Integrated Transcript and Genome Analyses Reveal NKX2-1 and MEF2C as Potential Oncogenes in T Cell Acute Lymphoblastic Leukemia

Cancer Cell

Volumn 19, Issue 4, 2011, Pages 484-497

  Homminga, Irene ^a   Pieters, Rob ^a   Langerak, Anton W ^b   de Rooi, Johan J ^b   Stubbs, Andrew ^b   Verstegen, Monique ^a   Vuerhard, Maartje ^a   Buijs Gladdines, Jessica ^a   Kooi, Clarissa ^a   Klous, Petra ^b,c   van Vlierberghe, Pieter ^d   Ferrando, Adolfo A ^e   Cayuela, Jean Michel ^f   Verhaaf, Brenda ^b   Beverloo, H Berna ^b   Horstmann, Martin ^g,h,i   de Haas, Valerie ^j   Wiekmeijer, Anna Sophia ^k   Pike Overzet, Karin ^k   Staal, Frank J T ^k   de Laat, Wouter ^b,c   Soulier, Jean ^f   Sigaux, Francois ^f   Meijerink, Jules P P ^a   more..

^a SOPHIA CHILDREN S HOSPITAL   (Netherlands)

^b ERASMUS MEDICAL CENTER   (Netherlands)

^c UNIVERSITY MEDICAL CENTER UTRECHT   (Netherlands)

^d GHENT UNIVERSITY HOSPITAL   (Belgium)

^e Och Spine at New York Presbyterian Hospitals   (United States)

^f Institut Universitaire d'Hématologie   (France)

^g Research Institute Children's Cancer Center   (Germany)

^h UNIVERSITY MEDICAL CENTER HAMBURG EPPENDORF   (Germany)

ⁱ German Cooperative Study Group for Childhood Acute Lymphoblastic Leukemia (COALL)   (Germany)

^j Dutch Childhood Oncology Group   (Netherlands)

^k LEIDEN UNIVERSITY MEDICAL CENTER   (Netherlands)

more..

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR;

ACUTE LYMPHOBLASTIC LEUKEMIA; ADOLESCENT; ARTICLE; CHILD; FEMALE; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENE REARRANGEMENT; GENOME ANALYSIS; HUMAN; HUMAN TISSUE; MALE; MEF2C GENE; NKX2 1 GENE; NKX2 2 GENE; ONCOGENE; PRIORITY JOURNAL; TRANSCRIPTOMICS;

EID: 79953735093     PISSN: 15356108     EISSN: 18783686     Source Type: Journal    
DOI: 10.1016/j.ccr.2011.02.008     Document Type: Article

References (49)

