single-cell spatial transcriptomics count data with Crescendo improves visualization and detection of spatial gene patterns. Genome Biol 2025; 26:36. PubMed
Braun DA, Moranzoni G, Chea V, McGregor BA, Blass E, Tu CR, Vanasse AP, Forman C, Forman J, Afeyan AB, Schindler NR, Liu Y, Li S, Southard J, Chang SL, Hirsch MS, LeBoeuf NR, Olive O, Mehndiratta A, Greenslade H, Shetty K, Klaeger S, Sarkizova S, Pedersen CB, Mossanen M, Carulli I, Tarren A, Duke-Cohan J, Howard AA, Iorgulescu JB, Shim B, Simon JM, Signoretti S, Aster JC, Elagina L, Carr SA, Leshchiner I, Getz G, Gabriel S, Hacohen N, Olsen LR, Oliveira G, Neuberg DS, Livak KJ, Shukla SA, Fritsch EF, Wu CJ, Keskin DB, Ott PA, Choueiri TK. A neoantigen vaccine generates antitumour immunity in renal cell carcinoma. Nature 2025. PubMed
Gentili M, Carlson RJ, Liu B, Hellier Q, Andrews J, Qin Y, Blainey PC, Hacohen N. Classification and functional characterization of regulators of intracellular STING trafficking identified by genome-wide optical pooled screening. Cell Syst 2024; 15:1264-1277.e8. PubMed
Monette A, Aguilar-Mahecha A, Altinmakas E, Angelos MG, Assad N, Batist G, Bommareddy PK, Bonilla DL, Borchers CH, Church SE, Ciliberto G, Cogdill AP, Fattore L, Hacohen N, Haris M, Lacasse V, Lie WR, Mehta A, Ruella M, Sater HA, Spatz A, Taouli B, Tarhoni I, Gonzalez-Kozlova E, Tirosh I, Wang X, Gnjatic S. The Society for Immunotherapy of Cancer Perspective on Tissue-Based Technologies for Immuno-Oncology Biomarker Discovery and Application. Clin Cancer Res 2024. PubMed
LaFleur MW, D'Andrea JM, Patterson DG, Streeter ISL, Coxe MA, Osborn JF, Milling LE, Tjokrosurjo Q, Gillis JE, Nguyen TH, Schwartz MA, Hacohen N, Doench JG, Sharpe AH. In Vivo CRISPR Screening Reveals CHD7 as a Positive Regulator of Short-lived Effector Cells. J Immunol 2024. PubMed
Chudnovskiy A, Castro TBR, Nakandakari-Higa S, Cui A, Lin CH, Sade-Feldman M, Phillips BK, Pae J, Mesin L, Bortolatto J, Schweitzer LD, Pasqual G, Lu LF, Hacohen N, Victora GD. Proximity-dependent labeling identifies dendritic cells that drive the tumor-specific CD4 T cell response. Sci Immunol 2024; 9:eadq8843. PubMed
Chen JH, Elmelech L, Tang AL, Hacohen N. Powerful microscopy technologies decode spatially organized cellular networks that drive response to immunotherapy in humans. Curr Opin Immunol 2024; 91:102463. PubMed
Mooradian MJ, Fintelmann FJ, LaSalle TJ, Simon J, Graur A, Muzikansky A, Mino-Kenudson M, Shalhout S, Kaufman HL, Jenkins RW, Lawrence D, Lawless A, Sharova T, Uppot RN, Fang J, Blaum EM, Gonye ALK, Gushterova I, Boland GM, Azzoli C, Hacohen N, Sade-Feldman M, Sullivan RJ. Cryoablation and post-progression immune checkpoint inhibition in metastatic melanoma: a phase II trial. Nat Commun 2024; 15:7357. PubMed
Osmani Z, Villanueva MA, Joseph-Chazan J, Beudeker BJ, de Knegt RJ, Chung RT, Hacohen N, Aerssens J, Bollekens J, Janssen HLA, Gehring AJ, Lauer GM, Shalek AK, van de Werken HJG, Boonstra A. Intrahepatic plasma cells, but not atypical memory B cells, associate with clinical phases of chronic hepatitis B. Eur J Immunol 2024. PubMed
Chen ACY, Jaiswal S, Martinez D, Yerinde C, Ji K, Miranda V, Fung ME, Weiss SA, Zschummel M, Taguchi K, Garris CS, Mempel TR, Hacohen N, Sen DR. The aged tumor microenvironment limits T cell control of cancer. Nat Immunol 2024. PubMed
