Genome-wide DNA methylation analysis using MethylCap-seq in canine high-grade B-cell lymphoma

Abstract

DNA methylation is a comprehensively studied epigenetic modification and plays crucial roles in cancer development. In the present study, MethylCap-seq was used to characterize the genome-wide DNA methylation patterns in canine high-grade B-cell lymphoma (cHGBL). Canine methylated DNA fragments were captured and the MEDIUM-HIGH and LOW fraction of methylated DNA was obtained based on variation in CpG methylation density. In the MEDIUM-HIGH and LOW fraction, 2144 and 1987 cHGBL-specific hypermethylated genes, respectively, were identified. Functional analysis highlighted pathways strongly related to oncogenesis. The relevant signaling pathways associated with neuronal system were also revealed, echoing recent novel findings that neurogenesis plays key roles in tumor establishment. In addition, 14 genes were hypermethylated in all the cHGBL cases but not in the healthy dogs. These genes might be potential signatures for tracing cHGBL, and some of them have been reported to play roles in various types of cancers. Further, the distinct methylation pattern of cHGBL showed a concordance with the clinical outcome, suggesting that aberrant epigenetic changes may influence tumor behavior.In summary, our study characterized genome-wide DNA methylation patterns using MethylCapseq in cHGBL; the findings suggest that specific DNA hypermethylation holds promise for dissecting tumorigenesis and uncovering biomarkers for monitoring the progression of cHGBL.

Epigenetic Alterations in Canine Malignant Lymphoma: Future and Clinical Outcomes

“…Thus, the CpG island in the upstream region of the exon 2 in the ABCB1 gene is hypermethylated (and presents low expression) in drug-sensitive canine lymphoma cell lines, whereas it is hypomethylated in drug-resistant canine lymphoma cell lines, and these results have been corroborated in in vivo studies [134]. Furthermore, O-methyl guanine DNA methyltransferase expression has been correlated to lomustine resistance in canine lymphoma cell lines [135], and canine cell lines resistant to doxorubicin show hypermethylation in gene promoter regions and low expression of 24 differentiated genes [67]. These results indicate that, as in humans, demethylating drugs could be interesting to use in CML with poor prognosis or resistant to chemotherapy.…”

“…Different GWAS (genome-wide association studies) have been carried out with relevant results. Specifically, in gastrointestinal lymphoma, 773 CpG islands are methylated, including promoter regions of 61 genes, including homeobox genes [66], whereas in highgrade B-cell lymphoma, Hsu et al, (2021) found 14 specific hypermethylated genes in samples of sick dogs but not in healthy dogs [67]. In canine diffuse large B-cell lymphoma, 1194 target loci are hypermethylated, including HOX, BMP and WNT genes, in promoter, 5 -UTRs upstream and exonic regions [68].…”

Exploring DNA methylation data for diagnostic classification of Diffuse large B-cell lymphoma in Dogs

“…The differential methylation analysis revealed expectedly that there were differences in methylation between cDLBCL and the control samples. Indeed, aberrant DNA methylation is characteristic of cancer (Dong et al, 2014), and cDLBCL (Ferraresso et al, 2017;Fujiwara-Igarashi et al, 2014;Hsu et al, 2021;Sato et al, 2018). The accuracy of the clustering despite using all 1701 significant probes substantiated the differential methylation analysis result and indicated their possible utility for classification.…”

“…Few studies have been done to characterize the epigenetic landscape of cDLBCL and these have been focused on DNA methylation. These included DNA methylation studies that focused on single gene (Sato et al, 2014;Fujiwara-Igarashi et al, 2014;Tomiyasu et al, 2014;Ferraresso et al, 2014), and genome-wide (Ferraresso et al, 2017;Aresu et al, 2019;Hsu et al, 2021). The full understanding of the molecular mechanisms underlying cDLBCL is still incomplete.…”

Use of genome‐wide DNA methylation analysis to identify prognostic CpG site markers associated with longer survival time in dogs with multicentric high‐grade B‐cell lymphoma

“…In human DLBCL, epigenetic heterogeneity in DNA methylation pattern correlates with a poorer prognosis, 22 signifying the feasibility of DNA methylation studies in detecting candidate CpG site prognostic biomarkers in dogs with MHGL. In dogs, while there are multiple studies which have utilized next‐generation sequencing based methylation analysis to relate molecular signature of DNA methylation and transcriptome with the prognosis of MHGL, 23 , 24 , 25 there is currently only 1 study which described the use of a singular CpG site methylation in the gene DAPK as a possible prognostic marker of nodal high‐grade B‐cell lymphoma. 26 Despite the presence in statistical significance in predicting a poorer outcome of dogs with high‐grade‐B‐cell lymphoma, the study focused only a singular CpG site with a rather smaller study group.…”