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

Abstract

Despite improvements in the prognosis of childhood acute lymphoblastic leukemia (ALL), subgroups of patients would benefit from alternative treatment approaches. Our aim was to identify genes with DNA methylation profiles that could identify such groups. We determined the methylation levels of 1320 CpG sites in regulatory regions of 416 genes in cells from 401 children diagnosed with ALL. Hierarchical clustering of 300 CpG sites distinguished between T-lineage ALL and B-cell precursor (BCP) ALL and between the main cytogenetic subtypes of BCP ALL. It also stratified patients with high hyperdiploidy and t(12;21) ALL into 2 subgroups with different probability of relapse. By using supervised learning, we constructed multivariate classifiers by external cross-validation procedures. We identified 40 genes that consistently contributed to accurate discrimination between the main subtypes of BCP ALL and gene sets that discriminated between subtypes of ALL and between ALL and controls in pairwise classification analyses. We also identified 20 individual genes with DNA methylation levels that predicted relapse of leukemia. Thus, methylation analysis should be explored as a method to improve stratification of ALL patients. The genes highlighted in our study are not enriched to specific pathways, but the gene expression levels are inversely correlated to the methylation levels. (Blood. 2010;115:1214-1225)

DNA Hypermethylation of Cell Cycle (p15 and p16) and Apoptotic (p14, p53, DAPK and TMS1) Genes in Peripheral Blood of Leukemia Patients

“…Nevertheless, methylation analysis of multiple genes in leukemia is yet to be explored as a method for grouping patients (Milani et al, 2010).…”

Initial Diagnostic Workup of Acute Leukemia: Guideline From the College of American Pathologists and the American Society of Hematology

“…This statement was supported by 4 PCSs [193][194][195][196] that met the inclusion criteria for our SR. Two of the studies 193,194 were deemed to have a low risk of bias, and the other 2 195,196 were deemed to have a low to moderate risk of bias. None of these studies were found to have methodological flaws that would raise concerns about the studies' findings.…”

“…Nevertheless, only a few studies in the SR specifically mention or allude to the use of preserved cells as the specimen source for the studies performed. [193][194][195][196] Historically, cryopreservation was the most commonly employed method of preserving cells. 197 Cryopreserved leukemia cells can be used for the extraction of DNA and RNA for molecular genetic studies.…”

“…106,112,413,414 Molecular studies confirming mutations and gene rearrangements as part of clinical trials were typically performed at a central laboratory or tertiary care center § § § § § § § § as were DNA methylation studies. 196 If testing involves making specimens for routine or cytochemical staining or performing flow cytometry on BM at a central laboratory, the sample should be shipped overnight and processed within 24 hours of being obtained. 112,297 For testing involving cytogenetics performed centrally, overnight shipping of a heparinized BM sample is recommended.…”

Aberrant Proliferative and Apoptotic Pathways in Acute Lymphoblastic Leukemia (ALL): Molecular Therapies to Overcome Chemo-Resistance

“…Data reported by Yang et al (2009) demonstrated that detection of epigenetic alterations allows the identification of ALL patients with poor prognosis within the standard-risk group. More recently, Milani L et al (2010), analyzing the methylation patterns of CpG sites in 416 genes, have found a striking difference in the methylation patterns within a large number of samples from ALL patients. Notably, they observed a correlation between the methylation level and clinical outcome within major subgroups of ALL patients, identifying 20 genes with DNA methylation levels capable to predict leukemia relapse.…”