Canine mammary tumor (CMT) has long been considered as a good animal model for human breast cancer (HBC) due to their pathological and biological similarities. However, only a few aspects of the epigenome have been explored in both HBC and CMT. Moreover, DNA methylation studies have mainly been limited to the promoter regions of genes. Genome-wide methylation analysis was performed in CMT and adjacent normal tissues and focused on the intron regions as potential targets for epigenetic regulation. As expected, many tumor suppressors and oncogenes were identified. Of note, most cancer-associated biological processes were enriched in differentially methylated genes (DMGs) that included intron DMRs (differentially methylated regions). Interestingly, two PAX motifs, PAX5 (tumor suppressive) and PAX6 (oncogenic), were frequently found in hyper- and hypomethylated intron DMRs, respectively. Hypermethylation at the PAX5 motifs in the intron regions of CDH5 and LRIG1 genes were found to be anti-correlated with gene expression, while CDH2 and ADAM19 genes harboring hypomethylated PAX6 motifs in their intron region were upregulated. These results were validated from the specimens originally MBD-sequenced as well as additional clinical samples. We also comparatively investigated the intron methylation and downstream gene expression of these genes using human breast invasive carcinoma (BRCA) datasets in TCGA (The Cancer Genome Atlas) public database. Regional alteration of methylation was conserved in the corresponding intron regions and, consequently, gene expression was also altered in HBC. This study provides good evidence for the conservation of epigenetic regulation in CMT and HBC, and suggests that intronic methylation can be an important factor in better understanding gene regulation in both CMT and HBC.

中文翻译：

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内含子基序的替代甲基化与犬乳腺肿瘤和人类乳腺癌中的癌症相关基因表达有关。

由于其病理和生物学相似性，犬乳腺肿瘤（CMT）长期以来一直被认为是人类乳腺癌（HBC）的良好动物模型。然而，在 HBC 和 CMT 中只探索了表观基因组的几个方面。此外，DNA 甲基化研究主要限于基因的启动子区域。在 CMT 和邻近的正常组织中进行全基因组甲基化分析，并将重点放在内含子区域作为表观遗传调控的潜在目标。正如预期的那样，鉴定了许多肿瘤抑制基因和癌基因。值得注意的是，大多数与癌症相关的生物过程都富含差异甲基化基因 (DMG)，其中包括内含子 DMR（差异甲基化区域）。有趣的是，两个 PAX 基序，PAX5（肿瘤抑制）和 PAX6（致癌），分别在高甲基化和低甲基化内含子 DMR 中经常发现。发现 CDH5 和 LRIG1 基因内含子区域中 PAX5 基序的高甲基化与基因表达反相关，而在内含子区域中含有低甲基化 PAX6 基序的 CDH2 和 ADAM19 基因被上调。这些结果从最初 MBD 测序的样本以及其他临床样本中得到了验证。我们还使用 TCGA（癌症基因组图谱）公共数据库中的人类乳腺癌浸润性癌（BRCA）数据集比较研究了这些基因的内含子甲基化和下游基因表达。甲基化的区域改变在相应的内含子区域中是保守的，因此，HBC 中的基因表达也发生了改变。