Latest Publications

1.

 Polycomb deficiency drives a FOXP2-high aggressive state targetable by epigenetic inhibitors.

Chen F, Byrd AL, Liu J, Flight RM, DuCote TJ, Naughton KJ, Song X, Edgin AR, Lukyanchuk A, Dixon DT, Gosser CM, Esoe DP, Jayswal RD, Orkin SH, Moseley HNB, Wang C, Brainson CF.

Nat Commun. 2023 Jan 20;14(1):336. doi: 10.1038/s41467-023-35784-x.

PMID: 36670102 

2.

 Evolution of nanobodies specific for BCL11A.

Yin M, Izadi M, Tenglin K, Viennet T, Zhai L, Zheng G, Arthanari H, Dassama LMK, Orkin SH.

Proc Natl Acad Sci U S A. 2023 Jan 17;120(3):e2218959120. doi: 10.1073/pnas.2218959120. Epub 2023 Jan 10.

PMID: 36626555

3.

 A Cell-Permeant Nanobody-Based Degrader That Induces Fetal Hemoglobin.

Shen F, Zheng G, Setegne M, Tenglin K, Izadi M, Xie H, Zhai L, Orkin SH, Dassama LMK.

ACS Cent Sci. 2022 Dec 28;8(12):1695-1703. doi: 10.1021/acscentsci.2c00998. Epub 2022 Dec 14.

PMID: 36589886 

4.

 Temporal resolution of gene derepression and proteome changes upon PROTAC-mediated degradation of BCL11A protein in erythroid cells.

Mehta S, Buyanbat A, Kai Y, Karayel O, Goldman SR, Seruggia D, Zhang K, Fujiwara Y, Donovan KA, Zhu Q, Yang H, Nabet B, Gray NS, Mann M, Fischer ES, Adelman K, Orkin SH.

Cell Chem Biol. 2022 Aug 18;29(8):1273-1287.e8. doi: 10.1016/j.chembiol.2022.06.007. Epub 2022 Jul 14.

PMID: 35839780

5.

 CD49b identifies functionally and epigenetically distinct subsets of lineage-biased hematopoietic stem cells.

Somuncular E, Hauenstein J, Khalkar P, Johansson AS, Dumral Ö, Frengen NS, Gustafsson C, Mocci G, Su TY, Brouwer H, Trautmann CL, Vanlandewijck M, Orkin SH, Månsson R, Luc S.

Stem Cell Reports. 2022 Jul 12;17(7):1546-1560. doi: 10.1016/j.stemcr.2022.05.014. Epub 2022 Jun 16.

PMID: 35714596

6.

 Transcriptional Plasticity Drives Leukemia Immune Escape.

Eagle K, Harada T, Kalfon J, Perez MW, Heshmati Y, Ewers J, Koren JV, Dempster JM, Kugener G, Paralkar VR, Lin CY, Dharia NV, Stegmaier K, Orkin SH, Pimkin M.

Blood Cancer Discov. 2022 Sep 6;3(5):394-409. doi: 10.1158/2643-3230.BCD-21-0207.

PMID: 35709529

7.

 Hypoxic, glycolytic metabolism is a vulnerability of B-acute lymphoblastic leukemia-initiating cells.

Morris V, Wang D, Li Z, Marion W, Hughes T, Sousa P, Harada T, Sui SH, Naumenko S, Kalfon J, Sensharma P, Falchetti M, Vinicius da Silva R, Candelli T, Schneider P, Margaritis T, Holstege FCP, Pikman Y, Harris M, Stam RW, Orkin SH, Koehler AN, Shalek AK, North TE, Pimkin M, Daley GQ, Lummertz da Rocha E, Rowe RG.

Cell Rep. 2022 Apr 26;39(4):110752. doi: 10.1016/j.celrep.2022.110752.

PMID: 35476984

8.

 Unleashing Cell-Intrinsic Inflammation as a Strategy to Kill AML Blasts.

