Li Yueqi, Wei Wudi, An Sanqi, Jiang Junjun, He Jinhao, Zhang Hong, Wang Gang, Han Jing, Liang Bingyu, Ye Li, Liang Hao
Guangxi Collaborative Innovation Center for Biomedicine & Guangxi-ASEAN Collaborative Innovation Center for Major Disease Prevention and Treatment, Life Science Institute, Guangxi Medical University, Nanning, Guangxi, China.
Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China.
PeerJ. 2021 Jan 13;9:e10529. doi: 10.7717/peerj.10529. eCollection 2021.
Competitive endogenous RNA (ceRNA) reveals new mechanisms for interactions between RNAs, which have been considered to play a significant role in pathogen-host innate immune response. However, knowledge of ceRNA regulatory networks in (TM)-macrophages is still limited.
Next-generation sequencing technology (NGS) was used to obtain mRNA, miRNA and lncRNA expression profiles in TM-infected macrophages. The R package DESeq2 was used to identify differentially expressed lncRNA, miRNA and mRNA. The R package GOseq was used for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, and the ceRNA network of lncRNA-miRNA-mRNA interaction was constructed in Cytoscape. Similarly, functional enrichment analysis on mRNA in the ceRNA network. Finally, two mRNAs and four lncRNAs in the ceRNA network were randomly selected to verify the expression using qRT-PCR.
In total, 119 lncRNAs, 28 miRNAs and 208 mRNAs were identified as differentially expressed RNAs in TM-infected macrophages. The constructed ceRNA network contains 38 lncRNAs, 10 miRNAs and 45 mRNAs. GO and KEGG analysis of mRNA in the ceRNA network indicated that activated pathways in TM-infected macrophages were related to immunity, inflammation and metabolism. The quantitative validation of the expression of four randomly selected differentially expressed lncRNAs, AC006252.1, AC090197.1, IL6R-AS1, LINC02009 and two mRNAs, CSF1, NR4A3 showed that the expression levels were consistent with those in the RNA-sequencing.
The ceRNA network related to immunity, inflammation and metabolism plays an important role in TM-macrophage interaction. This study may provide effective and novel insights for further understanding the underlying mechanism of TM infection.
竞争性内源性RNA（ceRNA）揭示了RNA之间相互作用的新机制，其被认为在病原体-宿主先天免疫反应中发挥重要作用。然而，关于（TM）-巨噬细胞中ceRNA调控网络的知识仍然有限。
使用下一代测序技术（NGS）获取TM感染的巨噬细胞中的mRNA、miRNA和lncRNA表达谱。R包DESeq2用于鉴定差异表达的lncRNA、miRNA和mRNA。R包GOseq用于基因本体论（GO）和京都基因与基因组百科全书（KEGG）分析，并在Cytoscape中构建lncRNA-miRNA-mRNA相互作用的ceRNA网络。同样，对ceRNA网络中的mRNA进行功能富集分析。最后，随机选择ceRNA网络中的两个mRNA和四个lncRNA，使用qRT-PCR验证其表达。
总共，119个lncRNA、28个miRNA和208个mRNA被鉴定为TM感染的巨噬细胞中差异表达的RNA。构建的ceRNA网络包含38个lncRNA、10个miRNA和45个mRNA。ceRNA网络中mRNA的GO和KEGG分析表明，TM感染的巨噬细胞中激活的通路与免疫、炎症和代谢有关。对随机选择的四个差异表达lncRNA（AC006252.1、AC090197.1、IL6R-AS1、LINC02009）和两个mRNA（CSF1、NR4A3）表达的定量验证表明，表达水平与RNA测序中的一致。
与免疫、炎症和代谢相关的ceRNA网络在TM-巨噬细胞相互作用中起重要作用。本研究可能为进一步了解TM感染的潜在机制提供有效且新颖的见解。
