DNA methylation for subtype classification and prediction of treatment outcome in patients with childhood acute lymphoblastic leukemia

Blood

Volumn 115, Issue 6, 2010, Pages 1214-1225

  Milani, Lili ^a   Lundmark, Anders ^a   Kiialainen, Anna ^a   Nordlund, Jessica ^a   Flaegstad, Trond ^b   Forestier, Erik ^c   Heyman, Mats ^d   Jonmundsson, Gudmundur ^e   Kanerva, Jukka ^f   Schmiegelow, Kjeld ^g   Söderhäll, Stefan ^d   Gustafsson, Mats G ^a   Lönnerholm, Gudmar ^h   Syvänen, Ann Christine ^a  

^a UPPSALA UNIVERSITY   (Sweden)

^b UNIVERSITY HOSPITAL OF NORTH NORWAY   (Norway)

^c UMEÅ UNIVERSITY   (Sweden)

^d KAROLINSKA UNIVERSITY HOSPITAL   (Sweden)

^e Department of Pediatrics ^*  (Iceland)

^f UNIVERSITY OF HELSINKI   (Finland)

^g UNIVERSITY OF COPENHAGEN   (Denmark)

^h UNIVERSITY CHILDREN S HOSPITAL   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

CD31 ANTIGEN; CHST13 PROTEIN; COBL PROTEIN; COL6A2 PROTEIN; CPVL PROTEIN; DFNB31 PROTEIN; EVC PROTEIN; EYA4 PROTEIN; FAM24B PROTEIN; FAT1 PROTEIN; FUCA2 PROTEIN; GBE1 PROTEIN; INADL PROTEIN; LRP1B PROTEIN; MYBPC2 PROTEIN; MYO3A PROTEIN; PCDHGA12 PROTEIN; PROTEIN; ROR1 PROTEIN; SDCBP2 PROTEIN; SEC31B PROTEIN; SPON2 PROTEIN; SYNM PROTEIN; TRANSCRIPTION FACTOR PAX8; UNCLASSIFIED DRUG; ZNF502 PROTEIN; DNA; TUMOR PROTEIN;

ACUTE LYMPHOBLASTIC LEUKEMIA; ADOLESCENT; ARTICLE; CANCER PATIENT; CELL LINEAGE; CHILD; CHILDHOOD LEUKEMIA; CPG ISLAND; DNA METHYLATION; FEMALE; GENE EXPRESSION; GENE IDENTIFICATION; HUMAN; INFANT; LEUKEMIA RELAPSE; MAJOR CLINICAL STUDY; MALE; OUTCOME ASSESSMENT; PATIENT CODING; PRE B LYMPHOCYTE; PREDICTION; PRESCHOOL CHILD; PRIORITY JOURNAL; SCHOOL CHILD; SINGLE NUCLEOTIDE POLYMORPHISM; T LYMPHOCYTE; B LYMPHOCYTE; CHROMOSOME 12; CHROMOSOME 21; CLASSIFICATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; NEWBORN; PATHOLOGY; POLYMERASE CHAIN REACTION; PROGNOSIS; TREATMENT OUTCOME;

ADOLESCENT; B-LYMPHOCYTES; CHILD; CHILD, PRESCHOOL; CHROMOSOMES, HUMAN, PAIR 12; CHROMOSOMES, HUMAN, PAIR 21; CPG ISLANDS; DNA METHYLATION; DNA, NEOPLASM; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, LEUKEMIC; HUMANS; INFANT; INFANT, NEWBORN; MALE; NEOPLASM PROTEINS; POLYMERASE CHAIN REACTION; PRECURSOR CELL LYMPHOBLASTIC LEUKEMIA-LYMPHOMA; PROGNOSIS; TREATMENT OUTCOME;

EID: 77949536178     PISSN: 00064971     EISSN: 15280020     Source Type: Journal    
DOI: 10.1182/blood-2009-04-214668     Document Type: Article

References (48)