Thomas MF, Slowikowski K, Manakongtreecheep K, Sen P, Samanta N, Tantivit J, Nasrallah M, Zubiri L, Smith NP, Tirard A, Ramesh S, Arnold BY, Nieman LT, Chen JH, Eisenhaure T, Pelka K, Song Y, Xu KH, Jorgji V, Pinto CJ, Sharova T, Glasser R, Chan P, Sullivan RJ, Khalili H, Juric D, Boland GM, Dougan M, Hacohen N, Li B, Reynolds KL, Villani AC. Single-cell transcriptomic analyses reveal distinct immune cell contributions to epithelial barrier dysfunction in checkpoint inhibitor colitis. Nat Med 2024; 30:1349-1362. PubMed
Milling LE, Markson SC, Tjokrosurjo Q, Derosia NM, Streeter ISL, Hickok GH, Lemmen AM, Nguyen TH, Prathima P, Fithian W, Schwartz MA, Hacohen N, Doench JG, LaFleur MW, Sharpe AH. Framework for in vivo T cell screens. J Exp Med 2024. PubMed
Chen JH, Nieman LT, Spurrell M, Jorgji V, Elmelech L, Richieri P, Xu KH, Madhu R, Parikh M, Zamora I, Mehta A, Nabel CS, Freeman SS, Pirl JD, Lu C, Meador CB, Barth JL, Sakhi M, Tang AL, Sarkizova S, Price C, Fernandez NF, Emanuel G, He J, Van Raay K, Reeves JW, Yizhak K, Hofree M, Shih A, Sade-Feldman M, Boland GM, Pelka K, Aryee MJ, Mino-Kenudson M, Gainor JF, Korsunsky I, Hacohen N. Human lung cancer harbors spatially organized stem-immunity hubs associated with response to immunotherapy. Nat Immunol 2024. PubMed
Cui A, Huang T, Li S, Ma A, Pérez JL, Sander C, Keskin DB, Wu CJ, Fraenkel E, Hacohen N. Dictionary of immune responses to cytokines at single-cell resolution. Nature 2024; 625:377-384. PubMed
Alvarez-Breckenridge C, Anderson KG, Correia AL, Demehri S, Dinh HQ, Dixon KO, Dunn GP, Evgin L, Goc J, Good Z, Hacohen N, Han P, Hanč P, Hickey J, Kersten K, Liu BC, Buque A, Miao Y', Milner JJ, Pritykin Y, Pucci F, Scharping NE, Sudmeier L, Wang Y, Wieland A, Williams MM. Lessons for the Next Generation of Scientists from the Second Annual Arthur and Sandra Irving Cancer Immunology Symposium. Cancer Immunol Res 2023. PubMed
Liu B, Carlson RJ, Pires IS, Gentili M, Feng E, Hellier Q, Schwartz MA, Blainey PC, Irvine DJ, Hacohen N. Human STING is a proton channel. Science 2023; 381:508-514. PubMed
Bill R, Wirapati P, Messemaker M, Roh W, Zitti B, Duval F, Kiss M, Park JC, Saal TM, Hoelzl J, Tarussio D, Benedetti F, Tissot S, Kandalaft L, Varrone M, Ciriello G, McKee TA, Monnier Y, Mermod M, Blaum EM, Gushterova I, Gonye ALK, Hacohen N, Getz G, Mempel TR, Klein AM, Weissleder R, Faquin WC, Sadow PM, Lin D, Pai SI, Sade-Feldman M, Pittet MJ. macrophage polarity identifies a network of cellular programs that control human cancers. Science 2023; 381:515-524. PubMed
Al'Khafaji AM, Smith JT, Garimella KV, Babadi M, Popic V, Sade-Feldman M, Gatzen M, Sarkizova S, Schwartz MA, Blaum EM, Day A, Costello M, Bowers T, Gabriel S, Banks E, Philippakis AA, Boland GM, Blainey PC, Hacohen N. High-throughput RNA isoform sequencing using programmed cDNA concatenation. Nat Biotechnol 2023. PubMed
Genshaft AS, Subudhi S, Keo A, Sanchez Vasquez JD, Conceição-Neto N, Mahamed D, Boeijen LL, Alatrakchi N, Oetheimer C, Vilme M, Drake R, Fleming I, Tran N, Tzouanas C, Joseph-Chazan J, Arreola Villanueva M, van de Werken HJG, van Oord GW, Groothuismink ZMA, Beudeker BJ, Osmani Z, Nkongolo S, Mehrotra A, Spittaels K, Feld J, Chung RT, de Knegt RJ, Janssen HLA, Aerssens J, Bollekens J, Hacohen N, Lauer GM, Boonstra A, Shalek AK, Gehring AJ. Single-cell RNA sequencing of liver fine-needle aspirates captures immune diversity in the blood and liver in chronic hepatitis B patients. Hepatology 2023. PubMed
