Promoter DNA Methylation Pattern Identifies Prognostic Subgroups in Childhood T-Cell Acute Lymphoblastic Leukemia

PLoS ONE

Volumn 8, Issue 6, 2013, Pages

  Borssén, Magnus ^a   Palmqvist, Lars ^b   Karrman, Kristina ^c   Abrahamsson, Jonas ^b   Behrendtz, Mikael ^d   Heldrup, Jesper ^c   Forestier, Erik ^a   Roos, Göran ^a   Degerman, Sofie ^a  

^a UMEÅ UNIVERSITY   (Sweden)

^b SAHLGRENSKA UNIVERSITY HOSPITAL   (Sweden)

^c LUND UNIVERSITY HOSPITAL   (Sweden)

^d LINKÖPING UNIVERSITY HOSPITAL   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

LIGAND; POLYCOMB GROUP PROTEIN; TRANSCRIPTION FACTOR; TUMOR PROTEIN;

ACUTE LYMPHOBLASTIC LEUKEMIA; ADOLESCENT; AGE; ARTICLE; CANCER PROGNOSIS; CANCER SURVIVAL; CHILD; CHILDHOOD LEUKEMIA; CONTROLLED STUDY; CPG ISLAND; DNA METHYLATION; EVENT FREE SURVIVAL; GENDER; GENE TARGETING; HUMAN; INFANT; LEUKOCYTE COUNT; NUCLEOTIDE SEQUENCE; OUTCOME ASSESSMENT; PHENOTYPE; PRESCHOOL CHILD; SCHOOL CHILD; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC ASSOCIATION; GENETICS; HUMAN GENOME; MALE; METABOLISM; MORTALITY; MULTIVARIATE ANALYSIS; PRECURSOR T-CELL LYMPHOBLASTIC LEUKEMIA-LYMPHOMA; PROGNOSIS; PROMOTER REGION; SURVIVAL;

ADOLESCENT; CHILD; CHILD, PRESCHOOL; CPG ISLANDS; DNA METHYLATION; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, LEUKEMIC; GENOME, HUMAN; GENOME-WIDE ASSOCIATION STUDY; HUMANS; INFANT; MALE; MULTIVARIATE ANALYSIS; NEOPLASM PROTEINS; PHENOTYPE; PRECURSOR T-CELL LYMPHOBLASTIC LEUKEMIA-LYMPHOMA; PROGNOSIS; PROMOTER REGIONS, GENETIC; SURVIVAL ANALYSIS;

EID: 84878807245     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0065373     Document Type: Article

References (48)