1. Buijs A., van Rompaey L., Molijn A.C., Davis J.N., Vertegaal A.C., Potter M.D., Adams C., van Baal S., Zwarthoff E.C., Roussel M.F., Grosveld G.C. The MN1-TEL fusion protein, encoded by the translocation (12;22)(p13;q11) in myeloid leukemia, is a transcription factor with transforming activity. Mol. Cell. Biol. 2000, 20:9281-9293.
2. Chen S.L., Dowhan D.H., Hosking B.M., Muscat G.E. The steroid receptor coactivator, GRIP-1, is necessary for MEF-2C-dependent gene expression and skeletal muscle differentiation. Genes Dev. 2000, 14:1209-1228.
3. Clappier E., Cuccuini W., Kalota A., Crinquette A., Cayuela J.M., Dik W.A., Langerak A.W., Montpellier B., Nadel B., Walrafen P., et al. The C-MYB locus is involved in chromosomal translocation and genomic duplications in human T-cell acute leukemia (T-ALL), the translocation defining a new T-ALL subtype in very young children. Blood 2007, 110:1251-1261.
4. Coustan-Smith E., Mullighan C.G., Onciu M., Behm F.G., Raimondi S.C., Pei D., Cheng C., Su X., Rubnitz J.E., Basso G., et al. Early T-cell precursor leukaemia: a subtype of very high-risk acute lymphoblastic leukaemia. Lancet Oncol. 2009, 10:147-156.
5. Dik W.A., Pike-Overzet K., Weerkamp F., de Ridder D., de Haas E.F., Baert M.R., van der Spek P., Koster E.E., Reinders M.J., van Dongen J.J., et al. New insights on human T cell development by quantitative T cell receptor gene rearrangement studies and gene expression profiling. J. Exp. Med. 2005, 201:1715-1723.
6. Du Y., Spence S.E., Jenkins N.A., Copeland N.G. Cooperating cancer-gene identification through oncogenic-retrovirus-induced insertional mutagenesis. Blood 2005, 106:2498-2505.
7. Ferrando A.A., Neuberg D.S., Staunton J., Loh M.L., Huard C., Raimondi S.C., Behm F.G., Pui C.H., Downing J.R., Gilliland D.G., et al. Gene expression signatures define novel oncogenic pathways in T cell acute lymphoblastic leukemia. Cancer Cell 2002, 1:75-87.
8. Grosveld G.C. MN1, a novel player in human AML. Blood Cells Mol. Dis. 2007, 39:336-339.
9. Grounds M.D. Towards understanding skeletal muscle regeneration. Pathol. Res. Pract. 1991, 187:1-22.
10. Hebert J., Cayuela J.M., Berkeley J., Sigaux F. Candidate tumor-suppressor genes MTS1 (p16INK4A) and MTS2 (p15INK4B) display frequent homozygous deletions in primary cells from T- but not from B-cell lineage acute lymphoblastic leukemias. Blood 1994, 84:4038-4044.
11. Hoshida Y., Brunet J.P., Tamayo P., Golub T.R., Mesirov J.P. Subclass mapping: identifying common subtypes in independent disease data sets. PLoS ONE 2007, 2:e1195.
12. Huber W., von Heydebreck A., Sultmann H., Poustka A., Vingron M. Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics 2002, 18(Suppl 1):S96-S104.
13. Irizarry R.A., Hobbs B., Collin F., Beazer-Barclay Y.D., Antonellis K.J., Scherf U., Speed T.P. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 2003, 4:249-264.
14. Johnson W.E., Li C., Rabinovic A. Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 2007, 8:118-127.
15. Katsumata M., Siegel R.M., Louie D.C., Miyashita T., Tsujimoto Y., Nowell P.C., Greene M.I., Reed J.C. Differential effects of Bcl-2 on T and B cells in transgenic mice. Proc. Natl. Acad. Sci. USA 1992, 89:11376-11380.
16. Kawamura M., Ohnishi H., Guo S.X., Sheng X.M., Minegishi M., Hanada R., Horibe K., Hongo T., Kaneko Y., Bessho F., et al. Alterations of the p53, p21, p16, p15 and RAS genes in childhood T-cell acute lymphoblastic leukemia. Leuk. Res. 1999, 23:115-126.