Ravi A, Hellmann MD, Arniella MB, Holton M, Freeman SS, Naranbhai V, Stewart C, Leshchiner I, Kim J, Akiyama Y, Griffin AT, Vokes NI, Sakhi M, Kamesan V, Rizvi H, Ricciuti B, Forde PM, Anagnostou V, Riess JW, Gibbons DL, Pennell NA, Velcheti V, Digumarthy SR, Mino-Kenudson M, Califano A, Heymach JV, Herbst RS, Brahmer JR, Schalper KA, Velculescu VE, Henick BS, Rizvi N, Jänne PA, Awad MM, Chow A, Greenbaum BD, Luksza M, Shaw AT, Wolchok J, Hacohen N, Getz G, Gainor JF. Genomic and transcriptomic analysis of checkpoint blockade response in advanced non-small cell lung cancer. Nat Genet 2023; 55:807-819. PubMed
Carlson RJ, Leiken MD, Guna A, Hacohen N, Blainey PC. A genome-wide optical pooled screen reveals regulators of cellular antiviral responses. Proc Natl Acad Sci U S A 2023; 120:e2210623120. PubMed
Hasegawa T, Oka T, Son HG, Oliver-García VS, Azin M, Eisenhaure TM, Lieb DJ, Hacohen N, Demehri S. Cytotoxic CD4 T cells eliminate senescent cells by targeting cytomegalovirus antigen. Cell 2023; 186:1417-1431.e20. PubMed
Cui A, Li B, Wallace MS, Gonye ALK, Oetheimer C, Patel H, Tonnerre P, Holmes JA, Lieb D, Yao BS, Ma A, Roberts K, Damasio M, Chen JH, Piou D, Carlton-Smith C, Brown J, Mylvaganam R, Hon Fung JM, Sade-Feldman M, Aneja J, Gustafson J, Epstein ET, Salloum S, Brisac C, Thabet A, Kim AY, Lauer GM, Hacohen N, Chung RT, Alatrakchi N. Single-cell atlas of the liver myeloid compartment before and after cure of chronic viral hepatitis. J Hepatol 2023. PubMed
Fox DB, Ebright RY, Hong X, Russell HC, Guo H, LaSalle TJ, Wittner BS, Poux N, Vuille JA, Toner M, Hacohen N, Boland GM, Sen DR, Sullivan RJ, Maheswaran S, Haber DA. Downregulation of KEAP1 in melanoma promotes resistance to immune checkpoint blockade. NPJ Precis Oncol 2023; 7:25. PubMed
Reyes M, Leff SM, Gentili M, Hacohen N, Blainey PC. Microscale combinatorial stimulation of human myeloid cells reveals inflammatory priming by viral ligands. Sci Adv 2023; 9:eade5090. PubMed
Gonye ALK, LaSalle TJ, Freeman SS, Reyes M, Hacohen N, Villani AC, Sade-Feldman M. Protocol for bulk RNA sequencing of enriched human neutrophils from whole blood and estimation of sample purity. STAR Protoc 2023; 4:102125. PubMed
Gentili M, Liu B, Papanastasiou M, Dele-Oni D, Schwartz MA, Carlson RJ, Al'Khafaji AM, Krug K, Brown A, Doench JG, Carr SA, Hacohen N. ESCRT-dependent STING degradation inhibits steady-state and cGAMP-induced signalling. Nat Commun 2023; 14:611. PubMed
Sun Y, Revach OY, Anderson S, Kessler EA, Wolfe CH, Jenney A, Mills CE, Robitschek EJ, Davis TGR, Kim S, Fu A, Ma X, Gwee J, Tiwari P, Du PP, Sindurakar P, Tian J, Mehta A, Schneider AM, Yizhak K, Sade-Feldman M, LaSalle T, Sharova T, Xie H, Liu S, Michaud WA, Saad-Beretta R, Yates KB, Iracheta-Vellve A, Spetz JKE, Qin X, Sarosiek KA, Zhang G, Kim JW, Su MY, Cicerchia AM, Rasmussen MQ, Klempner SJ, Juric D, Pai SI, Miller DM, Giobbie-Hurder A, Chen JH, Pelka K, Frederick DT, Stinson S, Ivanova E, Aref AR, Paweletz CP, Barbie DA, Sen DR, Fisher DE, Corcoran RB, Hacohen N, Sorger PK, Flaherty KT, Boland GM, Manguso RT, Jenkins RW. Targeting TBK1 to overcome resistance to cancer immunotherapy. Nature 2023. PubMed
