PEDV 感染中 mRNAs、lncRNAs 和 miRNAs 表达谱的差异表达分析及 ceRNA 网络的构建。

Differential expression analysis of mRNAs, lncRNAs, and miRNAs expression profiles and construction of ceRNA networks in PEDV infection.

机构信息

College of Veterinary Medicine, Northwest A&F University, Yangling, Xianyang, 712100, Shaanxi, China.

出版信息

BMC Genomics. 2022 Aug 13;23(1):586. doi: 10.1186/s12864-022-08805-0.

BACKGROUND

Porcine Epidemic Diarrhea Virus (PEDV) is a coronavirus that seriously affects the swine industry. MicroRNAs and long noncoding RNAs are two relevant non-coding RNAs (ncRNAs) class and play crucial roles in a variety of physiological processes. Increased evidence indicates a complex interaction between mRNA and ncRNA. However, our understanding of the function of ncRNA involved in host-PEDV interaction is limited.

RESULTS

A total of 1,197 mRNA transcripts, 539 lncRNA transcripts, and 208 miRNA transcripts were differentially regulated at 24 h and 48 h post-infection. Gene ontology (GO) and KEGG pathway enrichment analysis showed that DE mRNAs and DE lncRNAs were mainly involved in biosynthesis, innate immunity, and lipid metabolism. Moreover, we constructed a miRNA-mRNA-pathway network using bioinformatics, including 12 DE mRNAs, 120 DE miRNAs, and 11 pathways. Finally, the target genes of DE miRNAs were screened by bioinformatics, and we constructed immune-related lncRNA-miRNA-mRNA ceRNA networks. Then, the selected DE genes were validated by qRT-PCR, which were consistent with the results from RNA-Seq data.

CONCLUSIONS

This study provides the comprehensive analysis of the expression profiles of mRNAs, lncRNAs, and miRNAs during PEDV infection. We characterize the ceRNA networks which can provide new insights into the pathogenesis of PEDV.

背景

猪流行性腹泻病毒（PEDV）是一种严重影响养猪业的冠状病毒。microRNAs 和长链非编码 RNA 是两种相关的非编码 RNA（ncRNA），在各种生理过程中发挥着关键作用。越来越多的证据表明，mRNA 和 ncRNA 之间存在复杂的相互作用。然而，我们对参与宿主- PEDV 相互作用的 ncRNA 的功能的理解是有限的。

结果

在感染后 24 和 48 小时，共检测到 1197 个 mRNA 转录本、539 个 lncRNA 转录本和 208 个 miRNA 转录本的差异表达。基因本体（GO）和 KEGG 通路富集分析显示，差异表达的 mRNAs 和 lncRNAs 主要参与生物合成、先天免疫和脂质代谢。此外，我们利用生物信息学构建了 miRNA-mRNA-通路网络，其中包括 12 个差异表达的 mRNAs、120 个差异表达的 miRNAs 和 11 条通路。最后，通过生物信息学筛选差异表达 miRNAs 的靶基因，并构建免疫相关 lncRNA-miRNA-mRNA ceRNA 网络。然后，通过 qRT-PCR 验证了所选的差异表达基因，结果与 RNA-Seq 数据一致。