INCLIVA Biomedical Research Institute, Hospital Clínico Universitario Valencia, University of Valencia, Valencia, Spain.
Department of Surgery and Cancer, Imperial College London, London, UK.
Sci Rep. 2018 Sep 26;8(1):14373. doi: 10.1038/s41598-018-32393-3.
MiRNAs are part of the epigenetic machinery, and are also epigenetically modified by DNA methylation. MiRNAs regulate expression of different genes, so any alteration in their methylation status may affect their expression. We aimed to identify methylation differences in miRNA encoding genes in breast cancer affecting women under 35 years old (BCVY), in order to identify potential biomarkers in these patients. In Illumina Infinium MethylationEPIC BeadChip samples (metEPICVal), we analysed the methylation of 9,961 CpG site regulators of miRNA-encoding genes present in the array. We identified 193 differentially methylated CpG sites in BCVY (p-value < 0.05 and methylation differences ±0.1) that regulated 83 unique miRNA encoding genes. We validated 10 CpG sites using two independent datasets based on Infinium Human Methylation 450k array. We tested gene expression of miRNAs with differential methylation in BCVY in a meta-analysis using The Cancer Genome Atlas (TCGA), Clariom D and Affymetrix datasets. Five miRNAs (miR-9, miR-124-2, miR-184, miR-551b and miR-196a-1) were differently expressed (FDR p-value < 0.01). Finally, only miR-124-2 shows a significantly different gene expression by quantitative real-time PCR. MiR-124-hypomethylation presents significantly better survival rates for older patients as opposed to the worse prognosis observed in BCVY, identifying it as a potential specific survival biomarker in BCVY.
miRNAs 是表观遗传机制的一部分，也可被 DNA 甲基化修饰。miRNAs 调节不同基因的表达，因此其甲基化状态的任何改变都可能影响其表达。我们旨在鉴定影响 35 岁以下乳腺癌女性（BCVY）的 miRNA 编码基因的甲基化差异，以确定这些患者的潜在生物标志物。在 Illumina Infinium MethylationEPIC BeadChip 样本（metEPICVal）中，我们分析了阵列中存在的 miRNA 编码基因的 9961 个 CpG 位点调控子的甲基化情况。我们在 BCVY 中鉴定出 193 个差异甲基化 CpG 位点（p 值<0.05，甲基化差异±0.1），这些 CpG 位点调节 83 个独特的 miRNA 编码基因。我们使用基于 Infinium Human Methylation 450k 阵列的两个独立数据集验证了 10 个 CpG 位点。我们使用 The Cancer Genome Atlas (TCGA)、Clariom D 和 Affymetrix 数据集进行荟萃分析，测试了 BCVY 中具有差异甲基化的 miRNA 的基因表达。5 个 miRNA（miR-9、miR-124-2、miR-184、miR-551b 和 miR-196a-1）的表达存在差异（FDR p 值<0.01）。最后，只有 miR-124-2 通过定量实时 PCR 显示出显著不同的基因表达。miR-124-低甲基化在年龄较大的患者中表现出显著更好的生存率，而在 BCVY 中观察到的预后较差，表明其为 BCVY 中潜在的特异性生存生物标志物。
