Integration of High-Resolution Methylome and Transcriptome Analyses to Dissect Epigenomic Changes in Childhood Acute Lymphoblastic Leukemia

Abstract

B-cell precursor acute lymphoblastic leukemia (pre-B ALL) is the most common pediatric cancer. Although the genetic determinants underlying disease onset remain unclear, epigenetic modifications including DNA methylation are suggested to contribute significantly to leukemogenesis. Using the Illumina 450K array, we assessed DNA methylation in matched tumor-normal samples of 46 childhood patients with pre-B ALL, extending single CpG-site resolution analysis of the pre-B ALL methylome beyond CpG-islands (CGI). Unsupervised hierarchical clustering of CpG-site neighborhood, gene, or microRNA (miRNA) gene-associated methylation levels separated the tumor cohort according to major pre-B ALL subtypes, and methylation in CGIs, CGI shores, and in regions around the transcription start site was found to significantly correlate with transcript expression. Focusing on samples carrying the t(12;21) ETV6-RUNX1 fusion, we identified 119 subtype-specific high-confidence marker CpG-loci. Pathway analyses linked the CpG-loci-associated genes with hematopoiesis and cancer. Further integration with whole-transcriptome data showed the effects of methylation on expression of 17 potential drivers of leukemogenesis. Independent validation of array methylation and sequencing-derived transcript expression with Sequenom Epityper technology and realtime quantitative reverse transcriptase PCR, respectively, indicates more than 80% empirical accuracy of our genome-wide findings. In summary, genome-wide DNA methylation profiling enabled us to separate pre-B ALL according to major subtypes, to map epigenetic biomarkers specific for the t(12;21) subtype, and through a combined methylome and transcriptome approach to identify downstream effects on candidate drivers of leukemogenesis. Cancer Res; 73(14); 4323-36. Ó2013 AACR.

Integrated methylome and transcriptome analysis reveals novel regulatory elements in pediatric acute lymphoblastic leukemia

“…Previous studies in ALL have identified inverse correlations between gene expression and DNA methylation in CGIs, CGI shores and gene promoters. 32 In this study, 99% of DMRs associated with a CGI were hypermethylated in ALL; however, these only accounted for a small number of the total DMRs. In fact, more than 80% of DMRs were identified in intronic or intergenic regions and not within a CGI context.…”

Differences in DNA Methylation Signatures Reveal Multiple Pathways of Progression From Adenoma to Colorectal Cancer

“…We and others have reported previously that results from the HumanMethylation450 BeadChips (HM450) are technically robust but that there is a measurable false discovery rate [24, 25] . Thus, we initially conducted technical validation studies and biological validation studies of a subset of differentially methylated CpGs (N=4) found on the HM450 arrays (described in detail in Supplemental Methods and Results).…”

Pathogenesis of ETV6/RUNX1-positive childhood acute lymphoblastic leukemia and mechanisms underlying its relapse

“…Maximal repression requires the binding of mSin3A, N-CoR and histone deacetylase-3 (HDAC3) to ETV6 [72]. Although the E/R chimeric protein is assumed to act as transcriptional repressor of RUNX1 target genes, several studies have reported similar levels of gene repression and activation for protein-coding and miRNA genes [68, 71, 75]. In addition, the E/R fusion gene product can disrupt the transcriptional repression of wild-type ETV6 by dimerization via the PNT domain [76].…”