Dna methylation-based subtype prediction for pediatric acute lymphoblastic leukemia

Clinical Epigenetics

Volumn 7, Issue 1, 2015, Pages

  Nordlund, Jessica ^a   Bäcklin, Christofer L ^b   Zachariadis, Vasilios ^c   Cavelier, Lucia ^d   Dahlberg, Johan ^a   Öfverholm, Ingegerd ^c   Barbany, Gisela ^c   Nordgren, Ann ^c   Övernäs, Elin ^a   Abrahamsson, Jonas ^e   Flaegstad, Trond ^f   Heyman, Mats M ^g   Jónsson, Ólafur G ^h   Kanerva, Jukka ⁱ   Larsson, Rolf ^b   Palle, Josefine ^a,b   Schmiegelow, Kjeld ^j   Gustafsson, Mats G ^b   Lönnerholm, Gudmar ^b   Forestier, Erik ^k   Syvänen, Ann Christine ^a   more..

^a UPPSALA UNIVERSITY   (Sweden)

^b UPPSALA UNIVERSITY HOSPITAL   (Sweden)

^c KAROLINSKA INSTITUTE   (Sweden)

^d UPPSALA UNIVERSITY   (Sweden)

^e QUEEN SILVIA CHILDREN'S HOSPITAL   (Sweden)

^f UNIVERSITY OF TROMSØ   (Norway)

^g KAROLINSKA UNIVERSITY HOSPITAL   (Sweden)

^h LANDSPITALI UNIVERSITY HOSPITAL   (Iceland)

ⁱ UNIVERSITY OF HELSINKI AND HELSINKI UNIVERSITY HOSPITAL   (Finland)

^j UNIVERSITY OF COPENHAGEN   (Denmark)

^k UMEÅ UNIVERSITY   (Sweden)

more..

Author keywords

450 k array; CpG site; Cytogenetics; DNA methylation; Epigenetics; Pediatric acute lymphoblastic leukemia; RNA seq; Subtyping

Indexed keywords

TRANSCRIPTION FACTOR ETV6; TRANSCRIPTION FACTOR PAX5; TRANSCRIPTION FACTOR RUNX1;

ACUTE LYMPHOBLASTIC LEUKEMIA; ADOLESCENT; ADULT; ARTICLE; B CELL PRECURSOR ACUTE LYMPHOBLASTIC LEUKEMIA; CHILD; CLASSIFIER; CONTROLLED STUDY; COPY NUMBER VARIATION; CPG ISLAND; CYTOGENETICS; DNA METHYLATION; DOWN SYNDROME; ETV6 GENE; FEMALE; FLUORESCENCE IN SITU HYBRIDIZATION; FUSION GENE; HUMAN; INFANT; KARYOTYPE; MAJOR CLINICAL STUDY; MALE; PAX5 GENE; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA SEQUENCE; RUNX1 GENE; SENSITIVITY AND SPECIFICITY; T CELL ACUTE LYMPHOBLASTIC LEUKEMIA;

EID: 84927126704     PISSN: 18687075     EISSN: 18687083     Source Type: Journal    
DOI: 10.1186/s13148-014-0039-z     Document Type: Article

References (48)

