Changing expression profiles of mRNA, miRNA, lncRNA, and circRNA reveal the key regulators and interaction networks of ceRNA in pulmonary fibrosis [ncRNA-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构与细胞外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）以及环状RNA（circular RNA，circRNA）在肺纤维化的发生与进展调控过程中同样发挥关键作用。本研究采用全转录组测序分析技术，对信使RNA（mRNA）、长链非编码RNA（lncRNA）、环状RNA（circRNA）以及微小RNA（miRNA）的表达谱进行探究。通过对比博莱霉素诱导的肺纤维化模型肺组织样本与正常对照样本，本研究共筛选得到286个差异表达长链非编码RNA（lncRNA）、192个差异表达信使RNA（mRNA）、605个差异表达环状RNA（circRNA）以及32个差异表达微小RNA（miRNA）。本研究开展了基因本体（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，以探究这些差异表达信使RNA（mRNA）及非编码RNA（ncRNA）的潜在功能。多种相关的基因本体-生物过程（GO-BP）术语被显著富集，包括"炎症反应"（inflammatory response）、"白细胞介素-2生物合成过程正调控"（positive regulation of interleukin-2 biosynthetic process）、"肌动蛋白细胞骨架调控"（Regulation of actin cytoskeleton）、"Notch信号通路"（Notch signaling pathway）、"血管内皮生长因子刺激下细胞应答的负调控"（negative regulation of cellular response to vascular endothelial growth factor stimulus）；同时富集到的京都基因与基因组百科全书信号通路包括"Wnt信号通路"（Wnt signaling pathway）、"肿瘤坏死因子（TNF）信号通路"（TNF signaling pathway）、"丝裂原活化蛋白激酶（MAPK）信号通路"（MAPK signaling pathway）以及"肌动蛋白细胞骨架调控"（Regulation of actin cytoskeleton），上述富集结果提示这些RNA分子在肺纤维化的调控过程中具备潜在功能。此外，本研究还构建了两条共表达网络（lncRNA-miRNA-mRNA以及circRNA-miRNA-mRNA），以解析这些信使RNA与非编码RNA之间的内在调控关系。本研究为肺纤维化（PF）进程中这些差异表达信使RNA与非编码RNA的潜在功能提供了系统性视角，同时可为这款凶险且复杂的疾病开发有效治疗手段奠定基础。