Dubrot J, Du PP, Lane-Reticker SK, Kessler EA, Muscato AJ, Mehta A, Freeman SS, Allen PM, Olander KE, Ockerman KM, Wolfe CH, Wiesmann F, Knudsen NH, Tsao HW, Iracheta-Vellve A, Schneider EM, Rivera-Rosario AN, Kohnle IC, Pope HW, Ayer A, Mishra G, Zimmer MD, Kim SY, Mahapatra A, Ebrahimi-Nik H, Frederick DT, Boland GM, Haining WN, Root DE, Doench JG, Hacohen N, Yates KB, Manguso RT. In vivo CRISPR screens reveal the landscape of immune evasion pathways across cancer. Nat Immunol 2022; 23:1495-1506. PubMed
Freeman SS, Sade-Feldman M, Kim J, Stewart C, Gonye ALK, Ravi A, Arniella MB, Gushterova I, LaSalle TJ, Blaum EM, Yizhak K, Frederick DT, Sharova T, Leshchiner I, Elagina L, Spiro OG, Livitz D, Rosebrock D, Aguet F, Carrot-Zhang J, Ha G, Lin Z, Chen JH, Barzily-Rokni M, Hammond MR, Vitzthum von Eckstaedt HC, Blackmon SM, Jiao YJ, Gabriel S, Lawrence DP, Duncan LM, Stemmer-Rachamimov AO, Wargo JA, Flaherty KT, Sullivan RJ, Boland GM, Meyerson M, Getz G, Hacohen N. Combined tumor and immune signals from genomes or transcriptomes predict outcomes of checkpoint inhibition in melanoma. Cell Rep Med 2022; 3:100500. PubMed
Oliveira G, Stromhaug K, Cieri N, Iorgulescu JB, Klaeger S, Wolff JO, Rachimi S, Chea V, Krause K, Freeman SS, Zhang W, Li S, Braun DA, Neuberg D, Carr SA, Livak KJ, Frederick DT, Fritsch EF, Wind-Rotolo M, Hacohen N, Sade-Feldman M, Yoon CH, Keskin DB, Ott PA, Rodig SJ, Boland GM, Wu CJ. Landscape of helper and regulatory antitumour CD4 T cells in melanoma. Nature 2022; 605:532-538. PubMed
Ouspenskaia T, Law T, Clauser KR, Klaeger S, Sarkizova S, Aguet F, Li B, Christian E, Knisbacher BA, Le PM, Hartigan CR, Keshishian H, Apffel A, Oliveira G, Zhang W, Chen S, Chow YT, Ji Z, Jungreis I, Shukla SA, Justesen S, Bachireddy P, Kellis M, Getz G, Hacohen N, Keskin DB, Carr SA, Wu CJ, Regev A. Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer. Nat Biotechnol 2021. PubMed
Pelka K, Hofree M, Chen JH, Sarkizova S, Pirl JD, Jorgji V, Bejnood A, Dionne D, Ge WH, Xu KH, Chao SX, Zollinger DR, Lieb DJ, Reeves JW, Fuhrman CA, Hoang ML, Delorey T, Nguyen LT, Waldman J, Klapholz M, Wakiro I, Cohen O, Albers J, Smillie CS, Cuoco MS, Wu J, Su MJ, Yeung J, Vijaykumar B, Magnuson AM, Asinovski N, Moll T, Goder-Reiser MN, Applebaum AS, Brais LK, DelloStritto LK, Denning SL, Phillips ST, Hill EK, Meehan JK, Frederick DT, Sharova T, Kanodia A, Todres EZ, Jané-Valbuena J, Biton M, Izar B, Lambden CD, Clancy TE, Bleday R, Melnitchouk N, Irani J, Kunitake H, Berger DL, Srivastava A, Hornick JL, Ogino S, Rotem A, Vigneau S, Johnson BE, Corcoran RB, Sharpe AH, Kuchroo VK, Ng K, Giannakis M, Nieman LT, Boland GM, Aguirre AJ, Anderson AC, Rozenblatt-Rosen O, Regev A, Hacohen N. Spatially organized multicellular immune hubs in human colorectal cancer. Cell 2021; 184:4734-4752.e20. PubMed
Klaeger S, Apffel A, Clauser KR, Sarkizova S, Oliveira G, Rachimi S, Le PM, Tarren A, Chea V, Abelin JG, Braun DA, Ott PA, Keshishian H, Hacohen N, Keskin DB, Wu CJ, Carr SA. Optimized liquid and gas phase fractionation increases HLA-peptidome coverage for primary cell and tissue samples. Mol Cell Proteomics 2021. PubMed
