My Bibliography

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Iyer AR, Gurumurthy A, Chu SA, Kodgule R, Aguilar AR, Saari T, Ramzan A, Rosa J, Gupta J, Emmanuel A, Hall CN, Runge JS, Owczarczyk AB, Cho JW, Weiss MB, Anyoha R, Sikkink K, Gemus S, Fulco CP, Perry AM, Schmitt AD, Engreitz JM, Brown NA, Cieslik MP, Ryan RJH. Selective Enhancer Dependencies in MYC-Intact and MYC-Rearranged Germinal Center B-cell Diffuse Large B-cell Lymphoma. Blood Cancer Discov. 2025 May 5;6(3):233-253. doi: 10.1158/2643-3230.BCD-24-0126. PubMed PMID: 40067173; PubMed Central PMCID: PMC12050968.

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Wang Q, Boccalatte F, Xu J, Gambi G, Nadorp B, Akter F, Mullin C, Melnick AF, Choe E, McCarter AC, Jerome NA, Chen S, Lin K, Khan S, Kodgule R, Sussman JH, Pölönen P, Rodriguez-Hernaez J, Narang S, Avrampou K, King B, Tsirigos A, Ryan RJH, Mullighan CG, Teachey DT, Tan K, Aifantis I, Chiang MY. Native stem cell transcriptional circuits define cardinal features of high-risk leukemia. J Exp Med. 2025 Apr 7;222(4). doi: 10.1084/jem.20231349. Epub 2025 Feb 19. PubMed PMID: 39969525; PubMed Central PMCID: PMC11837855.

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Rahmat M, Clement K, Alberge JB, Sklavenitis-Pistofidis R, Kodgule R, Fulco CP, Heilpern-Mallory D, Nilsson K, Dorfman D, Engreitz JM, Getz G, Pinello L, Ryan RJH, Ghobrial IM. Selective Enhancer Gain-of-Function Deregulates MYC Expression in Multiple Myeloma. Cancer Res. 2024 Dec 16;84(24):4173-4183. doi: 10.1158/0008-5472.CAN-24-1440. PubMed PMID: 39312195; PubMed Central PMCID: PMC11649448.

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Monovich AC, Gurumurthy A, Ryan RJH. The Diverse Roles of ETV6 Alterations in B-Lymphoblastic Leukemia and Other Hematopoietic Cancers. Adv Exp Med Biol. 2024;1459:291-320. doi: 10.1007/978-3-031-62731-6_13. Review. PubMed PMID: 39017849.

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Melnick AF, Mullin C, Lin K, McCarter AC, Liang S, Liu YE, Wang Q, Jerome NA, Choe E, Kunnath N, Bodanapu G, Akter F, Magnuson B, Kumar S, Lombard DB, Muntean AG, Ljungman M, Sekiguchi J, Ryan RJH, Chiang MY. Cdc73 protects Notch-induced T-cell leukemia cells from DNA damage and mitochondrial stress. Blood. 2023 Dec 21;142(25):2159-2174. doi: 10.1182/blood.2023020144. PubMed PMID: 37616559; PubMed Central PMCID: PMC10733839.

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Barnett KR, Mobley RJ, Diedrich JD, Bergeron BP, Bhattarai KR, Monovich AC, Narina S, Yang W, Crews KR, Manring CS, Jabbour E, Paietta E, Litzow MR, Kornblau SM, Stock W, Inaba H, Jeha S, Pui CH, Mullighan CG, Relling MV, Pruett-Miller SM, Ryan RJH, Yang JJ, Evans WE, Savic D. Epigenomic mapping reveals distinct B cell acute lymphoblastic leukemia chromatin architectures and regulators. Cell Genom. 2023 Dec 13;3(12):100442. doi: 10.1016/j.xgen.2023.100442. eCollection 2023 Dec 13. PubMed PMID: 38116118; PubMed Central PMCID: PMC10726428.

