Ouyang Shuai, Ma Jingyu, Sun Qihang, Li Jinyan, Chen Yijia, Luo Lixia
State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Centre, Sun Yat-sen University, Guangzhou, China.
Front Genet. 2022 Jun 7;13:896780. doi: 10.3389/fgene.2022.896780. eCollection 2022.
Keratoconus (KC) is the most common corneal ectatic disease, with its pathological mechanisms unclear. We mainly performed bioinformatics approaches to reveal core RNA targets and hub competitive endogenous RNA (ceRNA) network and explored the potential regulatory mechanisms of ceRNA in KC. The high-throughput sequencing datasets GSE77938 and GSE151631 were downloaded from the Gene Expression Omnibus (GEO) database. The differential expression of mRNAs and lncRNAs was identified using the DESeq2 package. Functional enrichment analyses and protein-protein interaction (PPI) were executed. Then, the hub genes were filtered and molecular docking analysis was performed. Moreover, we predicted miRNAs through a website database and validated them using quantitative PCR (qPCR). Eventually, the lncRNA-miRNA-mRNA regulatory network was constructed by Cytoscape. We revealed that 428 intersected differentially expressed mRNA (DEGs) and 68 intersected differentially expressed lncRNA (DELs) were shared between the two datasets. Functional enrichment results innovatively showed that the ubiquitin-dependent protein catabolic process was upregulated in KC. The pathway enrichment showed that DEGs were mainly involved in NF-kB signaling and neurodegenerative diseases. In addition, we uncovered the top 20 hub genes in which , , , and were validated by qPCR. Particularly, a small-molecule drug triptolide was predicted by molecular docking to be a candidate drug for treating KC. Moreover, we innovatively predicted and validated four core miRNAs (miR-4257, miR-4494, miR-4263, and miR-4298) and constructed a ceRNA network that contained 165 mRNA, eight lncRNAs, and four core miRNAs. Finally, we proposed a potential regulatory mechanism for KC. Overall, we uncovered a hub ceRNA network that might underlie a critical posttranslational regulatory mechanism in KC, in which miR-4257, miR-4494, miR-4263, and miR-4298 could be valuable biomarkers and provided core RNAs therapeutic targets for KC.
圆锥角膜（KC）是最常见的角膜扩张性疾病，其病理机制尚不清楚。我们主要采用生物信息学方法来揭示核心RNA靶点和枢纽竞争性内源性RNA（ceRNA）网络，并探讨ceRNA在KC中的潜在调控机制。从基因表达综合数据库（GEO）下载了高通量测序数据集GSE77938和GSE151631。使用DESeq2软件包鉴定mRNA和lncRNA的差异表达。进行了功能富集分析和蛋白质-蛋白质相互作用（PPI）分析。然后，筛选出枢纽基因并进行分子对接分析。此外，我们通过网站数据库预测miRNA，并使用定量PCR（qPCR）进行验证。最终，用Cytoscape构建lncRNA-miRNA-mRNA调控网络。我们发现两个数据集中共有428个交集差异表达mRNA（DEG）和68个交集差异表达lncRNA（DEL）。功能富集结果创新性地表明，泛素依赖性蛋白分解代谢过程在KC中上调。通路富集表明，DEG主要参与NF-κB信号通路和神经退行性疾病。此外，我们发现了前20个枢纽基因，其中 、 、 和 通过qPCR得到验证。特别地，通过分子对接预测小分子药物雷公藤内酯醇是治疗KC的候选药物。此外，我们创新性地预测并验证了四个核心miRNA（miR-4257、miR-4494、miR-4263和miR-4298），并构建了一个包含165个mRNA、8个lncRNA和4个核心miRNA的ceRNA网络。最后，我们提出了KC的潜在调控机制。总体而言，我们发现了一个枢纽ceRNA网络，它可能是KC中关键的翻译后调控机制的基础，其中miR-4257、miR-4494、miR-4263和miR-4298可能是有价值的生物标志物，并为KC提供了核心RNA治疗靶点。
