Hypermethylation-Mediated Silencing of CIDEA, MAL and PCDH17 Tumour Suppressor Genes in Canine DLBCL: From Multi-Omics Analyses to Mechanistic Studies

Abstract

Gene expression is controlled by epigenetic deregulation, a hallmark of cancer. The DNA methylome of canine diffuse large B-cell lymphoma (cDLBCL), the most frequent malignancy of B-lymphocytes in dog, has recently been investigated, suggesting that aberrant hypermethylation of CpG loci is associated with gene silencing. Here, we used a multi-omics approach (DNA methylome, transcriptome and copy number variations) combined with functional in vitro assays, to identify putative tumour suppressor genes subjected to DNA methylation in cDLBCL. Using four cDLBCL primary cell cultures and CLBL-1 cells, we found that CiDEA, MAL and PCDH17, which were significantly suppressed in DLBCL samples, were hypermethylated and also responsive (at the DNA, mRNA and protein level) to pharmacological unmasking with hypomethylating drugs and histone deacetylase inhibitors. The regulatory mechanism underneath the methylation-dependent inhibition of those target genes expression was then investigated through luciferase and in vitro methylation assays. In the most responsive CpG-rich regions, an in silico analysis allowed the prediction of putative transcription factor binding sites influenced by DNA methylation. Interestingly, regulatory elements for AP2, MZF1, NF-kB, PAX5 and SP1 were commonly identified in all three genes. This study provides a foundation for characterisation and experimental validation of novel epigenetically-dysregulated pathways in cDLBCL.

Epigenetic Alterations in Canine Malignant Lymphoma: Future and Clinical Outcomes

“…Another tumour suppressor gene, DAPK, has been found hypermethylated in canine nodal high-grade B-cell lymphomas [79,80]. Recently, silencing of tumour suppressor genes CIDEA, MAL and PCDH17 by hypermethylation in canine diffuse large B-cell lymphoma in vitro has been demonstrated [81].…”

Omics Technologies in Veterinary Medicine: Literature Review and Perspectives in Transfusion Medicine

“…Major attention has been paid to veterinary oncology, not least because of the comparative insights with humans it provides. In particular, neoplastic diseases investigated through omics technologies are hematopoietic neoplasms [79][80][81][82], mammary tumors [83][84][85], oral neoplasms [86], neuroendocrine tumors [87], and melanocytic tumors [73,88]. Further disorders addressed by omics approaches include cardiopathies [89][90][91], endocrinopathies such as hyperadrenocorticism [92] and diabetes mellitus [93,94], hepatopathies [95][96][97], chronic kidney disease [98,99], and inflammatory/infectious diseases(i.e., sepsis [100], pyometra [101], and vector-borne diseases [102,103]).…”