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Shestakova A, Shao L, Smith LB, Ryan R, Bedell V, Murata-Collins J, Zhang W, Perry AM, Song JY. High-grade B-cell lymphoma with concurrent MYC rearrangement and 11q aberrations: clinicopathologic, cytogenetic, and molecular characterization of 4 cases. Hum Pathol. 2023 Jun;136:34-43. doi: 10.1016/j.humpath.2023.03.013. Epub 2023 Mar 29. PubMed PMID: 36997031.

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Iyer AR, Gurumurthy A, Kodgule R, Aguilar AR, Saari T, Ramzan A, Rausch D, Gupta J, Hall CN, Runge JS, Weiss MB, Rahmat M, Anyoha R, Fulco CP, Ghobrial IM, Engreitz JM, Cieslik MP, Ryan RJ. Selective Enhancer Dependencies in MYC-Intact and MYC-Rearranged Germinal Center B-cell Diffuse Large B-cell Lymphoma. [preprint]. 2023 May. Available from: https://www.biorxiv.org/content/10.1101/2023.05.02.538892v1. doi: 10.1101/2023.05.02.538892.

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Kodgule R, Goldman JW, Monovich AC, Saari T, Aguilar AR, Hall CN, Rajesh N, Gupta J, Chu SA, Ye L, Gurumurthy A, Iyer A, Brown NA, Chiang MY, Cieslik MP, Ryan RJH. ETV6 Deficiency Unlocks ERG-Dependent Microsatellite Enhancers to Drive Aberrant Gene Activation in B-Lymphoblastic Leukemia. Blood Cancer Discov. 2023 Jan 6;4(1):34-53. doi: 10.1158/2643-3230.BCD-21-0224. PubMed PMID: 36350827; PubMed Central PMCID: PMC9820540.

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Apfelbaum AA, Wu F, Hawkins AG, Magnuson B, Jiménez JA, Taylor SD, Wrenn ED, Waltner O, Pfaltzgraff ER, Song JY, Hall C, Wellik DM, Ljungman M, Furlan SN, Ryan RJH, Sarthy JF, Lawlor ER. EWS::FLI1 and HOXD13 Control Tumor Cell Plasticity in Ewing Sarcoma. Clin Cancer Res. 2022 Oct 14;28(20):4466-4478. doi: 10.1158/1078-0432.CCR-22-0384. PubMed PMID: 35653119; PubMed Central PMCID: PMC9588607.

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Gómez Atria D, Gaudette BT, Londregan J, Kelly S, Perkey E, Allman A, Srivastava B, Koch U, Radtke F, Ludewig B, Siebel CW, Ryan RJ, Robertson TF, Burkhardt JK, Pear WS, Allman D, Maillard I. Stromal Notch ligands foster lymphopenia-driven functional plasticity and homeostatic proliferation of naive B cells. J Clin Invest. 2022 Jul 1;132(13). doi: 10.1172/JCI158885. PubMed PMID: 35579963; PubMed Central PMCID: PMC9246379.

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Shukla S, Ying W, Gray F, Yao Y, Simes ML, Zhao Q, Miao H, Cho HJ, González-Alonso P, Winkler A, Lund G, Purohit T, Kim E, Zhang X, Ray JM, He S, Nikolaidis C, Ndoj J, Wang J, Jaremko Ł, Jaremko M, Ryan RJH, Guzman ML, Grembecka J, Cierpicki T. Small-molecule inhibitors targeting Polycomb repressive complex 1 RING domain. Nat Chem Biol. 2021 Jul;17(7):784-793. doi: 10.1038/s41589-021-00815-5. Epub 2021 Jun 21. PubMed PMID: 34155404; PubMed Central PMCID: PMC8238916.

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Crotty R, Hu K, Stevenson K, Pontius MY, Sohani AR, Ryan RJH, Rueckert E, Brauer HA, Hudson B, Berlin AM, Rodenbaugh M, Licon A, Haimes J, Iafrate AJ, Nardi V, Louissaint A. Simultaneous Identification of Cell of Origin, Translocations, and Hotspot Mutations in Diffuse Large B-Cell Lymphoma Using a Single RNA-Sequencing Assay. Am J Clin Pathol. 2021 Apr 26;155(5):748-754. doi: 10.1093/ajcp/aqaa185. PubMed PMID: 33258912; PubMed Central PMCID: PMC8244124.

