Whole transcriptome sequencing identifies key lncRNAs,circRNAs, and mRNAs for exploring the pathogenesis and therapeutic target of mouse pneumoconiosis

The purpose of this study was to characterize the lncRNA, circRNA, and mRNA profile of silica-treated pneumoconiosis mice model and to analyze the changes in differential expression genes, biological processes, and signaling pathways based on the differently expressed genes. Lung tissues from 12 mice, 6 silicosis mice, and 6 normal saline were collected and analyzed for their lncRNA, circRNA, and mRNA profile profiles. After qualified library inspection, Illumina PE150 sequencing was performed after pooling according to the effective concentration of the library and data output requirements. Differentially expressed mRNAs/lncRNAs/circRNAs (DEMs) were identified between the different groups, the target miRNAs (co-pre-miRNAs) were obtained by intersecting the miRNAs predicted by DElncRNA and DEcircRNA, respectively, and the target mRNAs (co-mRNA) were obtained by intersecting the mRNAs predicted by target miRNA and DEGs. Then, the lncRNA/circRNA-miRNA-mRNA networks were constructed by Cytoscape. Next, the key mRNAs were obtained by protein-protein interaction (PPI) analysis, and the key lncRNAs/circRNAs were selected by correlation analysis. Moreover, the expression of the key lncRNAs, circRNAs and mRNAs on chromosome were studied by the “circlize” package. Furthermore, the TFs-miRNA-mRNA network was constructed and the function of DEGs were explored by Ingenuity Pathway Analysis (IPA). Finally, We used the Drug-Gene Interaction database to predict potential drugs that could interfere with key genes,which may help to find promising treatment. This study constructed the lncRNA/circRNA-miRNA-mRNA and TFs-miRNA-mRNA networks, which could deepen the potential molecular regulatory mechanism of pneumoconiosis/silicosis. RNA-sequence of circRNA,lncRNA and mRNA in the silica-treated silicosis mice model and sterile normal saline sample were performed and analysed by Novogene (Beijing, China)

本研究旨在表征二氧化硅染尘尘肺病小鼠模型的长链非编码RNA（long non-coding RNA，lncRNA）、环状RNA（circular RNA，circRNA）及信使RNA（messenger RNA，mRNA）表达谱，并基于差异表达基因（differentially expressed genes，DEGs）分析差异表达基因的表达变化、相关生物学过程及信号通路的改变。本研究收集12只小鼠的肺组织，其中矽肺模型小鼠6只、生理盐水对照组小鼠6只，对其lncRNA、circRNA及mRNA表达谱进行分析。文库质检合格后，根据文库有效浓度及数据产出需求进行混样，随后采用Illumina PE150测序技术完成测序。通过组间比较鉴定差异表达的mRNA/lncRNA/circRNA（differentially expressed mRNAs/lncRNAs/circRNAs，DEMs）；分别对差异表达lncRNA（DElncRNA）与差异表达circRNA（DEcircRNA）预测的miRNA取交集，得到共同靶标miRNA（co-pre-miRNAs）；再将该靶标miRNA与DEGs预测的mRNA取交集，获得共同靶标mRNA（co-mRNA）。借助Cytoscape软件构建lncRNA/circRNA-miRNA-mRNA调控网络。通过蛋白质相互作用（protein-protein interaction，PPI）分析筛选关键mRNA，通过相关性分析筛选关键lncRNA与circRNA。此外，利用"circlize"R包研究关键lncRNA、circRNA及mRNA在染色体上的表达分布情况。进一步构建转录因子（transcription factors，TFs）-miRNA-mRNA调控网络，并通过Ingenuity Pathway Analysis（IPA）分析DEGs的功能。本研究借助Drug-Gene Interaction数据库预测可干预关键基因的潜在药物，为探索尘肺病/矽肺的潜在治疗策略提供参考。本研究中二氧化硅染尘矽肺小鼠模型及无菌生理盐水对照组样本的circRNA、lncRNA与mRNA RNA测序及分析工作，由北京诺禾致源（Novogene，北京，中国）完成。