1. Inaba H, Greaves M, Mullighan CG. Acute lymphoblastic leukaemia. Lancet. 2013;381:1943–55.
2. Harrison CJ. Targeting signaling pathways in acute lymphoblastic leukemia: new insights. Hematology Am Soc Hematol Educ Program. 2013;2013:118–25.
3. Dario Campana M, Pui C-H. Diagnosis and treatment of childhood acute lymphoblastic leukemia. In: Neoplastic diseases of the blood. New York: Springer; 2013. p. 305–29.
4. Schmiegelow K, Forestier E, Hellebostad M, Heyman M, Kristinsson J, Soderhall S, et al. Long-term results of NOPHO ALL-92 and ALL-2000 studies of childhood acute lymphoblastic leukemia. Leukemia. 2010;24:345–54.
5. Pui CH, Carroll WL, Meshinchi S, Arceci RJ. Biology, risk stratification, and therapy of pediatric acute leukemias: an update. J Clin Oncol. 2011;29:551–65.
6. Olde Nordkamp L, Mellink C, van der Schoot E, van den Berg H. Karyotyping, FISH, and PCR in acute lymphoblastic leukemia: competing or complementary diagnostics? J Pediatr Hematol Oncol. 2009;31:930–5.
7. Easwaran H, Tsai HC, Baylin SB. Cancer epigenetics: tumor heterogeneity, plasticity of stem-like states, and drug resistance. Mol Cell. 2014;54:716–27.
8. Deaton AM, Bird A. CpG islands and the regulation of transcription. Genes Dev. 2011;25:1010–22.
9. Nordlund J, Milani L, Lundmark A, Lonnerholm G, Syvanen AC. DNA methylation analysis of bone marrow cells at diagnosis of acute lymphoblastic leukemia and at remission. PLoS One. 2012;7:e34513.
10. Martin-Subero JI, Ammerpohl O, Bibikova M, Wickham-Garcia E, Agirre X, Alvarez S, et al. A comprehensive microarray-based DNA methylation study of 367 hematological neoplasms. PLoS One. 2009;4:e6986.
11. Chatterton Z, Morenos L, Mechinaud F, Ashley DM, Craig JM, Sexton-Oates A, et al. Epigenetic deregulation in pediatric acute lymphoblastic leukemia. Epigenetics. 2014;9:459–67.
12. Milani L, Lundmark A, Kiialainen A, Nordlund J, Flaegstad T, Forestier E, et al. DNA methylation for subtype classification and prediction of treatment outcome in patients with childhood acute lymphoblastic leukemia. Blood. 2010;115:1214–25.
13. You JS, Jones PA. Cancer genetics and epigenetics: two sides of the same coin? Cancer Cell. 2012;22:9–20.
14. Nordlund J, Backlin CL, Wahlberg P, Busche S, Berglund EC, Eloranta ML, et al. Genome-wide signatures of differential DNA methylation in pediatric acute lymphoblastic leukemia. Genome Biol. 2013;14:r105.
15. Figueroa ME, Chen SC, Andersson AK, Phillips LA, Li Y, Sotzen J, et al. Integrated genetic and epigenetic analysis of childhood acute lymphoblastic leukemia. J Clin Invest. 2013;123:3099–111.
16. Davidsson J, Lilljebjorn H, Andersson A, Veerla S, Heldrup J, Behrendtz M, et al. The DNA methylome of pediatric acute lymphoblastic leukemia. Hum Mol Genet. 2009;18:4054–65.
17. Rodriguez-Paredes M, Esteller M. Cancer epigenetics reaches mainstream oncology. Nat Med. 2011;17:330–9.
18. Busche S, Ge B, Vidal R, Spinella JF, Saillour V, Richer C, et al. Integration of high-resolution methylome and transcriptome analyses to dissect epigenomic changes in childhood acute lymphoblastic leukemia. Cancer Res. 2013;73:4323–36.
19. Sarhadi VK, Lahti L, Scheinin I, Tyybakinoja A, Savola S, Usvasalo A, et al. Targeted resequencing of 9p in acute lymphoblastic leukemia yields concordant results with array CGH and reveals novel genomic alterations. Genomics. 2013;102:182–8.
20. Strehl S, Konig M, Dworzak MN, Kalwak K, Haas OA. PAX5/ETV6 fusion defines cytogenetic entity dic(9;12)(p13;p13). Leukemia. 2003;17:1121–3.
21. Roberts KG, Morin RD, Zhang J, Hirst M, Zhao Y, Su X, et al. Genetic alterations activating kinase and cytokine receptor signaling in high-risk acute lymphoblastic leukemia. Cancer Cell. 2012;22:153–66.
22. Xu XJ, Johnson EB, Leverton L, Arthur A, Watson Q, Chang FL, et al. The advantage of using SNP array in clinical testing for hematological malignancies-a comparative study of three genetic testing methods. Cancer Genet. 2013;206:317–26.
23. Kwee I, Rinaldi A, Rancoita P, Rossi D, Capello D, Forconi F, et al. Integrated DNA copy number and methylation profiling of lymphoid neoplasms using a single array. Br J Haematol. 2012;156:354–7.
24. Feber A, Guilhamon P, Lechner M, Fenton T, Wilson GA, Thirlwell C, et al. Using high-density DNA methylation arrays to profile copy number alterations. Genome Biol. 2014;15:R30.
25. Den Boer ML, van Slegtenhorst M, De Menezes RX, Cheok MH, Buijs-Gladdines JG, Peters ST, et al. A subtype of childhood acute lymphoblastic leukaemia with poor treatment outcome: a genome-wide classification study. Lancet Oncol. 2009;10:125–34.