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McCarter AC, Della Gatta G, Melnick A, Kim E, Sha C, Wang Q, Nalamolu JK, Liu Y, Keeley TM, Yan R, Sun M, Kodgule R, Kunnath N, Ambesi-Impiombato A, Kuick R, Rao A, Ryan RJH, Kee BL, Samuelson LC, Ostrowski MC, Ferrando AA, Chiang MY. Combinatorial ETS1-dependent control of oncogenic NOTCH1 enhancers in T-cell leukemia. Blood Cancer Discov. 2020 Sep;1(2):178-197. doi: 10.1158/2643-3230.BCD-20-0026. PubMed PMID: 32924017; PubMed Central PMCID: PMC7482717.

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Lee WY, Pfau RB, Choi SM, Yang J, Xiao H, Putnam EM, Ryan RJ, Bixby DL, Shao L. The diagnostic challenges and clinical course of a myeloid/lymphoid neoplasm with eosinophilia and ZBTB20-JAK2 gene fusion presenting as B-lymphoblastic leukemia. Cold Spring Harb Mol Case Stud. 2020 Apr;6(2). doi: 10.1101/mcs.a004937. Print 2020 Apr. PubMed PMID: 32238402; PubMed Central PMCID: PMC7133749.

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Ryan RJH, Wilcox RA. Ontogeny, Genetics, Molecular Biology, and Classification of B- and T-Cell Non-Hodgkin Lymphoma. Hematol Oncol Clin North Am. 2019 Aug;33(4):553-574. doi: 10.1016/j.hoc.2019.04.003. Epub 2019 May 18. Review. PubMed PMID: 31229154; PubMed Central PMCID: PMC7216062.

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Huang G, Kaufman AJ, Ryan RJH, Romin Y, Huryn L, Bains S, Manova-Todorova K, Morris PL, Hunnicutt GR, Adelman CA, Petrini JHJ, Ramanathan Y, Singh B. Mouse DCUN1D1 (SCCRO) is required for spermatogenetic individualization. PLoS One. 2019;14(1):e0209995. doi: 10.1371/journal.pone.0209995. eCollection 2019. PubMed PMID: 30653527; PubMed Central PMCID: PMC6336273.

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Ryan RJH, Petrovic J, Rausch DM, Zhou Y, Lareau CA, Kluk MJ, Christie AL, Lee WY, Tarjan DR, Guo B, Donohue LKH, Gillespie SM, Nardi V, Hochberg EP, Blacklow SC, Weinstock DM, Faryabi RB, Bernstein BE, Aster JC, Pear WS. A B Cell Regulome Links Notch to Downstream Oncogenic Pathways in Small B Cell Lymphomas. Cell Rep. 2017 Oct 17;21(3):784-797. doi: 10.1016/j.celrep.2017.09.066. PubMed PMID: 29045844; PubMed Central PMCID: PMC5687286.

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Gupta RM, Hadaya J, Trehan A, Zekavat SM, Roselli C, Klarin D, Emdin CA, Hilvering CRE, Bianchi V, Mueller C, Khera AV, Ryan RJH, Engreitz JM, Issner R, Shoresh N, Epstein CB, de Laat W, Brown JD, Schnabel RB, Bernstein BE, Kathiresan S. A Genetic Variant Associated with Five Vascular Diseases Is a Distal Regulator of Endothelin-1 Gene Expression. Cell. 2017 Jul 27;170(3):522-533.e15. doi: 10.1016/j.cell.2017.06.049. PubMed PMID: 28753427; PubMed Central PMCID: PMC5785707.

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Fu W, Sun J, Huang G, Liu JC, Kaufman A, Ryan RJ, Ramanathan SY, Venkatesh T, Singh B. Squamous Cell Carcinoma-related Oncogene (SCCRO) Family Members Regulate Cell Growth and Proliferation through Their Cooperative and Antagonistic Effects on Cullin Neddylation. J Biol Chem. 2016 Mar 18;291(12):6200-17. doi: 10.1074/jbc.M115.692756. Epub 2016 Jan 20. PubMed PMID: 26792857; PubMed Central PMCID: PMC4813546.