Tonnerre P, Wolski D, Subudhi S, Aljabban J, Hoogeveen RC, Damasio M, Drescher HK, Bartsch LM, Tully DC, Sen DR, Bean DJ, Brown J, Torres-Cornejo A, Robidoux M, Kvistad D, Alatrakchi N, Cui A, Lieb D, Cheney JA, Gustafson J, Lewis-Ximenez LL, Massenet-Regad L, Eisenhaure T, Aneja J, Haining WN, Chung RT, Hacohen N, Allen TM, Kim AY, Lauer GM. Differentiation of exhausted CD8 T cells after termination of chronic antigen stimulation stops short of achieving functional T cell memory. Nat Immunol 2021; 22:1030-1041. PubMed
Nasser J, Bergman DT, Fulco CP, Guckelberger P, Doughty BR, Patwardhan TA, Jones TR, Nguyen TH, Ulirsch JC, Lekschas F, Mualim K, Natri HM, Weeks EM, Munson G, Kane M, Kang HY, Cui A, Ray JP, Eisenhaure TM, Collins RL, Dey K, Pfister H, Price AL, Epstein CB, Kundaje A, Xavier RJ, Daly MJ, Huang H, Finucane HK, Hacohen N, Lander ES, Engreitz JM. Genome-wide enhancer maps link risk variants to disease genes. Nature 2021; 593:238-243. PubMed
Hajaj E, Zisman E, Tzaban S, Merims S, Cohen J, Klein S, Frankenburg S, Sade-Feldman M, Tabach Y, Yizhak K, Navon A, Stepensky P, Hacohen N, Peretz T, Veillette A, Karni R, Eisenberg G, Lotem M. Alternative Splicing of the Inhibitory Immune Checkpoint Receptor SLAMF6 Generates a Dominant Positive Form, Boosting T-cell Effector Functions. Cancer Immunol Res 2021. PubMed
Lo JA, Kawakubo M, Juneja VR, Su MY, Erlich TH, LaFleur MW, Kemeny LV, Rashid M, Malehmir M, Rabi SA, Raghavan R, Allouche J, Kasumova G, Frederick DT, Pauken KE, Weng QY, Pereira da Silva M, Xu Y, van der Sande AAJ, Silkworth W, Roider E, Browne EP, Lieb DJ, Wang B, Garraway LA, Wu CJ, Flaherty KT, Brinckerhoff CE, Mullins DW, Adams DJ, Hacohen N, Hoang MP, Boland GM, Freeman GJ, Sharpe AH, Manstein D, Fisher DE. Epitope spreading toward wild-type melanocyte-lineage antigens rescues suboptimal immune checkpoint blockade responses. Sci Transl Med 2021. PubMed
Parikh AR, Szabolcs A, Allen JN, Clark JW, Wo JY, Raabe M, Thel H, Hoyos D, Mehta A, Arshad S, Lieb DJ, Drapek LC, Blaszkowsky LS, Giantonio BJ, Weekes CD, Zhu AX, Goyal L, Nipp RD, Dubois JS, Van Seventer EE, Foreman BE, Matlack LE, Ly L, Meurer JA, Hacohen N, Ryan DP, Yeap BY, Corcoran RB, Greenbaum BD, Ting DT, Hong TS. Radiation therapy enhances immunotherapy response in microsatellite stable colorectal and pancreatic adenocarcinoma in a phase II trial. 2021; 2:1124-1135. PubMed
Chen B, Scurrah CR, McKinley ET, Simmons AJ, Ramirez-Solano MA, Zhu X, Markham NO, Heiser CN, Vega PN, Rolong A, Kim H, Sheng Q, Drewes JL, Zhou Y, Southard-Smith AN, Xu Y, Ro J, Jones AL, Revetta F, Berry LD, Niitsu H, Islam M, Pelka K, Hofree M, Chen JH, Sarkizova S, Ng K, Giannakis M, Boland GM, Aguirre AJ, Anderson AC, Rozenblatt-Rosen O, Regev A, Hacohen N, Kawasaki K, Sato T, Goettel JA, Grady WM, Zheng W, Washington MK, Cai Q, Sears CL, Goldenring JR, Franklin JL, Su T, Huh WJ, Vandekar S, Roland JT, Liu Q, Coffey RJ, Shrubsole MJ, Lau KS. Differential pre-malignant programs and microenvironment chart distinct paths to malignancy in human colorectal polyps. Cell 2021; 184:6262-6280.e26. PubMed
Raychowdhury R, Gentili M, Cui A, Schweitzer LD, Li B, Hacohen N. Macrophages from Rosa26-Integrated Cas9-Expressing C57BL/6J Mice Have a Putative TRIF-Mediated Defect in the TLR-3/4 Signaling. Immunohorizons 2021; 5:818-829. PubMed
