Whole-genome noncoding sequence analysis in T-cell acute lymphoblastic leukemia identifies oncogene enhancer mutations

Blood

Volumn 129, Issue 24, 2017, Pages 3264-3268

  Hu, Shaoyan ^a   Qian, Maoxiang ^b   Zhang, Hui ^b,c   Guo, Yu ^d   Yang, Jin ^a   Zhao, Xujie ^b   He, Hailong ^a   Lu, Jun ^a   Pan, Jian ^a   Chang, Meimei ^d   Du, Guoqing ^b   Lin, Ting Nien ^b   Kham, Shirley Kow Yin ^e   Quah, Thuan Chong ^e,f   Ariffin, Hany ^g   Tan, Ah Moy ^h   Cheng, Yong ^b   Li, Chunliang ^b   Yeoh, Allen Eng Juh ^e,f   Pui, Ching Hon ^b   Skanderup, Anders Jacobsen ^d   Yang, Jun J ^b   more..

^a CHILDREN S HOSPITAL OF SOOCHOW UNIVERSITY   (China)

^b ST JUDE CHILDREN S RESEARCH HOSPITAL   (United States)

^c GUANGZHOU MEDICAL UNIVERSITY   (China)

^d GENOME INSTITUTE OF SINGAPORE   (Singapore)

^e National University Health Systems   (Singapore)

^f NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^g UNIVERSITY MALAYA MEDICAL CENTRE   (Malaysia)

^h KK WOMEN'S AND CHILDREN'S HOSPITAL   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

NOTCH1 RECEPTOR; PHOSPHATIDYLINOSITOL 3,4,5 TRISPHOSPHATE 3 PHOSPHATASE; PROTEIN MYB; TRANSCRIPTION FACTOR GATA 3; TRANSCRIPTION FACTOR RUNX1; TRANSCRIPTION FACTOR TAL1;

ACUTE LYMPHOBLASTIC LEUKEMIA; CD3+ T LYMPHOCYTE; CD4+ T LYMPHOCYTE; CD8+ T LYMPHOCYTE; CHINESE; CLINICAL ARTICLE; FBXW7 GENE; GENE; GENE EXPRESSION; GENE MUTATION; GENETIC ASSOCIATION; HUMAN; LETTER; LMO1 GENE; LMO2 GENE; ONCOGENE; POINT MUTATION; PRIORITY JOURNAL; PROMOTER REGION; TRANSCRIPTION INITIATION SITE; USP7 GENE; WHOLE GENOME SEQUENCING; ENHANCER REGION; FEMALE; GENE LOCUS; GENETICS; GENOME-WIDE ASSOCIATION STUDY; MALE; MUTATION;

ENHANCER ELEMENTS, GENETIC; FEMALE; GENETIC LOCI; GENOME-WIDE ASSOCIATION STUDY; HUMANS; MALE; MUTATION; PRECURSOR T-CELL LYMPHOBLASTIC LEUKEMIA-LYMPHOMA;

EID: 85021068404     PISSN: 00064971     EISSN: 15280020     Source Type: Journal    
DOI: 10.1182/blood-2017-03-771162     Document Type: Letter

References (24)

1. Roberts KG, Mullighan CG. Genomics in acute lymphoblastic leukaemia: insights and treatment implications. Nat Rev Clin Oncol. 2015;12(6):344-357.
2. Pui CH, Yang JJ, Hunger SP, et al. Childhood acute lymphoblastic leukemia: progress through collaboration. J Clin Oncol. 2015;33(27):2938-2948.
3. Inaba H, Greaves M, Mullighan CG. Acute lymphoblastic leukaemia. Lancet. 2013;381(9881):1943-1955.
4. Belver L, Ferrando A. The genetics and mechanisms of T cell acute lymphoblastic leukaemia. Nat Rev Cancer. 2016;16(8):494-507.
5. Aifantis I, Raetz E, Buonamici S. Molecular pathogenesis of T-cell leukaemia and lymphoma. Nat Rev Immunol. 2008;8(5):380-390.
6. Mansour MR, Abraham BJ, Anders L, et al. Oncogene regulation. An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element. Science. 2014;346(6215):1373-1377.
7. Mullighan CG, Collins-Underwood JR, Phillips LA, et al. Rearrangement of CRLF2 in B-progenitor-and Down syndrome-associated acute lymphoblastic leukemia. Nat Genet. 2009;41(11):1243-1246.
8. Consortium EP; ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012;489(7414):57-74.
9. Bauer DE, Kamran SC, Lessard S, et al. An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level. Science. 2013; 342(6155):253-257.
10. Claussnitzer M, Dankel SN, Kim KH, et al. FTO obesity variant circuitry and adipocyte browning in humans. N Engl J Med. 2015;373(10):895-907.
11. Oldridge DA, Wood AC, Weichert-Leahey N, et al. Genetic predisposition to neuroblastoma mediated by a LMO1 super-enhancer polymorphism. Nature. 2015;528(7582):418-421.
12. Ferrando AA. The role of NOTCH1 signaling in T-ALL. Hematology (Am Soc Hematol Educ Program). 2009;353-361.
13. Navarro JM, Touzart A, Pradel LC, et al. Site-and allele-specific polycomb dysregulation in T-cell leukaemia. Nat Commun. 2015;6:6094.
14. Sanda T, Lawton LN, Barrasa MI, et al. Core transcriptional regulatory circuit controlled by the TAL1 complex in human T cell acute lymphoblastic leukemia. Cancer Cell. 2012;22(2):209-221.
15. Fan X, Zhang X, Wu X, et al. Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos. Genome Biol. 2015;16:148.
16. Larson RC, Lavenir I, Larson TA, et al. Protein dimerization between Lmo2 (Rbtn2) and Tal1 alters thymocyte development and potentiates T cell tumorigenesis in transgenic mice. EMBO J. 1996;15(5):1021-1027.
17. Zhang JA, Mortazavi A, Williams BA, Wold BJ, Rothenberg EV. Dynamic transformations of genome-wide epigenetic marking and transcriptional control establish T cell identity. Cell. 2012;149(2):467-482.
18. Draheim KM, Hermance N, Yang Y, Arous E, Calvo J, Kelliher MA. A DNAbinding mutant of TAL1 cooperates with LMO2 to cause T cell leukemia in mice. Oncogene. 2011;30(10):1252-1260.
19. Nam CH, Rabbitts TH. The role of LMO2 in development and in T cell leukemia after chromosomal translocation or retroviral insertion. Mol Ther. 2006;13(1): 15-25.
20. Gerby B, Tremblay CS, Tremblay M, et al. SCL, LMO1 and Notch1 reprogram thymocytes into self-renewing cells. PLoS Genet. 2014;10(12):e1004768.
21. Tremblay M, Tremblay CS, Herblot S, et al. Modeling T-cell acute lymphoblastic leukemia induced by the SCL and LMO1 oncogenes. Genes Dev. 2010;24(11): 1093-1105.
22. Tamborero D, Gonzalez-Perez A, Perez-Llamas C, et al. Comprehensive identification of mutational cancer driver genes across 12 tumor types. Sci Rep. 2013;3:2650.
23. Rahman S, Magnussen M, León TE, et al. Activation of the LMO2 oncogene through a somatically acquired neomorphic promoter in T-cell acute lymphoblastic leukemia [published online ahead of print 7 March 2017]. Blood. doi:10.1182/blood-2016-09-742148.
24. Abraham BJ, Hnisz D, Weintraub AS, et al. Small genomic insertions form enhancers that misregulate oncogenes. Nat Commun. 2017;8:14385.