Roodnat Anton W, Doyle Chelsey, Callaghan Breedge, Lester Karen, Henry Megan, Sheridan Carl, McKenna Declan J, Willoughby Colin E, Atkinson Sarah D
Biomedical Sciences Research Institute, Centre for Genomic Medicine, Ulster University, Coleraine, Northern Ireland, United Kingdom.
Department of Eye and Vision Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom.
PLoS One. 2025 Jan 30;20(1):e0318125. doi: 10.1371/journal.pone.0318125. eCollection 2025.
Pseudoexfoliation glaucoma is a severe form of secondary open angle glaucoma and is associated with activation of the TGF-β pathway by TGF-β1. MicroRNAs (miRNAs) are small non-coding RNA species that are involved in regulation of mRNA expression and translation. To investigate what glaucomatous changes occur in the trabecular meshwork and how these changes may be regulated by miRNAs, we performed a bioinformatics analysis resulting in a miRNA-mRNA interactome. Primary human trabecular meshwork cells originating from normal donors were treated with TGF-β1 at 5 ng/mL for 24h; total RNA was extracted followed by RNA-Seq and miRNA-Seq. For both mRNA and miRNA species, differential expression was determined using a bioinformatics pipeline consisting of FastQC, STAR, FeatureCounts, edgeR (for miRNA) and DESeq2 (for mRNA). Putative mRNA-miRNA interactions between differentially expressed mRNA and miRNA species were determined using interaction databases miRWalk, miRTarBase, TarBase and TargetScan. To classify mRNA species by function and pathway, gene enrichment was performed using Enrichr. The resulting miRNA-mRNA interactome consisted of 1202 interactions. Some highly connected microRNAs were hsa-let-7e-5p, hsa-miR-20a-5p, hsa-miR-122-5p, and hsa-miR-29c-3p. Most differentially expressed genes were indicated to be regulated by miRNAs. The sub-interactomes of genes involved in specific pseudoexfoliation glaucoma related enrichment terms such as oxidative stress, unfolded protein response, signal molecules and ECM remodelling were determined. This is the first study to present a genome-wide microRNA-mRNA regulatory network for human trabecular meshwork cells treated with TGF-β1 and may serve to generate unbiased hypotheses about regulatory functions and mRNA targets of miRNAs in pseudoexfoliation glaucoma and may help to develop miRNA-based therapeutics.
假性剥脱性青光眼是继发性开角型青光眼的一种严重形式，与转化生长因子-β1（TGF-β1）激活TGF-β信号通路有关。微小RNA（miRNA）是一类小的非编码RNA，参与mRNA表达和翻译的调控。为了研究小梁网中发生了哪些青光眼性改变，以及这些改变如何受到miRNA的调控，我们进行了生物信息学分析，得出了一个miRNA-mRNA相互作用组。将来自正常供体的原代人小梁网细胞用5 ng/mL的TGF-β1处理24小时；提取总RNA，随后进行RNA测序和miRNA测序。对于mRNA和miRNA种类，使用由FastQC、STAR、FeatureCounts、edgeR（用于miRNA）和DESeq2（用于mRNA）组成的生物信息学流程来确定差异表达。使用相互作用数据库miRWalk、miRTarBase、TarBase和TargetScan来确定差异表达的mRNA和miRNA种类之间的假定mRNA-miRNA相互作用。为了按功能和通路对mRNA种类进行分类，使用Enrichr进行基因富集分析。所得的miRNA-mRNA相互作用组由1202个相互作用组成。一些高度连接的微小RNA有hsa-let-7e-5p、hsa-miR-20a-5p、hsa-miR-122-5p和hsa-miR-29c-3p。大多数差异表达基因表明受miRNA调控。确定了参与特定假性剥脱性青光眼相关富集术语（如氧化应激、未折叠蛋白反应、信号分子和细胞外基质重塑）的基因的子相互作用组。这是第一项针对用TGF-β1处理的人小梁网细胞呈现全基因组miRNA-mRNA调控网络的研究，可能有助于产生关于假性剥脱性青光眼中miRNA的调控功能和mRNA靶点的无偏假设，并可能有助于开发基于miRNA的治疗方法。