Wang C, Cui A, Bukenya M, Aung A, Pradhan D, Whittaker CA, Agarwal Y, Thomas A, Liang S, Amlashi P, Suh H, Spranger S, Hacohen N, Irvine DJ. Reprogramming NK cells and macrophages via combined antibody and cytokine therapy primes tumors for elimination by checkpoint blockade. Cell Rep 2021; 37:110021. PubMed
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Zhu Z, Aref AR, Cohoon TJ, Barbie TU, Imamura Y, Yang S, Moody SE, Shen RR, Schinzel AC, Thai TC, Reibel JB, Tamayo P, Godfrey JT, Qian ZR, Page AN, Maciag K, Chan EM, Silkworth W, Labowsky MT, Rozhansky L, Mesirov JP, Gillanders WE, Ogino S, Hacohen N, Gaudet S, Eck MJ, Engelman JA, Corcoran RB, Wong KK, Hahn WC, Barbie DA. Inhibition of KRAS-driven tumorigenicity by interruption of an autocrine cytokine circuit. 2014; 4:452-65. PubMed
Lee MN, Ye C, Villani AC, Raj T, Li W, Eisenhaure TM, Imboywa SH, Chipendo PI, Ran FA, Slowikowski K, Ward LD, Raddassi K, McCabe C, Lee MH, Frohlich IY, Hafler DA, Kellis M, Raychaudhuri S, Zhang F, Stranger BE, Benoist CO, De Jager PL, Regev A, Hacohen N. Common genetic variants modulate pathogen-sensing responses in human dendritic cells. Science 2014; 343:1246980. PubMed
Bachireddy P, Hainz U, Rooney M, Pozdnyakova O, Aldridge J, Zhang W, Liao X, Hodi FS, O'Connell K, Haining WN, Goldstein NR, Canning CM, Soiffer RJ, Ritz J, Hacohen N, Alyea EP, Kim HT, Wu CJ. Reversal of in situ T-cell exhaustion during effective human antileukemia responses to donor lymphocyte infusion. Blood 2014; 123:1412-21. PubMed
Zhou P, Shaffer DR, Alvarez Arias DA, Nakazaki Y, Pos W, Torres AJ, Cremasco V, Dougan SK, Cowley GS, Elpek K, Brogdon J, Lamb J, Turley SJ, Ploegh HL, Root DE, Love JC, Dranoff G, Hacohen N, Cantor H, Wucherpfennig KW. In vivo discovery of immunotherapy targets in the tumour microenvironment. Nature 2014; 506:52-7. PubMed
Filone CM, Caballero IS, Dower K, Mendillo ML, Cowley GS, Santagata S, Rozelle DK, Yen J, Rubins KH, Hacohen N, Root DE, Hensley LE, Connor J. The master regulator of the cellular stress response (HSF1) is critical for orthopoxvirus infection. PLoS Pathog. 2014; 10:e1003904. PubMed
Giraud M, Jmari N, Du L, Carallis F, Nieland TJ, Perez-Campo FM, Bensaude O, Root DE, Hacohen N, Mathis D, Benoist C. An RNAi screen for Aire cofactors reveals a role for Hnrnpl in polymerase release and Aire-activated ectopic transcription. Proc Natl Acad Sci U S A 2014; 111:1491-6. PubMed
Park SM, Deering RP, Lu Y, Tivnan P, Lianoglou S, Al-Shahrour F, Ebert BL, Hacohen N, Leslie C, Daley GQ, Lengner CJ, Kharas MG. Musashi-2 controls cell fate, lineage bias, and TGF-β signaling in HSCs. J Exp Med 2014; 211:71-87. PubMed
Fritsch EF, Hacohen N, Wu CJ. Personal neoantigen cancer vaccines: The momentum builds. Oncoimmunology 2014; 3:e29311. PubMed
Ramirez-Ortiz ZG, Pendergraft WF, Prasad A, Byrne MH, Iram T, Blanchette CJ, Luster AD, Hacohen N, El Khoury J, Means TK. The scavenger receptor SCARF1 mediates the clearance of apoptotic cells and prevents autoimmunity. Nat Immunol 2013; 14:917-26. PubMed
Hacohen N, Fritsch EF, Carter TA, Lander ES, Wu CJ. Getting personal with neoantigen-based therapeutic cancer vaccines. Cancer Immunol Res 2013; 1:11-5. PubMed
Shalek AK, Satija R, Adiconis X, Gertner RS, Gaublomme JT, Raychowdhury R, Schwartz S, Yosef N, Malboeuf C, Lu D, Trombetta JJ, Gennert D, Gnirke A, Goren A, Hacohen N, Levin JZ, Park H, Regev A. Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells. Nature 2013; 498:236-40. PubMed
