Photo of Stuart H. Orkin, MD

Stuart H. Orkin, MD

Dana-Farber Cancer Institute

Dana-Farber Cancer Institute
Phone: (617) 632-3564
Fax: (617) 632-4367


stuart_orkin@dfci.harvard.edu

Photo of Stuart H. Orkin, MD

Dana-Farber Cancer Institute
Phone: (617) 632-3564
Fax: (617) 632-4367


stuart_orkin@dfci.harvard.edu

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Stuart H. Orkin, MD

Dana-Farber Cancer Institute

EDUCATIONAL TITLES

  • David G. Nathan Professor of Pediatrics, Pediatrics, Harvard Medical School
  • Chairman, Pediatric Oncology, Dana-Farber Cancer Institute
  • Investigator, Pediatrics, Boston Children's Hospital

DF/HCC PROGRAM AFFILIATION

Research Abstract

1. Molecular genetics and biology of human disease

2. Thalassemia syndromes and hemoglobin synthesis

3. Prenatal diagnosis of genetic disease

4. Molecular genetics and biochemistry of the phagocytic cell

5. Gene transfer and expression in hematopoietic cells

6. Hematopoietic cell development

Publications from Harvard Catalyst Profiles

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  • Shen Y, Verboon JM, Zhang Y, Liu N, Kim YJ, Marglous S, Nandakumar SK, Voit RA, Fiorini C, Ejaz A, Basak A, Orkin SH, Xu J, Sankaran VG. A unified model of human hemoglobin switching through single-cell genome editing. Nat Commun 2021; 12:4991. PubMed
  • Kai Y, Li BE, Zhu M, Li GY, Chen F, Han Y, Cha HJ, Orkin SH, Cai W, Huang J, Yuan GC. Mapping the evolving landscape of super-enhancers during cell differentiation. Genome Biol 2021; 22:269. PubMed
  • Beyaz S, Chung C, Mou H, Bauer-Rowe KE, Xifaras ME, Ergin I, Dohnalova L, Biton M, Shekhar K, Eskiocak O, Papciak K, Ozler K, Almeqdadi M, Yueh B, Fein M, Annamalai D, Valle-Encinas E, Erdemir A, Dogum K, Shah V, Alici-Garipcan A, Meyer HV, Özata DM, Elinav E, Kucukural A, Kumar P, McAleer JP, Fox JG, Thaiss CA, Regev A, Roper J, Orkin SH, Yilmaz ÖH. Dietary suppression of MHC class II expression in intestinal epithelial cells enhances intestinal tumorigenesis. Cell Stem Cell 2021; 28:1922-1935.e5. PubMed
  • Cha HJ, Uyan Ö, Kai Y, Liu T, Zhu Q, Tothova Z, Botten GA, Xu J, Yuan GC, Dekker J, Orkin SH. Inner nuclear protein Matrin-3 coordinates cell differentiation by stabilizing chromatin architecture. Nat Commun 2021; 12:6241. PubMed
  • Barthlott T, Handel AE, Teh HY, Wirasinha RC, Hafen K, Žuklys S, Roch B, Orkin SH, de Villartay JP, Daley SR, Holländer GA. Indispensable epigenetic control of thymic epithelial cell development and function by polycomb repressive complex 2. Nat Commun 2021; 12:3933. PubMed
  • King AJ, Songdej D, Downes DJ, Beagrie RA, Liu S, Buckley M, Hua P, Suciu MC, Marieke Oudelaar A, Hanssen LLP, Jeziorska D, Roberts N, Carpenter SJ, Francis H, Telenius J, Olijnik AA, Sharpe JA, Sloane-Stanley J, Eglinton J, Kassouf MT, Orkin SH, Pennacchio LA, Davies JOJ, Hughes JR, Higgs DR, Babbs C. Reactivation of a developmentally silenced embryonic globin gene. Nat Commun 2021; 12:4439. PubMed
  • Liu N, Xu S, Yao Q, Zhu Q, Kai Y, Hsu JY, Sakon P, Pinello L, Yuan GC, Bauer DE, Orkin SH. Transcription factor competition at the γ-globin promoters controls hemoglobin switching. Nat Genet 2021; 53:511-520. PubMed
  • Terzi Cizmecioglu N, Huang J, Keskin EG, Wang X, Esen I, Chen F, Orkin SH. ARID4B is critical for mouse embryonic stem cell differentiation towards mesoderm and endoderm, linking epigenetics to pluripotency exit. J Biol Chem 2020; 295:17738-17751. PubMed
  • Canver MC, Tripathi P, Bullen MJ, Olshansky M, Kumar Y, Wong LH, Turner SJ, Lessard S, Pinello L, Orkin SH, Das PP. A saturating mutagenesis CRISPR-Cas9 mediated functional genomic screen identifies cis- and trans-regulatory elements of Oct4 in murine ESCs. J Biol Chem 2020. PubMed
  • Cai W, Huang J, Zhu Q, Li BE, Seruggia D, Zhou P, Nguyen M, Fujiwara Y, Xie H, Yang Z, Hong D, Ren P, Xu J, Pu WT, Yuan GC, Orkin SH. Enhancer dependence of cell-type-specific gene expression increases with developmental age. Proc Natl Acad Sci U S A 2020; 117:21450-21458. PubMed
  • Bowling S, Sritharan D, Osorio FG, Nguyen M, Cheung P, Rodriguez-Fraticelli A, Patel S, Yuan WC, Fujiwara Y, Li BE, Orkin SH, Hormoz S, Camargo FD. An Engineered CRISPR-Cas9 Mouse Line for Simultaneous Readout of Lineage Histories and Gene Expression Profiles in Single Cells. Cell 2020; 181:1410-1422.e27. PubMed
  • Liu X, Chen Y, Zhang Y, Liu Y, Liu N, Botten GA, Cao H, Orkin SH, Zhang MQ, Xu J. Multiplexed capture of spatial configuration and temporal dynamics of locus-specific 3D chromatin by biotinylated dCas9. Genome Biol 2020; 21:59. PubMed
  • Basak A, Munschauer M, Lareau CA, Montbleau KE, Ulirsch JC, Hartigan CR, Schenone M, Lian J, Wang Y, Huang Y, Wu X, Gehrke L, Rice CM, An X, Christou HA, Mohandas N, Carr SA, Chen JJ, Orkin SH, Lander ES, Sankaran VG. Control of human hemoglobin switching by LIN28B-mediated regulation of BCL11A translation. Nat Genet 2020; 52:138-145. PubMed
  • Christodoulou C, Spencer JA, Yeh SA, Turcotte R, Kokkaliaris KD, Panero R, Ramos A, Guo G, Seyedhassantehrani N, Esipova TV, Vinogradov SA, Rudzinskas S, Zhang Y, Perkins AS, Orkin SH, Calogero RA, Schroeder T, Lin CP, Camargo FD. Live-animal imaging of native haematopoietic stem and progenitor cells. Nature 2020; 578:278-283. PubMed
  • Zhu Q, Liu N, Orkin SH, Yuan GC. CUT&RUNTools: a flexible pipeline for CUT&RUN processing and footprint analysis. Genome Biol 2019; 20:192. PubMed
  • Debruyne DN, Dries R, Sengupta S, Seruggia D, Gao Y, Sharma B, Huang H, Moreau L, McLane M, Day DS, Marco E, Chen T, Gray NS, Wong KK, Orkin SH, Yuan GC, Young RA, George RE. BORIS promotes chromatin regulatory interactions in treatment-resistant cancer cells. Nature 2019; 572:676-680. PubMed
  • Sher F, Hossain M, Seruggia D, Schoonenberg VAC, Yao Q, Cifani P, Dassama LMK, Cole MA, Ren C, Vinjamur DS, Macias-Trevino C, Luk K, McGuckin C, Schupp PG, Canver MC, Kurita R, Nakamura Y, Fujiwara Y, Wolfe SA, Pinello L, Maeda T, Kentsis A, Orkin SH, Bauer DE. Rational targeting of a NuRD subcomplex guided by comprehensive in situ mutagenesis. Nat Genet 2019; 51:1149-1159. PubMed
  • Seruggia D, Oti M, Tripathi P, Canver MC, LeBlanc L, Di Giammartino DC, Bullen MJ, Nefzger CM, Sun YBY, Farouni R, Polo JM, Pinello L, Apostolou E, Kim J, Orkin SH, Das PP. TAF5L and TAF6L Maintain Self-Renewal of Embryonic Stem Cells via the MYC Regulatory Network. Mol Cell 2019; 74:1148-1163.e7. PubMed
