Epigenetic analysis reveals significant differential expression of miR-378C and miR-128-2-5p in a cohort of relapsed pediatric B-acute lymphoblastic leukemia cases.

Abstract

Epigenetic changes play a major role in mediating chemoresistance and relapse in pediatric ALL, and hence in current pilot study, we tried to identify DNA methylation, miRNA expression, and copy number variations (CNVs) in a cohort of relapse pediatric B-ALL cases. DNA methylation, miRNA expression, and CNV analysis were performed in a total of 14, 16, and 18 cases as diagnosis-relapse samples. Briefly, DNA methylation was performed using Infinium HumanMethylation850 chip and data analyzed using RnBeads. miRNA was sequenced on illumina NextSeq500 platform for 20M 75bp SE reads and analyzed by DESeq2. CNVs were assessed by MLPA assay using the ALL P-335 probemix kit and analyzed by coffalyzer.net. On methylation analysis, oncogenes MYCN, MYB, and EGFR and tumor suppressor genes MDM4 & BCL11B were found differentially expressed as compared to controls (p-0.03). In addition, protooncogenes-AXL, HCK, MED12, and ETS2-were hypomethylated/overexpressed in 4 or more cases (P<.05). miRNA analysis revealed significant differential expression of miR-128-2-5p and miR-378C (p-4.4e-15 and p-6.4E-12) in relapse samples. CNV analysis revealed that frequency of good and intermediate/poor risk CNV profile at diagnosis was nearly equal (40% vs 60%). However, CDKN2A/2B and IKZF1 gene CNVs if present in initial diagnostic clone usually persisted in relapse clone. Our pilot study highlights two miRNAs (miR-128-2-5p and miR-378C) as possible candidate biomarkers of relapsed B-ALL. However, these miRNAs and hypomethylated protooncogene signature noted in our data needs validation in a larger series of B-ALL.