Gat-Viks I, Chevrier N, Wilentzik R, Eisenhaure T, Raychowdhury R, Steuerman Y, Shalek AK, Hacohen N, Amit I, Regev A. Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli. Nat Biotechnol 2013; 31:342-9. PubMed
Landau DA, Carter SL, Stojanov P, McKenna A, Stevenson K, Lawrence MS, Sougnez C, Stewart C, Sivachenko A, Wang L, Wan Y, Zhang W, Shukla SA, Vartanov A, Fernandes SM, Saksena G, Cibulskis K, Tesar B, Gabriel S, Hacohen N, Meyerson M, Lander ES, Neuberg D, Brown JR, Getz G, Wu CJ. Evolution and impact of subclonal mutations in chronic lymphocytic leukemia. Cell 2013; 152:714-26. PubMed
Lee MN, Roy M, Ong SE, Mertins P, Villani AC, Li W, Dotiwala F, Sen J, Doench JG, Orzalli MH, Kramnik I, Knipe DM, Lieberman J, Carr SA, Hacohen N. Identification of regulators of the innate immune response to cytosolic DNA and retroviral infection by an integrative approach. Nat Immunol 2013; 14:179-85. PubMed
Shalek AK, Gaublomme JT, Wang L, Yosef N, Chevrier N, Andersen MS, Robinson JT, Pochet N, Neuberg D, Gertner RS, Amit I, Brown JR, Hacohen N, Regev A, Wu CJ, Park H. Nanowire-mediated delivery enables functional interrogation of primary immune cells: application to the analysis of chronic lymphocytic leukemia. Nano Lett 2012; 12:6498-504. PubMed
Garber M, Yosef N, Goren A, Raychowdhury R, Thielke A, Guttman M, Robinson J, Minie B, Chevrier N, Itzhaki Z, Blecher-Gonen R, Bornstein C, Amann-Zalcenstein D, Weiner A, Friedrich D, Meldrim J, Ram O, Cheng C, Gnirke A, Fisher S, Friedman N, Wong B, Bernstein BE, Nusbaum C, Hacohen N, Regev A, Amit I. A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. Mol Cell 2012; 47:810-22. PubMed
Moita CF, Chora Â, Hacohen N, Moita LF. RNAi screen for kinases and phosphatases that play a role in antigen presentation by dendritic cells. Eur J Immunol 2012; 42:1843-9. PubMed
Lin Y, Zhang L, Cai AX, Lee M, Zhang W, Neuberg D, Canning CM, Soiffer RJ, Alyea EP, Ritz J, Hacohen N, Means TK, Wu CJ. Effective posttransplant antitumor immunity is associated with TLR-stimulating nucleic acid-immunoglobulin complexes in humans. J Clin Invest 2011. PubMed
Pe'er D, Hacohen N. Principles and strategies for developing network models in cancer. Cell 2011; 144:864-73. PubMed
Dougan M, Dougan S, Slisz J, Firestone B, Vanneman M, Draganov D, Goyal G, Li W, Neuberg D, Blumberg R, Hacohen N, Porter D, Zawel L, Dranoff G. IAP inhibitors enhance co-stimulation to promote tumor immunity. J Exp Med 2010; 207:2195-206. PubMed
Colvin RA, Means TK, Diefenbach TJ, Moita LF, Friday RP, Sever S, Campanella GS, Abrazinski T, Manice LA, Moita C, Andrews NW, Wu D, Hacohen N, Luster AD. Synaptotagmin-mediated vesicle fusion regulates cell migration. Nat Immunol 2010; 11:495-502. PubMed
Dixit E, Boulant S, Zhang Y, Lee AS, Odendall C, Shum B, Hacohen N, Chen ZJ, Whelan SP, Fransen M, Nibert ML, Superti-Furga G, Kagan JC. Peroxisomes are signaling platforms for antiviral innate immunity. Cell 2010; 141:668-81. PubMed
Astier AL, Beriou G, Eisenhaure TM, Anderton SM, Hafler DA, Hacohen N. RNA interference screen in primary human T cells reveals FLT3 as a modulator of IL-10 levels. J Immunol 2010; 184:685-93. PubMed
