RNA sequencing analysis of long non-coding RNA expression in ocular posterior poles of guinea pig myopia models

• Published in: Molecular vision Vol. 26; pp. 117 - 134
• Main Authors: Geng, Chao, Li, Yahong, Guo, Fang, Wang, Jindan, Yue, Yiyun, Zhou, Kewen, Wei, Ruihua, Zhang, Yan
• Format: Journal Article
• Language: English
• Published: United States Molecular Vision 2020
• Subjects: Animal models; Animals; Biometry; Cornea; Disease Models, Animal; Extracellular matrix; Extracellular Matrix - metabolism; Eye; Gene Expression Regulation - genetics; Gene Ontology; Genomes; Glycosaminoglycans; Glycosaminoglycans - metabolism; Guinea Pigs; Kinases; Latex; Male; mRNA; Mucin; Myopia; Myopia - genetics; Myopia - metabolism; Myopia - pathology; Non-coding RNA; Polymorphism, Single Nucleotide; Polysaccharides - biosynthesis; Real-Time Polymerase Chain Reaction; Refraction, Ocular - genetics; Refraction, Ocular - physiology; Retina - metabolism; Retina - pathology; RNA, Long Noncoding - genetics; RNA, Long Noncoding - metabolism; RNA-Seq; Sclera - metabolism; Sclera - pathology; Sequence analysis; Signal Transduction - genetics
• ISSN: 1090-0535; 1090-0535

To detect the differential expression of long non-coding RNAs (lncRNAs) in the ocular posterior poles of two guinea pig myopia models and explore the pathogenic role of lncRNAs in myopia. Form-deprived myopia (FDM) and lens-induced myopia (LIM) models were induced in guinea pig right eyes by wearing a translucent latex balloon head mask and a -10.00 diopter (D) lens, respectively. Ocular biometric parameters were measured biweekly. At 6 weeks after the induction of myopia, the guinea pig eyeballs were processed for hematoxylin and eosin staining to examine the ocular morphology. The ocular posterior poles from the normal control, FDM, and LIM groups were collected to analyze the differential expression of lncRNAs between the groups with high-throughput RNA sequencing (RNA-seq). Further, the lncRNA-mRNA colocation network was delineated to predict the functions of the differentially expressed lncRNAs. Last, Gene Ontology (GO) functional enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed on the colocated mRNAs of the differentially expressed lncRNAs. Additionally, the expression of the most differentially expressed lncRNAs in the myopia-induced eyes and the contralateral eyes was validated with quantitative real-time PCR (qPCR). Compared with the normal controls and the contralateral eyes, the myopia-induced eyes in the FDM and LIM groups exhibited decreased scleral and choroidal thicknesses, reduced refraction, and increased ocular axial length but without changes in the corneal curvature radius at 6 weeks after myopia was induced. RNA-seq showed that 372 and 247 lncRNAs were differentially expressed in the FDM and LIM groups, respectively, in comparison to the normal counterparts. There were 380 differentially expressed lncRNAs in the LIM group compared to the FDM group. The GO and KEGG analyses showed that the colocated mRNAs of the differentially expressed lncRNAs were enriched in cellular components such as the extracellular matrix (ECM) structural constituent; in molecular functions such as kinase activity, metabolism, and growth; as well as in pathways including ECM-receptor interaction, glycosaminoglycan degradation, and mucin type O-Glycan biosynthesis. The expression patterns of the selected lncRNAs were verified with qPCR. High-throughput RNA-seq revealed previously undescribed lncRNA expression profiling in guinea pig FDM and LIM models. These results may shed light on the molecular pathogenesis of myopia and provide clues for interventional targets for this highly prevalent visual disorder.