RNA sequencing reveals a transcriptomic portrait of human mesenchymal stem cells from bone marrow, adipose tissue, and palatine tonsils

Abstract

Human mesenchymal stem cells (MSCs) are adult multipotent cells that have plasticity and inhabit the stroma of diverse tissues. The potential utility of MSCs has been heavily investigated in the fields of regenerative medicine and cell therapy. However, MSCs represent diverse populations that may depend on the tissue of origin. Thus, the ability to identify specific MSC populations has remained difficult. Using RNA sequencing, we analyzed the whole transcriptomes of bone marrow-derived MSCs (BMs), adipose tissue-derived MSCs (AMs), and tonsil-derived MSCs (TMs). We categorized highly regulated genes from these MSC groups according to functional gene ontology (GO) classification. AMs and TMs showed higher expression of genes encoding proteins that function in protein binding, growth factor, or cytokine activity in extracellular compartments than BMs. Interestingly, TM were highly enriched for genes coding extracellular, protein-binding proteins compared with AMs. Functional Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis also showed differentially enriched signaling pathways between the three MSC groups. Further, we confirmed surface antigens expressed in common and in a tissue-specific manner on BMs, AMs, and TMs by flow cytometry analysis. This study provides comprehensive characteristics of MSCs derived from different tissues to better understand their cellular and molecular biology.

Figure 1

RNA-seq data analysis of BMs, AMs, and TMs. (A) Heatmap of hierarchical clustering indicate differentially expressed genes (rows) between BMs, AMs, and four samples of TMs. (fold-change > 2, P < 0.05). Red indicates up-regulation and green indicates down-regulation. (B) Dendrogram of hierarchical clustering indicates the interclass correlation between the three MSC groups. (C) The differentially expressed genes between AMs, BMs, and TMs are shown as up-regulated or down-regulated.

Figure 2

Functional enrichment analysis of highly regulated genes: AMs and BMs. Distribution of gene ontology (GO) terms of DEG between AMs and BMs were annotated in three ontology categories: (A) Biological Process, (B) Cellular Component, and (C) Molecular Function (P-value < 0.001).

Figure 3

Functional enrichment analysis of highly regulated genes: TMs and BMs. Distribution of gene ontology (GO) terms of DEG between TMs and BMs were annotated in three ontology categories: (A) Biological Process, (B) Cellular Component, and (C) Molecular Function (P-value < 0.001).

Figure 4

Functional enrichment analysis of highly regulated genes: TMs and AMs. Distribution of gene ontology (GO) terms of DEG between TMs and AMs were annotated in three ontology categories: (A) Biological Process, (B) Cellular Component, and (C) Molecular Function (P-value < 0.001).

Figure 5

Functional enrichment analysis of highly regulated genes: TMs 3,4 and TMs 1, 2. Distribution of gene ontology (GO) terms of DEG between TMs and AMs were annotated in three ontology categories: (A) Biological Process, (B) Cellular Component, and (C) Molecular Function (*P < 0.05, **P < 0.01, ***P < 0.001).

Figure 6

Venn diagrams of surface marker expression on BMs, AMs, and TMs. Lyoplate analysis of surface marker expression on BMs, AMs, and TMs was performed by flow cytometry. The commonly expressed markers among all MSC groups, markers shared between two MSC groups, and tissue-specific markers are shown.