Genome-wide analysis of long noncoding RNA profiling in PRRSV-infected PAM cells by RNA sequencing

Abstract

Porcine reproductive and respiratory syndrome (PRRS) is a major threat to the global swine industry and causes tremendous economic losses. Its causative agent, porcine reproductive and respiratory syndrome virus (PRRSV), primarily infects immune cells, such as porcine alveolar macrophages and dendritic cells. PRRSV infection results in immune suppression, antibody-dependent enhancement, and persistent infection. Highly pathogenic strains in China cause high fever and severe inflammatory responses in the lungs. However, the pathogenesis of PRRSV is still not fully understood. In this study, we analysed the long noncoding RNA (lncRNA) and mRNA expression profiles of the HP-PRRSV GSWW15 and the North American strain FL-12 in infected porcine alveolar macrophages (PAMs) at 12 and 24 hours post-infection. We predicted 12,867 novel lncRNAs, 299 of which were differentially expressed after viral infection. The Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) analyses of the genes adjacent to lncRNAs showed that they were enriched in pathways related to viral infection and immune response, indicating that lncRNAs might play regulatory roles in virus-host interactions. Our study provided information about lncRNAs in the porcine immune system and offers new insights into the pathogenic mechanism of PRRSV infection and novel antiviral therapy development.

Transcriptome Analysis Reveals Dynamic Gene Expression Profiles in Porcine Alveolar Macrophages in Response to the Chinese Highly Pathogenic Porcine Reproductive and Respiratory Syndrome Virus

“…In addition to protein-coding genes, a total of 17624 novel and 12987 annotated lncRNAs were obtained from the great amounts of uncharacterized transcripts identified in our study. Zhang et al characterized 12867 novel lncRNAs during PRRSV infection [19], while our study predicted more novel lncRNAs. Meanwhile we predicted the annotated lncRNAs XR 297549.1 with a highly decreased level during PRRSV infection that was both cis-regulated and trans-regulated by the PTSG2 gene.…”

“…The microRNA transcriptome of PAMs in response to different strains of PRRSV has expanded our understanding of cellular noncoding RNAs in PRRSV infection [73,74]. A latest study analyzed the lncRNA expression profiles of PAMs in response to different pathogenic PRRSV strains, further expanding our understanding of predicted lncRNAs and their potential role in antiviral immune response [19].…”

“…It is of great significance to focus on PAMs in the study of PRRSV, because they play essential roles in lung tissue homeostasis, early pathogen recognition, initiation of the local immune responses, and resolution of inflammation [16]. To date, a considerable number of transcriptomic experiments have been conducted to reveal the gene expression profiles of PRRSV-infected PAMs either in an in vitro infection model or in vivo challenge model [17][18][19][20][21][22][23][24]. Although the in vivo model enabled us to evaluate the overall effects of PRRSV infection on the respiratory tract, the in vitro model helps us to assess the direct impacts of PAMs in response to PRRSV infection independently of the respiratory immune system.…”

“…PAMs have been shown to present distinct gene expression profiles at different time points during PPRSV infection, indicating the dynamic interaction between PRRSV and PAMs at the transcriptional levels [17,25]. Moreover, it has been illustrated that the transcriptome differences of PAMs existed in response to PRRSV strains with divergent virulence [18,19], expanding the understanding of unique performance of defined PRRSV strain in PAMs at the transcriptional level [26]. However, majority of the studies mentioned above were performed using either microarrays or Digital Gene Expression (DGE) tag profiling with some limitations.…”

Comprehensive analysis of long noncoding RNA and mRNA in five colorectal cancer tissues and five normal tissues

“…LncRNA forms an RNA regulatory network by regulating the expression of protein-coding genes, and participates in the physiological and pathological processes of the organism. Therefore, the change in the expression level of lncRNA is closely related to the occurrence and development of various diseases [8,9]. Annotation of eukaryotic transcriptomes by binding sequencing and biological information methods can reveal the functions of lncRNA in epigenetic modifications, transcriptional regulation and post-transcriptional regulation [10,11].…”