  • Jadhav U, Cavazza A, Banerjee KK, Xie H, O'Neill NK, Saenz-Vash V, Herbert Z, Madha S, Orkin SH, Zhai H, Shivdasani RA. Extensive Recovery of Embryonic Enhancer and Gene Memory Stored in Hypomethylated Enhancer DNA. Mol Cell 2019. PubMed
  • Barros-Silva JD, Linn DE, Steiner I, Guo G, Ali A, Pakula H, Ashton G, Peset I, Brown M, Clarke NW, Bronson RT, Yuan GC, Orkin SH, Li Z, Baena E. Single-Cell Analysis Identifies LY6D as a Marker Linking Castration-Resistant Prostate Luminal Cells to Prostate Progenitors and Cancer. Cell Rep 2018; 25:3504-3518.e6. PubMed
  • Ariës IM, Bodaar K, Karim SA, Chonghaile TN, Hinze L, Burns MA, Pfirrmann M, Degar J, Landrigan JT, Balbach S, Peirs S, Menten B, Isenhart R, Stevenson KE, Neuberg DS, Devidas M, Loh ML, Hunger SP, Teachey DT, Rabin KR, Winter SS, Dunsmore KP, Wood BL, Silverman LB, Sallan SE, Van Vlierberghe P, Orkin SH, Knoechel B, Letai AG, Gutierrez A. PRC2 loss induces chemoresistance by repressing apoptosis in T cell acute lymphoblastic leukemia. J Exp Med 2018; 215:3094-3114. PubMed
  • Hsu JY, Fulco CP, Cole MA, Canver MC, Pellin D, Sher F, Farouni R, Clement K, Guo JA, Biasco L, Orkin SH, Engreitz JM, Lander ES, Joung JK, Bauer DE, Pinello L. CRISPR-SURF: discovering regulatory elements by deconvolution of CRISPR tiling screen data. Nat Methods 2018; 15:992-993. PubMed
  • Singarapu N, Ma K, Reeh KAG, Shen J, Lancaster JN, Yi S, Xie H, Orkin SH, Manley NR, Ehrlich LIR, Jiang N, Richie ER. Polycomb Repressive Complex 2 is essential for development and maintenance of a functional TEC compartment. Sci Rep 2018; 8:14335. PubMed
  • Michalak EM, Milevskiy MJG, Joyce RM, Dekkers JF, Jamieson PR, Pal B, Dawson CA, Hu Y, Orkin SH, Alexander WS, Lindeman GJ, Smyth GK, Visvader JE. Canonical PRC2 function is essential for mammary gland development and affects chromatin compaction in mammary organoids. PLoS Biol. 2018; 16:e2004986. PubMed
  • MacLean GA, McEldoon J, Huang J, Allred J, Canver MC, Orkin SH. Downregulation of Endothelin Receptor B Contributes to Defective B Cell Lymphopoiesis in Trisomy 21 Pluripotent Stem Cells. Sci Rep 2018; 8:8001. PubMed
  • Canver MC, Haeussler M, Bauer DE, Orkin SH, Sanjana NE, Shalem O, Yuan GC, Zhang F, Concordet JP, Pinello L. Integrated design, execution, and analysis of arrayed and pooled CRISPR genome-editing experiments. Nat Protoc 2018; 13:946-986. PubMed
  • Liu N, Hargreaves VV, Zhu Q, Kurland JV, Hong J, Kim W, Sher F, Macias-Trevino C, Rogers JM, Kurita R, Nakamura Y, Yuan GC, Bauer DE, Xu J, Bulyk ML, Orkin SH. Direct Promoter Repression by BCL11A Controls the Fetal to Adult Hemoglobin Switch. Cell 2018. PubMed
  • Yamauchi T, Masuda T, Canver MC, Seiler M, Semba Y, Shboul M, Al-Raqad M, Maeda M, Schoonenberg VAC, Cole MA, Macias-Trevino C, Ishikawa Y, Yao Q, Nakano M, Arai F, Orkin SH, Reversade B, Buonamici S, Pinello L, Akashi K, Bauer DE, Maeda T. Genome-wide CRISPR-Cas9 Screen Identifies Leukemia-Specific Dependence on a Pre-mRNA Metabolic Pathway Regulated by DCPS. Cancer Cell 2018; 33:386-400.e5. PubMed
  • Han X, Wang R, Zhou Y, Fei L, Sun H, Lai S, Saadatpour A, Zhou Z, Chen H, Ye F, Huang D, Xu Y, Huang W, Jiang M, Jiang X, Mao J, Chen Y, Lu C, Xie J, Fang Q, Wang Y, Yue R, Li T, Huang H, Orkin SH, Yuan GC, Chen M, Guo G. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell 2018; 172:1091-1107.e17. PubMed
  • Vo LT, Kinney MA, Liu X, Zhang Y, Barragan J, Sousa PM, Jha DK, Han A, Cesana M, Shao Z, North TE, Orkin SH, Doulatov S, Xu J, Daley GQ. Regulation of embryonic haematopoietic multipotency by EZH1. Nature 2018; 553:506-510. PubMed
  • LeBlanc L, Lee BK, Yu AC, Kim M, Kambhampati AV, Dupont SM, Seruggia D, Ryu BU, Orkin SH, Kim J. Yap1 safeguards mouse embryonic stem cells from excessive apoptosis during differentiation. Elife 2018. PubMed
  • Huang J, Li K, Cai W, Liu X, Zhang Y, Orkin SH, Xu J, Yuan GC. Dissecting super-enhancer hierarchy based on chromatin interactions. Nat Commun 2018; 9:943. PubMed
  • Lessard S, Francioli L, Alfoldi J, Tardif JC, Ellinor PT, MacArthur DG, Lettre G, Orkin SH, Canver MC. Human genetic variation alters CRISPR-Cas9 on- and off-targeting specificity at therapeutically implicated loci. Proc Natl Acad Sci U S A 2017; 114:E11257-E11266. PubMed
  • Moody JD, Levy S, Mathieu J, Xing Y, Kim W, Dong C, Tempel W, Robitaille AM, Dang LT, Ferreccio A, Detraux D, Sidhu S, Zhu L, Carter L, Xu C, Valensisi C, Wang Y, Hawkins RD, Min J, Moon RT, Orkin SH, Baker D, Ruohola-Baker H. First critical repressive H3K27me3 marks in embryonic stem cells identified using designed protein inhibitor. Proc Natl Acad Sci U S A 2017; 114:10125-10130. PubMed
  • Xie Y, Koch ML, Zhang X, Hamblen MJ, Godinho FJ, Fujiwara Y, Xie H, Klusmann JH, Orkin SH, Li Z. Reduced Erg Dosage Impairs Survival of Hematopoietic Stem and Progenitor Cells. Stem Cells 2017; 35:1773-1785. PubMed
  • Hsu JH, Hubbell-Engler B, Adelmant G, Huang J, Joyce CE, Vazquez F, Weir BA, Montgomery P, Tsherniak A, Giacomelli AO, Perry JA, Trowbridge J, Fujiwara Y, Cowley GS, Xie H, Kim W, Novina CD, Hahn WC, Marto JA, Orkin SH. Prmt1-mediated translation regulation is a crucial vulnerability of cancer. Cancer Res 2017. PubMed
  • Pittermann E, Lachmann N, MacLean G, Emmrich S, Ackermann M, Göhring G, Schlegelberger B, Welte K, Schambach A, Heckl D, Orkin SH, Cantz T, Klusmann JH. Gene correction of HAX1 reversed Kostmann disease phenotype in patient-specific induced pluripotent stem cells. Blood Adv 2017; 1:903-914. PubMed
  • Han X, Yu H, Huang D, Xu Y, Saadatpour A, Li X, Wang L, Yu J, Pinello L, Lai S, Jiang M, Tian X, Zhang F, Cen Y, Fujiwara Y, Zhu W, Zhou B, Zhou T, Ouyang H, Wang J, Yuan GC, Duan S, Orkin SH, Guo G. A molecular roadmap for induced multi-lineage trans-differentiation of fibroblasts by chemical combinations. Cell Res 2017; 27:842. PubMed
  • Han X, Yu H, Huang D, Xu Y, Saadatpour A, Li X, Wang L, Yu J, Pinello L, Lai S, Jiang M, Tian X, Zhang F, Cen Y, Fujiwara Y, Zhu W, Zhou B, Zhou T, Ouyang H, Wang J, Yuan GC, Duan S, Orkin SH, Guo G. A molecular roadmap for induced multi-lineage trans-differentiation of fibroblasts by chemical combinations. Cell Res 2017; 27:843. PubMed