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Drier Y, Cotton MJ, Williamson KE, Gillespie SM, Ryan RJ, Kluk MJ, Carey CD, Rodig SJ, Sholl LM, Afrogheh AH, Faquin WC, Queimado L, Qi J, Wick MJ, El-Naggar AK, Bradner JE, Moskaluk CA, Aster JC, Knoechel B, Bernstein BE. An oncogenic MYB feedback loop drives alternate cell fates in adenoid cystic carcinoma. Nat Genet. 2016 Mar;48(3):265-72. doi: 10.1038/ng.3502. Epub 2016 Feb 1. PubMed PMID: 26829750; PubMed Central PMCID: PMC4767593.

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van Galen P, Viny AD, Ram O, Ryan RJ, Cotton MJ, Donohue L, Sievers C, Drier Y, Liau BB, Gillespie SM, Carroll KM, Cross MB, Levine RL, Bernstein BE. A Multiplexed System for Quantitative Comparisons of Chromatin Landscapes. Mol Cell. 2016 Jan 7;61(1):170-80. doi: 10.1016/j.molcel.2015.11.003. Epub 2015 Dec 10. PubMed PMID: 26687680; PubMed Central PMCID: PMC4707994.

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Ryan RJ, Drier Y, Whitton H, Cotton MJ, Kaur J, Issner R, Gillespie S, Epstein CB, Nardi V, Sohani AR, Hochberg EP, Bernstein BE. Detection of Enhancer-Associated Rearrangements Reveals Mechanisms of Oncogene Dysregulation in B-cell Lymphoma. Cancer Discov. 2015 Oct;5(10):1058-71. doi: 10.1158/2159-8290.CD-15-0370. Epub 2015 Jul 30. PubMed PMID: 26229090; PubMed Central PMCID: PMC4592453.

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Farh KK, Marson A, Zhu J, Kleinewietfeld M, Housley WJ, Beik S, Shoresh N, Whitton H, Ryan RJ, Shishkin AA, Hatan M, Carrasco-Alfonso MJ, Mayer D, Luckey CJ, Patsopoulos NA, De Jager PL, Kuchroo VK, Epstein CB, Daly MJ, Hafler DA, Bernstein BE. Genetic and epigenetic fine mapping of causal autoimmune disease variants. Nature. 2015 Feb 19;518(7539):337-43. doi: 10.1038/nature13835. Epub 2014 Oct 29. PubMed PMID: 25363779; PubMed Central PMCID: PMC4336207.

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Ryan DP, Friedmann AM, Schmitz MD, Ryan RJ. Case records of the Massachusetts General Hospital. Case 11-2013. A 4-year-old boy with fever and abdominal pain. N Engl J Med. 2013 Apr 11;368(15):1435-44. doi: 10.1056/NEJMcpc1209304. PubMed PMID: 23574123.

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Ryan RJ, Akin C, Castells M, Wills M, Selig MK, Nielsen GP, Ferry JA, Hornick JL. Mast cell sarcoma: a rare and potentially under-recognized diagnostic entity with specific therapeutic implications. Mod Pathol. 2013 Apr;26(4):533-43. doi: 10.1038/modpathol.2012.199. Epub 2012 Nov 30. PubMed PMID: 23196796.

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Cortez-Retamozo V, Etzrodt M, Newton A, Ryan R, Pucci F, Sio SW, Kuswanto W, Rauch PJ, Chudnovskiy A, Iwamoto Y, Kohler R, Marinelli B, Gorbatov R, Wojtkiewicz G, Panizzi P, Mino-Kenudson M, Forghani R, Figueiredo JL, Chen JW, Xavier R, Swirski FK, Nahrendorf M, Weissleder R, Pittet MJ. Angiotensin II drives the production of tumor-promoting macrophages. Immunity. 2013 Feb 21;38(2):296-308. doi: 10.1016/j.immuni.2012.10.015. Epub 2013 Jan 17. PubMed PMID: 23333075; PubMed Central PMCID: PMC3582771.

