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

Abstract

IntroductionThe porcine reproductive and respiratory syndrome virus (PRRSV) continues to pose a significant threat to the global swine industry, attributed largely to its immunosuppressive properties and the chronic nature of its infection. The absence of effective vaccines and therapeutics amplifies the urgency to deepen our comprehension of PRRSV’s intricate pathogenic mechanisms. Previous transcriptomic studies, although informative, are partially constrained by their predominant reliance on in vitro models or lack of long-term infections. Moreover, the role of circular RNAs (circRNAs) during PRRSV invasion is yet to be elucidated.MethodsIn this study, we employed an in vivo approach, exposing piglets to a PRRSV challenge over varied durations of 3, 7, or 21 days. Subsequently, porcine alveolar macrophages were isolated for a comprehensive transcriptomic investigation, examining the expression patterns of mRNAs, miRNAs, circRNAs, and long non-coding RNAs (lncRNAs).ResultsDifferentially expressed RNAs from all four categories were identified, underscoring the dynamic interplay among these RNA species during PRRSV infection. Functional enrichment analyses indicate that these differentially expressed RNAs, as well as their target genes, play a pivotal role in immune related pathways. For the first time, we integrated circRNAs into the lncRNA-miRNA-mRNA relationship, constructing a competitive endogenous RNA (ceRNA) network. Our findings highlight the immune-related genes, CTLA4 and SAMHD1, as well as their associated miRNAs, lncRNAs, and circRNAs, suggesting potential therapeutic targets for PRRS. Importantly, we corroborated the expression patterns of selected RNAs through RT-qPCR, ensuring consistency with our transcriptomic sequencing data.DiscussionThis study sheds lights on the intricate RNA interplay during PRRSV infection and provides a solid foundation for future therapeutic strategizing.

Transcriptomic and metabolomic correlation analysis: effect of initial SO2 addition on higher alcohol synthesis in Saccharomyces cerevisiae and identification of key regulatory genes

“…The RNA chain was degraded with RNase H, and the second strand of cDNA was synthesized using dNTPs as the raw material in the DNA polymerase I system. Purified double-stranded cDNA was end-repaired, A-tailed, and connected to sequencing adapters ( Peng et al, 2023 ). AMPure XP beads were used to screen approximately 200 bp of cDNA.…”

MicroRNAs: exploring their role in farm animal disease and mycotoxin challenges

“…Further, more research exploring miR-c89, miR-142-3p, and their roles in preventing PRRSV entry into porcine alveolar macrophages provides promising avenues for therapeutic development ( 128 , 129 ). Moreover, recent investigations into miRNAs associated with immune-related genes, including CTLA4 and SAMHD1, and their associated miRNAs, LncRNAs, and circRNA offer potential targets for controlling PRRSV infections ( 130 , 131 ). The multifaceted roles of miRNAs in PRRS indicate their significance in regulating host-pathogen interactions.…”