  • Chung J, Wittig JG, Ghamari A, Maeda M, Dailey TA, Bergonia H, Kafina MD, Coughlin EE, Minogue CE, Hebert AS, Li L, Kaplan J, Lodish HF, Bauer DE, Orkin SH, Cantor AB, Maeda T, Phillips JD, Coon JJ, Pagliarini DJ, Dailey HA, Paw BH. Erythropoietin signaling regulates heme biosynthesis. Elife 2017. PubMed
  • Yuan GC, Cai L, Elowitz M, Enver T, Fan G, Guo G, Irizarry R, Kharchenko P, Kim J, Orkin S, Quackenbush J, Saadatpour A, Schroeder T, Shivdasani R, Tirosh I. Challenges and emerging directions in single-cell analysis. Genome Biol 2017; 18:84. PubMed
  • Canver MC, Lessard S, Pinello L, Wu Y, Ilboudo Y, Stern EN, Needleman AJ, Galactéros F, Brugnara C, Kutlar A, McKenzie C, Reid M, Chen DD, Das PP, A Cole M, Zeng J, Kurita R, Nakamura Y, Yuan GC, Lettre G, Bauer DE, Orkin SH. Variant-aware saturating mutagenesis using multiple Cas9 nucleases identifies regulatory elements at trait-associated loci. Nat Genet 2017; 49:625-634. PubMed
  • Canver MC, Bauer DE, Orkin SH. Functional interrogation of non-coding DNA through CRISPR genome editing. Methods 2017. PubMed
  • Erb MA, Scott TG, Li BE, Xie H, Paulk J, Seo HS, Souza A, Roberts JM, Dastjerdi S, Buckley DL, Sanjana NE, Shalem O, Nabet B, Zeid R, Offei-Addo NK, Dhe-Paganon S, Zhang F, Orkin SH, Winter GE, Bradner JE. Transcription control by the ENL YEATS domain in acute leukaemia. Nature 2017; 543:270-274. PubMed
  • Canver MC, Bauer DE, Dass A, Yien YY, Chung J, Masuda T, Maeda T, Paw BH, Orkin SH. Characterization of genomic deletion efficiency mediated by clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 nuclease system in mammalian cells. J Biol Chem 2017; 292:2556. PubMed
  • Beyaz S, Kim JH, Pinello L, Xifaras ME, Hu Y, Huang J, Kerenyi MA, Das PP, Barnitz RA, Herault A, Dogum R, Haining WN, Yilmaz ÖH, Passegue E, Yuan GC, Orkin SH, Winau F. The histone demethylase UTX regulates the lineage-specific epigenetic program of invariant natural killer T cells. Nat Immunol 2017; 18:184-195. PubMed
  • Han X, Yu H, Huang D, Xu Y, Saadatpour A, Li X, Wang L, Yu J, Pinello L, Lai S, Jiang M, Tian X, Zhang F, Cen Y, Fujiwara Y, Zhu W, Zhou B, Zhou T, Ouyang H, Wang J, Yuan GC, Duan S, Orkin SH, Guo G. A molecular roadmap for induced multi-lineage trans-differentiation of fibroblasts by chemical combinations. Cell Res 2017. PubMed
  • Smith EC, Luc S, Croney DM, Woodworth MB, Greig LC, Fujiwara Y, Nguyen M, Sher F, Macklis JD, Bauer DE, Orkin SH. Strict in vivo specificity of the Bcl11a erythroid enhancer. Blood 2016. PubMed
  • Brendel C, Guda S, Renella R, Bauer DE, Canver MC, Kim YJ, Heeney MM, Klatt D, Fogel J, Milsom MD, Orkin SH, Gregory RI, Williams DA. Lineage-specific BCL11A knockdown circumvents toxicities and reverses sickle phenotype. J Clin Invest 2016; 126:3868-3878. PubMed
  • Luc S, Huang J, McEldoon JL, Somuncular E, Li D, Rhodes C, Mamoor S, Hou S, Xu J, Orkin SH. Bcl11a Deficiency Leads to Hematopoietic Stem Cell Defects with an Aging-like Phenotype. Cell Rep 2016; 16:3181-94. PubMed
  • Xie H, Peng C, Huang J, Li BE, Kim W, Smith EC, Fujiwara Y, Qi J, Cheloni G, Das PP, Nguyen M, Li S, Bradner JE, Orkin SH. Chronic myelogenous leukemia initiating cells require Polycomb group protein EZH2. 2016. PubMed
  • Kim TH, Saadatpour A, Guo G, Saxena M, Cavazza A, Desai N, Jadhav U, Jiang L, Rivera MN, Orkin SH, Yuan GC, Shivdasani RA. Single-Cell Transcript Profiles Reveal Multilineage Priming in Early Progenitors Derived from Lgr5(+) Intestinal Stem Cells. Cell Rep 2016; 16:2053-60. PubMed
  • Shimizu T, Kubovcakova L, Nienhold R, Zmajkovic J, Meyer SC, Hao-Shen H, Geier F, Dirnhofer S, Guglielmelli P, Vannucchi AM, Feenstra JD, Kralovics R, Orkin SH, Skoda RC. Loss of Ezh2 synergizes with JAK2-V617F in initiating myeloproliferative neoplasms and promoting myelofibrosis. J Exp Med 2016; 213:1479-96. PubMed
  • Pinello L, Canver MC, Hoban MD, Orkin SH, Kohn DB, Bauer DE, Yuan GC. Analyzing CRISPR genome-editing experiments with CRISPResso. Nat Biotechnol 2016; 34:695-7. PubMed
  • Balbach ST, Orkin SH. An Achilles' Heel for MLL-Rearranged Leukemias: Writers and Readers of H3 Lysine 36 Dimethylation. 2016; 6:700-2. PubMed
  • Liddicoat BJ, Hartner JC, Piskol R, Ramaswami G, Chalk AM, Kingsley PD, Sankaran VG, Wall M, Purton LE, Seeburg PH, Palis J, Orkin SH, Lu J, Li JB, Walkley CR. Adenosine-to-insoine RNA editing by ADAR1 is essential for normal murine erythropoiesis. Exp Hematol 2016. PubMed
  • Smith EC, Orkin SH. Hemoglobin genetics: recent contributions of GWAS and gene editing. Hum Mol Genet 2016. PubMed
  • Altrock PM, Brendel C, Renella R, Orkin SH, Williams DA, Michor F. Mathematical modeling of erythrocyte chimerism informs genetic intervention strategies for sickle cell disease. Am J Hematol 2016. PubMed
  • Jadhav U, Nalapareddy K, Saxena M, O'Neill NK, Pinello L, Yuan GC, Orkin SH, Shivdasani RA. Acquired Tissue-Specific Promoter Bivalency Is a Basis for PRC2 Necessity in Adult Cells. Cell 2016; 165:1389-400. PubMed
  • Kim PG, Canver MC, Rhee C, Ross SJ, Harriss JV, Tu HC, Orkin SH, Tucker HO, Daley GQ. Interferon-alpha signaling promotes embryonic HSC maturation. Blood 2016. PubMed
  • Townsend EC, Murakami MA, Christodoulou A, Christie AL, Köster J, DeSouza TA, Morgan EA, Kallgren SP, Liu H, Wu SC, Plana O, Montero J, Stevenson KE, Rao P, Vadhi R, Andreeff M, Armand P, Ballen KK, Barzaghi-Rinaudo P, Cahill S, Clark RA, Cooke VG, Davids MS, DeAngelo DJ, Dorfman DM, Eaton H, Ebert BL, Etchin J, Firestone B, Fisher DC, Freedman AS, Galinsky IA, Gao H, Garcia JS, Garnache-Ottou F, Graubert TA, Gutierrez A, Halilovic E, Harris MH, Herbert ZT, Horwitz SM, Inghirami G, Intlekoffer AM, Ito M, Izraeli S, Jacobsen ED, Jacobson CA, Jeay S, Jeremias I, Kelliher MA, Koch R, Konopleva M, Kopp N, Kornblau SM, Kung AL, Kupper TS, LaBoeuf N, LaCasce AS, Lees E, Li LS, Look AT, Murakami M, Muschen M, Neuberg D, Ng SY, Odejide OO, Orkin SH, Paquette RR, Place AE, Roderick JE, Ryan JA, Sallan SE, Shoji B, Silverman LB, Soiffer RJ, Steensma DP, Stegmaier K, Stone RM, Tamburini J, Thorner AR, van Hummelen P, Wadleigh M, Wiesmann M, Weng AP, Wuerthner JU, Williams DA, Wollison BM, Lane AA, Letai A, Bertagnolli MM, Ritz J, Brown M, Long H, Aster JC, Shipp MA, Griffin JD, Weinstock DM. The Public Repository of Xenografts Enables Discovery and Randomized Phase II-like Trials in Mice. Cancer Cell 2016; 29:574-86. PubMed
