Qu L, Ma S C, Xu L L, Jiang X Z, Sun X W, Dong Z Y, Wu Y L
School of Basic Medical Sciences, Binzhou Medical University, Yantai, Shandong 264003, China.
Co-first authors.
Zhongguo Xue Xi Chong Bing Fang Zhi Za Zhi. 2022 Apr 11;34(2):128-140. doi: 10.16250/j.32.1374.2021299.
To investigate long non-coding RNA (lncRNA)-microRNA (miRNA)-messenger RNA (mRNA) interactions and identify the critical gene regulatory network during infections and praziquantel treatment using whole transcriptome sequencing.
A total of 110 male C57BL/6 mice were randomly divided into the control group, the infection group and the treatment group. Mice in the infection treatment and the control group were infected with cercariae via the abdomen, and liver specimens were sampled from 10 mice 3, 6, 8 weeks post-infection. Praziquantel treatment was given to mice in the treatment group 8 weeks post-infection, and liver specimens were sampled from 10 mice 2, 4, 6, 8, 10 weeks post-treatment. Total RNA was isolated from mouse liver specimens, and the transcriptome library was constructed for highthroughput whole transcriptome sequencing. The significant differentially expressed genes were subjected to functional annotations, Gene Ontology (GO) terms enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Correlation analysis of liver specimens was performed using R Corrplot and Himsc functions, and the lncRNAmiRNA-mRNA interaction network analysis was performed using R MixOmics and Himsc functions.
There were 1 176 differentially expressed miRNAs, 5 270 differentially expressed mRNAs, and 2 682 differentially expressed lncRNAs between the infection group and the control group, 1 289 differentially expressed miRNAs, 7 differentially expressed mRNAs, and 69 differentially expressed lncRNAs between the treatment group and the infection group, and 1 210 differentially expressed miRNAs, 4 456 differentially expressed mRNAs, and 2 016 differentially expressed lncRNAs between the treatment group and the control group. Correlation analysis showed a higher correlation of gene expression between the treatment group and the control group. Principal component analysis showed obvious separate clustering between the infection group and the treatment group. The differentially expressed genes with significant relevance were significantly enriched in 24 GO terms, including arachidonic acid metabolic process, xenobiotic catabolic process, unsaturated fatty acid metabolic process, xenobiotic metabolic process, long-chain fatty acid metabolic process, and 8 KEGG metabolic pathways, including cholesterol metabolism, tyrosine metabolism, linoleic acid metabolism, retinol metabolism, and steroid hormone biometabolism.
There were 23 mRNAs including Cyp2b9 and 14 lncRNAs including Rmrpr in the core position of the gene regulatory network, which may play a critical role in infections and praziquantel treatment, and 9 miRNAs including miR-8105 may serve as potential molecular markers for diagnosis of infections.
利用全转录组测序研究长链非编码RNA（lncRNA）-微小RNA（miRNA）-信使RNA（mRNA）相互作用，并确定感染和吡喹酮治疗期间的关键基因调控网络。
将110只雄性C57BL/6小鼠随机分为对照组、感染组和治疗组。感染组和对照组小鼠经腹部感染尾蚴，并在感染后3、6、8周从10只小鼠采集肝脏标本。治疗组小鼠在感染后8周给予吡喹酮治疗，并在治疗后2、4、6、8、10周从10只小鼠采集肝脏标本。从小鼠肝脏标本中分离总RNA，构建转录组文库进行高通量全转录组测序。对显著差异表达基因进行功能注释、基因本体论（GO）术语富集分析和京都基因与基因组百科全书（KEGG）通路富集分析。使用R语言的Corrplot和Himsc函数对肝脏标本进行相关性分析，使用R语言的MixOmics和Himsc函数进行lncRNA-miRNA-mRNA相互作用网络分析。
感染组与对照组之间有1176个差异表达的miRNA、5270个差异表达的mRNA和2682个差异表达的lncRNA；治疗组与感染组之间有1289个差异表达的miRNA、7个差异表达的mRNA和69个差异表达的lncRNA；治疗组与对照组之间有1210个差异表达的miRNA、4456个差异表达的mRNA和2016个差异表达的lncRNA。相关性分析显示治疗组与对照组之间基因表达的相关性更高。主成分分析显示感染组和治疗组之间有明显的单独聚类。具有显著相关性的差异表达基因在24个GO术语中显著富集，包括花生四烯酸代谢过程、异源物质分解代谢过程、不饱和脂肪酸代谢过程、异源物质代谢过程、长链脂肪酸代谢过程，以及8条KEGG代谢通路，包括胆固醇代谢、酪氨酸代谢、亚油酸代谢、视黄醇代谢和类固醇激素生物合成。
Cyp2b9等23个mRNA和Rmrpr等14个lncRNA处于基因调控网络的核心位置，可能在感染和吡喹酮治疗中起关键作用，miR-8105等9个miRNA可能作为感染诊断的潜在分子标志物。
