MicroRNA transcriptome analysis of porcine vital organ responses to immunosuppressive porcine cytomegalovirus infection

Abstract

BackgroundPorcine 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.MethodsIn 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.ResultsIn 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.ConclusionsThis 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.Electronic supplementary materialThe online version of this article (10.1186/s12985-018-0922-x) contains supplementary material, which is available to authorized users.

Effects of gE/gI deletions on the miRNA expression of PRV-infected PK-15 cells

“…4), indicating that gE and gI genes affect PRV-to-host infection by interfering with miRNA expression. This is in agreement with previous work showing that a series of miR-NAs are significantly DE in different viral-infected cell lines or tissues [26,[30][31][32], indicating that these miRNAs play similar regulatory roles during viral infection (Table S5). The host-encoded miR-182 was significantly upregulated in PRV Fa ΔgE/gI strain-infected PK-15 cells, while miR-182 inhibits virus replication through activation of type I IFN response by targeting FOXO3 in neural cells [33], this suggested that upregulation of miR-182 after gE/gI deletion may inhibit PRV replication in the host.…”

“…The present study also showed that 46.8% and 43.9% miRNAs were significantly DE in PRV Fa wild-type strain-infected and PRV Fa ΔgE/gI strain-infected PK-15 cells compared with non-infected PK-15 cells, respectively, suggesting that PRV invasion significantly affected host miRNA expression. Sequencing results showed that ssc-miR-21, ssc-miR-10b, ssc-miR-10a-5p, ssc-let-7a, ssc-let-7f, and ssc-miR-30a-5p miRNAs had the highest expression in each cell sample (Table S1), which agrees with previous findings in various mammals, suggesting that these miRNAs are conserved under PRV infection [25,26]. Among these miRNAs, hostencoded ssc-miR-10a-5p can reduce PRRSV replication by inhibiting the expression of the host-encoded signal recognition particle 14 gene, while miR-10a was reported to inhibit the activation of T helper (Th)1/Th7 cells by targeting interleukin (IL)-12/ IL-23p40 [27,28].…”

MicroRNA Profiling Reveals an Abundant ssc-miRNA-148a-3p that Promotes Proliferation and Differentiation during Intramuscular Adipogenesis in Chinese Guizhou Congjiang Pigs Breeds by targeting PPARGC1A

“…The rst nucleotide bias of known 20 nt, 22 nt, 24 nt miRNAs is U which was similar to others [12]. While, the rst nucleotide bias of known 21nt and 23nt miRNA and novel miRNA was different from other researches [7,8]. The length of predicted novel miRNA was largely aggregated in 22 nt, while the length of known miRNA was mainly clustered in 23 nt which was different from other reports [26].…”

“…MicroRNAs (miRNA) are a kind of 22~nt small non-coding RNAs that direct posttranscriptional repression of mRNA targets in mammals [6]. In recent years, a large number of miRNAs have been identi ed in eukaryotic organisms from nematodes to humans [7][8][9]. Moreover, miRNAs have been regarded as key regulators because they play a critical role in various biological processes, such as animal development, cell proliferation, and differentiation, transcriptional regulation, and homeostasis [10].…”

Comparative Analysis of Roseoloviruses in Humans, Pigs, Mice, and Other Species

“…When porcine micro-RNAs (miRNA) were analyzed in PCMV/PRV-infected and non-infected porcine macrophages, the differentially expressed miRNAs are mainly involved in immune and metabolic processes [176]. Ninety-two, 107, 95, 77, and 111 miRNAs were significantly differentially expressed in lung, liver, spleen, kidney, and thymus after PCMV/PRV infection, providing insights into the regulatory mechanisms of miRNAs during infection by immunosuppressive viruses [179].…”