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The aging mouse lens transcriptome. Experimental eye research Age is a major risk factor for cataract (ARC). However, the influence of aging on the lens transcriptome is under studied. Lens epithelial (LEC) and fiber cells (LFC) were isolated from young (3 month old) and aged (24 month old) C57BL/6J mice, and the transcriptome elucidated via RNAseq. EdgeR estimated differential gene expression in pairwise contrasts, and Advaita's Ipathway guide and custom R scripts were used to evaluate the potential biological significance of differentially expressed genes (DEGs). This analysis revealed age-dependent decreases in lens differentiation marker expression in both LECs and LFCs, with gamma crystallin transcripts downregulating nearly 50 fold in aged LFCs. The expression of the transcription factors Hsf4 and Maf, which are known to activate lens fiber cell preferred genes, are downregulated, while FoxE3, which represses gamma crystallin expression, is upregulated in aged fibers. Aged LECs upregulate genes controlling the immune response, complement pathways, and cellular stress responses, including glutathione peroxidase 3 (Gpx3). Aged LFCs exhibit broad changes in the expression of genes regulating cell communication, and upregulate genes involved in antigen processing/presentation and cholesterol metabolism, while changes in the expression of mitochondrial respiratory chain genes are consistent with mitochondrial stress, including upregulation of NDufa4l2, which encodes an alternate electron transport chain protein. However, age did not profoundly affect the response of LECs to injury as both young and aged LECs upregulate inflammatory gene signatures at 24 h post injury to similar extents. These RNAseq profiles provide a rich data set that can be mined to understand the genetic regulation of lens aging and how this impinges on the pathophysiology of age related cataract. 10.1016/j.exer.2021.108663
Identification and Integrated Analysis of the miRNA-mRNA Regulatory Network in Lens from an HO-Induced Zebrafish Cataract Model. Current eye research PURPOSE:This study aimed to explore the regulatory mechanisms of age-related cataract (ARC) formation. METHODS:Cataracts in zebrafish were induced by injecting hydrogen peroxide into the fish anterior chamber. The mRNA and miRNA expression profiles of the lens from HO-injected and PBS-injected zebrafishes were detected by RNA sequencing. The LIMMA package was applied to identify differentially expressed genes (DEGs). Gene Ontology categories were enriched by the R "cluster Profiler" package and Kyoto Encyclopedia of Genes and Genomes pathway enrichment was performed based on hypergeometric distribution using the R "phyper" function. The protein-protein interaction network of DEGs was built the STRING. Target genes of differentially expressed miRNAs (DEmiRs) were predicted by miRanda. Furthermore, DEGs were selected as DEmiR targets and a DEmiR-DEG regulatory network was constructed Cytoscape. RESULTS:In total, 3689 DEGs (such as opn1mw4, LOC103908930, si:dkeyp-1h4.8, crispld1b, cyp1a, and gdpd3a) including 2478 upregulated and 1211 downregulated genes were identified. 177 DEmiRs (such as dre-miR-96-3p, dre-miR-182-5p, dre-miR-9-7-3p, and dre-miR-124-4-5p) including 108 upregulated and 69 downregulated miRNAs were detected. The DEGs are involved in cell death, DNA repair, and cell development-related pathways. A protein-protein interaction network including 79 node genes was constructed to explore the interactions of DEGs. Furthermore, a DEmiR-DEG regulatory network focusing on the DNA repair process was constructed, including 21 hub DEGs and 15 hub DEmiRs. CONCLUSIONS:We identified several DEGs and constructed a miRNA-mRNA regulatory network related to the DNA repair process in a zebrafish cataract model. These genes participate in the oxidative stress response of lens epithelium cells and finally contribute to the formation of zebrafish cataracts. The hub DEGs and hub DEmiRs could be potential therapeutic targets for ARC. 10.1080/02713683.2022.2050263
Genome-Wide Repertoire of Transfer RNA-Derived Fragments in a Mouse Model of Age-Related Cataract. Current eye research PURPOSE:To investigate the roles of tRNA-derived small RNAs (tsRNAs) containing transfer RNA-derived fragments (tRFs) and tRNA halves in age-related cataracts (ARCs). METHODS:Lens capsule tissue from Emory mice at 3 months and 8 months of age were dissected for integrated tsRNA and gene transcriptome sequencing. A quantitative real-time PCR assay (qRT-PCR) was performed for validating sequencing results. Bioinformatics analysis was constructed to reveal the roles of tsRNAs. RESULTS:A total of 422 differential expression (DE) tsRNAs were changed, in which 156 were elevated while 266 were declined in 8-month-old mice. Subsequently, the gene sequencing data exhibited 375 upregulated and 456 downregulated DE genes. Validation by qRT-PCR in 5 selected upregulated tRFs was consistent with tsRNAs sequencing results. Moreover, bioinformatics analysis identified 25 downregulated target genes of the 5 validated tRFs. Furthermore, GO analysis revealed that these target genes were mainly enriched in camera-type eye development, sensory organ development, and so on. CONCLUSION:Our study provides a novel perspective on the role of tsRNAs in the pathogenesis of ARC, and thus therapeutic potential targets for ARC. 10.1080/02713683.2022.2110263