Southwest University, College of Animal Science and technology, Chongqing, 400715, China.
Key Laboratory of Animal Disease and Human Health of Sichuan Province and Animal Biotechnology Center, College of Veterinary Medicine of Sichuan Agricultural University, 211#Huimin Road, Wenjiang District, Chengdu, Sichuan Province, 610000, China.
Virol J. 2018 Jan 18;15(1):16. doi: 10.1186/s12985-018-0922-x.
Porcine cytomegalovirus (PCMV) is an immunosuppressive virus that mainly inhibits T-lymphocyte and macrophage immune functions; it has significantly damaged the farming industry. Although recent studies have shown that miRNAs play important roles in immune responses, the regulatory mechanisms of miRNAs during immunosuppressive virus infection remain unclear.
In this study, porcine small-RNA transcriptomes of PCMV-infected and uninfected vital organs were first characterised by high-throughput sequencing. miRDeep2 software was used to predict novel pig-encoded miRNAs. To verify the accuracy of the high-throughput sequencing results, stem-loop qRT-PCR was performed on 12 significantly DE miRNAs. The physical and functional interactions between the immune-related target genes of the DE miRNAs in PCMV-infected organs were analysed using the STRING database.
In total, 306 annotated and 295 novel miRNAs were identified from PCMV-infected and uninfected porcine organs, respectively, through alignment with known Sus scrofa pre-miRNAs. Overall, 92, 107, 95, 77 and 111 miRNAs were significantly differentially expressed in lung, liver, spleen, kidney and thymus after PCMV infection, respectively. According to Gene Ontology enrichment analysis, target genes of the differentially expressed miRNAs associated with immune system processes, regulation of biological processes and metabolic processes were enriched in every sample. Integrated expression analysis of the differentially expressed miRNAs and their target mRNAs in PCMV-infected thymus showed that the significant differential expression of specific miRNAs under the pressure of PCMV infection in central immune organs interfered with the expression of genes involved in important immune-related signalling pathways, thus promoting the viral infection.
This is the first comprehensive analysis of the responses of host small-RNA transcriptomes to PCMV infection in vital porcine organs. It provides new insights into the regulatory mechanisms of miRNAs during infection by immunosuppressive viruses.
猪巨细胞病毒（PCMV）是一种免疫抑制性病毒，主要抑制 T 淋巴细胞和巨噬细胞的免疫功能；它对养殖业造成了严重损害。尽管最近的研究表明 miRNA 在免疫反应中发挥着重要作用，但 miRNA 在免疫抑制性病毒感染过程中的调控机制尚不清楚。
本研究首先通过高通量测序对 PCMV 感染和未感染的重要器官的猪小 RNA 转录组进行了特征描述。使用 miRDeep2 软件预测新的猪编码 miRNA。为了验证高通量测序结果的准确性，对 12 个差异表达的 miRNA 进行了茎环 qRT-PCR 验证。使用 STRING 数据库分析了 PCMV 感染器官中差异表达 miRNA 的免疫相关靶基因之间的物理和功能相互作用。
总共从 PCMV 感染和未感染的猪器官中鉴定出 306 个注释 miRNA 和 295 个新 miRNA，通过与已知的猪前体 miRNA 进行比对。总体而言，肺、肝、脾、肾和胸腺在 PCMV 感染后分别有 92、107、95、77 和 111 个 miRNA 显著差异表达。根据基因本体论富集分析，差异表达 miRNA 的靶基因与免疫系统过程、生物过程调控和代谢过程相关，在每个样本中都有富集。对 PCMV 感染胸腺中差异表达 miRNA 及其靶 mRNA 的综合表达分析表明，在中枢免疫器官中受到 PCMV 感染压力的特定 miRNA 的显著差异表达，干扰了参与重要免疫相关信号通路的基因表达，从而促进了病毒感染。
这是首次全面分析宿主小 RNA 转录组对重要猪器官中 PCMV 感染的反应，为免疫抑制性病毒感染过程中 miRNA 的调控机制提供了新的见解。