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Fathi AT, Chen YB, Carter BW, Ryan RJ. Case records of the Massachusetts General Hospital. Case 24-2012. A 38-year-old man with abdominal pain and altered mental status. N Engl J Med. 2012 Aug 9;367(6):552-63. doi: 10.1056/NEJMcpc1110049. PubMed PMID: 22873536.

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Ryan RJ, Bernstein BE. Molecular biology. Genetic events that shape the cancer epigenome. Science. 2012 Jun 22;336(6088):1513-4. doi: 10.1126/science.1223730. PubMed PMID: 22723401.

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Cortez-Retamozo V, Etzrodt M, Newton A, Rauch PJ, Chudnovskiy A, Berger C, Ryan RJ, Iwamoto Y, Marinelli B, Gorbatov R, Forghani R, Novobrantseva TI, Koteliansky V, Figueiredo JL, Chen JW, Anderson DG, Nahrendorf M, Swirski FK, Weissleder R, Pittet MJ. Origins of tumor-associated macrophages and neutrophils. Proc Natl Acad Sci U S A. 2012 Feb 14;109(7):2491-6. doi: 10.1073/pnas.1113744109. Epub 2012 Jan 30. PubMed PMID: 22308361; PubMed Central PMCID: PMC3289379.

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Ryan RJ, Sloan JM, Collins AB, Mansouri J, Raje NS, Zukerberg LR, Ferry JA. Extranodal marginal zone lymphoma of mucosa-associated lymphoid tissue with amyloid deposition: a clinicopathologic case series. Am J Clin Pathol. 2012 Jan;137(1):51-64. doi: 10.1309/AJCPI08WAKYVLHHA. PubMed PMID: 22180478.

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Ryan RJ, Nitta M, Borger D, Zukerberg LR, Ferry JA, Harris NL, Iafrate AJ, Bernstein BE, Sohani AR, Le LP. EZH2 codon 641 mutations are common in BCL2-rearranged germinal center B cell lymphomas. PLoS One. 2011;6(12):e28585. doi: 10.1371/journal.pone.0028585. Epub 2011 Dec 14. PubMed PMID: 22194861; PubMed Central PMCID: PMC3237460.

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Restivo G, Nguyen BC, Dziunycz P, Ristorcelli E, Ryan RJ, Özuysal ÖY, Di Piazza M, Radtke F, Dixon MJ, Hofbauer GF, Lefort K, Dotto GP. IRF6 is a mediator of Notch pro-differentiation and tumour suppressive function in keratinocytes. EMBO J. 2011 Nov 16;30(22):4571-85. doi: 10.1038/emboj.2011.325. PubMed PMID: 21909072; PubMed Central PMCID: PMC3243593.

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Kim AY, Bommeljé CC, Lee BE, Yonekawa Y, Choi L, Morris LG, Huang G, Kaufman A, Ryan RJ, Hao B, Ramanathan Y, Singh B. SCCRO (DCUN1D1) is an essential component of the E3 complex for neddylation. J Biol Chem. 2008 Nov 28;283(48):33211-20. doi: 10.1074/jbc.M804440200. Epub 2008 Sep 30. PubMed PMID: 18826954; PubMed Central PMCID: PMC2586271.

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Sarkaria I, O-charoenrat P, Talbot SG, Reddy PG, Ngai I, Maghami E, Patel KN, Lee B, Yonekawa Y, Dudas M, Kaufman A, Ryan R, Ghossein R, Rao PH, Stoffel A, Ramanathan Y, Singh B. Squamous cell carcinoma related oncogene/DCUN1D1 is highly conserved and activated by amplification in squamous cell carcinomas. Cancer Res. 2006 Oct 1;66(19):9437-44. doi: 10.1158/0008-5472.CAN-06-2074. PubMed PMID: 17018598.

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Selective Enhancer Dependencies in MYC-Intact and MYC-Rearranged Germinal Center B-cell Diffuse Large B-cell Lymphoma. Blood cancer discovery. . NIHMSID: NIHMS2064838.