Identification and Integrated Analysis of the miRNA-mRNA Regulatory Network in Lens from an H₂O₂-Induced Zebrafish Cataract Model

Abstract

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 H₂O₂-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 via 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 via 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.

Keywords:

• Age-related cataract
• oxidative damage
• RNA-sequencing
• zebrafish
• regulatory network

Author contributions

Peirong Lu and Huaijin Guan designed the project. Mu Zhang and Jiawei Luo established the animal model. Jiawei Luo and Xiaoqing Chen acquired the data. Yanhua Chen, Pengfei Li, and Guowei Zhang analyzed and interpreted the data. Jiawei Luo and Mu Zhang wrote the article.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data availability statement

The data that support the findings of this study are available from the corresponding author upon reasonable request.

Additional information

Funding

This work was supported by the National Natural Science Foundation of China under Grant [81974129, 81770906, and 81500706]; the Postdoctoral Science Foundation of China under Grant [2020M671562]; and the Postdoctoral Science Foundation of Jiangsu Province under Grant [2020Z318].