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Items: 43

1.

JDP2: An oncogenic bZIP transcription factor in T cell acute lymphoblastic leukemia.

Mansour MR, He S, Li Z, Lobbardi R, Abraham BJ, Hug C, Rahman S, Leon TE, Kuang YY, Zimmerman MW, Blonquist T, Gjini E, Gutierrez A, Tang Q, Garcia-Perez L, Pike-Overzet K, Anders L, Berezovskaya A, Zhou Y, Zon LI, Neuberg D, Fielding AK, Staal FJT, Langenau DM, Sanda T, Young RA, Look AT.

J Exp Med. 2018 Jul 2;215(7):1929-1945. doi: 10.1084/jem.20170484. Epub 2018 Jun 25.

2.

Coactivator condensation at super-enhancers links phase separation and gene control.

Sabari BR, Dall'Agnese A, Boija A, Klein IA, Coffey EL, Shrinivas K, Abraham BJ, Hannett NM, Zamudio AV, Manteiga JC, Li CH, Guo YE, Day DS, Schuijers J, Vasile E, Malik S, Hnisz D, Lee TI, Cisse II, Roeder RG, Sharp PA, Chakraborty AK, Young RA.

Science. 2018 Jul 27;361(6400). pii: eaar3958. doi: 10.1126/science.aar3958. Epub 2018 Jun 21.

PMID:
29930091
3.

Integrated genomic analyses of de novo pathways underlying atypical meningiomas.

Harmancı AS, Youngblood MW, Clark VE, Coşkun S, Henegariu O, Duran D, Erson-Omay EZ, Kaulen LD, Lee TI, Abraham BJ, Simon M, Krischek B, Timmer M, Goldbrunner R, Omay SB, Baranoski J, Baran B, Carrión-Grant G, Bai H, Mishra-Gorur K, Schramm J, Moliterno J, Vortmeyer AO, Bilgüvar K, Yasuno K, Young RA, Günel M.

Nat Commun. 2018 Apr 20;9:16215. doi: 10.1038/ncomms16215.

4.

Cross-Cohort Analysis Identifies a TEAD4-MYCN Positive Feedback Loop as the Core Regulatory Element of High-Risk Neuroblastoma.

Rajbhandari P, Lopez G, Capdevila C, Salvatori B, Yu J, Rodriguez-Barrueco R, Martinez D, Yarmarkovich M, Weichert-Leahey N, Abraham BJ, Alvarez MJ, Iyer A, Harenza JL, Oldridge D, De Preter K, Koster J, Asgharzadeh S, Seeger RC, Wei JS, Khan J, Vandesompele J, Mestdagh P, Versteeg R, Look AT, Young RA, Iavarone A, Lasorella A, Silva JM, Maris JM, Califano A.

Cancer Discov. 2018 May;8(5):582-599. doi: 10.1158/2159-8290.CD-16-0861. Epub 2018 Mar 6.

5.

High MITF Expression Is Associated with Super-Enhancers and Suppressed by CDK7 Inhibition in Melanoma.

Eliades P, Abraham BJ, Ji Z, Miller DM, Christensen CL, Kwiatkowski N, Kumar R, Njauw CN, Taylor M, Miao B, Zhang T, Wong KK, Gray NS, Young RA, Tsao H.

J Invest Dermatol. 2018 Jul;138(7):1582-1590. doi: 10.1016/j.jid.2017.09.056. Epub 2018 Feb 8.

PMID:
29408204
6.

EWS/FLI Confers Tumor Cell Synthetic Lethality to CDK12 Inhibition in Ewing Sarcoma.

Iniguez AB, Stolte B, Wang EJ, Conway AS, Alexe G, Dharia NV, Kwiatkowski N, Zhang T, Abraham BJ, Mora J, Kalev P, Leggett A, Chowdhury D, Benes CH, Young RA, Gray NS, Stegmaier K.

Cancer Cell. 2018 Feb 12;33(2):202-216.e6. doi: 10.1016/j.ccell.2017.12.009. Epub 2018 Jan 18.

