RNA-sequencing analysis reveals the long noncoding RNA profile in the mouse myopic retina

Abstract

Aim: Myopia is a prevalent public health problem. The long noncoding RNA (lncRNA) mechanisms for dysregulated retinal signaling in the myopic eye have remained elusive. The aim of this study was to analyze the expression profiles and possible pathogenic roles of lncRNAs in mouse form-deprived myopia (FDM) retinas.Methods: A mouse FDM model was induced and retinas from the FDM right eyes and the contralateral eyes were collected for RNA sequencing. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, and lncRNA-mRNA coexpression network analyses were conducted to explore the biological functions of the differentially expressed lncRNAs. In addition, the levels of differentially expressed lncRNAs in the myopic retinas were validated by quantitative real-time PCR (qRT–PCR). Fluorescence in situ hybridization (FISH) was used to detect the localization of lncRNAs in mouse retinas.Results: FDM eyes exhibited reduced refraction and increased ocular axial length compared to control fellow eyes. RNA sequencing revealed that there were 655 differentially expressed lncRNAs between the FDM and control retinas. Functional enrichment analysis indicated that the differentially expressed RNAs were mostly enriched in cellular processes, cytokine-cytokine receptor interactions, retinol metabolism, and rhythmic processes. Differentially expressed lncRNAs were validated by qRT–PCR. Additionally, RNA FISH showed that XR_384718.4 (Gm35369) localized in the ganglion cell (GCL) and inner nuclear layers (INL).Conclusion: This study identified the differential expression profiles of lncRNAs in myopic mouse retinas. Our results provide scientific evidence for investigations of myopia and the development of putative interventions in the future.

RNA-Sequencing Analysis Reveals the Role of Mitochondrial Energy Metabolism Alterations and Immune Cell Activation in Form-Deprivation and Lens-Induced Myopia in Mice

“…Previous studies have identified possible differentially expressed genes and pathways involved in myopia models [8][9][10][11]. However, there is not much of a consensus among the existing studies due to variations in animal models and experimental designs.…”

LncRNA-XR_002792574.1-mediated ceRNA network reveals potential biomarkers in myopia-induced retinal ganglion cell damage

“…Recent studies have shown that lncRNAs play a crucial role in the pathogenesis of myopia [ 15 , 37 ]. It has been found that lncRNA Gm35369 might be related to myopia, and this lncRNA is mainly located in ganglion cells and horizontal cells [ 14 ]. Studies have reported that RGC alterations are associated with the occurrence and development of myopia, including changes in the number of RGCs, abnormal axonal projections and changes in protein expression in RGCs [ 19 – 22 , 38 ].…”

“…For example, the abnormal expression profiles of lncRNAs in the retinas of form-deprived myopia (FDM) mouse models were analyzed in a prior study. It was found that lncRNA Gm35369 might be related to myopia and that this lncRNA was mainly located in ganglion cells and horizontal cells [ 14 ]. Assessment of the differential expression of lncRNAs in the ocular posterior poles of two guinea pig myopia models (FDM and lens-induced myopia (LIM)) has revealed that lncRNA-related extracellular matrix (ECM), kinase activity, metabolism, ECM receptor interactions, glycosaminoglycan degradation and multiple functional pathways are involved in the pathogenesis of myopia [ 15 ].…”

Epitranscriptomic investigation of myopia-associated RNA editing in the retina

“…FASTQ files of RNA-Seq raw reads were retrieved from the Gene Expression Omnibus (GEO). 1 The dataset (PRJNA832969) contains 12 retinal samples of male C57BL/6 J mice from six FDM and six fellow controls, and each sample contains three retinas ( Li et al, 2022 ). According to the original study, FDM was induced in the male C57BL/6 J mice at three weeks of age.…”