26. Nordlund J, Kiialainen A, Karlberg O, Berglund EC, Goransson-Kultima H, Sonderkaer M, et al. Digital gene expression profiling of primary acute lymphoblastic leukemia cells. Leukemia. 2012;26:1218–27.
27. Ross ME, Zhou X, Song G, Shurtleff SA, Girtman K, Williams WK, et al. Classification of pediatric acute lymphoblastic leukemia by gene expression profiling. Blood. 2003;102:2951–9.
28. Yeoh EJ, Ross ME, Shurtleff SA, Williams WK, Patel D, Mahfouz R, et al. Classification, subtype discovery, and prediction of outcome in pediatric acute lymphoblastic leukemia by gene expression profiling. Cancer Cell. 2002;1:133–43.
29. Gandemer V, Rio AG, de Tayrac M, Sibut V, Mottier S, Ly Sunnaram B, et al. Five distinct biological processes and 14 differentially expressed genes characterize TEL/AML1-positive leukemia. BMC Genomics. 2007;8:385.
30. Caudell D, Harper DP, Novak RL, Pierce RM, Slape C, Wolff L, et al. Retroviral insertional mutagenesis identifies Zeb2 activation as a novel leukemogenic collaborating event in CALM-AF10 transgenic mice. Blood. 2010;115:1194–203.
31. Meyer JA, Wang JH, Hogan LE, Yang JJ, Dandekar S, Patel JP, et al. Relapse-specific mutations in NT5C2 in childhood acute lymphoblastic leukemia. Nat Genet. 2013;45:290–4.
32. Tzoneva G, Perez-Garcia A, Carpenter Z, Khiabanian H, Tosello V, Allegretta M, et al. Activating mutations in the NT5C2 nucleotidase gene drive chemotherapy resistance in relapsed ALL. Nat Med. 2013;19:368–71.
33. Liang DC, Liu HC, Yang CP, Jaing TH, Hung IJ, Yeh TC, et al. Cooperating gene mutations in childhood acute myeloid leukemia with special reference on mutations of ASXL1, TET2, IDH1, IDH2, and DNMT3A. Blood. 2013;121:2988–95.
34. Collins EC, Rabbitts TH. The promiscuous MLL gene links chromosomal translocations to cellular differentiation and tumour tropism. Trends Mol Med. 2002;8:436–42.
35. French CA, Kutok JL, Faquin WC, Toretsky JA, Antonescu CR, Griffin CA, et al. Midline carcinoma of children and young adults with NUT rearrangement. J Clin Oncol. 2004;22:4135–9.
36. French CA, Miyoshi I, Kubonishi I, Grier HE, Perez-Atayde AR, Fletcher JA. BRD4-NUT fusion oncogene: a novel mechanism in aggressive carcinoma. Cancer Res. 2003;63:304–7.
37. Roberts KG, Li Y, Payne-Turner D, Harvey RC, Yang YL, Pei D, et al. Targetable kinase-activating lesions in Ph-like acute lymphoblastic leukemia. N Engl J Med. 2014;371:1005–15.
38. Ofverholm I, Tran AN, Heyman M, Zachariadis V, Nordenskjold M, Nordgren A, et al. Impact of IKZF1 deletions and PAX5 amplifications in pediatric B-cell precursor ALL treated according to NOPHO protocols. Leukemia. 2013;27:1936–9.
39. Olsson L, Castor A, Behrendtz M, Biloglav A, Forestier E, Paulsson K, et al. Deletions of IKZF1 and SPRED1 are associated with poor prognosis in a population-based series of pediatric B-cell precursor acute lymphoblastic leukemia diagnosed between 1992 and 2011. Leukemia. 2013;28:302–10.
40. Pieters R, Schrappe M, De Lorenzo P, Hann I, De Rossi G, Felice M, 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;370:240–50.
41. Biondi A, Schrappe M, De Lorenzo P, Castor A, Lucchini G, Gandemer V, et al. Imatinib after induction for treatment of children and adolescents with Philadelphia-chromosome-positive acute lymphoblastic leukaemia (EsPhALL): a randomised, open-label, intergroup study. Lancet Oncol. 2012;13:936–45.
42. Paulsson K, Johansson B. High hyperdiploid childhood acute lymphoblastic leukemia. Genes Chromosomes Cancer. 2009;48:637–60.
43. Zachariadis V, Gauffin F, Kuchinskaya E, Heyman M, Schoumans J, Blennow E, et al. The frequency and prognostic impact of dic(9;20)(p13.2;q11.2) in childhood B-cell precursor acute lymphoblastic leukemia: results from the NOPHO ALL-2000 trial. Leukemia. 2011;25:622–8.
44. Zachariadis V, Schoumans J, Ofverholm I, Barbany G, Halvardsson E, Forestier E, et al. Detecting dic(9;20)(p13.2;p11.2)-positive B-cell precursor acute lymphoblastic leukemia in a clinical setting using fluorescence in situ hybridization. Leukemia. 2013;28:196–8.
45. Tibshirani R, Hastie T, Narasimhan B, Chu G. Diagnosis of multiple cancer types by shrunken centroids of gene expression. Proc Natl Acad Sci U S A. 2002;99:6567–72.
46. 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;19:185–93.
47. Thorvaldsdottir H, Robinson JT, Mesirov JP. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform. 2013;14:178–92.
48. Nicorici D, Satalan M, Edgren H, Kangaspeska S, Murumagi A, Kallioniemi O, et al. FusionCatcher—a tool for finding somatic fusion genes in paired-end RNA-sequencing data. bioRxiv. 2014. http://dx.doi.org/10.1101/011650.