  • Beyaz S, Mana MD, Roper J, Kedrin D, Saadatpour A, Hong SJ, Bauer-Rowe KE, Xifaras ME, Akkad A, Arias E, Pinello L, Katz Y, Shinagare S, Abu-Remaileh M, Mihaylova MM, Lamming DW, Dogum R, Guo G, Bell GW, Selig M, Nielsen GP, Gupta N, Ferrone CR, Deshpande V, Yuan GC, Orkin SH, Sabatini DM, Yilmaz ÖH. High-fat diet enhances stemness and tumorigenicity of intestinal progenitors. Nature 2016; 531:53-8. PubMed
  • Danis E, Yamauchi T, Echanique K, Zhang X, Haladyna JN, Riedel SS, Zhu N, Xie H, Orkin SH, Armstrong SA, Bernt KM, Neff T. Ezh2 Controls an Early Hematopoietic Program and Growth and Survival Signaling in Early T Cell Precursor Acute Lymphoblastic Leukemia. Cell Rep 2016; 14:1953-65. PubMed
  • Orkin SH. Recent advances in globin research using genome-wide association studies and gene editing. Ann N Y Acad Sci 2016. PubMed
  • Guo G, Pinello L, Han X, Lai S, Shen L, Lin TW, Zou K, Yuan GC, Orkin SH. Serum-Based Culture Conditions Provoke Gene Expression Variability in Mouse Embryonic Stem Cells as Revealed by Single-Cell Analysis. Cell Rep 2016; 14:956-65. PubMed
  • Masuda T, Wang X, Maeda M, Canver MC, Sher F, Funnell AP, Fisher C, Suciu M, Martyn GE, Norton LJ, Zhu C, Kurita R, Nakamura Y, Xu J, Higgs DR, Crossley M, Bauer DE, Orkin SH, Kharchenko PV, Maeda T. Transcription factors LRF and BCL11A independently repress expression of fetal hemoglobin. Science 2016; 351:285-9. PubMed
  • Huang J, Liu X, Li D, Shao Z, Cao H, Zhang Y, Trompouki E, Bowman TV, Zon LI, Yuan GC, Orkin SH, Xu J. Dynamic Control of Enhancer Repertoires Drives Lineage and Stage-Specific Transcription during Hematopoiesis. Dev Cell 2016; 36:9-23. PubMed
  • Mirzamohammadi F, Papaioannou G, Inloes JB, Rankin EB, Xie H, Schipani E, Orkin SH, Kobayashi T. Polycomb repressive complex 2 regulates skeletal growth by suppressing Wnt and TGF-β signalling. Nat Commun 2016; 7:12047. PubMed
  • Miles WO, Lepesant JM, Bourdeaux J, Texier M, Kerenyi MA, Nakakido M, Hamamoto R, Orkin SH, Dyson NJ, Di Stefano L. The LSD1 Family of Histone Demethylases and the Pumilio Posttranscriptional Repressor Function in a Complex Regulatory Feedback Loop. Mol Cell Biol 2015; 35:4199-211. PubMed
  • Yin J, Leavenworth JW, Li Y, Luo Q, Xie H, Liu X, Huang S, Yan H, Fu Z, Zhang LY, Zhang L, Hao J, Wu X, Deng X, Roberts CW, Orkin SH, Cantor H, Wang X. Ezh2 regulates differentiation and function of natural killer cells through histone methyltransferase activity. Proc Natl Acad Sci U S A 2015. PubMed
  • Kim KH, Kim W, Howard TP, Vazquez F, Tsherniak A, Wu JN, Wang W, Haswell JR, Walensky LD, Hahn WC, Orkin SH, Roberts CW. SWI/SNF-mutant cancers depend on catalytic and non-catalytic activity of EZH2. Nat Med 2015; 21:1491-6. PubMed
  • Canver MC, Smith EC, Sher F, Pinello L, Sanjana NE, Shalem O, Chen DD, Schupp PG, Vinjamur DS, Garcia SP, Luc S, Kurita R, Nakamura Y, Fujiwara Y, Maeda T, Yuan GC, Zhang F, Orkin SH, Bauer DE. BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis. Nature 2015. PubMed
  • Danis E, Yamauchi T, Echanique K, Haladyna J, Kalkur R, Riedel S, Zhu N, Xie H, Bernt KM, Orkin SH, Armstrong SA, Neff T. Inactivation of Eed impedes MLL-AF9-mediated leukemogenesis through Cdkn2a-dependent and Cdkn2a-independent mechanisms in a murine model. Exp Hematol 2015. PubMed
  • Renneville A, Van Galen P, Canver MC, McConkey M, Krill-Burger JM, Dorfman DM, Holson EB, Bernstein BE, Orkin SH, Bauer DE, Ebert BL. EHMT1 and EHMT2 inhibition induces fetal hemoglobin expression. Blood 2015. PubMed
  • Vierstra J, Reik A, Chang KH, Stehling-Sun S, Zhou Y, Hinkley SJ, Paschon DE, Zhang L, Psatha N, Bendana YR, O'Neil CM, Song AH, Mich AK, Liu PQ, Lee G, Bauer DE, Holmes MC, Orkin SH, Papayannopoulou T, Stamatoyannopoulos G, Rebar EJ, Gregory PD, Urnov FD, Stamatoyannopoulos JA. Functional footprinting of regulatory DNA. Nat Methods 2015; 12:927-30. PubMed
  • De Los Angeles A, Ferrari F, Fujiwara Y, Mathieu R, Lee S, Lee S, Tu HC, Ross S, Chou S, Nguyen M, Wu Z, Theunissen TW, Powell BE, Imsoonthornruksa S, Chen J, Borkent M, Krupalnik V, Lujan E, Wernig M, Hanna JH, Hochedlinger K, Pei D, Jaenisch R, Deng H, Orkin SH, Park PJ, Daley GQ. Failure to replicate the STAP cell phenomenon. Nature 2015; 525:E6-9. PubMed
  • Anderson H, Patch TC, Reddy PN, Hagedorn EJ, Kim PG, Soltis KA, Chen MJ, Tamplin OJ, Frye M, MacLean GA, Hübner K, Bauer DE, Kanki JP, Vogin G, Huston NC, Nguyen M, Fujiwara Y, Paw BH, Vestweber D, Zon LI, Orkin SH, Daley GQ, Shah DI. Hematopoietic stem cells develop in the absence of endothelial cadherin 5 expression. Blood 2015. PubMed
  • Bauer DE, Orkin SH. Hemoglobin switching's surprise: the versatile transcription factor BCL11A is a master repressor of fetal hemoglobin. Curr Opin Genet Dev 2015; 33:62-70. PubMed
  • Guda S, Brendel C, Renella R, Du P, Bauer DE, Canver MC, Grenier JK, Grimson AW, Kamran SC, Thornton J, de Boer H, Root DE, Milsom MD, Orkin SH, Gregory RI, Williams DA. miRNA-embedded shRNAs for Lineage-specific BCL11A Knockdown and Hemoglobin F Induction. Mol Ther 2015. PubMed
  • Das PP, Hendrix DA, Apostolou E, Buchner AH, Canver MC, Beyaz S, Ljuboja D, Kuintzle R, Kim W, Karnik R, Shao Z, Xie H, Xu J, De Los Angeles A, Zhang Y, Choe J, Jun DL, Shen X, Gregory RI, Daley GQ, Meissner A, Kellis M, Hochedlinger K, Kim J, Orkin SH. PRC2 Is Required to Maintain Expression of the Maternal Gtl2-Rian-Mirg Locus by Preventing De Novo DNA Methylation in Mouse Embryonic Stem Cells. Cell Rep 2015; 12:1456-70. PubMed
  • Maier VK, Feeney CM, Taylor JE, Creech AL, Qiao JW, Szanto A, Das PP, Chevrier N, Cifuentes-Rojas C, Orkin SH, Carr SA, Jaffe JD, Mertins P, Lee JT. Functional Proteomic Analysis of Repressive Histone Methyltransferase Complexes Reveals ZNF518B as a G9A Regulator. Mol Cell Proteomics 2015. PubMed
  • Yin Y, Yan P, Lu J, Song G, Zhu Y, Li Z, Zhao Y, Shen B, Huang X, Zhu H, Orkin SH, Shen X. Opposing Roles for the lncRNA Haunt and Its Genomic Locus in Regulating HOXA Gene Activation during Embryonic Stem Cell Differentiation. Cell Stem Cell 2015; 16:504-16. PubMed
  • Kim PG, Nakano H, Das PP, Chen MJ, Rowe RG, Chou SS, Ross SJ, Sakamoto KM, Zon LI, Schlaeger TM, Orkin SH, Nakano A, Daley GQ. Flow-induced protein kinase A-CREB pathway acts via BMP signaling to promote HSC emergence. J Exp Med 2015; 212:633-48. PubMed