PMID:
29358035
7.

MYC Drives a Subset of High-Risk Pediatric Neuroblastomas and Is Activated through Mechanisms Including Enhancer Hijacking and Focal Enhancer Amplification.

Zimmerman MW, Liu Y, He S, Durbin AD, Abraham BJ, Easton J, Shao Y, Xu B, Zhu S, Zhang X, Li Z, Weichert-Leahey N, Young RA, Zhang J, Look AT.

Cancer Discov. 2018 Mar;8(3):320-335. doi: 10.1158/2159-8290.CD-17-0993. Epub 2017 Dec 28.

PMID:
29284669
8.

YY1 Is a Structural Regulator of Enhancer-Promoter Loops.

Weintraub AS, Li CH, Zamudio AV, Sigova AA, Hannett NM, Day DS, Abraham BJ, Cohen MA, Nabet B, Buckley DL, Guo YE, Hnisz D, Jaenisch R, Bradner JE, Gray NS, Young RA.

Cell. 2017 Dec 14;171(7):1573-1588.e28. doi: 10.1016/j.cell.2017.11.008. Epub 2017 Dec 7.

9.

Suppression of Adaptive Responses to Targeted Cancer Therapy by Transcriptional Repression.

Rusan M, Li K, Li Y, Christensen CL, Abraham BJ, Kwiatkowski N, Buczkowski KA, Bockorny B, Chen T, Li S, Rhee K, Zhang H, Chen W, Terai H, Tavares T, Leggett AL, Li T, Wang Y, Zhang T, Kim TJ, Hong SH, Poudel-Neupane N, Silkes M, Mudianto T, Tan L, Shimamura T, Meyerson M, Bass AJ, Watanabe H, Gray NS, Young RA, Wong KK, Hammerman PS.

Cancer Discov. 2018 Jan;8(1):59-73. doi: 10.1158/2159-8290.CD-17-0461. Epub 2017 Oct 20.

PMID:
29054992
10.

Activation of the p53 Transcriptional Program Sensitizes Cancer Cells to Cdk7 Inhibitors.

Kalan S, Amat R, Schachter MM, Kwiatkowski N, Abraham BJ, Liang Y, Zhang T, Olson CM, Larochelle S, Young RA, Gray NS, Fisher RP.

Cell Rep. 2017 Oct 10;21(2):467-481. doi: 10.1016/j.celrep.2017.09.056.

11.

O-GlcNAcase is an RNA polymerase II elongation factor coupled to pausing factors SPT5 and TIF1β.

Resto M, Kim BH, Fernandez AG, Abraham BJ, Zhao K, Lewis BA.

J Biol Chem. 2017 Oct 6;292(40):16524-16525. doi: 10.1074/jbc.A116.751420. No abstract available.

12.

TOX Regulates Growth, DNA Repair, and Genomic Instability in T-cell Acute Lymphoblastic Leukemia.

Lobbardi R, Pinder J, Martinez-Pastor B, Theodorou M, Blackburn JS, Abraham BJ, Namiki Y, Mansour M, Abdelfattah NS, Molodtsov A, Alexe G, Toiber D, de Waard M, Jain E, Boukhali M, Lion M, Bhere D, Shah K, Gutierrez A, Stegmaier K, Silverman LB, Sadreyev RI, Asara JM, Oettinger MA, Haas W, Look AT, Young RA, Mostoslavsky R, Dellaire G, Langenau DM.

Cancer Discov. 2017 Nov;7(11):1336-1353. doi: 10.1158/2159-8290.CD-17-0267. Epub 2017 Oct 3.

PMID:
28974511
13.

The long noncoding RNA Wisper controls cardiac fibrosis and remodeling.

Micheletti R, Plaisance I, Abraham BJ, Sarre A, Ting CC, Alexanian M, Maric D, Maison D, Nemir M, Young RA, Schroen B, González A, Ounzain S, Pedrazzini T.

Sci Transl Med. 2017 Jun 21;9(395). pii: eaai9118. doi: 10.1126/scitranslmed.aai9118.

