Department of Animal Science, College of Agriculture, Isfahan University of Technology, 84156-83111, Isfahan, Iran.
Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Tehran, 3391653755, Iran.
J Appl Genet. 2022 Dec;63(4):771-782. doi: 10.1007/s13353-022-00722-y. Epub 2022 Sep 6.
MicroRNAs (miRNAs) as post-transcriptionally regulators of gene expression have been shown to be critical regulators to fine-tuning immune responses, besides their criteria for being an ideal biomarker. The regulatory role of miRNAs in responses to most mastitis-causing pathogens is not well understood. Gram-positive Streptococcus uberis (Str. uberis), the leading pathogen in dairy herds, cause both clinical and subclinical infections. In this study, a system biology approach was used to better understand the main post-transcriptional regulatory functions and elements of bovine mammary gland response to Str. uberis infection. Publicly available miRNA-Seq data containing 50 milk samples of the ten dairy cows (five controls and five infected) were retrieved for this current research. Functional enrichment analysis of predicted targets revealed that highly confident responsive miRNAs (4 up- and 19 downregulated) mainly regulate genes involved in the regulation of transcription, apoptotic process, regulation of cell adhesion, and pro-inflammatory signaling pathways. Time series analysis showed that six gene clusters significantly differed in comparisons between Str. uberis-induced samples with controls. Additionally, other bioinformatic analysis, including upstream network analysis, showed essential genes, including TP53 and TGFB1 and some small molecules, including glucose, curcumin, and LPS, commonly regulate most of the downregulated miRNAs. Upregulated miRNAs are commonly controlled by the most important genes, including IL1B, NEAT1, DICER1 enzyme and small molecules including estradiol, tamoxifen, estrogen, LPS, and epigallocatechin. Our study used results of next-generation sequencing to reveal key miRNAs as the main regulator of gene expression responses to a Gram-positive bacterial infection. Furthermore, by gene regulatory network (GRN) analysis, we can introduce the common upregulator transcription factor of these miRNAs. Such milk-based miRNA signature(s) would facilitate risk stratification for large-scale prevention programs and provide an opportunity for early diagnosis and therapeutic intervention.
微小 RNA（miRNA）作为基因表达的转录后调控因子，除了作为理想生物标志物的标准外，还被证明是精细调节免疫反应的关键调节剂。miRNA 在对大多数引起乳腺炎的病原体的反应中的调节作用尚未得到很好的理解。革兰氏阳性菌停乳链球菌（Str. uberis）是奶牛群中的主要病原体，可引起临床和亚临床感染。在这项研究中，采用系统生物学方法来更好地理解牛乳腺对 Str. uberis 感染的主要转录后调控功能和元素。为此项研究检索了包含 10 头奶牛（5 头对照和 5 头感染）的 50 个乳样的公开 miRNA-Seq 数据。对预测靶标的功能富集分析表明，高可信度反应性 miRNA（4 个上调和 19 个下调）主要调节参与转录调节、凋亡过程、细胞粘附调节和促炎信号通路的基因。时间序列分析表明，Str. uberis 诱导的样品与对照之间的 6 个基因簇在比较中差异显著。此外，其他生物信息学分析，包括上游网络分析，表明包括 TP53 和 TGFB1 在内的重要基因和包括葡萄糖、姜黄素和 LPS 在内的一些小分子共同调节大多数下调的 miRNA。上调的 miRNA 通常受包括 IL1B、NEAT1、DICER1 酶和小分子在内的最重要基因的控制，包括雌二醇、他莫昔芬、雌激素、LPS 和表没食子儿茶素没食子酸酯。我们的研究使用下一代测序的结果揭示了关键 miRNA 作为对革兰氏阳性细菌感染的基因表达反应的主要调节剂。此外，通过基因调控网络（GRN）分析，我们可以引入这些 miRNA 的常见上调转录因子。这种基于乳的 miRNA 特征将有助于大规模预防计划的风险分层，并为早期诊断和治疗干预提供机会。