  • Org T, Duan D, Ferrari R, Montel-Hagen A, Van Handel B, Kerényi MA, Sasidharan R, Rubbi L, Fujiwara Y, Pellegrini M, Orkin SH, Kurdistani SK, Mikkola HK. Scl binds to primed enhancers in mesoderm to regulate hematopoietic and cardiac fate divergence. EMBO J 2015; 34:759-77. PubMed
  • Xu J, Shao Z, Li D, Xie H, Kim W, Huang J, Taylor JE, Pinello L, Glass K, Jaffe JD, Yuan GC, Orkin SH. Developmental control of polycomb subunit composition by GATA factors mediates a switch to non-canonical functions. Mol Cell 2015; 57:304-16. PubMed
  • Kim J, Singh AK, Takata Y, Lin K, Shen J, Lu Y, Kerenyi MA, Orkin SH, Chen T. LSD1 is essential for oocyte meiotic progression by regulating CDC25B expression in mice. Nat Commun 2015; 6:10116. PubMed
  • Chung J, Bauer DE, Ghamari A, Nizzi CP, Deck KM, Kingsley PD, Yien YY, Huston NC, Chen C, Schultz IJ, Dalton AJ, Wittig JG, Palis J, Orkin SH, Lodish HF, Eisenstein RS, Cantor AB, Paw BH. The mTORC1/4E-BP pathway coordinates hemoglobin production with L-leucine availability. Sci Signal 2015; 8:ra34. PubMed
  • Lin MI, Price EN, Boatman S, Hagedorn EJ, Trompouki E, Satishchandran S, Carspecken CW, Uong A, DiBiase A, Yang S, Canver MC, Dahlberg A, Lu Z, Zhang CC, Orkin SH, Bernstein ID, Aster JC, White RM, Zon LI. Angiopoietin-like proteins stimulate HSPC development through interaction with notch receptor signaling. Elife 2015. PubMed
  • Perry JA, Kiezun A, Tonzi P, Van Allen EM, Carter SL, Baca SC, Cowley GS, Bhatt AS, Rheinbay E, Pedamallu CS, Helman E, Taylor-Weiner A, McKenna A, DeLuca DS, Lawrence MS, Ambrogio L, Sougnez C, Sivachenko A, Walensky LD, Wagle N, Mora J, de Torres C, Lavarino C, Dos Santos Aguiar S, Yunes JA, Brandalise SR, Mercado-Celis GE, Melendez-Zajgla J, Cárdenas-Cardós R, Velasco-Hidalgo L, Roberts CW, Garraway LA, Rodriguez-Galindo C, Gabriel SB, Lander ES, Golub TR, Orkin SH, Getz G, Janeway KA. Complementary genomic approaches highlight the PI3K/mTOR pathway as a common vulnerability in osteosarcoma. Proc Natl Acad Sci U S A 2014; 111:E5564-73. PubMed
  • Li Y, Esain V, Teng L, Xu J, Kwan W, Frost IM, Yzaguirre AD, Cai X, Cortes M, Maijenburg MW, Tober J, Dzierzak E, Orkin SH, Tan K, North TE, Speck NA. Inflammatory signaling regulates embryonic hematopoietic stem and progenitor cell production. Genes Dev 2014; 28:2597-612. PubMed
  • Vierstra J, Rynes E, Sandstrom R, Zhang M, Canfield T, Hansen RS, Stehling-Sun S, Sabo PJ, Byron R, Humbert R, Thurman RE, Johnson AK, Vong S, Lee K, Bates D, Neri F, Diegel M, Giste E, Haugen E, Dunn D, Wilken MS, Josefowicz S, Samstein R, Chang KH, Eichler EE, De Bruijn M, Reh TA, Skoultchi A, Rudensky A, Orkin SH, Papayannopoulou T, Treuting PM, Selleri L, Kaul R, Groudine M, Bender MA, Stamatoyannopoulos JA. Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution. Science 2014; 346:1007-12. PubMed
  • Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD, Shen Y, Pervouchine DD, Djebali S, Thurman RE, Kaul R, Rynes E, Kirilusha A, Marinov GK, Williams BA, Trout D, Amrhein H, Fisher-Aylor K, Antoshechkin I, DeSalvo G, See LH, Fastuca M, Drenkow J, Zaleski C, Dobin A, Prieto P, Lagarde J, Bussotti G, Tanzer A, Denas O, Li K, Bender MA, Zhang M, Byron R, Groudine MT, McCleary D, Pham L, Ye Z, Kuan S, Edsall L, Wu YC, Rasmussen MD, Bansal MS, Kellis M, Keller CA, Morrissey CS, Mishra T, Jain D, Dogan N, Harris RS, Cayting P, Kawli T, Boyle AP, Euskirchen G, Kundaje A, Lin S, Lin Y, Jansen C, Malladi VS, Cline MS, Erickson DT, Kirkup VM, Learned K, Sloan CA, Rosenbloom KR, Lacerda de Sousa B, Beal K, Pignatelli M, Flicek P, Lian J, Kahveci T, Lee D, Kent WJ, Ramalho Santos M, Herrero J, Notredame C, Johnson A, Vong S, Lee K, Bates D, Neri F, Diegel M, Canfield T, Sabo PJ, Wilken MS, Reh TA, Giste E, Shafer A, Kutyavin T, Haugen E, Dunn D, Reynolds AP, Neph S, Humbert R, Hansen RS, De Bruijn M, Selleri L, Rudensky A, Josefowicz S, Samstein R, Eichler EE, Orkin SH, Levasseur D, Papayannopoulou T, Chang KH, Skoultchi A, Gosh S, Disteche C, Treuting P, Wang Y, Weiss MJ, Blobel GA, Cao X, Zhong S, Wang T, Good PJ, Lowdon RF, Adams LB, Zhou XQ, Pazin MJ, Feingold EA, Wold B, Taylor J, Mortazavi A, Weissman SM, Stamatoyannopoulos JA, Snyder MP, Guigo R, Gingeras TR, Gilbert DM, Hardison RC, Beer MA, Ren B, . A comparative encyclopedia of DNA elements in the mouse genome. Nature 2014; 515:355-64. PubMed
  • Lundberg P, Takizawa H, Kubovcakova L, Guo G, Hao-Shen H, Dirnhofer S, Orkin SH, Manz MG, Skoda RC. Myeloproliferative neoplasms can be initiated from a single hematopoietic stem cell expressing JAK2-V617F. J Exp Med 2014; 211:2213-30. PubMed
  • Yien YY, Robledo RF, Schultz IJ, Takahashi-Makise N, Gwynn B, Bauer DE, Dass A, Yi G, Li L, Hildick-Smith GJ, Cooney JD, Pierce EL, Mohler K, Dailey TA, Miyata N, Kingsley PD, Garone C, Hattangadi SM, Huang H, Chen W, Keenan EM, Shah DI, Schlaeger TM, DiMauro S, Orkin SH, Cantor AB, Palis J, Koehler CM, Lodish HF, Kaplan J, Ward DM, Dailey HA, Phillips JD, Peters LL, Paw BH. TMEM14C is required for erythroid mitochondrial heme metabolism. J Clin Invest 2014; 124:4294-304. PubMed
  • Canver MC, Bauer DE, Dass A, Yien YY, Chung J, Masuda T, Maeda T, Paw BH, Orkin SH. Characterization of genomic deletion efficiency mediated by clustered regularly interspaced palindromic repeats (CRISPR)/Cas9 nuclease system in mammalian cells. J Biol Chem 2014. PubMed
  • Yao H, Goldman DC, Nechiporuk T, Kawane S, McWeeney SK, Tyner JW, Fan G, Kerenyi MA, Orkin SH, Fleming WH, Mandel G. Corepressor Rcor1 is essential for murine erythropoiesis. Blood 2014. PubMed
  • Foudi A, Kramer DJ, Qin J, Ye D, Behlich AS, Mordecai S, Preffer FI, Amzallag A, Ramaswamy S, Hochedlinger K, Orkin SH, Hock H. Distinct, strict requirements for Gfi-1b in adult bone marrow red cell and platelet generation. J Exp Med 2014. PubMed
  • Riddell J, Gazit R, Garrison BS, Guo G, Saadatpour A, Mandal PK, Ebina W, Volchkov P, Yuan GC, Orkin SH, Rossi DJ. Reprogramming committed murine blood cells to induced hematopoietic stem cells with defined factors. Cell 2014; 157:549-64. PubMed
  • Pinello L, Xu J, Orkin SH, Yuan GC. Analysis of chromatin-state plasticity identifies cell-type-specific regulators of H3K27me3 patterns. Proc Natl Acad Sci U S A 2014; 111:E344-53. PubMed