14.

Corrigendum: Small genomic insertions form enhancers that misregulate oncogenes.

Abraham BJ, Hnisz D, Weintraub AS, Kwiatkowski N, Li CH, Li Z, Weichert-Leahey N, Rahman S, Liu Y, Etchin J, Li B, Shen S, Lee TI, Zhang J, Look AT, Mansour MR, Young RA.

Nat Commun. 2017 Jun 1;8:15797. doi: 10.1038/ncomms15797.

15.

A CD47-associated super-enhancer links pro-inflammatory signalling to CD47 upregulation in breast cancer.

Betancur PA, Abraham BJ, Yiu YY, Willingham SB, Khameneh F, Zarnegar M, Kuo AH, McKenna K, Kojima Y, Leeper NJ, Ho P, Gip P, Swigut T, Sherwood RI, Clarke MF, Somlo G, Young RA, Weissman IL.

Nat Commun. 2017 Apr 5;8:14802. doi: 10.1038/ncomms14802.

16.

Activation of the LMO2 oncogene through a somatically acquired neomorphic promoter in T-cell acute lymphoblastic leukemia.

Rahman S, Magnussen M, León TE, Farah N, Li Z, Abraham BJ, Alapi KZ, Mitchell RJ, Naughton T, Fielding AK, Pizzey A, Bustraan S, Allen C, Popa T, Pike-Overzet K, Garcia-Perez L, Gale RE, Linch DC, Staal FJT, Young RA, Look AT, Mansour MR.

Blood. 2017 Jun 15;129(24):3221-3226. doi: 10.1182/blood-2016-09-742148. Epub 2017 Mar 7.

17.

APOBEC signature mutation generates an oncogenic enhancer that drives LMO1 expression in T-ALL.

Li Z, Abraham BJ, Berezovskaya A, Farah N, Liu Y, Leon T, Fielding A, Tan SH, Sanda T, Weintraub AS, Li B, Shen S, Zhang J, Mansour MR, Young RA, Look AT.

Leukemia. 2017 Oct;31(10):2057-2064. doi: 10.1038/leu.2017.75. Epub 2017 Mar 6.

18.

Integrated genomic analyses of de novo pathways underlying atypical meningiomas.

Harmancı AS, Youngblood MW, Clark VE, Coşkun S, Henegariu O, Duran D, Erson-Omay EZ, Kaulen LD, Lee TI, Abraham BJ, Simon M, Krischek B, Timmer M, Goldbrunner R, Omay SB, Baranoski J, Baran B, Carrión-Grant G, Bai H, Mishra-Gorur K, Schramm J, Moliterno J, Vortmeyer AO, Bilgüvar K, Yasuno K, Young RA, Günel M.

Nat Commun. 2017 Feb 14;8:14433. doi: 10.1038/ncomms14433. Erratum in: Nat Commun. 2018 Apr 20;9:16215.

19.

Small genomic insertions form enhancers that misregulate oncogenes.

Abraham BJ, Hnisz D, Weintraub AS, Kwiatkowski N, Li CH, Li Z, Weichert-Leahey N, Rahman S, Liu Y, Etchin J, Li B, Shen S, Lee TI, Zhang J, Look AT, Mansour MR, Young RA.

Nat Commun. 2017 Feb 9;8:14385. doi: 10.1038/ncomms14385.

20.

Genome-wide Trans-ethnic Meta-analysis Identifies Seven Genetic Loci Influencing Erythrocyte Traits and a Role for RBPMS in Erythropoiesis.

