Wang Mengqi, Bissonnette Nathalie, Laterrière Mario, Dudemaine Pier-Luc, Gagné David, Roy Jean-Philippe, Zhao Xin, Sirard Marc-André, Ibeagha-Awemu Eveline M
Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, Quebec, Canada.
Department of Animal Science, Laval University, Quebec, Quebec, Canada.
J Anim Sci Biotechnol. 2022 Nov 7;13(1):136. doi: 10.1186/s40104-022-00779-z.
Mastitis caused by different pathogens including Streptococcus uberis (S. uberis) is responsible for huge economic losses to the dairy industry. In order to investigate the potential genetic and epigenetic regulatory mechanisms of subclinical mastitis due to S. uberis, the DNA methylome (whole genome DNA methylation sequencing) and transcriptome (RNA sequencing) of milk somatic cells from cows with naturally occurring S. uberis subclinical mastitis and healthy control cows (n = 3/group) were studied.
Globally, the DNA methylation levels of CpG sites were low in the promoters and first exons but high in inner exons and introns. The DNA methylation levels at the promoter, first exon and first intron regions were negatively correlated with the expression level of genes at a whole-genome-wide scale. In general, DNA methylation level was lower in S. uberis-positive group (SUG) than in the control group (CTG). A total of 174,342 differentially methylated cytosines (DMCs) (FDR < 0.05) were identified between SUG and CTG, including 132,237, 7412 and 34,693 DMCs in the context of CpG, CHG and CHH (H = A or T or C), respectively. Besides, 101,612 methylation haplotype blocks (MHBs) were identified, including 451 MHBs that were significantly different (dMHB) between the two groups. A total of 2130 differentially expressed (DE) genes (1378 with up-regulated and 752 with down-regulated expression) were found in SUG. Integration of methylome and transcriptome data with MethGET program revealed 1623 genes with significant changes in their methylation levels and/or gene expression changes (MetGDE genes, MethGET P-value < 0.001). Functional enrichment of genes harboring ≥ 15 DMCs, DE genes and MetGDE genes suggest significant involvement of DNA methylation changes in the regulation of the host immune response to S. uberis infection, especially cytokine activities. Furthermore, discriminant correlation analysis with DIABLO method identified 26 candidate biomarkers, including 6 DE genes, 15 CpG-DMCs and 5 dMHBs that discriminated between SUG and CTG.
The integration of methylome and transcriptome of milk somatic cells suggests the possible involvement of DNA methylation changes in the regulation of the host immune response to subclinical mastitis due to S. uberis. The presented genetic and epigenetic biomarkers could contribute to the design of management strategies of subclinical mastitis and breeding for mastitis resistance.
由包括乳房链球菌（S. uberis）在内的不同病原体引起的乳腺炎给乳制品行业造成了巨大的经济损失。为了研究由S. uberis引起的亚临床乳腺炎的潜在遗传和表观遗传调控机制，对自然发生S. uberis亚临床乳腺炎的奶牛和健康对照奶牛（每组n = 3）的乳体细胞进行了DNA甲基化组（全基因组DNA甲基化测序）和转录组（RNA测序）研究。
总体而言，启动子和首个外显子中CpG位点的DNA甲基化水平较低，而内部外显子和内含子中的水平较高。在全基因组范围内，启动子、首个外显子和首个内含子区域的DNA甲基化水平与基因表达水平呈负相关。一般来说，S. uberis阳性组（SUG）的DNA甲基化水平低于对照组（CTG）。在SUG和CTG之间共鉴定出174,342个差异甲基化胞嘧啶（DMC）（FDR < 0.05），其中在CpG、CHG和CHH（H = A或T或C）背景下分别有132,237、7,412和34,693个DMC。此外，鉴定出101,612个甲基化单倍型块（MHB），其中两组之间有451个显著不同的MHB（dMHB）。在SUG中总共发现了2,130个差异表达（DE）基因（1,378个上调和752个下调）。使用MethGET程序整合甲基化组和转录组数据，发现1,623个基因的甲基化水平和/或基因表达发生了显著变化（甲基化和差异表达基因，MethGET P值< 0.001）。对含有≥ 15个DMC的基因、DE基因和甲基化和差异表达基因进行功能富集分析，表明DNA甲基化变化在宿主对S. uberis感染的免疫反应调节中起重要作用，尤其是细胞因子活性。此外，使用DIABLO方法进行判别相关分析，确定了26个候选生物标志物，包括6个DE基因、15个CpG-DMC和5个dMHB，可区分SUG和CTG。
乳体细胞甲基化组和转录组的整合表明，DNA甲基化变化可能参与宿主对S. uberis引起亚临床乳腺炎的免疫反应调节。所呈现的遗传和表观遗传生物标志物有助于亚临床乳腺炎管理策略的设计和抗乳腺炎育种。