1. Pui CH, Relling MV, Downing JR. Acute lymphoblastic leukemia. N Engl J Med. 2004;350(15):1535-1548.
2. Graux C, Cools J, Michaux L, Vandenberghe P, Hagemeijer A. Cytogenetics and molecular genetics of T-cell acute lymphoblastic leukemia: from thymocyte to lymphoblast. Leukemia. 2006;20(9):1496-1510.
3. Karrman K, Forestier E, Heyman M, et al. 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. 2009;48(9):795-805.
4. Pui CH, Robison LL, Look AT. Acute lymphoblastic leukaemia. Lancet. 2008;371(9617):1030-1043.
5. Gutierrez MI, Siraj AK, Bhargava M, et al. Concurrent methylation of multiple genes in childhood ALL: correlation with phenotype and molecular subgroup. Leukemia. 2003;17(9):1845-1850.
6. Roman-Gomez J, Jimenez-Velasco A, Castillejo JA, et al. Promoter hypermethylation of cancer-related genes: a strong independent prognostic factor in acute lymphoblastic leukemia. Blood. 2004;104(8):2492-2498.
7. Kuang SQ, Tong WG, Yang H, et al. Genomewide identification of aberrantly methylated promoter associated CpG islands in acute lymphocytic leukemia. Leukemia. 2008;22(8):1529-1538.
8. Taylor KH, Pena-Hernandez KE, Davis JW, et al. Large-scale CpG methylation analysis identifies novel candidate genes and reveals methylation hotspots in acute lymphoblastic leukemia. Cancer Res. 2007;67(6):2617-2625.
9. Figueroa ME, Reimers M, Thompson RF, et al. An integrative genomic and epigenomic approach for the study of transcriptional regulation. PLoS ONE. 2008;3(3):e1882.
10. Taylor KH, Kramer RS, Davis JW, et al. Ultradeep bisulfite sequencing analysis of DNA methylation patterns in multiple gene promoters by 454 sequencing. Cancer Res. 2007;67(18):8511-8518.
11. Suzuki MM, Bird A. DNA methylation landscapes: provocative insights from epigenomics. Nat Rev Genet. 2008;9(6):465-476.
12. Irizarry RA, Ladd-Acosta C, Carvalho B, et al. Comprehensive high-throughput arrays for relative methylation (CHARM). Genome Res. 2008;18(5):780-790.
13. Bhojwani D, Kang H, Menezes RX, et al. Gene expression signatures predictive of early response and outcome in high-risk childhood acute lymphoblastic leukemia: A Children's Oncology Group Study [corrected]. J Clin Oncol. 2008;26(27):4376-4384.
14. Flotho C, Coustan-Smith E, Pei D, et al. A set of genes that regulate cell proliferation predicts treatment outcome in childhood acute lymphoblastic leukemia. Blood. 2007;110(4):1271-1277.
15. van Delft FW, Bellotti T, Luo Z, et al. Prospective gene expression analysis accurately subtypes acute leukaemia in children and establishes a commonality between hyperdiploidy and t(12;21) in acute lymphoblastic leukaemia. Br J Haematol. 2005;130(1):26-35.
16. Willenbrock H, Juncker AS, Schmiegelow K, Knudsen S, Ryder LP. Prediction of immunophenotype, treatment response, and relapse in childhood acute lymphoblastic leukemia using DNA microarrays. Leukemia. 2004;18(7):1270-1277.
17. Winter SS, Jiang Z, Khawaja HM, et al. Identification of genomic classifiers that distinguish induction failure in T-lineage acute lymphoblastic leukemia: a report from the Children's Oncology Group. Blood. 2007;110(5):1429-1438.
18. Ross ME, Zhou X, Song G, et al. Classification of pediatric acute lymphoblastic leukemia by gene expression profiling. Blood. 2003;102(8):2951- 2959. (Pubitemid 37248870)
19. Den Boer ML, van Slegtenhorst M, De Menezes RX, et al. A subtype of childhood acute lymphoblastic leukaemia with poor treatment outcome: a genome-wide classification study. Lancet Oncol. 2009;10(2):125-134.
20. Milani L, Lundmark A, Nordlund J, et al. Allelespecific gene expression patterns in primary leukemic cells reveal regulation of gene expression by CpG site methylation. Genome Res. 2009;19(1):1-11.
21. Gustafsson G, Schmiegelow K, Forestier E, et al. 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. 2000; 14(12):2267-2275.
22. Pieters R, Schrappe M, De Lorenzo P, et al. A treatment protocol for infants younger than 1 year with acute lymphoblastic leukaemia (Interfant-99): an observational study and a multicentre randomised trial. Lancet. 2007;370(9583):240-250.
23. Bibikova M, Lin Z, Zhou L, et al. High-throughput DNA methylation profiling using universal bead arrays. Genome Res. 2006;16(3):383-393.