van Rooij FJA, Qayyum R, Smith AV, Zhou Y, Trompet S, Tanaka T, Keller MF, Chang LC, Schmidt H, Yang ML, Chen MH, Hayes J, Johnson AD, Yanek LR, Mueller C, Lange L, Floyd JS, Ghanbari M, Zonderman AB, Jukema JW, Hofman A, van Duijn CM, Desch KC, Saba Y, Ozel AB, Snively BM, Wu JY, Schmidt R, Fornage M, Klein RJ, Fox CS, Matsuda K, Kamatani N, Wild PS, Stott DJ, Ford I, Slagboom PE, Yang J, Chu AY, Lambert AJ, Uitterlinden AG, Franco OH, Hofer E, Ginsburg D, Hu B, Keating B, Schick UM, Brody JA, Li JZ, Chen Z, Zeller T, Guralnik JM, Chasman DI, Peters LL, Kubo M, Becker DM, Li J, Eiriksdottir G, Rotter JI, Levy D, Grossmann V, Patel KV, Chen CH; BioBank Japan Project, Ridker PM, Tang H, Launer LJ, Rice KM, Li-Gao R, Ferrucci L, Evans MK, Choudhuri A, Trompouki E, Abraham BJ, Yang S, Takahashi A, Kamatani Y, Kooperberg C, Harris TB, Jee SH, Coresh J, Tsai FJ, Longo DL, Chen YT, Felix JF, Yang Q, Psaty BM, Boerwinkle E, Becker LC, Mook-Kanamori DO, Wilson JG, Gudnason V, O'Donnell CJ, Dehghan A, Cupples LA, Nalls MA, Morris AP, Okada Y, Reiner AP, Zon LI, Ganesh SK.

Am J Hum Genet. 2017 Jan 5;100(1):51-63. doi: 10.1016/j.ajhg.2016.11.016. Epub 2016 Dec 22.

21.

O-GlcNAcase Is an RNA Polymerase II Elongation Factor Coupled to Pausing Factors SPT5 and TIF1β.

Resto M, Kim BH, Fernandez AG, Abraham BJ, Zhao K, Lewis BA.

J Biol Chem. 2016 Oct 21;291(43):22703-22713. Epub 2016 Sep 6. Erratum in: J Biol Chem. 2017 Oct 6;292(40):16524-16525.

22.

Covalent targeting of remote cysteine residues to develop CDK12 and CDK13 inhibitors.

Zhang T, Kwiatkowski N, Olson CM, Dixon-Clarke SE, Abraham BJ, Greifenberg AK, Ficarro SB, Elkins JM, Liang Y, Hannett NM, Manz T, Hao M, Bartkowiak B, Greenleaf AL, Marto JA, Geyer M, Bullock AN, Young RA, Gray NS.

Nat Chem Biol. 2016 Oct;12(10):876-84. doi: 10.1038/nchembio.2166. Epub 2016 Aug 29.

23.

Recurrent somatic mutations in POLR2A define a distinct subset of meningiomas.

Clark VE, Harmancı AS, Bai H, Youngblood MW, Lee TI, Baranoski JF, Ercan-Sencicek AG, Abraham BJ, Weintraub AS, Hnisz D, Simon M, Krischek B, Erson-Omay EZ, Henegariu O, Carrión-Grant G, Mishra-Gorur K, Durán D, Goldmann JE, Schramm J, Goldbrunner R, Piepmeier JM, Vortmeyer AO, Günel JM, Bilgüvar K, Yasuno K, Young RA, Günel M.

Nat Genet. 2016 Oct;48(10):1253-9. doi: 10.1038/ng.3651. Epub 2016 Aug 22.

24.

Parkinson-associated risk variant in distal enhancer of α-synuclein modulates target gene expression.

Soldner F, Stelzer Y, Shivalila CS, Abraham BJ, Latourelle JC, Barrasa MI, Goldmann J, Myers RH, Young RA, Jaenisch R.

Nature. 2016 May 5;533(7601):95-9. doi: 10.1038/nature17939. Epub 2016 Apr 20.

25.

Models of human core transcriptional regulatory circuitries.

Saint-André V, Federation AJ, Lin CY, Abraham BJ, Reddy J, Lee TI, Bradner JE, Young RA.

Genome Res. 2016 Mar;26(3):385-96. doi: 10.1101/gr.197590.115. Epub 2016 Feb 3.

26.

Genetic predisposition to neuroblastoma mediated by a LMO1 super-enhancer polymorphism.