  • Das PP, Shao Z, Beyaz S, Apostolou E, Pinello L, De Los Angeles A, O'Brien K, Atsma JM, Fujiwara Y, Nguyen M, Ljuboja D, Guo G, Woo A, Yuan GC, Onder T, Daley G, Hochedlinger K, Kim J, Orkin SH. Distinct and combinatorial functions of Jmjd2b/Kdm4b and Jmjd2c/Kdm4c in mouse embryonic stem cell identity. Mol Cell 2014; 53:32-48. PubMed
  • Xie H, Xu J, Hsu JH, Nguyen M, Fujiwara Y, Peng C, Orkin SH. Polycomb repressive complex 2 regulates normal hematopoietic stem cell function in a developmental-stage-specific manner. Cell Stem Cell 2014; 14:68-80. PubMed
  • Saadatpour A, Guo G, Orkin SH, Yuan GC. Characterizing heterogeneity in leukemic cells using single-cell gene expression analysis. Genome Biol 2014; 15:525. PubMed
  • Elagib KE, Rubinstein JD, Delehanty LL, Ngoh VS, Greer PA, Li S, Lee JK, Li Z, Orkin SH, Mihaylov IS, Goldfarb AN. Calpain 2 activation of P-TEFb drives megakaryocyte morphogenesis and is disrupted by leukemogenic GATA1 mutation. Dev Cell 2013; 27:607-20. PubMed
  • Bauer DE, Kamran SC, Lessard S, Xu J, Fujiwara Y, Lin C, Shao Z, Canver MC, Smith EC, Pinello L, Sabo PJ, Vierstra J, Voit RA, Yuan GC, Porteus MH, Stamatoyannopoulos JA, Lettre G, Orkin SH. An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level. Science 2013; 342:253-7. PubMed
  • Guo G, Luc S, Marco E, Lin TW, Peng C, Kerenyi MA, Beyaz S, Kim W, Xu J, Das PP, Neff T, Zou K, Yuan GC, Orkin SH. Mapping cellular hierarchy by single-cell analysis of the cell surface repertoire. Cell Stem Cell 2013; 13:492-505. PubMed
  • Kim W, Bird GH, Neff T, Guo G, Kerenyi MA, Walensky LD, Orkin SH. Targeted disruption of the EZH2-EED complex inhibits EZH2-dependent cancer. Nat Chem Biol 2013; 9:643-50. PubMed
  • Luc S, Orkin SH. Delineating the mixed lineage leukemia gene expression network in hematopoietic stem cells. Proc Natl Acad Sci U S A 2013; 110:11670-1. PubMed
  • Sankaran VG, Orkin SH. Genome-wide association studies of hematologic phenotypes: a window into human hematopoiesis. Curr Opin Genet Dev 2013. PubMed
  • Baena E, Shao Z, Linn DE, Glass K, Hamblen MJ, Fujiwara Y, Kim J, Nguyen M, Zhang X, Godinho FJ, Bronson RT, Mucci LA, Loda M, Yuan GC, Orkin SH, Li Z. ETV1 directs androgen metabolism and confers aggressive prostate cancer in targeted mice and patients. Genes Dev 2013; 27:683-98. PubMed
  • Staber PB, Zhang P, Ye M, Welner RS, Nombela-Arrieta C, Bach C, Kerenyi M, Bartholdy BA, Zhang H, Alberich-Jordà M, Lee S, Yang H, Ng F, Zhang J, Leddin M, Silberstein LE, Hoefler G, Orkin SH, Göttgens B, Rosenbauer F, Huang G, Tenen DG. Sustained PU.1 levels balance cell-cycle regulators to prevent exhaustion of adult hematopoietic stem cells. Mol Cell 2013; 49:934-46. PubMed
  • Bai X, Trowbridge JJ, Riley E, Lee JA, DiBiase A, Kaartinen VM, Orkin SH, Zon LI. TiF1-gamma plays an essential role in murine hematopoiesis and regulates transcriptional elongation of erythroid genes. Dev Biol 2013. PubMed
  • Kerenyi MA, Shao Z, Hsu YJ, Guo G, Luc S, O'Brien K, Fujiwara Y, Peng C, Nguyen M, Orkin SH. Histone demethylase Lsd1 represses hematopoietic stem and progenitor cell signatures during blood cell maturation. Elife 2013; 2:e00633. PubMed
  • Maclean GA, Menne TF, Guo G, Sanchez DJ, Park IH, Daley GQ, Orkin SH. Altered hematopoiesis in trisomy 21 as revealed through in vitro differentiation of isogenic human pluripotent cells. Proc Natl Acad Sci U S A 2012; 109:17567-72. PubMed
  • Xu J, Shao Z, Glass K, Bauer DE, Pinello L, Van Handel B, Hou S, Stamatoyannopoulos JA, Mikkola HK, Yuan GC, Orkin SH. Combinatorial assembly of developmental stage-specific enhancers controls gene expression programs during human erythropoiesis. Dev Cell 2012; 23:796-811. PubMed
  • Bauer DE, Kamran SC, Orkin SH. Reawakening fetal hemoglobin: prospects for new therapies for the β-globin disorders. Blood 2012; 120:2945-53. PubMed
  • Sankaran VG, Ludwig LS, Sicinska E, Xu J, Bauer DE, Eng JC, Patterson HC, Metcalf RA, Natkunam Y, Orkin SH, Sicinski P, Lander ES, Lodish HF. Cyclin D3 coordinates the cell cycle during differentiation to regulate erythrocyte size and number. Genes Dev 2012; 26:2075-87. PubMed
  • Funnell AP, Norton LJ, Mak KS, Burdach J, Artuz CM, Twine NA, Wilkins MR, Power CA, Hung TT, Perdomo J, Koh P, Bell-Anderson KS, Orkin SH, Fraser ST, Perkins AC, Pearson RC, Crossley M. The CACCC-binding protein KLF3/BKLF represses a subset of KLF1/EKLF target genes and is required for proper erythroid maturation in vivo. Mol Cell Biol 2012; 32:3281-92. PubMed
  • Sankaran VG, Ghazvinian R, Do R, Thiru P, Vergilio JA, Beggs AH, Sieff CA, Orkin SH, Nathan DG, Lander ES, Gazda HT. Exome sequencing identifies GATA1 mutations resulting in Diamond-Blackfan anemia. J Clin Invest 2012; 122:2439-43. PubMed
  • Snow JW, Trowbridge JJ, Johnson KD, Fujiwara T, Emambokus NE, Grass JA, Orkin SH, Bresnick EH. Context-dependent function of "GATA switch" sites in vivo. Blood 2011. PubMed
  • Xu J, Orkin SH. The erythroid/myeloid lineage fate paradigm takes a new player. EMBO J 2011; 30:983-5. PubMed
  • Wilber A, Hargrove PW, Kim YS, Riberdy JM, Sankaran VG, Papanikolaou E, Georgomanoli M, Anagnou NP, Orkin SH, Nienhuis AW, Persons DA. Therapeutic levels of fetal hemoglobin in erythroid progeny of β-thalassemic CD34+ cells after lentiviral vector-mediated gene transfer. Blood 2011; 117:2817-26. PubMed
  • Koh KP, Yabuuchi A, Rao S, Huang Y, Cunniff K, Nardone J, Laiho A, Tahiliani M, Sommer CA, Mostoslavsky G, Lahesmaa R, Orkin SH, Rodig SJ, Daley GQ, Rao A. Tet1 and Tet2 regulate 5-hydroxymethylcytosine production and cell lineage specification in mouse embryonic stem cells. Cell Stem Cell 2011; 8:200-13. PubMed
  • Bauer DE, Orkin SH. Update on fetal hemoglobin gene regulation in hemoglobinopathies. Curr Opin Pediatr 2011; 23:1-8. PubMed
  • Sankaran VG, Menne TF, Šćepanović D, Vergilio JA, Ji P, Kim J, Thiru P, Orkin SH, Lander ES, Lodish HF. MicroRNA-15a and -16-1 act via MYB to elevate fetal hemoglobin expression in human trisomy 13. Proc Natl Acad Sci U S A 2011; 108:1519-24. PubMed
  • Rao S, Zhen S, Roumiantsev S, McDonald LT, Yuan GC, Orkin SH. Differential roles of sall4 isoforms in embryonic stem cell pluripotency. Mol Cell Biol 2010; 30:5364-80. PubMed