Ellegast JM, Alexe G, Hamze A, Lin S, Uckelmann HJ, Rauch PJ, Pimkin M, Ross LS, Dharia NV, Robichaud AL, Conway AS, Khalid D, Perry JA, Wunderlich M, Benajiba L, Pikman Y, Nabet B, Gray NS, Orkin SH, Stegmaier K.

Cancer Discov. 2022 Jul 6;12(7):1760-1781. doi: 10.1158/2159-8290.CD-21-0956.

PMID: 35405016

9.

 Developmental maturation of the hematopoietic system controlled by a Lin28b-let-7-Cbx2 axis.

Wang D, Tanaka-Yano M, Meader E, Kinney MA, Morris V, Lummertz da Rocha E, Liu N, Liu T, Zhu Q, Orkin SH, North TE, Daley GQ, Rowe RG.

Cell Rep. 2022 Apr 5;39(1):110587. doi: 10.1016/j.celrep.2022.110587.

PMID: 35385744

10.

 A distinct core regulatory module enforces oncogene expression in KMT2A-rearranged leukemia.

Harada T, Heshmati Y, Kalfon J, Perez MW, Xavier Ferrucio J, Ewers J, Hubbell Engler B, Kossenkov A, Ellegast JM, Yi JS, Bowker A, Zhu Q, Eagle K, Liu T, Kai Y, Dempster JM, Kugener G, Wickramasinghe J, Herbert ZT, Li CH, Vrabič Koren J, Weinstock DM, Paralkar VR, Nabet B, Lin CY, Dharia NV, Stegmaier K, Orkin SH, Pimkin M.

Genes Dev. 2022 Mar 1;36(5-6):368-389. doi: 10.1101/gad.349284.121. Epub 2022 Mar 17.

PMID: 35301220

11.

 Congenital anemia reveals distinct targeting mechanisms for master transcription factor GATA1.

Ludwig LS, Lareau CA, Bao EL, Liu N, Utsugisawa T, Tseng AM, Myers SA, Verboon JM, Ulirsch JC, Luo W, Muus C, Fiorini C, Olive ME, Vockley CM, Munschauer M, Hunter A, Ogura H, Yamamoto T, Inada H, Nakagawa S, Ohzono S, Subramanian V, Chiarle R, Glader B, Carr SA, Aryee MJ, Kundaje A, Orkin SH, Regev A, McCavit TL, Kanno H, Sankaran VG.

Blood. 2022 Apr 21;139(16):2534-2546. doi: 10.1182/blood.2021013753.

PMID: 35030251

12.

 Transcription factor-mediated intestinal metaplasia and the role of a shadow enhancer.

Singh H, Seruggia D, Madha S, Saxena M, Nagaraja AK, Wu Z, Zhou J, Huebner AJ, Maglieri A, Wezenbeek J, Hochedlinger K, Orkin SH, Bass AJ, Hornick JL, Shivdasani RA.

Genes Dev. 2022 Jan 1;36(1-2):38-52. doi: 10.1101/gad.348983.121. Epub 2021 Dec 30.

PMID: 34969824

13.

 Inner nuclear protein Matrin-3 coordinates cell differentiation by stabilizing chromatin architecture.

Cha HJ, Uyan Ö, Kai Y, Liu T, Zhu Q, Tothova Z, Botten GA, Xu J, Yuan GC, Dekker J, Orkin SH.

Nat Commun. 2021 Oct 29;12(1):6241. doi: 10.1038/s41467-021-26574-4.

PMID: 34716321

14.

 Dietary suppression of MHC class II expression in intestinal epithelial cells enhances intestinal tumorigenesis.

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.

Cell Stem Cell. 2021 Nov 4;28(11):1922-1935.e5. doi: 10.1016/j.stem.2021.08.007. Epub 2021 Sep 15.

PMID: 34529935

15.

 Mapping the evolving landscape of super-enhancers during cell differentiation.