24. Shen R, Fan JB, Campbell D, et al. High-throughput SNP genotyping on universal bead arrays. Mutat Res. 2005;573(1-2):70-82.
25. Bolstad BM, Irizarry RA, Astrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics. 2003;19(2):185-193.
26. R Development Team. R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing; 2008.
27. Gray RJ. A class of K-sample tests for comparing the cumulative incidence of a competing risk. Ann Stat. 1988;16(3):1141-1154.
28. Fine JP, Gray RJ. A proportional hazards model for subdistribution of a competing risk. J Am Stat Assoc. 1999;94(446):496-509.
29. Tibshirani R, Hastie T, Narasimhan B, Chu G. Diagnosis of multiple cancer types by shrunken centroids of gene expression. Proc Natl Acad Sci U SA. 2002;99(10):6567-6572.
30. Soeria-Atmadja D, Wallman M, Bjorklund AK, Isaksson A, Hammerling U, Gustafsson MG. External cross-validation for unbiased evaluation of protein family detectors: application to allergens. Proteins. 2005;61(4):918-925.
31. Wood IA, Visscher PM, Mengersen KL. Classification based upon gene expression data: bias and precision of error rates. Bioinformatics. 2007;23(11):1363-1370.
32. Leonard Kaufman PJR. Divisive Analysis (Program DIANA). In: Leonard Kaufman PJR, ed. Finding Groups in Data: An Introduction to Cluster Analysis. New York, NY: John Wiley & Sons, Inc; 1990:253-279.
33. Agirre X, Roman-Gomez J, Jimenez-Velasco A, et al. ASPP1, a common activator of TP53, is inactivated by aberrant methylation of its promoter in acute lymphoblastic leukemia. Oncogene. 2006;25(13):1862-1870.
34. Roman-Gomez J, Jimenez-Velasco A, Agirre X, et al. CpG island methylator phenotype redefines the prognostic effect of t(12;21) in childhood acute lymphoblastic leukemia. Clin Cancer Res. 2006;12(16):4845-4850.
35. San José-Enériz E, Agirre X, Roman-Gomez J, et al. Downregulation of DBC1 expression in acute lymphoblastic leukaemia is mediated by aberrant methylation of its promoter. Br J Haematol. 2006;134(2):137-144.
36. Aifantis I, Raetz E, Buonamici S. Molecular pathogenesis of T-cell leukaemia and lymphoma. Nat Rev Immunol. 2008;8(5):380-390.
37. Flotho C, Coustan-Smith E, Pei D, et al. Genes contributing to minimal residual disease in childhood acute lymphoblastic leukemia: prognostic significance of CASP8AP2. Blood. 2006;108(3):1050-1057.
38. Hogarth LA, Hall AG. Increased BAX expression is associated with an increased risk of relapse in childhood acute lymphocytic leukemia. Blood. 1999;93(8):2671-2678.
39. Holleman A, Cheok MH, den Boer ML, et al. Gene-expression patterns in drug-resistant acute lymphoblastic leukemia cells and response to treatment. N Engl J Med. 2004;351(6):533-542.
40. Holleman A, den Boer ML, de Menezes RX, et al. The expression of 70 apoptosis genes in relation to lineage, genetic subtype, cellular drug resistance, and outcome in childhood acute lymphoblastic leukemia. Blood. 2006;107(2):769-776.
41. Mullighan CG, Goorha S, Radtke I, et al. Genome-wide analysis of genetic alterations in acute lymphoblastic leukaemia. Nature. 2007;446(7137):758-764.
42. Irizarry RA, Ladd-Acosta C, Wen B, et al. The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat Genet. 2009;41(2):178-186.
43. Zhao Z, Tavoosidana G, Sjolinder M, et al. Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions. Nat Genet. 2006;38(11):1341-1347.
44. Breit S, Nees M, Schaefer U, et al. Impact of preanalytical handling on bone marrow mRNA gene expression. Br J Haematol. 2004;126(2):231-243.
45. Greaves MF, Wiemels J. Origins of chromosome translocations in childhood leukaemia. Nat Rev Cancer. 2003;3(9):639-649.
46. Tsai AG, Lu H, Raghavan SC, Muschen M, Hsieh CL, Lieber MR. Human chromosomal translocations at CpG sites and a theoretical basis for their lineage and stage specificity. Cell. 2008;135(6):1130-1142.
47. Shabani M, Asgarian-Omran H, Vossough P, et al. Expression profile of orphan receptor tyrosine kinase (ROR1) and Wilms' tumor gene 1 (WT1) in different subsets of B-cell acute lymphoblastic leukemia. Leuk Lymphoma. 2008;49(7):1360-1367.
48. Bellavia D, Mecarozzi M, Campese AF, Grazioli P, Gulino A, Screpanti I. Notch and Ikaros: not only converging players in T-cell leukemia. Cell Cycle. 2007;6(22):2730-2734.