Oldridge DA, Wood AC, Weichert-Leahey N, Crimmins I, Sussman R, Winter C, McDaniel LD, Diamond M, Hart LS, Zhu S, Durbin AD, Abraham BJ, Anders L, Tian L, Zhang S, Wei JS, Khan J, Bramlett K, Rahman N, Capasso M, Iolascon A, Gerhard DS, Guidry Auvil JM, Young RA, Hakonarson H, Diskin SJ, Look AT, Maris JM.

Nature. 2015 Dec 17;528(7582):418-21. doi: 10.1038/nature15540. Epub 2015 Nov 11.

27.

Transcription factor trapping by RNA in gene regulatory elements.

Sigova AA, Abraham BJ, Ji X, Molinie B, Hannett NM, Guo YE, Jangi M, Giallourakis CC, Sharp PA, Young RA.

Science. 2015 Nov 20;350(6263):978-81. doi: 10.1126/science.aad3346. Epub 2015 Oct 29.

28.

CDK7-dependent transcriptional addiction in triple-negative breast cancer.

Wang Y, Zhang T, Kwiatkowski N, Abraham BJ, Lee TI, Xie S, Yuzugullu H, Von T, Li H, Lin Z, Stover DG, Lim E, Wang ZC, Iglehart JD, Young RA, Gray NS, Zhao JJ.

Cell. 2015 Sep 24;163(1):174-86. doi: 10.1016/j.cell.2015.08.063.

29.

Convergence of developmental and oncogenic signaling pathways at transcriptional super-enhancers.

Hnisz D, Schuijers J, Lin CY, Weintraub AS, Abraham BJ, Lee TI, Bradner JE, Young RA.

Mol Cell. 2015 Apr 16;58(2):362-70. doi: 10.1016/j.molcel.2015.02.014. Epub 2015 Mar 19.

30.

Chromatin proteomic profiling reveals novel proteins associated with histone-marked genomic regions.

Ji X, Dadon DB, Abraham BJ, Lee TI, Jaenisch R, Bradner JE, Young RA.

Proc Natl Acad Sci U S A. 2015 Mar 24;112(12):3841-6. doi: 10.1073/pnas.1502971112. Epub 2015 Mar 9.

31.

Targeting transcriptional addictions in small cell lung cancer with a covalent CDK7 inhibitor.

Christensen CL, Kwiatkowski N, Abraham BJ, Carretero J, Al-Shahrour F, Zhang T, Chipumuro E, Herter-Sprie GS, Akbay EA, Altabef A, Zhang J, Shimamura T, Capelletti M, Reibel JB, Cavanaugh JD, Gao P, Liu Y, Michaelsen SR, Poulsen HS, Aref AR, Barbie DA, Bradner JE, George RE, Gray NS, Young RA, Wong KK.

Cancer Cell. 2014 Dec 8;26(6):909-922. doi: 10.1016/j.ccell.2014.10.019. Erratum in: Cancer Cell. 2015 Jan 12;27(1):149.

32.

CDK7 inhibition suppresses super-enhancer-linked oncogenic transcription in MYCN-driven cancer.

Chipumuro E, Marco E, Christensen CL, Kwiatkowski N, Zhang T, Hatheway CM, Abraham BJ, Sharma B, Yeung C, Altabef A, Perez-Atayde A, Wong KK, Yuan GC, Gray NS, Young RA, George RE.

Cell. 2014 Nov 20;159(5):1126-1139. doi: 10.1016/j.cell.2014.10.024. Epub 2014 Nov 6.

33.

Popliteal artery thrombosis following total knee arthroplasty managed successfully with percutaneous intervention.

Mathew A, Abraham BJ, Fischer L, Punnoose E.

BMJ Case Rep. 2014 Nov 20;2014. pii: bcr2014206936. doi: 10.1136/bcr-2014-206936.

34.

Oncogene regulation. An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element.

Mansour MR, Abraham BJ, Anders L, Berezovskaya A, Gutierrez A, Durbin AD, Etchin J, Lawton L, Sallan SE, Silverman LB, Loh ML, Hunger SP, Sanda T, Young RA, Look AT.

