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

Abstract

Acute lymphoblastic leukemia (ALL) is the most common cancer diagnosed in children under the age of 15. In addition to genetic aberrations, epigenetic modifications such as DNA methylation are altered in cancer and impact gene expression. To identify epigenetic alterations in ALL, genome-wide methylation profiles were generated using the methylated CpG island recovery assay followed by next-generation sequencing. More than 25,000 differentially methylated regions (DMR) were observed in ALL patients with »90% present within intronic or intergenic regions. To determine the regulatory potential of the DMR, whole-transcriptome analysis was performed and integrated with methylation data. Aberrant promoter methylation was associated with the altered expression of genes involved in transcriptional regulation, apoptosis, and proliferation. Novel enhancer-like sequences were identified within intronic and intergenic DMR. Aberrant methylation in these regions was associated with the altered expression of neighboring genes involved in cell cycle processes, lymphocyte activation and apoptosis. These genes include potential epi-driver genes, such as SYNE1, PTPRS, PAWR, HDAC9, RGCC, MCOLN2, LYN, TRAF3, FLT1, and MELK, which may provide a selective advantage to leukemic cells. In addition, the differential expression of epigenetic modifier genes, pseudogenes, and non-coding RNAs was also observed accentuating the role of erroneous epigenetic gene regulation in ALL.

RNA methylation in lymphoid malignancies

“…To determine if the trends observed in cell lines are consistent in primary cells, data generated from pre-B ALL patients and normal precursor B-cells was analyzed [23] . In these samples the gene expression of METTL3 was lower while FTO was higher in patients diagnosed with ALL compared to healthy donors ( Figure 2D), although the m 6 A status in these samples needs to be determined.…”

Role of TRAF3 in neurological and cardiovascular diseases: an overview of recent studies

“…TRAF3 was found to be epigenetically regulated in three conditions: cardiac hypertrophy (25), acute lymphoblastic leukaemia (ALL) (26) and vascular recurrence in patients treated with clopidogrel (22).…”

“…Regarding the epigenetic regulation of TRAF3 in ALL, the genome-wide methylation profile was analysed in ALL using methylated CpG island recovery assay followed by next-generation sequencing (26). Then, the authors performed whole-transcriptome analysis and integrated this data with the methylation data.…”

“…The authors found DMRs in 'enhancer-like' regions, in which altered methylation was associated with altered expression in neighbouring genes. Among these genes, TRAF3 was downregulated by hypermethylation of an 'enhancerlike' region (26). In addition, TRAF3 methylation has been associated with vascular recurrence after ischaemic stroke in patients treated with clopidogrel.…”

Inferring a role for methylation of intergenic DNA in the regulation of genes aberrantly expressed in precursor B-cell acute lymphoblastic leukemia

“…Aberrant DNA methylation in vital regulatory regions of the genome, like enhancers, may cause initiation of many hematopoietic disease conditions including pre-B ALL. We have previously shown that aberrant methylation in enhancer regions was associated with the altered expression of neighboring genes involved in cell cycle processes, lymphocyte activation and apoptosis in pre-B ALL [10]. To further the understanding of the role that intergenic DNA methylation and/or differential eRNA expression plays in regulating the expression of target genes in pre-B ALL, the regulatory potential of putatively active enhancers has been investigated.…”