Identification and function of differentially expressed long noncoding RNAs in the chondrogenesis of human adipose-derived mesenchymal stem cells

doi:10.12307/2023.370

Abstract

Abstract: BACKGROUND: The chondrogenic differentiation of human adipose-derived mesenchymal stem cells is affected by many factors. Studies have confirmed that long noncoding RNAs (lncRNAs) play important roles in epigenetic regulation, transcription and post-transcriptional regulation. However, there are few reports on the changes of its expression profile and its regulatory role during the chondrogenic differentiation of human adipose-derived mesenchymal stem cells.
OBJECTIVE: To preliminarily analyze the differentially expressed lncRNAs and their potential functions during the chondrogenesis of human adipose-derived mesenchymal stem cells.
METHODS: The human adipose-derived mesenchymal stem cells at 0 day (undifferentiated group) and 14 days (differentiated group) after chondrogenic differentiation were used as research objects. RNA-seq was used to screen lncRNAs and messenger RNAs (mRNAs) with expressed fold change larger than twice between groups. Quantitative real time PCR (qRT-PCR) was used to verify the sequencing results. Bioinformatics analyses including GO function analysis and KEGG pathway analysis were performed for differentially expressed genes to screen adjacent genes and co-expressed genes of lncRNAs.
RESULTS AND CONCLUSION: (1) Compared with the undifferentiated group, a total of 816 lncRNAs and 5 138 mRNAs were significantly differentially expressed in the differentiated group. (2) GO function and KEGG signaling pathway analysis showed that differentially expressed genes were enriched in several biological processes including cellular processes, biological regulation, and metabolic processes, and multiple pathways including focal adhesion kinase, insulin signaling pathway, and Wnt signaling pathway. (3) Analysis results of adjacent genes and co-expressed genes of differentially expressed lncRNAs indicated that some lncRNAs such as SNHG16 and XLOC_003886 might play critical roles in the chondrogenic differentiation of adipose-derived mesenchymal stem cells and cartilage degeneration. (4) These findings suggest that the expression profiles of lncRNAs were significantly altered during the chondrogenesis of adipose-derived mesenchymal stem cells. The biological functions of differentially expressed lncRNAs may be closely related to the functions of adjacent genes and co-expressed genes, thereby regulating the chondrogenic differentiation of adipose-derived mesenchymal stem cells. However, further experiments should be employed to uncover the regulatory roles and underlying molecular mechanisms of differentially expressed lncRNAs.

Key words: long noncoding RNA, adipose-derived mesenchymal stem cell, chondrogenesis, RNA-seq, bioinformatics analysis

CLC Number:

Sun Hong, Deng Jin, Peng Guoxuan, Zhuang Yong, Liu Miao, Ning Xu, Yang Hua. Identification and function of differentially expressed long noncoding RNAs in the chondrogenesis of human adipose-derived mesenchymal stem cells[J]. Chinese Journal of Tissue Engineering Research, 2023, 27(15): 2325-2332.

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