1. Aifantis I, Raetz E, Buonamici S, (2008) Molecular pathogenesis of T-cell leukaemia and lymphoma. Nat Rev Immunol 8: 380-390.
2. Karrman K, Forestier E, Heyman M, Andersen MK, Autio K, et al. (2009) Clinical and cytogenetic features of a population-based consecutive series of 285 pediatric T-cell acute lymphoblastic leukemias: rare T-cell receptor gene rearrangements are associated with poor outcome. Genes Chromosomes Cancer 48: 795-805.
3. Weng AP, Ferrando AA, Lee W, Morris JPt, Silverman LB, et al. (2004) Activating mutations of NOTCH1 in human T cell acute lymphoblastic leukemia. Science 306: 269-271.
4. Ma J, Wu M, (2012) The indicative effect of Notch1 expression for the prognosis of T-cell acute lymphocytic leukemia: a systematic review. Mol Biol Rep 39: 6095-6100.
5. Jones PA, Baylin SB, (2007) The epigenomics of cancer. Cell 128: 683-692.
6. Esteller M, (2008) Epigenetics in cancer. N Engl J Med 358: 1148-1159.
7. Ang PW, Loh M, Liem N, Lim PL, Grieu F, et al. (2010) Comprehensive profiling of DNA methylation in colorectal cancer reveals subgroups with distinct clinicopathological and molecular features. BMC Cancer 10: 227.
8. Noushmehr H, Weisenberger DJ, Diefes K, Phillips HS, Pujara K, et al. (2010) Identification of a CpG island methylator phenotype that defines a distinct subgroup of glioma. Cancer Cell 17: 510-522.
9. Van der Auwera I, Yu W, Suo L, Van Neste L, van Dam P, et al. (2011) Array-based DNA methylation profiling for breast cancer subtype discrimination. PLoS One 5: e12616.
10. Shen L, Kantarjian H, Guo Y, Lin E, Shan J, et al. (2010) DNA methylation predicts survival and response to therapy in patients with myelodysplastic syndromes. J Clin Oncol 28: 605-613.
11. Quintas-Cardama A, Santos FP, Garcia-Manero G, (2010) Therapy with azanucleosides for myelodysplastic syndromes. Nat Rev Clin Oncol 7: 433-444.
12. Roman-Gomez J, Jimenez-Velasco A, Agirre X, Castillejo JA, Navarro G, et al. (2006) Promoter hypermethylation and global hypomethylation are independent epigenetic events in lymphoid leukemogenesis with opposing effects on clinical outcome. Leukemia 20: 1445-1448.
13. Milani L, Lundmark A, Kiialainen A, Nordlund J, Flaegstad T, et al. (2010) DNA methylation for subtype classification and prediction of treatment outcome in patients with childhood acute lymphoblastic leukemia. Blood 115: 1214-1225.
14. Deneberg S, Guardiola P, Lennartsson A, Qu Y, Gaidzik V, et al. (2011) Prognostic DNA methylation patterns in cytogenetically normal acute myeloid leukemia are predefined by stem cell chromatin marks. Blood 118: 5573-5582.
15. Gustafsson G, Schmiegelow K, Forestier E, Clausen N, Glomstein A, et al. (2000) Improving outcome through two decades in childhood ALL in the Nordic countries: the impact of high-dose methotrexate in the reduction of CNS irradiation. Nordic Society of Pediatric Haematology and Oncology (NOPHO). Leukemia 14: 2267-2275.
16. Schmiegelow K, Forestier E, Hellebostad M, Heyman M, Kristinsson J, et al. (2010) Long-term results of NOPHO ALL-92 and ALL-2000 studies of childhood acute lymphoblastic leukemia. Leukemia 24: 345-354.
17. Degerman S, Siwicki JK, Osterman P, Lafferty-Whyte K, Nicol Keith W, et al. (2010) Telomerase upregulation is a postcrisis event during senescence bypass and immortalization of two Nijmegen breakage syndrome T cell cultures. Aging Cell.
18. Siwicki JK, Hedberg Y, Nowak R, Loden M, Zhao J, et al. (2000) Long-term cultured IL-2-dependent T cell lines demonstrate p16(INK4a) overexpression, normal pRb/p53, and upregulation of cyclins E or D2. Experimental Gerontology 35: 375-388.
19. Weisenberger DJ, Trinh BN, Campan M, Sharma S, Long TI, et al. (2008) DNA methylation analysis by digital bisulfite genomic sequencing and digital MethyLight. Nucleic Acids Res 36: 4689-4698.
20. Weisenberger DJ, Campan M, Long TI, Kim M, Woods C, et al. (2005) Analysis of repetitive element DNA methylation by MethyLight. Nucleic Acids Res 33: 6823-6836.
21. Bibikova M, Le J, Barnes B, et al. (2009) Genome-wide DNA methylation profiling using infinium assay. Epigenomics 1: 177-200.
22. Takai D, Jones PA, (2002) Comprehensive analysis of CpG islands in human chromosomes 21 and 22. Proc Natl Acad Sci U S A 99: 3740-3745.
23. Huang da W, Sherman BT, Lempicki RA, (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4: 44-57.
24. Bracken AP, Dietrich N, Pasini D, Hansen KH, Helin K, (2006) Genome-wide mapping of Polycomb target genes unravels their roles in cell fate transitions. Genes Dev 20: 1123-1136.
