Multiomics global landscape of stemness-related gene clusters in adipose-derived mesenchymal stem cells

Abstract

Background: Adipose-derived mesenchymal stem cells (AD-MSCs) are a type of stem cell that is abundant and widely used. The molecular characteristics of AD-MSCs from different passages from donors of different ages have not been well elucidated.

Methods: Six kinds of AD-MSCs ((E1, E2, E3, Y1, Y2, and Y3) with E denoting cells derived from an elderly patient, Y denoting cells derived from a young patient, and 1, 2, and 3 representing passages 3, 6, and 10) were obtained from human abdominal adipose tissue. We obtained the protein expression profile, the mRNA expression profile, the lncRNA expression profile, and the methylation profile of each kind of AD-MSC by sequencing. After calculating the stemness indices, genes related to stemness were extracted. The multiomics correlation analysis was performed in the stemness-related genes. In addition, short time-series expression miner (STEM) analysis was performed for all cell passages and donor ages. To further explore the biological functions of the stemness-related genes, we performed Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Finally, the lncRNA-KEGG network and transcription factor (TF)-KEGG network were constructed based on the RNAInter database and TRRUST v2 database.

Results: The stemness of the Y1, E1, and Y2 cells was higher than that of the E2, Y3, and E3 cells. The stemness was the highest for Y1 cells and the lowest for E3 cells. STEM analysis showed that five stemness-related gene clusters were associated with the cell passages, and only one gene cluster was associated with age. The enrichment analysis results showed that the biological processes (BPs) and KEGG pathways were mainly involved in the proliferation, differentiation, and migration of cells. The global regulatory landscape of AD-MSCs was constructed: 25 TFs and 16 lncRNAs regulated 21 KEGG pathways through 27 mRNAs. Furthermore, we obtained a core stemness-related gene set consisting of ITGAV, MAD2L1, and PCNA. These genes were expressed at higher levels in Y1 cells than in E3 cells.

Conclusion: The multiomics global landscape of stemness-related gene clusters was determined for AD-MSCs, which may be helpful for selecting AD-MSCs with increased stemness.

Keywords: AD-MSCs; Adipose-derived mesenchymal stem cells; Multiomics global landscape; Short time-series miner analysis; Stemness gene clusters.

Fig. 1

The workflow of the study

Fig. 2

Multiomics analysis of genes related to stemness. a mRNA stemness indices of 6 types of AD-MSCs. b Manhattan plot of the differentially expressed stemness-related genes. The three most significant genes are marked. The numbers above the plot indicate the positively and negatively related genes. c Circos plot. Twenty genes are highly related to mRNA and protein expression. d Heatmap plot. STARD13 is negatively related to methylation but positively related to lncRNA expression. AD-MSCs, adipose-derived mesenchymal stem cells

Fig. 3

STEM analysis of genes related to stemness. a STEM analysis of AD-MSCs from different passages. b STEM analysis of ages. The diagram in the left panel represents log₂|(fold change)|, and the fitted curve is in red. The figure in the middle panel shows the expression of each gene cluster. The plot in the right panel shows the distribution of representative genes. STEM, short time-series expression miner

Fig. 4

Biological processes and pathways of the stemness-related genes in cells from different passages of AD-MSCs. a GO cluster-GSVA heatmap. The GO_BPs with more than 1 functional module were significantly enriched. b Bubble-GSVA heatmap. The KEGG pathways with more than 1 functional module were significantly enriched. c GO_BP network for different passages of AD-MSCs. d KEGG pathway network for different passages of AD-MSCs. Each node indicates a representative enrichment pathway. The connection of the nodes represents the number of genes in common between the pathways. The color represents the enrichment classification of the nodes. AD-MSCs, adipose-derived mesenchymal stem cells; GO, Gene Ontology; KEGG, Kyoto Encyclopedia of Genes and Genomes; BPs, biological processes

Fig. 5

Global regulatory landscape of the stemness-related gene clusters at the multiomics level. a Graphical summary of the lncRNAs associated with the stemness regulation of KEGG pathways through mRNAs. b Graphical summary of the transcription factors regulating KEGG pathways through mRNAs. c Comprehensive regulatory network of lncRNAs associated with stemness and transcription factors regulating KEGG pathways through mRNAs. d Nine pathways of interest in AD-MSCs. The triangles represent TFs. Circles represent KEGG-related genes. The squares represent the KEGG pathways. The kernels show the correlations between methylation and the transcriptome. The borders show the correlations between RNAs and proteins. The edges show the RNA correlations between nodes

Fig. 6

Multiomics characteristics of core stemness-related genes and their lncRNA regulators. a Three genes with the highest average semantic similarity. b Expression of core stemness-related genes in the mRNA expression profile, protein expression profile, and methylation profile in E3 and Y1 cells