Genome-wide DNA methylation and RNA-seq analyses identify genes and pathways associated with doxorubicin resistance in a canine diffuse large B-cell lymphoma cell line
Journal
PLoS ONE
Journal Volume
16
Journal Issue
May
Date Issued
2021
Author(s)
Abstract
Doxorubicin resistance is a major challenge in the successful treatment of canine diffuse large B-cell lymphoma (cDLBCL). In the present study, MethylCap-seq and RNA-seq were performed to characterize the genome-wide DNA methylation and differential gene expression patterns respectively in CLBL-1 8.0, a doxorubicin-resistant cDLBCL cell line, and in CLBL-1 as control, to investigate the underlying mechanisms of doxorubicin resistance in cDLBCL. A total of 20289 hypermethylated differentially methylated regions (DMRs) were detected. Among these, 1339 hypermethylated DMRs were in promoter regions, of which 24 genes showed an inverse correlation between methylation and gene expression. These 24 genes were involved in cell migration, according to gene ontology (GO) analysis. Also, 12855 hypermethylated DMRs were in gene-body regions. Among these, 353 genes showed a positive correlation between methylation and gene expression. Functional analysis of these 353 genes highlighted that TGF-β and lysosome-mediated signal pathways are significantly associated with the drug resistance of CLBL-1. The tumorigenic role of TGF-β signaling pathway in CLBL-1 8.0 was further validated by treating the cells with a TGF-β inhibitor(s) to show the increased chemo-sensitivity and intracellular doxorubicin accumulation, as well as decreased p-glycoprotein expression. In summary, the present study performed an integrative analysis of DNA methylation and gene expression in CLBL-1 8.0 and CLBL-1. The candidate genes and pathways identified in this study hold potential promise for overcoming doxorubicin resistance in cDLBCL. Copyright: ? 2021 Hsu et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Subjects
ABC transporter subfamily B
DNA
doxorubicin
RNA
transforming growth factor beta
animal cell
Article
carcinogenesis
cell migration
chemosensitivity
controlled study
diffuse large B cell lymphoma
diffuse large B-cell lymphoma cell line
DNA methylation
dog
drug cytotoxicity
drug resistance
gene
gene expression
gene identification
gene ontology
lysosome
nonhuman
promoter region
protein expression
real time polymerase chain reaction
RNA sequencing
signal transduction
Western blotting
animal
CpG island
genetics
genomics
pathology
tumor cell line
Animals
Cell Line, Tumor
CpG Islands
DNA Methylation
Dogs
Doxorubicin
Drug Resistance, Neoplasm
Genomics
Lymphoma, Large B-Cell, Diffuse
RNA-Seq
SDGs
Type
journal article