  • Wilson BG, Wang X, Shen X, McKenna ES, Lemieux ME, Cho YJ, Koellhoffer EC, Pomeroy SL, Orkin SH, Roberts CW. Epigenetic antagonism between polycomb and SWI/SNF complexes during oncogenic transformation. Cancer Cell 2010; 18:316-28. PubMed
  • Kim J, Woo AJ, Chu J, Snow JW, Fujiwara Y, Kim CG, Cantor AB, Orkin SH. A Myc network accounts for similarities between embryonic stem and cancer cell transcription programs. Cell 2010; 143:313-24. PubMed
  • Williams DA, Porter ES, Lux SE, Grier HE, Mack JW, Orkin SH. Training program in cancer and blood diseases: Pediatric Hematology/Oncology Fellowship Program, Children's Hospital Boston/Dana-Farber Cancer Institute. Am J Hematol 2010; 85:793-4. PubMed
  • Snow JW, Kim J, Currie CR, Xu J, Orkin SH. Sumoylation regulates interaction of FOG1 with C-terminal-binding protein (CTBP). J Biol Chem 2010; 285:28064-75. PubMed
  • Klusmann JH, Godinho FJ, Heitmann K, Maroz A, Koch ML, Reinhardt D, Orkin SH, Li Z. Developmental stage-specific interplay of GATA1 and IGF signaling in fetal megakaryopoiesis and leukemogenesis. Genes Dev 2010; 24:1659-72. PubMed
  • Sankaran VG, Xu J, Orkin SH. Transcriptional silencing of fetal hemoglobin by BCL11A. Ann N Y Acad Sci 2010; 1202:64-8. PubMed
  • Bai X, Kim J, Yang Z, Jurynec MJ, Akie TE, Lee J, LeBlanc J, Sessa A, Jiang H, DiBiase A, Zhou Y, Grunwald DJ, Lin S, Cantor AB, Orkin SH, Zon LI. TIF1gamma controls erythroid cell fate by regulating transcription elongation. Cell 2010; 142:133-43. PubMed
  • Trowbridge JJ, Orkin SH. DNA methylation in adult stem cells: New insights into self-renewal. Epigenetics 2010. PubMed
  • Xu J, Sankaran VG, Ni M, Menne TF, Puram RV, Kim W, Orkin SH. Transcriptional silencing of {gamma}-globin by BCL11A involves long-range interactions and cooperation with SOX6. Genes Dev 2010; 24:783-98. PubMed
  • Alford K, Slender A, Vanes L, Li Z, Fisher EM, Nizetic D, Orkin SH, Roberts I, Tybulewicz VL. Perturbed hematopoiesis in the Tc1 mouse model of Down Syndrome. Blood 2010; 115:2928-37. PubMed
  • Sankaran VG, Xu J, Orkin SH. Advances in the understanding of haemoglobin switching. British Journal of Haematology 2010; 149:181-94. PubMed
  • Klusmann JH, Li Z, Böhmer K, Maroz A, Koch ML, Emmrich S, Godinho FJ, Orkin SH, Reinhardt D. miR-125b-2 is a potential oncomiR on human chromosome 21 in megakaryoblastic leukemia. Genes Dev 2010; 24:478-90. PubMed
  • Kim J, Orkin SH. Systematic tracking of cell fate changes. Nat Biotechnol 2010; 28:146-7. PubMed
  • Nathan DG, Orkin SH. Musings on genome medicine: Hepatitis C. Genome Med 2010; 2:4. PubMed
  • Bjork BC, Fujiwara Y, Davis SW, Qiu H, Saunders TL, Sandy P, Orkin S, Camper SA, Beier DR. A transient transgenic RNAi strategy for rapid characterization of gene function during embryonic development. PLoS ONE 2010; 5:e14375. PubMed
  • Snow JW, Trowbridge JJ, Fujiwara T, Emambokus NE, Grass JA, Orkin SH, Bresnick EH. A single cis element maintains repression of the key developmental regulator Gata2. PLoS Genet. 2010. PubMed
  • Shen X, Kim W, Fujiwara Y, Simon MD, Liu Y, Mysliwiec MR, Yuan GC, Lee Y, Orkin SH. Jumonji modulates polycomb activity and self-renewal versus differentiation of stem cells. Cell 2009; 139:1303-14. PubMed
  • Yu M, Riva L, Xie H, Schindler Y, Moran TB, Cheng Y, Yu D, Hardison R, Weiss MJ, Orkin SH, Bernstein BE, Fraenkel E, Cantor AB. Insights into GATA-1-mediated gene activation versus repression via genome-wide chromatin occupancy analysis. Mol Cell 2009; 36:682-95. PubMed
  • Snow JW, Orkin SH. Translational isoforms of FOG1 regulate GATA1-interacting complexes. J Biol Chem 2009; 284:29310-9. PubMed
  • Trowbridge JJ, Snow JW, Kim J, Orkin SH. DNA methyltransferase 1 is essential for and uniquely regulates hematopoietic stem and progenitor cells. Cell Stem Cell 2009; 5:442-9. PubMed
  • Huang Z, Dore LC, Li Z, Orkin SH, Feng G, Lin S, Crispino JD. GATA-2 reinforces megakaryocyte development in the absence of GATA-1. Mol Cell Biol 2009; 29:5168-80. PubMed
  • Sankaran VG, Xu J, Ragoczy T, Ippolito GC, Walkley CR, Maika SD, Fujiwara Y, Ito M, Groudine M, Bender MA, Tucker PW, Orkin SH. Developmental and species-divergent globin switching are driven by BCL11A. Nature 2009; 460:1093-7. PubMed
  • Schindler JW, Van Buren D, Foudi A, Krejci O, Qin J, Orkin SH, Hock H. TEL-AML1 corrupts hematopoietic stem cells to persist in the bone marrow and initiate leukemia. Cell Stem Cell 2009; 5:43-53. PubMed
  • Gekas C,Rhodes KE,Gereige LM,Helgadottir H,Ferrari R,Kurdistani SK,Montecino-Rodriguez E,Bassel-Duby R,Olson E,Krivtsov AV,Armstrong S,Orkin SH,Pellegrini M,Mikkola HK. Mef2C is a lineage-restricted target of Scl/Tal1 and regulates megakaryopoiesis and B-cell homeostasis. Blood 2009; 113:3461-71. PubMed
  • Hu G,Kim J,Xu Q,Leng Y,Orkin SH,Elledge SJ. A genome-wide RNAi screen identifies a new transcriptional module required for self-renewal. Genes Dev 2009; 23:837-48. PubMed
  • Nathan DG,Orkin SH. Musings on genome medicine: the Obama effect. Genome Med 2009; 1:30. PubMed
  • Wang J,Cantor AB,Orkin SH. Tandem affinity purification of protein complexes in mouse embryonic stem cells using in vivo biotinylation. Curr Protoc Stem Cell Biol 2009; Chapter 1:Unit1B.5. PubMed
  • Nathan DG,Orkin SH. Musings on genome medicine: abuse of genetic tests. Genome Med 2009; 1:18. PubMed
  • Nathan DG,Orkin SH. Musings on genome medicine: genome wide association studies. Genome Med 2009; 1:3. PubMed
  • Shen X,Orkin SH. Glimpses of the epigenetic landscape. Cell Stem Cell 2009; 4:1-2. PubMed
  • Nathan DG, Orkin SH. Musings on genome medicine: Crohn's disease. Genome Med 2009; 1:103. PubMed
  • Nathan DG,Orkin SH. Musings on genome medicine: gene therapy. Genome Med 2009; 1:38. PubMed
  • Hartner JC,Walkley CR,Lu J,Orkin SH. ADAR1 is essential for the maintenance of hematopoiesis and suppression of interferon signaling. Nat Immunol 2009; 10:109-15. PubMed
  • Kim J,Cantor AB,Orkin SH,Wang J. Use of in vivo biotinylation to study protein-protein and protein-DNA interactions in mouse embryonic stem cells. Nat Protoc 2009; 4:506-17. PubMed
  • Nathan DG, Orkin SH. Musings on genome medicine: enzyme-replacement therapy of the lysosomal storage diseases. Genome Med 2009; 1:114. PubMed
