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This highlights\n                    <jats:italic>CREBBP<\/jats:italic>\n                    mutations as an attractive therapeutic target in FL and provides insight into their pathogenic mechanism.\n                  <\/jats:p>","DOI":"10.1073\/pnas.1501199112","type":"journal-article","created":{"date-parts":[[2015,2,25]],"date-time":"2015-02-25T17:27:01Z","timestamp":1424885221000},"update-policy":"https:\/\/doi.org\/10.1073\/pnas.cm10313","source":"Crossref","is-referenced-by-count":341,"title":["Mutations in early follicular lymphoma progenitors are associated with suppressed antigen presentation"],"prefix":"10.1073","volume":"112","author":[{"given":"Michael R.","family":"Green","sequence":"first","affiliation":[{"name":"Division of Oncology,"},{"name":"Center for Cancer Systems Biology,"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shingo","family":"Kihira","sequence":"additional","affiliation":[{"name":"Division of Oncology,"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chih Long","family":"Liu","sequence":"additional","affiliation":[{"name":"Division of Oncology,"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ramesh V.","family":"Nair","sequence":"additional","affiliation":[{"name":"Division of Oncology,"},{"name":"Division of Radiology,"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Raheleh","family":"Salari","sequence":"additional","affiliation":[{"name":"Department of Computer Science, and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew J.","family":"Gentles","sequence":"additional","affiliation":[{"name":"Center for Cancer Systems Biology,"},{"name":"Division of Radiology,"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jonathan","family":"Irish","sequence":"additional","affiliation":[{"name":"Division of Oncology,"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Henning","family":"Stehr","sequence":"additional","affiliation":[{"name":"Stanford Cancer Institute, Department of Medicine, Stanford University, Stanford, CA 94305;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carolina","family":"Vicente-Due\u00f1as","sequence":"additional","affiliation":[{"name":"Experimental Therapeutics and Translational Oncology Program, Instituto de Biolog\u00eda Molecular y Celular del C\u00e1ncer, Campus M. de Unamuno s\/n, Consejo Superior de Investigaciones Cientificas\/Universidad de Salamanca, Salamanca 37007, Spain;"},{"name":"Institute of Biomedical Research of Salamanca, Salamanca 37007, Spain; 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Annu Rev Immunol 10, 13\u201349 (1992).","journal-title":"Annu Rev Immunol"},{"key":"e_1_3_4_27_2","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1038\/ng.518","article-title":"Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin","volume":"42","author":"Morin RD","year":"2010","unstructured":"RD Morin, , Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin. Nat Genet 42, 181\u2013185 (2010).","journal-title":"Nat Genet"},{"key":"e_1_3_4_28_2","doi-asserted-by":"crossref","first-page":"298","DOI":"10.1038\/nature10351","article-title":"Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma","volume":"476","author":"Morin RD","year":"2011","unstructured":"RD Morin, , Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature 476, 298\u2013303 (2011).","journal-title":"Nature"},{"key":"e_1_3_4_29_2","doi-asserted-by":"crossref","first-page":"246","DOI":"10.1016\/j.ccr.2011.06.029","article-title":"Self-renewing hematopoietic stem cell is the primary target in pathogenesis of human chronic lymphocytic leukemia","volume":"20","author":"Kikushige Y","year":"2011","unstructured":"Y Kikushige, , Self-renewing hematopoietic stem cell is the primary target in pathogenesis of human chronic lymphocytic leukemia. Cancer Cell 20, 246\u2013259 (2011).","journal-title":"Cancer Cell"},{"key":"e_1_3_4_30_2","first-page":"238ra71","article-title":"Hematopoietic stem cell origin of BRAFV600E mutations in hairy cell leukemia","volume":"238","author":"Chung S","year":"2014","unstructured":"S Chung, , Hematopoietic stem cell origin of BRAFV600E mutations in hairy cell leukemia. Sci Transl Med 238, 238ra71 (2014).","journal-title":"Sci Transl Med"},{"key":"e_1_3_4_31_2","doi-asserted-by":"crossref","first-page":"108","DOI":"10.1038\/nature11606","article-title":"EZH2 inhibition as a therapeutic strategy for lymphoma with EZH2-activating mutations","volume":"492","author":"McCabe MT","year":"2012","unstructured":"MT McCabe, , EZH2 inhibition as a therapeutic strategy for lymphoma with EZH2-activating mutations. 