Kai Y, Li BE, Zhu M, Li GY, Chen F, Han Y, Cha HJ, Orkin SH, Cai W, Huang J, Yuan GC.

Genome Biol. 2021 Sep 15;22(1):269. doi: 10.1186/s13059-021-02485-x.

PMID: 34526084

16.

 A unified model of human hemoglobin switching through single-cell genome editing.

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.

Nat Commun. 2021 Aug 17;12(1):4991. doi: 10.1038/s41467-021-25298-9.

PMID: 34404810

17.

 Reactivation of a developmentally silenced embryonic globin gene.

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.

Nat Commun. 2021 Jul 21;12(1):4439. doi: 10.1038/s41467-021-24402-3.

PMID: 34290235

18.

 Indispensable epigenetic control of thymic epithelial cell development and function by polycomb repressive complex 2.

Barthlott T, Handel AE, Teh HY, Wirasinha RC, Hafen K, Žuklys S, Roch B, Orkin SH, de Villartay JP, Daley SR, Holländer GA.

Nat Commun. 2021 Jun 24;12(1):3933. doi: 10.1038/s41467-021-24158-w.

PMID: 34168132

19.

 Author Correction: Transcription factor competition at the γ-globin promoters controls hemoglobin switching.

Liu N, Xu S, Yao Q, Zhu Q, Kai Y, Hsu JY, Sakon P, Pinello L, Yuan GC, Bauer DE, Orkin SH.

Nat Genet. 2021 Apr;53(4):586. doi: 10.1038/s41588-021-00834-x.

PMID: 33731942

20.

 Transcription factor competition at the γ-globin promoters controls hemoglobin switching.

Liu N, Xu S, Yao Q, Zhu Q, Kai Y, Hsu JY, Sakon P, Pinello L, Yuan GC, Bauer DE, Orkin SH.

Nat Genet. 2021 Apr;53(4):511-520. doi: 10.1038/s41588-021-00798-y. Epub 2021 Mar 1.

PMID: 33649594

21.

 ARID4B is critical for mouse embryonic stem cell differentiation towards mesoderm and endoderm, linking epigenetics to pluripotency exit.

Terzi Cizmecioglu N, Huang J, Keskin EG, Wang X, Esen I, Chen F, Orkin SH.

J Biol Chem. 2020 Dec 18;295(51):17738-17751. doi: 10.1074/jbc.RA120.015534.

PMID: 33454011

22.

 A saturating mutagenesis CRISPR-Cas9-mediated functional genomic screen identifies cis- and trans-regulatory elements of Oct4 in murine ESCs.

Canver MC, Tripathi P, Bullen MJ, Olshansky M, Kumar Y, Wong LH, Turner SJ, Lessard S, Pinello L, Orkin SH, Das PP.

J Biol Chem. 2020 Nov 20;295(47):15797-15809. doi: 10.1074/jbc.RA120.013772. Epub 2020 Sep 29.

PMID: 32994224

23.

 Enhancer dependence of cell-type-specific gene expression increases with developmental age.

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.

Proc Natl Acad Sci U S A. 2020 Sep 1;117(35):21450-21458. doi: 10.1073/pnas.2008672117. Epub 2020 Aug 19.

PMID: 32817427

24.

 An Engineered CRISPR-Cas9 Mouse Line for Simultaneous Readout of Lineage Histories and Gene Expression Profiles in Single Cells.

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.

Cell. 2020 Jun 11;181(6):1410-1422.e27. doi: 10.1016/j.cell.2020.04.048. Epub 2020 May 14.

PMID: 32413320

25.

 Multiplexed capture of spatial configuration and temporal dynamics of locus-specific 3D chromatin by biotinylated dCas9.

Liu X, Chen Y, Zhang Y, Liu Y, Liu N, Botten GA, Cao H, Orkin SH, Zhang MQ, Xu J.

Genome Biol. 2020 Mar 5;21(1):59. doi: 10.1186/s13059-020-01973-w.

PMID: 32138752