25. Lee TI, Jenner RG, Boyer LA, Guenther MG, Levine SS, et al. (2006) Control of developmental regulators by Polycomb in human embryonic stem cells. Cell 125: 301-313.
26. Bracken AP, Helin K, (2009) Polycomb group proteins: navigators of lineage pathways led astray in cancer. Nat Rev Cancer 9: 773-784.
27. Widschwendter M, Fiegl H, Egle D, Mueller-Holzner E, Spizzo G, et al. (2007) Epigenetic stem cell signature in cancer. Nat Genet 39: 157-158.
28. Gutierrez A, Dahlberg SE, Neuberg DS, Zhang J, Grebliunaite R, et al. (2010) Absence of biallelic TCRgamma deletion predicts early treatment failure in pediatric T-cell acute lymphoblastic leukemia. J Clin Oncol 28: 3816-3823.
29. Gutierrez MI, Siraj AK, Bhargava M, Ozbek U, Banavali S, et al. (2003) Concurrent methylation of multiple genes in childhood ALL: Correlation with phenotype and molecular subgroup. Leukemia 17: 1845-1850.
30. Kraszewska MD, Dawidowska M, Larmonie NS, Kosmalska M, Sedek L, et al. (2011) DNA methylation pattern is altered in childhood T-cell acute lymphoblastic leukemia patients as compared with normal thymic subsets: insights into CpG island methylator phenotype in T-ALL. Leukemia.
31. Milani L, Lundmark A, Nordlund J, Kiialainen A, Flaegstad T, et al. (2009) Allele-specific gene expression patterns in primary leukemic cells reveal regulation of gene expression by CpG site methylation. Genome Res 19: 1-11.
32. Bibikova M, Barnes B, Tsan C, Ho V, Klotzle B, et al. (2011) High density DNA methylation array with single CpG site resolution. Genomics.
33. Bibikova M, Lin Z, Zhou L, Chudin E, Garcia EW, et al. (2006) High-throughput DNA methylation profiling using universal bead arrays. Genome Res 16: 383-393.
34. Herman JG, Graff JR, Myohanen S, Nelkin BD, Baylin SB, (1996) Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands. Proc Natl Acad Sci U S A 93: 9821-9826.
35. Sandoval J, Heyn H, Mendez-Gonzalez J, Gomez A, Moran S, et al. (2013) Genome-wide DNA methylation profiling predicts relapse in childhood B-cell acute lymphoblastic leukaemia. Br J Haematol 160: 406-409.
36. Ntziachristos P, Tsirigos A, Van Vlierberghe P, Nedjic J, Trimarchi T, et al. (2012) Genetic inactivation of the polycomb repressive complex 2 in T cell acute lymphoblastic leukemia. Nat Med 18: 298-301.
37. Martin-Perez D, Piris MA, Sanchez-Beato M, (2010) Polycomb proteins in hematologic malignancies. Blood 116: 5465-5475.
38. Zhang J, Ding L, Holmfeldt L, Wu G, Heatley SL, et al. (2012) The genetic basis of early T-cell precursor acute lymphoblastic leukaemia. Nature 481: 157-163.
39. Simon C, Chagraoui J, Krosl J, Gendron P, Wilhelm B, et al. (2012) A key role for EZH2 and associated genes in mouse and human adult T-cell acute leukemia. Genes Dev.
40. Costello JF, Fruhwald MC, Smiraglia DJ, Rush LJ, Robertson GP, et al. (2000) Aberrant CpG-island methylation has non-random and tumour-type-specific patterns. Nat Genet 24: 132-138.
41. Martin-Subero JI, Ammerpohl O, Bibikova M, Wickham-Garcia E, Agirre X, et al. (2009) A comprehensive microarray-based DNA methylation study of 367 hematological neoplasms. PLoS One 4: e6986.
42. Abecassis I, Maes J, Carrier JL, Hillion J, Goodhardt M, et al. (2008) Re-expression of DNA methylation-silenced CD44 gene in a resistant NB4 cell line: rescue of CD44-dependent cell death by cAMP. Leukemia 22: 511-520.
43. Lucchi S, Calebiro D, de Filippis T, Grassi ES, Borghi MO, et al. (2011) 8-Chloro-cyclic AMP and protein kinase A I-selective cyclic AMP analogs inhibit cancer cell growth through different mechanisms. PLoS One 6: e20785.
44. Rajendra Prasad VV, Peters GJ, Lemos C, Kathmann I, Mayur YC, (2011) Cytotoxicity studies of some novel fluoro acridone derivatives against sensitive and resistant cancer cell lines and their mechanistic studies. Eur J Pharm Sci 43: 217-224.
45. Jung S, Kim S, Gale M, Cherni I, Fonseca R, et al. (2012) DNA methylation in multiple myeloma is weakly associated with gene transcription. PLoS One 7: e52626.
46. Sanders YY, Ambalavanan N, Halloran B, Zhang X, Liu H, et al. (2012) Altered DNA methylation profile in idiopathic pulmonary fibrosis. Am J Respir Crit Care Med 186: 525-535.
47. van Eijk KR, de Jong S, Boks MP, Langeveld T, Colas F, et al. (2012) Genetic analysis of DNA methylation and gene expression levels in whole blood of healthy human subjects. BMC Genomics 13: 636.
48. Coustan-Smith E, Mullighan CG, Onciu M, Behm FG, Raimondi SC, et al. (2009) Early T-cell precursor leukaemia: a subtype of very high-risk acute lymphoblastic leukaemia. Lancet Oncol 10: 147-156.