Genome wide exploration of the methylome in aggressive B-cell lymphoma in Golden Retrievers reveals a conserved hypermethylome

Few recurrent DNA mutations are seen in aggressive canine B cell lymphomas (cBCL), suggesting other frequent drivers. The methylated island recovery assay (MIRA-seq) was used to define the genome wide methylation profiles in aggressive cBCL in Golden Retrievers to determine if cBCL can be better defined by epigenetic changes than by DNA mutations. DNA hypermethylation patterns were relatively homogenous within cBCL samples in Golden Retrievers, in different breeds and in geographical regions. Aberrant hypermethylation is thus suspected to be a central and early event in cBCL lymphomagenesis. Distinct subgroups within cBCL in Golden Retrievers were not identified with DNA methylation profiles. In comparison, the methylome profile of human DLBCL (hDLBCL) is relatively heterogenous. Only moderate similarity between hDLBCL and cBCL was seen and cBCL likely cannot be accurately classified into the subtypes seen in hDLBCL. Genes with hypermethylated regions in the promoter-TSS-first exon of cBCL compared to normal B cells often also had additional hyper- and hypomethylated regions distributed throughout the gene suggesting non-randomized repeat targeting of key genes by epigenetic mechanisms. The prevalence of hypermethylation in transcription factor families in aggressive cBCL may represent a fundamental step in lymphomagenesis. The data presented here represent the most comprehensive methylation profile of cBCL.

侵袭性犬B细胞淋巴瘤（canine B cell lymphomas, cBCL）中极少观察到复发性DNA突变，提示其存在其他高频驱动因素。本研究采用甲基化岛恢复测序（methylated island recovery assay, MIRA-seq），对金毛寻回犬侵袭性cBCL的全基因组甲基化谱进行分析，以探究相较于DNA突变，表观遗传改变是否能更精准地定义cBCL。在金毛寻回犬、不同品种以及不同地理区域的cBCL样本中，DNA高甲基化模式均呈现相对均一的特征。因此，异常高甲基化被认为是cBCL淋巴瘤发生过程中的核心早期事件。通过DNA甲基化谱未检测到金毛寻回犬cBCL存在明确亚群。相较而言，人类弥漫大B细胞淋巴瘤（human DLBCL, hDLBCL）的甲基化组谱呈现相对异质性特征。hDLBCL与cBCL仅存在中等程度的相似性，cBCL大概率无法被精准归类为hDLBCL的现有亚型。相较于正常B细胞，cBCL中启动子-转录起始位点（transcription start site, TSS）-第一外显子区域存在高甲基化的基因，往往在基因全长还分布有额外的高甲基化与低甲基化区域，这提示表观遗传机制会对关键基因进行非随机的重复靶向调控。侵袭性cBCL中转录因子家族基因出现高甲基化的现象，可能是淋巴瘤发生过程中的关键环节。本研究提供的数据为目前已报道的最为全面的cBCL甲基化谱数据集。