Science. 2014 Dec 12;346(6215):1373-7. doi: 10.1126/science.1259037. Epub 2014 Nov 13.

35.

Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes.

Dowen JM, Fan ZP, Hnisz D, Ren G, Abraham BJ, Zhang LN, Weintraub AS, Schujiers J, Lee TI, Zhao K, Young RA.

Cell. 2014 Oct 9;159(2):374-387. doi: 10.1016/j.cell.2014.09.030.

36.

The developmental potential of iPSCs is greatly influenced by reprogramming factor selection.

Buganim Y, Markoulaki S, van Wietmarschen N, Hoke H, Wu T, Ganz K, Akhtar-Zaidi B, He Y, Abraham BJ, Porubsky D, Kulenkampff E, Faddah DA, Shi L, Gao Q, Sarkar S, Cohen M, Goldmann J, Nery JR, Schultz MD, Ecker JR, Xiao A, Young RA, Lansdorp PM, Jaenisch R.

Cell Stem Cell. 2014 Sep 4;15(3):295-309. doi: 10.1016/j.stem.2014.07.003.

37.

Targeting transcription regulation in cancer with a covalent CDK7 inhibitor.

Kwiatkowski N, Zhang T, Rahl PB, Abraham BJ, Reddy J, Ficarro SB, Dastur A, Amzallag A, Ramaswamy S, Tesar B, Jenkins CE, Hannett NM, McMillin D, Sanda T, Sim T, Kim ND, Look T, Mitsiades CS, Weng AP, Brown JR, Benes CH, Marto JA, Young RA, Gray NS.

Nature. 2014 Jul 31;511(7511):616-20. doi: 10.1038/nature13393. Epub 2014 Jun 22.

38.

Novel mechanism of positive versus negative regulation by thyroid hormone receptor β1 (TRβ1) identified by genome-wide profiling of binding sites in mouse liver.

Ramadoss P, Abraham BJ, Tsai L, Zhou Y, Costa-e-Sousa RH, Ye F, Bilban M, Zhao K, Hollenberg AN.

J Biol Chem. 2014 Jan 17;289(3):1313-28. doi: 10.1074/jbc.M113.521450. Epub 2013 Nov 27.

39.

Multiple structural maintenance of chromosome complexes at transcriptional regulatory elements.

Dowen JM, Bilodeau S, Orlando DA, Hübner MR, Abraham BJ, Spector DL, Young RA.

Stem Cell Reports. 2013 Oct 24;1(5):371-8. doi: 10.1016/j.stemcr.2013.09.002. eCollection 2013.

40.

Super-enhancers in the control of cell identity and disease.

Hnisz D, Abraham BJ, Lee TI, Lau A, Saint-André V, Sigova AA, Hoke HA, Young RA.

Cell. 2013 Nov 7;155(4):934-47. doi: 10.1016/j.cell.2013.09.053. Epub 2013 Oct 10.

41.

Master transcription factors and mediator establish super-enhancers at key cell identity genes.

Whyte WA, Orlando DA, Hnisz D, Abraham BJ, Lin CY, Kagey MH, Rahl PB, Lee TI, Young RA.

Cell. 2013 Apr 11;153(2):307-19. doi: 10.1016/j.cell.2013.03.035.

42.

Dynamic regulation of epigenomic landscapes during hematopoiesis.

Abraham BJ, Cui K, Tang Q, Zhao K.

BMC Genomics. 2013 Mar 19;14:193. doi: 10.1186/1471-2164-14-193.

43.

Genome-wide analyses of transcription factor GATA3-mediated gene regulation in distinct T cell types.

Wei G, Abraham BJ, Yagi R, Jothi R, Cui K, Sharma S, Narlikar L, Northrup DL, Tang Q, Paul WE, Zhu J, Zhao K.

Immunity. 2011 Aug 26;35(2):299-311. doi: 10.1016/j.immuni.2011.08.007.

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