Comprehensive analysis of lncRNA-miRNA-mRNA ceRNA network in exosomes from lipoma tissue reveals differential impacts on biological functions

Abstract Background Our previous study found that both exosomes from lipoma tissue (Exo-LT) and exosomes from adipose tissue (Exo-AT) can promote the proliferation, migration, and adipogenesis of ADSCs. There is no significant difference between Exo-LT and Exo-AT in promoting the adipogenesis of ADSCs, but Exo-LT has a stronger ability to promote the proliferation and migration of ADSCs than Exo-AT. To elucidate the reason for this difference, we envisioned to explore the gene regulation mechanism of Exo-LT's stronger pro-proliferation effect than Exo-AT by comprehensively analyzing the differential genes between Exo-LT and Exo-AT. Methods Herein, we used high-throughput sequencing technology to analyze the expression of lncRNA, miRNA, and mRNA in Exo-LT and Exo-AT and screen out significantly differentially expressed genes, and then searched mRNAs related to cell proliferation and adipogenesis in GO enrichment and KEGG pathway analysis results for subsequent targeted analysis and construction of ceRNA networks. Results A total of 10 mRNAs were screened that met both significant differential expression conditions (|logFC|>2, p < 0.05) and abundance quality control (CPM༞100), of which 6 were up-regulated in Exo-LT and 4 were down-regulated in Exo-LT. Afterwards in the ceRNA regulatory network, we noticed 5 meaningful lncRNAs that were highly correlated with cell proliferation and adipogenesis, including HOXA11-AS, GAS5, HOTAIR, MALAT1, and PVT1, among which HOXA11-AS was significantly up-regulated in Exo-LT, while GAS5, HOTAIR, MALAT1, and PVT1 were expressed at high levels in both the Exo-LT and Exo-AT group. Interestingly, our follow-up analysis found that many of the lncRNA-miRNA targeting relationships predicted by these 5 lncRNAs in the ceRNA network have been well validated in a large number of previous studies. Conclusions Our first analysis of lncRNA, miRNA, and mRNA expression profiles and ceRNA networks in Exo-LT provides a preliminary explanation for the differences between Exo-LT and Exo-AT in promoting ADSCs proliferation and adipogenesis, as well as a new theoretical basis for the formation mechanism of lipoma tissue.