Identification and analysis of senescence-related genes in caudal fin cells of triploid crucian carp

Abstract

This research aims to identify the hub genes associated with the senescence of triploid caudal fin cells. Transcriptomic data are obtained from the high and low generation (P6, P60) of triploid crucian carp caudal fin cells by high-throughput sequencing technology. Initially, all differential genes between the high and low generations are screened, yielding 4140 significantly upregulated genes and 3724 significantly downregulated genes. Subsequently, an aging gene set containing 950 genes is downloaded from the CellAge database to extract the differentially expressed genes associated with caudal fin cell aging, totaling 29 genes. GO and KEGG enrichment analyses are performed on these 29 aging differential genes. The GO analysis shows enrichment mainly in cellular processes related to aging, such as regulation of cell division, chromatin organization, cell cycle regulation. KEGG analysis reveals that the 29 aging-related genes are primarily involved in cell cycle and cellular senescence pathways. A PPI network of aging-related genes is constructed using the STRING database and Cytoscape software. Top-ranked genes were identified by using Degree, MCC, MNC, and Closeness algorithms in the Cytohubba plugin in Cytoscape, resulting in hub genes EZH2, JUN, MYD88, RBL2, BMP4, CCND1, NFKB2, MMP9. Lastly, qRT-PCR validation of these eight hub genes further confirmed the involvement of four genes: EZH2, RBL2, BMP4, and CCND1. The hub gene screened in this study may become a potential biomarker of fish caudal fin cell senescence, which provides a valuable experimental basis for the senescence of fish caudal fin cells, especially the senescence of caudal fin cells in polyploid fish, and the reproduction and breeding improvement of polyploid fish. It also provides meaningful data for elucidating the molecular mechanism of polyploid formation in animals, as well as the formation of aging and tumour in human beings.