Ostrowski M, Carmo NB, Krumeich S, Fanget I, Raposo G, Savina A, Moita CF, Schauer K, Hume AN, Freitas RP, Goud B, Benaroch P, Hacohen N, Fukuda M, Desnos C, Seabra MC, Darchen F, Amigorena S, Moita LF, Thery C. Rab27a and Rab27b control different steps of the exosome secretion pathway. Nat Cell Biol 2010; 12:19-30; sup pp 1-13. PubMed
Shapira SD, Gat-Viks I, Shum BO, Dricot A, de Grace MM, Wu L, Gupta PB, Hao T, Silver SJ, Root DE, Hill DE, Regev A, Hacohen N. A physical and regulatory map of host-influenza interactions reveals pathways in H1N1 infection. Cell 2009; 139:1255-67. PubMed
Ali N,Karlsson C,Aspling M,Hu G,Hacohen N,Scadden DT,Larsson J. Forward RNAi screens in primary human hematopoietic stem/progenitor cells. Blood 2009; 113:3690-5. PubMed
Savina A,Peres A,Cebrian I,Carmo N,Moita C,Hacohen N,Moita LF,Amigorena S. The small GTPase Rac2 controls phagosomal alkalinization and antigen crosspresentation selectively in CD8(+) dendritic cells. Immunity 2009; 30:544-55. PubMed
Means TK,Mylonakis E,Tampakakis E,Colvin RA,Seung E,Puckett L,Tai MF,Stewart CR,Pukkila-Worley R,Hickman SE,Moore KJ,Calderwood SB,Hacohen N,Luster AD,El Khoury J. Evolutionarily conserved recognition and innate immunity to fungal pathogens by the scavenger receptors SCARF1 and CD36. J Exp Med 2009; 206:637-53. PubMed
Guttman M,Amit I,Garber M,French C,Lin MF,Feldser D,Huarte M,Zuk O,Carey BW,Cassady JP,Cabili MN,Jaenisch R,Mikkelsen TS,Jacks T,Hacohen N,Bernstein BE,Kellis M,Regev A,Rinn JL,Lander ES. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 2009; 458:223-7. PubMed
Luo B,Cheung HW,Subramanian A,Sharifnia T,Okamoto M,Yang X,Hinkle G,Boehm JS,Beroukhim R,Weir BA,Mermel C,Barbie DA,Awad T,Zhou X,Nguyen T,Piqani B,Li C,Golub TR,Meyerson M,Hacohen N,Hahn WC,Lander ES,Sabatini DM,Root DE. Highly parallel identification of essential genes in cancer cells. Proc Natl Acad Sci U S A 2008; 105:20380-5. PubMed
Oberdoerffer S,Moita LF,Neems D,Freitas RP,Hacohen N,Rao A. Regulation of CD45 alternative splicing by heterogeneous ribonucleoprotein, hnRNPLL. Science 2008; 321:686-91. PubMed
Adams EW, Ratner DM, Seeberger PH, Hacohen N. Carbohydrate-mediated targeting of antigen to dendritic cells leads to enhanced presentation of antigen to T cells. Chembiochem 2008; 9:294-303. PubMed
Moffat J, Grueneberg DA, Yang X, Kim SY, Kloepfer AM, Hinkle G, Piqani B, Eisenhaure TM, Luo B, Grenier JK, Carpenter AE, Foo SY, Stewart SA, Stockwell BR, Hacohen N, Hahn WC, Lander ES, Sabatini DM, Root DE. A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen. Cell 2006; 124:1283-98. PubMed
Bachireddy P, Hainz U, Rooney M, Pozdnyakova O, Aldridge J, Zhang W, Liao X, Hodi FS, O'Connell K, Haining WN, Goldstein NR, Canning CM, Soiffer RJ, Ritz J, Hacohen N, Alyea EP, Kim HT, Wu CJ. Reversal of in situ T cell exhaustion during effective human anti-leukemia responses to donor lymphocyte infusion Blood .
Chao S, Brenner MP, Hacohen N. Identifying Cell Type-Specific Chemokine Correlates with Hierarchical Signal Extraction from Single-Cell Transcriptomes. Pac Symp Biocomput ; 27:254-265. PubMed

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Nir Hacohen, PhD

Massachusetts General Hospital

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Nir Hacohen, PhD

Massachusetts General Hospital

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