Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, China.
Hubei Collaborative Innovation Center for Animal Nutrition and Feed Safety, Wuhan Polytechnic University, Wuhan, China.
Front Immunol. 2022 Feb 25;13:840399. doi: 10.3389/fimmu.2022.840399. eCollection 2022.
() can elicit serious inflammatory responses and cause meningitis in piglets. Previous epigenetic studies have indicated that alterations in host DNA methylation may modify the inflammatory response to bacterial infection. However, to date, genome-wide analysis of the DNA methylome during meningitis caused by infection is still lacking. In this study, we employed an unbiased approach using deep sequencing to profile the DNA methylome and transcriptome from infected porcine brain (cerebrum) and integrated the data to identify key differential methylation regions/sites involved in the regulation of the inflammatory response. Results showed that DNA methylation patterns and gene expression profiles from porcine brain were changed after infection. The majority of the altered DNA methylation regions were found in the intergenic regions and introns and not associated with CpG islands, with only a low percentage occurring at promoter or exon regions. Integrated analysis of the DNA methylome and transcriptome identified a number of inversely and positively correlated genes between DNA methylation and gene expression, following the criteria of |logFC| > 0.5, |diffMethy| > 0.1, and < 0.05. Differential expression and methylation of two significant genes, semaphoring 4D () and von Willebrand factor A domain containing 1 (), were validated by qRT-PCR and bisulfite sequencing. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses demonstrated that DNA methylation inversely correlated genes in infected porcine brains were mainly involved with cell adhesion molecules (CAMs), bacterial invasion of epithelial cells, RIG-1-like receptor signaling pathways, and hematopoietic cell lineage signaling pathways. In addition, a protein-protein interaction network of differentially methylated genes found potential candidate molecular interactions relevant to the pathology of infection. To the best of our knowledge, this is the first attempt to integrate the DNA methylome and transcriptome data from infected porcine brains. Our findings will help understanding the contribution of genome-wide DNA methylation to the pathogenesis of meningitis in pigs and developing epigenetic biomarkers and therapeutic targets for the treatment of induced meningitis.
可以引发严重的炎症反应，并导致仔猪脑膜炎。先前的表观遗传学研究表明，宿主 DNA 甲基化的改变可能会改变对细菌感染的炎症反应。然而，迄今为止，关于 感染引起的脑膜炎的全基因组 DNA 甲基组分析仍然缺乏。在这项研究中，我们采用了一种无偏的方法，使用深度测序来描绘 感染的猪脑（大脑）的 DNA 甲基组和转录组，并整合数据以识别参与调节炎症反应的关键差异甲基化区域/位点。结果表明，感染后猪脑的 DNA 甲基化模式和基因表达谱发生了变化。大多数改变的 DNA 甲基化区域位于基因间区域和内含子中，而与 CpG 岛无关，只有一小部分发生在启动子或外显子区域。DNA 甲基组和转录组的综合分析确定了一些在 DNA 甲基化和基因表达之间呈反相关和正相关的基因，其标准为 |logFC|>0.5、|diffMethy|>0.1 和 <0.05。通过 qRT-PCR 和亚硫酸氢盐测序验证了两个显著基因 semaphorin 4D()和 von Willebrand 因子 A 结构域包含 1()的差异表达和甲基化。基因本体论 (GO) 和京都基因与基因组百科全书 (KEGG) 富集分析表明，感染猪脑中与 DNA 甲基化呈反相关的基因主要参与细胞黏附分子 (CAMs)、细菌入侵上皮细胞、RIG-1 样受体信号通路和造血细胞谱系信号通路。此外，差异甲基化基因的蛋白质-蛋白质相互作用网络发现了与 感染病理学相关的潜在候选分子相互作用。据我们所知，这是首次尝试整合 感染猪脑的 DNA 甲基组和转录组数据。我们的研究结果将有助于了解全基因组 DNA 甲基化对猪脑膜炎发病机制的贡献，并为开发针对 诱导性脑膜炎的表观遗传生物标志物和治疗靶点提供帮助。