17. Krivtsov A.V., Twomey D., Feng Z., Stubbs M.C., Wang Y., Faber J., Levine J.E., Wang J., Hahn W.C., Gilliland D.G., et al. Transformation from committed progenitor to leukaemia stem cell initiated by MLL-AF9. Nature 2006, 442:818-822.
18. Kusy S., Gerby B., Goardon N., Gault N., Ferri F., Gerard D., Armstrong F., Ballerini P., Cayuela J.M., Baruchel A., et al. NKX3.1 is a direct TAL1 target gene that mediates proliferation of TAL1-expressing human T cell acute lymphoblastic leukemia. J. Exp. Med. 2010, 207:2141-2156.
19. Li C., Wong W.H. Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc. Natl. Acad. Sci. USA 2001, 98:31-36.
20. Lottaz C., Yang X., Scheid S., Spang R. OrderedList-a bioconductor package for detecting similarity in ordered gene lists. Bioinformatics 2006, 22. 2315-2136.
21. Nagel S., Kaufmann M., Drexler H.G., MacLeod R.A. The cardiac homeobox gene NKX2-5 is deregulated by juxtaposition with BCL11B in pediatric T-ALL cell lines via a novel t(5;14)(q35.1;q32.2). Cancer Res. 2003, 63:5329-5334.
22. Nagel S., Meyer C., Quentmeier H., Kaufmann M., Drexler H.G., MacLeod R.A. MEF2C is activated by multiple mechanisms in a subset of T-acute lymphoblastic leukemia cell lines. Leukemia 2008, 22:600-607.
23. Nguyen-Khac F., Barin C., Chapiro E., Macintyre E.A., Romana S., Bernard O.A. Cyclin D3 deregulation by juxtaposition with IGH locus in a t(6;14)(p21;q32)-positive T-cell acute lymphoblastic leukemia. Leuk. Res. 2010, 34:e13-e14.
24. Palomero T., Lim W.K., Odom D.T., Sulis M.L., Real P.J., Margolin A., Barnes K.C., O'Neil J., Neuberg D., Weng A.P., et al. NOTCH1 directly regulates c-MYC and activates a feed-forward-loop transcriptional network promoting leukemic cell growth. Proc. Natl. Acad. Sci. USA 2006, 103:18261-18266.
25. Pieters R., Carroll W.L. Biology and treatment of acute lymphoblastic leukemia. Pediatr. Clin. North Am. 2008, 55:1-20.
26. Prima V., Hunger S.P. Cooperative transformation by MEF2D/DAZAP1 and DAZAP1/MEF2D fusion proteins generated by the variant t(1;19) in acute lymphoblastic leukemia. Leukemia 2007, 21:2470-2475.
27. Przybylski G.K., Dik W.A., Grabarczyk P., Wanzeck J., Chudobska P., Jankowski K., von Bergh A., van Dongen J.J., Schmidt C.A., Langerak A.W. The effect of a novel recombination between the homeobox gene NKX2-5 and the TRD locus in T-cell acute lymphoblastic leukemia on activation of the NKX2-5 gene. Haematologica 2006, 91:317-321.
28. Pui C.H., Evans W.E. Treatment of acute lymphoblastic leukemia. N. Engl. J. Med. 2006, 354:166-178.
29. Rothenberg E.V. Regulatory factors for initial T lymphocyte lineage specification. Curr. Opin. Hematol. 2007, 14:322-329.
30. Schwieger M., Schüler A., Forster M., Engelmann A., Arnold M.A., Delwel R., Valk P.J., Löhler J., Slany R.K., Olson E.N., Stocking C. Homing and invasiveness of MLL/ENL leukemic cells is regulated by MEF2C. Blood 2009, 114:2476-2488.
31. Simonis M., Klous P., Splinter E., Moshkin Y., Willemsen R., de Wit E., van Steensel B., de Laat W. Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat. Genet. 2006, 38:1348-1354.
32. Simonis M., Klous P., Homminga I., Galjaard R.J., Rijkers E.J., Grosveld F., Meijerink J.P.P., de Laat W. High-resolution identification of balanced and complex chromosomal rearrangements by 4C technology. Nat. Methods 2009, 6:837-842.
33. Smith R., Owen L.A., Trem D.J., Wong J.S., Whangbo J.S., Golub T.R., Lessnick S.L. Expression profiling of EWS/FLI identifies NKX2.2 as a critical target gene in Ewing's sarcoma. Cancer Cell 2006, 9:405-416.
