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

Abstract

Previous studies have shown that interferon-mediated antiviral activity is subtype-dependent. Using a whole transcriptome procedure, we aimed to characterize the small RNA transcriptome (sRNA-Seq) and specifically the differential microRNA (miRNA) responses in porcine alveolar macrophages (PAMs) upon antiviral activation during viral infection and interferon (IFN) stimulation. Data showed that near 90% of the qualified reads of sRNA were miRNAs, and about 10% of the other sRNAs included rRNA, snoRNA, snRNA, and tRNA in order of enrichment. As the majority of sRNA (>98%) were commonly detected in all PAM samples under different treatments, about 2% sRNA were differentially expressed between the different antiviral treatments. Focusing on miRNA, 386 miRNA were profiled, including 331 known and 55 novel miRNA sequences, of which most were ascribed to miRNA families conserved among vertebrates, particularly mammalian species. Of the miRNA profiles comparably generated across the different treatments, in general, significantly differentially expressed miRNA (SEM) demonstrated that: (1) the wild-type and vaccine strains of a porcine arterivirus (a.k.a., PRRSV) induced nearly reversed patterns of up- or down-regulated SEMs; (2) similar SEM patterns were found among the treatments by the vaccine strain and antiviral IFN-α1/-ω5 subtypes; and (3) the weak antiviral IFN-ω1, however, remarked a suppressive SEM pattern as to SEMs upregulated in the antiviral treatments by the vaccine and IFN-α1/-ω5 subtypes. Further articulation identified SEMs commonly or uniquely expressed in different treatments, and experimentally validated that some SEMs including miR-10b and particularly miR-9-1 acted significantly in regulation of differential antiviral reactions stimulated by different IFN subtypes. Therefore, this study provides a general picture of porcine sRNA composition and pinpoints key SEMs underlying antiviral regulation in PAMs correlated to a typical respiratory RNA virus in pigs.

Current Status of Vaccines for Porcine Reproductive and Respiratory Syndrome: Interferon Response, Immunological Overview, and Future Prospects

“…Our recent research used an infectious DNA clone of the PRRSV-P129 for virus replication-competent expression of a cohort of optimized subtypes of porcine IFNs based on a functional characterization of their antiviral responses. As expected, these MLV-129p-IFN constructs induced comparable or better protection compared with a commercial vaccine in grower pigs regarding the body temperature, lung lesion score, and virus titer, as seen in [82,83] (and unpublished data). Furthermore, these studies also profiled signature gene-responsive pathways using transcriptomic analyses in the livers of pigs vaccinated with MLV-129p-IFNmix to reveal an obtained IFN response mediated by the virus replication-competent expression of IFNs in vivo [82].…”

Integrative transcriptomic profiling of mRNA, miRNA, circRNA, and lncRNA in alveolar macrophages isolated from PRRSV-infected porcine

“…Beyond those central miRNAs within the interaction network, ssc-miR-10b and ssc-miR-9-1 were observed to be upregulated at 3 dpi, and at 7 and 21 dpi, respectively. Both miRNAs are postulated to modify the distinct antiviral reactions triggered by various IFNs in PRRSV-infected PAMs ( 30 ). In our current study, ssc-miR-145-5p, which has been previously observed to induce alternative macrophage priming during PRRSV infection ( 26 ), exhibited a downregulated pattern at 7 dpi.…”

“…The lack of effective prevention or treatment strategies underscores the need for extensive investigations into PRRSV pathogenesis for the discovery of novel vaccines and drugs (1,5), for instance, targeting noncoding RNAs (51). However, previous research in the field has largely centered around limited RNA types and in vitro models, lacking a prolonged infection period (13,(26)(27)(28)(29)(30)(31)(32).…”

“…Transcriptomic investigations encompassing both gene expression and noncoding RNAs have significantly propelled our comprehension of PRRSV's pathogenesis and the interplay between PRRSV and pigs (13,(26)(27)(28)(29)(30)(31)(32). However, these studies are frequently limited by their reliance on in vitro models, which inherently fall short of capturing the complexity of the disease course, or lack relevance to persistent infections.…”

Research Progress on the NSP10 Protein of Porcine Reproductive and Respiratory Syndrome Virus

“…PRRSV primarily infects PAMs and induces apoptosis [ 68 , 69 ]. It has been shown that PRRSV infection of Marc-145 cells, which are derived from African green monkey kidney cells, can regulate apoptosis at different periods of infection [ 70 ].…”