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Mol Cell Biol 18, 6777\u20136783 (1998).","journal-title":"Mol Cell Biol"},{"key":"e_1_3_4_33_2","doi-asserted-by":"crossref","first-page":"941","DOI":"10.1128\/MCB.19.1.941","article-title":"Interactions between the class II transactivator and CREB binding protein increase transcription of major histocompatibility complex class II genes","volume":"19","author":"Fontes JD","year":"1999","unstructured":"JD Fontes, S Kanazawa, D Jean, BM Peterlin, Interactions between the class II transactivator and CREB binding protein increase transcription of major histocompatibility complex class II genes. Mol Cell Biol 19, 941\u2013947 (1999).","journal-title":"Mol Cell Biol"},{"key":"e_1_3_4_34_2","doi-asserted-by":"crossref","first-page":"652","DOI":"10.1038\/89810","article-title":"CIITA coordinates multiple histone acetylation modifications at the HLA-DRA promoter","volume":"2","author":"Beresford GW","year":"2001","unstructured":"GW Beresford, JM Boss, CIITA coordinates multiple histone acetylation modifications at the HLA-DRA promoter. Nat Immunol 2, 652\u2013657 (2001).","journal-title":"Nat Immunol"},{"key":"e_1_3_4_35_2","doi-asserted-by":"crossref","first-page":"4324","DOI":"10.1200\/JCO.2010.28.9793","article-title":"In situ vaccination with a TLR9 agonist induces systemic lymphoma regression: A phase I\/II study","volume":"28","author":"Brody JD","year":"2010","unstructured":"JD Brody, , In situ vaccination with a TLR9 agonist induces systemic lymphoma regression: A phase I\/II study. J Clin Oncol 28, 4324\u20134332 (2010).","journal-title":"J Clin Oncol"},{"key":"e_1_3_4_36_2","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1038\/nm.3442","article-title":"Fas ligand-mediated immune surveillance by T cells is essential for the control of spontaneous B cell lymphomas","volume":"20","author":"Afshar-Sterle S","year":"2014","unstructured":"S Afshar-Sterle, , Fas ligand-mediated immune surveillance by T cells is essential for the control of spontaneous B cell lymphomas. Nat Med 20, 283\u2013290 (2014).","journal-title":"Nat Med"},{"key":"e_1_3_4_37_2","doi-asserted-by":"crossref","first-page":"852","DOI":"10.1038\/nature01441","article-title":"CD4+ T cells are required for secondary expansion and memory in CD8+ T lymphocytes","volume":"421","author":"Janssen EM","year":"2003","unstructured":"EM Janssen, , CD4+ T cells are required for secondary expansion and memory in CD8+ T lymphocytes. Nature 421, 852\u2013856 (2003).","journal-title":"Nature"},{"key":"e_1_3_4_38_2","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1126\/science.1082305","article-title":"Requirement for CD4 T cell help in generating functional CD8 T cell memory","volume":"300","author":"Shedlock DJ","year":"2003","unstructured":"DJ Shedlock, H Shen, Requirement for CD4 T cell help in generating functional CD8 T cell memory. 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Genome Res 22, 568\u2013576 (2012).","journal-title":"Genome Res"},{"key":"e_1_3_4_45_2","doi-asserted-by":"crossref","first-page":"1297","DOI":"10.1101\/gr.107524.110","article-title":"The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data","volume":"20","author":"McKenna A","year":"2010","unstructured":"A McKenna, , The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20, 1297\u20131303 (2010).","journal-title":"Genome Res"},{"key":"e_1_3_4_46_2","doi-asserted-by":"crossref","first-page":"272","DOI":"10.1038\/nature08250","article-title":"Targeted capture and massively parallel sequencing of 12 human exomes","volume":"461","author":"Ng SB","year":"2009","unstructured":"SB Ng, , Targeted capture and massively parallel