34. Soulier J., Clappier E., Cayuela J.M., Regnault A., Garcia-Peydro M., Dombret H., Baruchel A., Toribio M.L., Sigaux F. HOXA genes are included in genetic and biologic networks defining human acute T-cell leukemia (T-ALL). Blood 2005, 106:274-286.
35. Stehling-Sun S., Dade J., Nutt S.L., DeKoter R.P., Camargo F.D. Regulation of lymphoid versus myeloid fate 'choice' by the transcription factor Mef2c. Nat. Immunol. 2009, 10:289-296.
36. Strasser A., Harris A.W., Cory S. bcl-2 transgene inhibits T cell death and perturbs thymic self-censorship. Cell 1991, 67:889-899.
37. Strehl S., Nebral K., Konig M., Harbott J., Strobl H., Ratei R., Struski S., Bielorai B., Lessard M., Zimmermann M., et al. ETV6-NCOA2: a novel fusion gene in acute leukemia associated with coexpression of T-lymphoid and myeloid markers and frequent NOTCH1 mutations. Clin. Cancer Res. 2008, 14:977-983.
38. Tibshirani R., Hastie T., Narasimhan B., Chu G. Diagnosis of multiple cancer types by shrunken centroids of gene expression. Proc. Natl. Acad. Sci. USA 2002, 99:6567-6572.
39. Tomlins S.A., Rhodes D.R., Perner S., Dhanasekaran S.M., Mehra R., Sun X.W., Varambally S., Cao X., Tchinda J., Kuefer R., et al. Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science 2005, 310:644-648.
40. Tusher V.G., Tibshirani R., Chu G. Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl. Acad. Sci. USA 2001, 98:5116-5121.
41. van Grotel M., Meijerink J.P., Beverloo H.B., Langerak A.W., Buys-Gladdines J.G., Schneider P., Poulsen T.S., den Boer M.L., Horstmann M., Kamps W.A., et al. The outcome of molecular-cytogenetic subgroups in pediatric T-cell acute lymphoblastic leukemia: a retrospective study of patients treated according to DCOG or COALL protocols. Haematologica 2006, 91:1212-1221.
42. Van Vlierberghe P., van Grotel M., Beverloo H.B., Lee C., Helgason T., Buijs-Gladdines J., Passier M., van Wering E.R., Veerman A.J., Kamps W.A., et al. The cryptic chromosomal deletion, del(11)(p12p13), as a new activation mechanism of LMO2 in pediatric T-cell acute lymphoblastic leukemia. Blood 2006, 108:3520-3529.
43. Van Vlierberghe P., Pieters R., Beverloo H.B., Meijerink J.P. Molecular-genetic insights in paediatric T-cell acute lymphoblastic leukaemia. Br. J. Haematol. 2008, 143:153-168.
44. Van Vlierberghe P., van Grotel M., Tchinda J., Lee C., Beverloo H.B., van der Spek P.J., Stubbs A., Cools J., Nagata K., Fornerod M., et al. The recurrent SET-NUP214 fusion as a new HOXA activation mechanism in pediatric T-cell acute lymphoblastic leukemia. Blood 2008, 111:4668-4680.
45. Weir B.A., Woo M.S., Getz G., Perner S., Ding L., Beroukhim R., Lin W.M., Province M.A., Kraja A., Johnson L.A., et al. Characterizing the cancer genome in lung adenocarcinoma. Nature 2007, 450:893-898.
46. Weng A.P., Ferrando A.A., Lee W., Morris J.P., Silverman L.B., Sanchez-Irizarry C., Blacklow S.C., Look A.T., Aster J.C. Activating mutations of NOTCH1 in human T cell acute lymphoblastic leukemia. Science 2004, 306:269-271.
47. Weng A.P., Millholland J.M., Yashiro-Ohtani Y., Arcangeli M.L., Lau A., Wai C., Del Bianco C., Rodriguez C.G., Sai H., Tobias J., et al. c-Myc is an important direct target of Notch1 in T-cell acute lymphoblastic leukemia/lymphoma. Genes Dev. 2006, 20:2096-2109.
48. Wilker P.R., Kohyama M., Sandau M.M., Albring J.C., Nakagawa O., Schwarz J.J., Murphy K.M. Transcription factor Mef2c is required for B cell proliferation and survival after antigen receptor stimulation. Nat. Immunol. 2008, 9:603-612.
49. Zhu B., Gulick T. Phosphorylation and alternative pre-mRNA splicing converge to regulate myocyte enhancer factor 2C activity. Mol. Cell. Biol. 2004, 24:8264-8275.