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

Congcong Li; Haoyuan Han; Xiuling Li; Jiao Wu; Xinfeng Li; Hui Niu; Wantao Li

doi:10.1155/2021/6666160

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

Int J Genomics. 2021 Jun 16:2021:6666160. doi: 10.1155/2021/6666160. eCollection 2021.

Authors

Congcong Li¹, Haoyuan Han¹, Xiuling Li², Jiao Wu¹, Xinfeng Li³, Hui Niu¹, Wantao Li¹

Affiliations

¹ College of Animal Science and Technology, Henan University of Animal Husbandry and Economy, Zhengzhou, Henan, China.
² College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan, China.
³ Henan Key Laboratory of Unconventional Feed Resources Innovative Utilization, Henan University of Animal Husbandry and Economy, Zhengzhou, Henan, China.

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.