Changing expression profiles of mRNA, miRNA, lncRNA, and circRNA reveal the key regulators and interaction networks of ceRNA in pulmonary fibrosis [miRNA-seq]

Pulmonary fibrosis is a kind of interstitial lung disease with architectural remodeling of tissues and excessive matrix deposition. Apart from mRNA, microRNA, long non-coding RNA (lncRNA) and circular RNA (circRNA) could also play important roles in the regulatory processes of occurrence and progression of pulmonary fibrosis. In the present study, whole transcriptome sequencing analysis was applied to investigate the expression profiles of mRNAs, lncRNAs, circRNAs and miRNAs. After comparing bleomycin-induced pulmonary fibrosis model lung samples and controls, 286 lncRNAs, 192 mRNAs, 605 circRNAs, and 32 miRNAs were found to be differentially expressed. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to investigate the potential functions of these DE mRNAs and ncRNAs. Various related GO-BP terms such as “inflammatory response”, “positive regulation of interleukin-2 biosynthetic process”, “Regulation of actin cytoskeleton”, “Notch signaling pathway”, “negative regulation of cellular response to vascular endothelial growth factor stimulus”, and KEGG signal pathways such as “Wnt signaling pathway”, “TNF signaling pathway”, “MAPK signaling pathway”, “Regulation of actin cytoskeleton” were enriched implying potential roles in regulatory process. In addition, two co-expression networks (lncRNA-miRNA-mRNA, circRNA-miRNA-mRNA) were also constructed to understand the internal regulating relationships of these mRNAs and ncRNAs. Our study provides a systematic perspective on the potential functions of these DE mRNAs and ncRNAs during PF process, and could help pave the way for effective therapeutics for this devastating and complex disease.肺纤维化（Pulmonary fibrosis）是一类以组织结构重塑与基质过度沉积为特征的间质性肺疾病。除信使RNA（mRNA）外，微小RNA（microRNA）、长链非编码RNA（long non-coding RNA，lncRNA）与环状RNA（circular RNA，circRNA）在肺纤维化发生与进展的调控过程中同样发挥重要作用。本研究采用全转录组测序（whole transcriptome sequencing）技术，分析信使RNA、长链非编码RNA、环状RNA与微小RNA的表达谱。通过对比博莱霉素诱导的肺纤维化模型肺组织样本与对照样本，共筛选得到286个差异表达长链非编码RNA、192个差异表达信使RNA、605个差异表达环状RNA以及32个差异表达微小RNA。本研究对上述差异表达信使RNA与非编码RNA开展基因本体论（Gene Ontology，GO）与京都基因与基因组百科全书（Kyoto Encyclopedia of Genes and Genomes，KEGG）富集分析，以探究其潜在功能。富集分析结果显示，多条GO生物过程（GO-BP）术语显著富集，包括“炎症反应”“白细胞介素-2生物合成过程正调控”“肌动蛋白细胞骨架调控”“Notch信号通路”“血管内皮生长因子刺激下细胞应答的负调控”；同时多条KEGG信号通路如“Wnt信号通路”“TNF信号通路”“MAPK信号通路”“肌动蛋白细胞骨架调控”亦显著富集，提示这些分子在肺纤维化的调控过程中具有潜在作用。此外，本研究还构建了两类共表达网络（lncRNA-miRNA-mRNA与circRNA-miRNA-mRNA），以解析上述信使RNA与非编码RNA之间的内在调控关系。本研究为肺纤维化过程中差异表达的信使RNA与非编码RNA的潜在功能提供了系统性视角，可为攻克这一致命性复杂疾病的有效治疗策略提供研究基础。