Department of Ophthalmology, the Second Hospital of Jilin University, Changchun 130000, Jilin Province, China.
Mol Vis. 2020 Feb 1;26:1-13. eCollection 2020.
As a disorder occurs in the eyes, keratoconus (KC) is induced by the thinning of the corneal stroma. This study was designed to reveal the key long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and mRNAs involved in the mechanisms of KC.
Transcriptome RNA-seq data set GSE112155 was acquired from the Gene Expression Omnibus database, which contained 10 KC samples and 10 myopic control samples. Using the edgeR package, the differentially expressed (DE)-mRNAs between KC and control samples were screened. The DE-lncRNAs and DE-miRNAs in this data set were identified using the HUGO Gene Nomenclature Committee (HGNC). Using the pheatmap package, bidirectional hierarchical clustering of the DE-RNAs was conducted. Then, an enrichment analysis of the DE-mRNAs was performed using the DAVID tool. Moreover, a competitive endogenous RNA (ceRNA) regulatory network was built using the Cytoscape software. After KC-associated pathways were searched within the Comparative Toxicogenomics Database, a KC-associated ceRNA regulatory network was constructed.
There were 282 DE-lncRNAs (192 upregulated and 90 downregulated), 40 DE-miRNAs (29 upregulated and 11 downregulated), and 910 DE-mRNAs (554 upregulated and 356 downregulated) between the KC and control samples. A total of 34 functional terms and 9 pathways were enriched for the DE-mRNAs. In addition, 6 mRNAs (including , , , and ), 5 miRNAs (including ), 9 lncRNAs (including ), and the axis were involved in the KC-associated ceRNA regulatory network.
, , , , , and might be correlated with the development of KC. Further, the axis might be implicated in the pathogenesis of KC.
圆锥角膜（KC）是由于角膜基质变薄而引起的眼部疾病。本研究旨在揭示与 KC 发病机制相关的关键长非编码 RNA（lncRNA）、微小 RNA（miRNA）和信使 RNA（mRNA）。
从基因表达综合数据库（GEO）中获取了包含 10 例 KC 样本和 10 例近视对照样本的转录组 RNA-seq 数据集 GSE112155。使用 edgeR 包筛选 KC 与对照样本之间的差异表达（DE）-mRNA。使用人类基因命名委员会（HGNC）识别该数据集的 DE-lncRNA 和 DE-miRNA。使用 pheatmap 包对 DE-RNAs 进行双向层次聚类。然后，使用 DAVID 工具对 DE-mRNAs 进行富集分析。此外，使用 Cytoscape 软件构建了竞争性内源性 RNA（ceRNA）调控网络。在比较毒理学基因组数据库中搜索与 KC 相关的通路后，构建了与 KC 相关的 ceRNA 调控网络。
KC 与对照样本之间有 282 个 DE-lncRNA（192 个上调，90 个下调）、40 个 DE-miRNA（29 个上调，11 个下调）和 910 个 DE-mRNAs（554 个上调，356 个下调）。DE-mRNAs 共富集到 34 个功能术语和 9 条通路。此外，在与 KC 相关的 ceRNA 调控网络中涉及 6 个 mRNA（包括、、、、和）、5 个 miRNA（包括）、9 个 lncRNA（包括）和 轴。
、、、、、和可能与 KC 的发生发展有关。此外，轴可能与 KC 的发病机制有关。
