Di-san junyi daxue xuebao (Aug 2021)
Comprehensive bioinformatics analysis of vitiligo melanocytes based on high-throughput sequencing
Abstract
Objective To screen the differentially expressed (DE) coding and non-coding RNAs in human vitiligo melanocytes and analyze their interactions and verify the expression of the identified key RNAs in order to explore their possible role in the pathogenesis of vitiligo. Methods High throughput sequencing was performed on human vitiligo melanocyte lines and normal human melanocyte lines. DE analysis was performed by R software. Protein-protein interaction (PPI) network was constructed by using the search tool STRING. The interaction loop of miRNA-mRNA and miRNA-lncRNA was identified by bioinformatics algorithm miRanda. The competitive endogenous RNA (CeRNA) network was constructed by Cytoscape software, and the functional enrichment and pathway analysis of DE mRNAs were performed by David database. Finally, the identified key RNAs were verified by Q-PCR. Results A total of 5 958 DE mRNAs, 1 650 DE lncRNAs and 450 DE miRNAs were screened out by DE analysis. The top10 hub genes (JUN, HIST2H3PS2, SOX2, EGR1, MMP9, NGF, BMP2, HSPA5, EDN1 and SERPINE1) in the PPI network are indicated closely related to the pathogenesis of vitiligo. Furthermore, 7 key lncRNAs that interact with top 20 hub genes are found. Among them, 3 lncRNAs (ENST0000623111, NONHSAT245258.1 and NONHSAT189782.1) with the most abundant molecular functions and signaling pathways were constructed into CeRNA subnetwork, and the expression of hsa-miR-92b-5p predicted in the CeRNA sub-network is significantly different in vitiligo melanocytes. In addition, the results of Q-PCR were basically consistent with our analysis. Conclusion The identified hub genes and non-coding RNAs in our study may play important roles in the pathogenesis of vitiligo. Our findings provide novel insights and strategies for researches on vitiligo.
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