PUBLICATION
Comprehensive analysis of the miRNA-mRNA regulatory network involved in spontaneous recovery of an H2O2-induced zebrafish cataract model
- Authors
- Luo, J., Zhang, M., Chen, Y., Zhang, G., Zhou, T., Kang, L., Chen, X., Guan, H.
- ID
- ZDB-PUB-240211-12
- Date
- 2024
- Source
- Experimental Eye Research 240: 109820 (Journal)
- Registered Authors
- Zhou, Tianqiu
- Keywords
- Opacity reversal, Oxidative stress, Zebrafish cataract, miRNA-mRNA network
- MeSH Terms
-
- Animals
- Gene Expression Profiling/methods
- Gene Regulatory Networks
- Hydrogen Peroxide
- MicroRNAs*/genetics
- MicroRNAs*/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Zebrafish/genetics
- PubMed
- 38340946 Full text @ Exp. Eye. Res.
Citation
Luo, J., Zhang, M., Chen, Y., Zhang, G., Zhou, T., Kang, L., Chen, X., Guan, H. (2024) Comprehensive analysis of the miRNA-mRNA regulatory network involved in spontaneous recovery of an H2O2-induced zebrafish cataract model. Experimental Eye Research. 240:109820.
Abstract
Objective To identify the hub miRNAs and mRNAs contributing to the spontaneous recovery of a zebrafish cataract model.
Methods Zebrafishes were divided into three groups, i.e., Group A, which included normal control fish (day 0), and Groups B and C, where fish were injected with hydrogen peroxide into the anterior chamber and reared for 14 and 30 days, respectively. Fish eyes were examined by stereomicroscope photography and OCT. RNA profiles of fish lenses were detected by RNA sequencing. Differentially expressed genes (DEGs) and differentially expressed miRNAs (DEmiRs) were identified among three groups. The DEGs and DEmiRs, which changed in opposite positions between "B vs. A" and "C vs. B" were defined as ODGs (opposite positions changed DEGs) and ODmiRs (opposite positions changed DEmiRs). Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) analysis were carried out by R language. The protein-protein interaction network (PPI) was constructed using STRING. Potential targets of miRNAs were obtained using miRanda. miRNA-mRNA networks were constructed using Cytoscape.
Results The fish lens opacity formed on day 14 and recovered to transparent on day 30. Compared to group B, 1366 DEGs and 54 DEmiRs were identified in group C. "C vs. B" DEGs were enriched in gene clusters related to development and oxidative phosphorylation. Target genes of DEmiRs were enriched in clusters such as development and cysteine metabolism. Among three groups, 786 ODGs and 27 ODmiRs were identified, and 480 ODGs were predicted as targets of ODmiRs. Target ODGs were enriched in pathways related to methionine metabolism, ubiquitin, sensory system development, and structural constituents of the eye lens. In addition, we established an ODmiRs-ODGs regulation network.
Conclusion We identified several hub mRNAs and altered miRNAs in the formation and reversal of zebrafish cataracts. These hub miRNAs/mRNAs could be new targets for the non-surgical treatment of ARC.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping