Publication Only: Chronic lymphocytic leukemia and related disorders - Biology & translational research
Asian chronic lymphocytic leukemia (CLL) is different from Caucasian CLL in terms of the incidence and the age of onset. Aberrant hyper- or hypomethylation might contribute to the pathogenesis of CLL.
We aimed at illucidating the ethnic difference of methylation pattern by performing a comprehensive investigation of a genome-wide DNA methylation profile of Asian CLL represented by a Korean cohort of eight IGHV-unmutated CLL using methylation binding domain sequencing (MBD-seq). To the best of our knowledge, this is the first genome-wide DNA methylation study in Asian CLL.
A total of eight Korean patients diagnosed with CLL/SLL without somatic hypermutation were enrolled. CD19 positive B-cell were collected from 5 healthy donors. MBD- sequencing was performed using HiSeq 2000 (Illumina, San Diego, CA). Differential methylation analysis between the CLL and control groups was performed at the window level. The windows with false discovery rate<0.01 were deemed as differentially methylated. Gene ontology (GO), pathway analysis and network-based prioritization of DMGs were performed.
There were more hypo-methylated regions (2,062 windows) than hyper-methylated regions (777 windows). Promoters contained the highest proportion of differentially methylated regions (DMRs) (around 0.08%), indicating that promoters are the preferential targets of differential methylation in CLL. Supervised clustering clearly separated CLL and normal groups. Protein-coding genes were the most abundant, followed by long noncoding genes, short noncoding genes and small nucleolar RNAs. Dysregulated KEGG pathways included those that are directly related to immune process and cancer. Among the signaling pathways, the most significantly dysregulated was B-cell receptor signaling pathway. In the network-based prioritization, a network of 1,094 nodes and 3,304 edges was obtained. We first selected top ten hub DMGs that were the most heavily linked to the known CLL-related genes, then extracted a subnetwork that consists of the top ten hub DMGs and their known CLL-related gene interactors. Among the ten hub DMGs, six (STAT3, PTPN6, SYK, STAT5B, XPO1, ABL1) had known CLL relevance, as indicated by the presence of blue tint, whereas the rest four (UBC, GRB2, CREBBP, GAB2) did not, as indicated by the absence of blue tint (Figure 1). The former indicates a corroboration of the knowns, while the latter implies a novel finding.
Figure 1. Interaction subnetwork between top ten hub DMGs and known CLL-related genes.
Aberrant hyper- and hypomethylation might contribute to the pathogenesis of CLL in Asians. Pathways related to immune process and cancer were main targets of aberrant methylation. While some genes with known CLL relevance in Caucasian CLL were affected in Asian CLL and Caucasian CLL, novel genes including UBC, GRB2, CREBBP and GAB2 were reported for the first time in our study, suggesting they might contribute to the ethnic differences of CLL between Asians and Caucasians.