Analysis of lncRNA, miRNA, and mRNA Expression Profiling in Type I IFN and Type II IFN Overexpressed in Porcine Alveolar Macrophages

Abstract

Current data is scarce regarding the function of noncoding RNAs (ncRNAs) such as microRNAs (miRNAs) and long noncoding RNAs (lncRNAs) in the interferon- (IFN-) mediated immune response. This is a comprehensive study that analyzes the lncRNA and miRNA expression profiles of the type I IFN and type II IFN in porcine alveolar macrophages using RNA sequencing. There was a total of 152 overexpressed differentially expressed (DE) lncRNAs and 21 DE miRNAs across type I IFN and type II IFN in porcine alveolar macrophages. Subsequent lncRNA-miRNA-mRNA network construction revealed the involvement of 36 DE lncRNAs and 12 DE miRNAs. LncRNAs such as the XLOC_211306, XLOC_100516, XLOC_00695, XLOC_149196, and XLOC_014459 were expressed at a higher degree in the type I IFN group, while XLOC_222640, XLOC_047290, XLOC_147777, XLOC_162298, XLOC_220210, and XLOC_165237 were expressed at a higher degree in the type II IFN group. These lncRNAs were found to act as “sponges” for miRNAs such as miR-34a, miR-328, miR-885-3p, miR-149, miR-30c-3p, miR-30b-5p, miR-708-5p, miR-193a-5p, miR-365-5p, and miR-7. Their target genes FADS2, RPS6KA1, PIM1, and NOD1 were found to be associated with several immune-related signaling pathways including the NOD-like receptor, Jak-STAT, mTOR, and PPAR signaling pathways. These experiments provide a comprehensive profile of overexpressed noncoding RNAs in porcine alveolar macrophages, providing new insights regarding the IFN-mediated immune response.

Comparative transcriptomics reveals small RNA composition and differential microRNA responses underlying interferon-mediated antiviral regulation in porcine alveolar macrophages

“…In contrast, slightly more novel sRNA/miRNA were detected in the P6 of IFN-w5 treatment (Table 4). More extensive or sRNA/miRNA-specific studies will be needed to test whether this general sRNA differential expression is associated with the respective samples across different treatments (21)(22)(23)(24)(25)(26)(27)(28)(29).…”

“…Most of our inter-sample RSQ for miRNA expression were larger than 0.97, indicating a critical experiment control across the samples, and shared expression patterns of the miRNA that correlates between the samples. Hence, the minor portion of sampleand miRNA-specific differential expression, which were hypothesized to underlie the observed difference of cellular responses across the samples, were pinpointed for further examination (20)(21)(22)(23)(24)(25)(26)(27)(28)(29).…”

“…The miRNA that play key roles in regulation of the AM response to IFNs and viral infection have not been critically investigated although several miRNA (such as miR-339-5p/-181d-5p) were differentially expressed in other cell types upon PRRSV infection (17)(18)(19)(20)(21)(22)(23)(24)(25). Similarly, a plethora of miRNA including miR-19/-122/-155 have been implicated in both IFN production and action signaling; however, no miRNA has been directly associated to differential antiviral regulation per different IFN subtypes and PRRSV strains with heterogeneous pathogenicity (17)(18)(19)(20)(21)(22)(23)(24)(25)(26)(27)(28).…”

Differential MicroRNA Expression in Porcine Endometrium Related to Spontaneous Embryo Loss during Early Pregnancy

“…The top miRNAs with more targets are miR-365-5p, miR-671-5p, miR-885, and miR-205. Studies have shown that miR-365-5p can target RNA-binding protein with serine-rich domain 1 ( RNPS1) , Keratin 14 ( KRT14) , and DnaJ heat shock protein family (Hsp40) member B6 ( DNAJB6) in porcine Alveolar Macrophages, thereby affecting interferon-mediated immune response [ 42 ]. Previous studies have shown that the differentially expressed miR-671-5p in the endometrium of Meishan and Duroc sows affects maternal placental development by targeting the Estrogen Receptor 1 ( ESR1) gene [ 5 , 43 ].…”

Insight into mechanisms of pig lncRNA FUT3-AS1 regulating E. coli F18-bacterial diarrhea

“…The library was sequenced on the Illumina Hiseq2500 platform by Oebiotech Corporation (Shanghai, China) and 50 bp single-end reads were produced. LncRNA transcriptome and miRNA analysis were performed as per the provided instructions, followed by data analysis as described previously [ 22 ]. LncRNA sequencing data has been submitted to NCBI′s SRA repository under BioProject IDs: PRJNA476718, PRJNA476720, PRJNA476721, PRJNA476722.…”