sequencing of 12 human exomes. Nature 461, 272\u2013276 (2009).","journal-title":"Nature"},{"key":"e_1_3_4_47_2","doi-asserted-by":"crossref","first-page":"1097","DOI":"10.1101\/gr.151670.112","article-title":"Genome evolution during progression to breast cancer","volume":"23","author":"Newburger DE","year":"2013","unstructured":"DE Newburger, , Genome evolution during progression to breast cancer. Genome Res 23, 1097\u20131108 (2013).","journal-title":"Genome Res"},{"key":"e_1_3_4_48_2","doi-asserted-by":"crossref","first-page":"725","DOI":"10.1016\/j.jmb.2006.02.057","article-title":"Crystal structure of the archaeal A1Ao ATP synthase subunit B from Methanosarcina mazei G\u00f61: Implications of nucleotide-binding differences in the major A1Ao subunits A and B","volume":"358","author":"Sch\u00e4fer IB","year":"2006","unstructured":"IB Sch\u00e4fer, , Crystal structure of the archaeal A1Ao ATP synthase subunit B from Methanosarcina mazei G\u00f61: Implications of nucleotide-binding differences in the major A1Ao subunits A and B. J Mol Biol 358, 725\u2013740 (2006).","journal-title":"J Mol Biol"},{"key":"e_1_3_4_49_2","doi-asserted-by":"crossref","first-page":"1040","DOI":"10.1038\/nsmb.2642","article-title":"Structure of the p300 catalytic core and implications for chromatin targeting and HAT regulation","volume":"20","author":"Delvecchio M","year":"2013","unstructured":"M Delvecchio, J Gaucher, C Aguilar-Gurrieri, E Ortega, D Panne, Structure of the p300 catalytic core and implications for chromatin targeting and HAT regulation. Nat Struct Mol Biol 20, 1040\u20131046 (2013).","journal-title":"Nat Struct Mol Biol"},{"key":"e_1_3_4_50_2","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s10969-008-9048-5","article-title":"The Protein Model Portal","volume":"10","author":"Arnold K","year":"2009","unstructured":"K Arnold, , The Protein Model Portal. J Struct Funct Genomics 10, 1\u20138 (2009).","journal-title":"J Struct Funct Genomics"},{"key":"e_1_3_4_51_2","doi-asserted-by":"crossref","first-page":"D336","DOI":"10.1093\/nar\/gkt1144","article-title":"ModBase, a database of annotated comparative protein structure models and associated resources","volume":"42","author":"Pieper U","year":"2014","unstructured":"U Pieper, , ModBase, a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res 42, D336\u2013D346 (2014).","journal-title":"Nucleic Acids Res"},{"key":"e_1_3_4_52_2","doi-asserted-by":"crossref","first-page":"D387","DOI":"10.1093\/nar\/gkn750","article-title":"The SWISS-MODEL Repository and associated resources","volume":"37","author":"Kiefer F","year":"2009","unstructured":"F Kiefer, K Arnold, M K\u00fcnzli, L Bordoli, T Schwede, The SWISS-MODEL Repository and associated resources. Nucleic Acids Res 37, D387\u2013D392 (2009).","journal-title":"Nucleic Acids Res"},{"key":"e_1_3_4_53_2","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1186\/gb-2003-4-5-p3","article-title":"DAVID: Database for annotation, visualization, and integrated discovery","volume":"4","author":"Dennis G","year":"2003","unstructured":"Jr G Dennis, , DAVID: Database for annotation, visualization, and integrated discovery. Genome Biol 4, 3 (2003).","journal-title":"Genome Biol"},{"key":"e_1_3_4_54_2","doi-asserted-by":"crossref","first-page":"3251","DOI":"10.1093\/bioinformatics\/btm369","article-title":"GSEA-P: A desktop application for gene set enrichment analysis","volume":"23","author":"Subramanian A","year":"2007","unstructured":"A Subramanian, H Kuehn, J Gould, P Tamayo, JP Mesirov, GSEA-P: A desktop application for gene set enrichment analysis. Bioinformatics 23, 3251\u20133253 (2007).","journal-title":"Bioinformatics"},{"key":"e_1_3_4_55_2","doi-asserted-by":"crossref","first-page":"12747","DOI":"10.1073\/pnas.1002057107","article-title":"B-cell signaling networks reveal a negative prognostic human lymphoma cell subset that emerges during tumor progression","volume":"107","author":"Irish JM","year":"2010","unstructured":"JM Irish, , B-cell signaling networks reveal a negative prognostic human lymphoma cell subset that emerges during tumor progression. 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