Japanese journal of ophthalmology · 2025
Transcriptome RNA sequencing reveals the global molecular responses and circRNA-miRNA-lncRNA interaction network in cataract.
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Jing Ruihua, Yang Zhuoyan, Ding Zhaodan, Deng Jiahui, Ma Bo
Аннотация
PURPOSE: Cataract, a clouding of the intraocular lens leading to blindness, is the most common eye disease globally. While whether and how circRNAs function in cataract is not fully understood.
STUDY DESIGN: Experimental study METHODS: We carried out circRNA RNA and lncRNA sequencing in a ribosome removal-specific transcriptome library. We then analyzed differentially expressed genes and their coding capacity. The enrichment results were visualized by use of the R ggplot2 package. KEGG pathway enrichment analysis was performed by use of the DAVID online tool. Quantitative real-time polymerase chain reactions (RT-PCR) were performed to verify the RNA levels of the top differentially expressed genes. The target genes miRNAs of circRNAs were found in circAtlas, and the targeted lncRNAs of miRNAs were searched in ENOCRI.
RESULTS: We identified 86 differentially expressed known circRNAs and 612 lncRNAs in cataract lenses by use of RNA-sequencing. Functional annotation revealed that differentially expressed circRNAs might function through the Wnt signaling pathway and that lncRNAs may be enriched in the metabolic pathways, Wnt signaling pathway, focal adhesion, and ECM-receptor interaction pathways. The RT-PCR verification results showed that 7 circRNAs and 7 lncRNAs were consistent with the RNA-seq data. Translation prediction showed high scores for has_circ_0026233 and has_circ_0006388. Finally, we found that the hsa_circ_0006388-AC008738.7-miR-378g network is probably the key regulator of cataract formation.
CONCLUSION: This study identified the hsa_circ_0006388-AC008738.7-miR-378g network as possibly functioning in cataract formation, providing new intervention targets.
STUDY DESIGN: Experimental study METHODS: We carried out circRNA RNA and lncRNA sequencing in a ribosome removal-specific transcriptome library. We then analyzed differentially expressed genes and their coding capacity. The enrichment results were visualized by use of the R ggplot2 package. KEGG pathway enrichment analysis was performed by use of the DAVID online tool. Quantitative real-time polymerase chain reactions (RT-PCR) were performed to verify the RNA levels of the top differentially expressed genes. The target genes miRNAs of circRNAs were found in circAtlas, and the targeted lncRNAs of miRNAs were searched in ENOCRI.
RESULTS: We identified 86 differentially expressed known circRNAs and 612 lncRNAs in cataract lenses by use of RNA-sequencing. Functional annotation revealed that differentially expressed circRNAs might function through the Wnt signaling pathway and that lncRNAs may be enriched in the metabolic pathways, Wnt signaling pathway, focal adhesion, and ECM-receptor interaction pathways. The RT-PCR verification results showed that 7 circRNAs and 7 lncRNAs were consistent with the RNA-seq data. Translation prediction showed high scores for has_circ_0026233 and has_circ_0006388. Finally, we found that the hsa_circ_0006388-AC008738.7-miR-378g network is probably the key regulator of cataract formation.
CONCLUSION: This study identified the hsa_circ_0006388-AC008738.7-miR-378g network as possibly functioning in cataract formation, providing new intervention targets.