  • Nathan DG, Orkin SH. Musings on genome medicine: cholesterol and coronary artery disease. Genome Med 2009; 1:60. PubMed
  • Nathan DG, Orkin SH. Musings on genome medicine: the Obama effect redux. Genome Med 2009; 1:86. PubMed
  • Nathan DG, Orkin SH. Musings on genome medicine: the slow but inexorable process of medical care reform in the United States. Genome Med 2009; 1:94. PubMed
  • Nathan DG,Orkin SH. Musings on genome medicine: cancer genetics and the promise of effective treatment. Genome Med 2009; 1:49. PubMed
  • Sankaran VG,Menne TF,Xu J,Akie TE,Lettre G,Van Handel B,Mikkola HK,Hirschhorn JN,Cantor AB,Orkin SH. Human fetal hemoglobin expression is regulated by the developmental stage-specific repressor BCL11A. Science 2008; 322:1839-42. PubMed
  • Shen X, Liu Y, Hsu YJ, Fujiwara Y, Kim J, Mao X, Yuan GC, Orkin SH. EZH1 mediates methylation on histone H3 lysine 27 and complements EZH2 in maintaining stem cell identity and executing pluripotency. Mol Cell 2008; 32:491-502. PubMed
  • Terranova R,Yokobayashi S,Stadler MB,Otte AP,van Lohuizen M,Orkin SH,Peters AH. Polycomb group proteins Ezh2 and Rnf2 direct genomic contraction and imprinted repression in early mouse embryos. Dev Cell 2008; 15:668-79. PubMed
  • Beuling E,Bosse T,aan de Kerk DJ,Piaseckyj CM,Fujiwara Y,Katz SG,Orkin SH,Grand RJ,Krasinski SD. GATA4 mediates gene repression in the mature mouse small intestine through interactions with friend of GATA (FOG) cofactors. Dev Biol 2008; 322:179-89. PubMed
  • Lettre G,Sankaran VG,Bezerra MA,Araujo AS,Uda M,Sanna S,Cao A,Schlessinger D,Costa FF,Hirschhorn JN,Orkin SH. DNA polymorphisms at the BCL11A, HBS1L-MYB, and beta-globin loci associate with fetal hemoglobin levels and pain crises in sickle cell disease. Proc Natl Acad Sci U S A 2008; 105:11869-74. PubMed
  • Walkley CR,Qudsi R,Sankaran VG,Perry JA,Gostissa M,Roth SI,Rodda SJ,Snay E,Dunning P,Fahey FH,Alt FW,McMahon AP,Orkin SH. Conditional mouse osteosarcoma, dependent on p53 loss and potentiated by loss of Rb, mimics the human disease. Genes Dev 2008; 22:1662-76. PubMed
  • Wang J, Levasseur DN, Orkin SH. Requirement of Nanog dimerization for stem cell self-renewal and pluripotency. Proc Natl Acad Sci U S A 2008; 105:6326-31. PubMed
  • Kim J, Chu J, Shen X, Wang J, Orkin SH. An extended transcriptional network for pluripotency of embryonic stem cells. Cell 2008; 132:1049-61. PubMed
  • Cantor AB, Iwasaki H, Arinobu Y, Moran TB, Shigematsu H, Sullivan MR, Akashi K, Orkin SH. Antagonism of FOG-1 and GATA factors in fate choice for the mast cell lineage. J Exp Med 2008; 205:611-24. PubMed
  • Rhodes KE, Gekas C, Wang Y, Lux CT, Francis CS, Chan DN, Conway S, Orkin SH, Yoder MC, Mikkola HK. The emergence of hematopoietic stem cells is initiated in the placental vasculature in the absence of circulation. Cell Stem Cell 2008; 2:252-63. PubMed
  • Levasseur DN, Wang J, Dorschner MO, Stamatoyannopoulos JA, Orkin SH. Oct4 dependence of chromatin structure within the extended Nanog locus in ES cells. Genes Dev 2008; 22:575-80. PubMed
  • Orkin SH, Zon LI. Hematopoiesis: an evolving paradigm for stem cell biology. Cell 2008; 132:631-44. PubMed
  • Orkin SH, Zon LI. SnapShot: hematopoiesis. Cell 2008; 132:712. PubMed
  • Sankaran VG, Orkin SH, Walkley CR. Rb intrinsically promotes erythropoiesis by coupling cell cycle exit with mitochondrial biogenesis. Genes Dev 2008; 22:463-75. PubMed
  • Walkley CR,Sankaran VG,Orkin SH. Rb and hematopoiesis: stem cells to anemia. Cell Div 2008; 3:13. PubMed
  • Wang J, Orkin SH. A Protein Roadmap to Pluripotency and Faithful Reprogramming. Cells Tissues Organs 2008; 188:23-30. PubMed
  • Wang J, Theunissen TW, Orkin SH. Site-directed, virus-free, and inducible RNAi in embryonic stem cells. Proc Natl Acad Sci U S A 2007; 104:20850-5. PubMed
  • Li Z, Tognon CE, Godinho FJ, Yasaitis L, Hock H, Herschkowitz JI, Lannon CL, Cho E, Kim SJ, Bronson RT, Perou CM, Sorensen PH, Orkin SH. ETV6-NTRK3 fusion oncogene initiates breast cancer from committed mammary progenitors via activation of AP1 complex. Cancer Cell 2007; 12:542-58. PubMed
  • Xie H, Orkin SH. Immunology: changed destiny. Nature 2007; 449:410-1. PubMed
  • Orkin SH, Pera M. Stem cells down under-ISSCR 2007. Cell Stem Cell 2007; 1:271-6. PubMed
  • Saleque S, Kim J, Rooke HM, Orkin SH. Epigenetic regulation of hematopoietic differentiation by Gfi-1 and Gfi-1b is mediated by the cofactors CoREST and LSD1. Mol Cell 2007; 27:562-72. PubMed
  • North TE, Goessling W, Walkley CR, Lengerke C, Kopani KR, Lord AM, Weber GJ, Bowman TV, Jang IH, Grosser T, Fitzgerald GA, Daley GQ, Orkin SH, Zon LI. Prostaglandin E2 regulates vertebrate haematopoietic stem cell homeostasis. Nature 2007; 447:1007-11. PubMed
  • Walkley CR, Shea JM, Sims NA, Purton LE, Orkin SH. Rb regulates interactions between hematopoietic stem cells and their bone marrow microenvironment. Cell 2007; 129:1081-95. PubMed
  • Ackerman KG, Wang J, Luo L, Fujiwara Y, Orkin SH, Beier DR. Gata4 is necessary for normal pulmonary lobar development. Am J Respir Cell Mol Biol 2007; 36:391-7. PubMed
  • Mikkola HK, Orkin SH. The journey of developing hematopoietic stem cells. Development 2006; 133:3733-44. PubMed
  • Walkley CR, Orkin SH. Rb is dispensable for self-renewal and multilineage differentiation of adult hematopoietic stem cells. Proc Natl Acad Sci U S A 2006; 103:9057-62. PubMed
  • Bourquin JP, Subramanian A, Langebrake C, Reinhardt D, Bernard O, Ballerini P, Baruchel A, Cavé H, Dastugue N, Hasle H, Kaspers GL, Lessard M, Michaux L, Vyas P, van Wering E, Zwaan CM, Golub TR, Orkin SH. Identification of distinct molecular phenotypes in acute megakaryoblastic leukemia by gene expression profiling. Proc Natl Acad Sci U S A 2006; 103:3339-44. PubMed
  • Nelms BD, Waldron L, Barrera LA, Weflen AW, Goettel JA, Guo G, Montgomery RK, Neutra MR, Breault DT, Snapper SB, Orkin SH, Bulyk ML, Huttenhower C, Lencer WI. CellMapper: rapid and accurate inference of gene expression in difficult-to-isolate cell types. Genome Biol ; 17:201. PubMed
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DF/HCC members that share similar concepts* with Stuart H. Orkin, MD but have yet to coauthor a publication with this researcher.

* Concepts are MeSH terms, automatically derived from member publications

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