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Single-Cell Transcriptomic Analysis Reveals The Cellular Heterogeneity Of Mesenchymal Stem Cells

Single-Cell Transcriptomic Analysis Reveals The Cellular Heterogeneity Of Mesenchymal Stem Cells

In February 2022, the single-cell platform of CapitaoBio Technology supported the Beijing Institute of Genomics, Chinese Academy of Sciences to publish research on the heterogeneity of mesenchymal stem cells in the journal “Genomics, Proteomics & Bioinformatics”.


Ex vivo-expanded mesenchymal stem cells (MSCs) have been demonstrated to be a heterogeneous mixture of cells exhibiting varying proliferative, multipotential, and immunomodulatory capacities. However, the exact characteristics of MSCs remain largely unknown. By single-cell RNA sequencing of 61,296 MSCs derived from bone marrow and Wharton’s jelly, researchers revealed six distinct subpopulations, the developmental trajectory was mapped. According to gene expression, it is divided into stem-like APCs, MPCs, preadipocytes, pre-Cos, prechondrocytes, pre-SMCs. The stem-like APCs, uniquely exhibited strong proliferation and stemness signatures; the prechondrocyte subpopulation specifically expressed immunomodulatory genes and was able to suppress activated CD3+ T cell proliferation in vitro, supporting the role of this population in immunoregulation. This study characterizes the cellular composition of MSCs and their specific functions, demonstrates the subpopulation heterogeneity of MSCs, reveals the molecular and functional heterogeneity of cultured MSCs, and lays the foundation for exploring their unique heterogeneity.

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1.Characterization and single-cell transcriptome of bone marrow and Wharton's jelly MSCs

Bone marrow MSCs (BMMSCs) and Wharton's jelly MSCs (WJMSCs) passaged to sixth to seventh passages in vitro were used for this study. scRNAseq was performed in 3 replicates per group. After

filtration, a total of 61,296 high-quality MSCs single-cell transcriptome data were obtained. Divided into 6 cell populations (Figure 1E). Typical MSC markers, including CD73/NT5E, CD90/THY1, CD105/ENG, and CD44, were expressed differently in each population, suggesting that traditional criteria cannot define MSC subpopulations.

Cells in Cluster 1 exhibited a stronger characteristic of proliferative activity, these cells highly expressed genes related to DNA replication and cell cycle progression, and were defined as stem-like APCs. Cluster 2 showed expression characteristics of trilineage differentiation, including osteogenic, chondrogenic, and adipogenic differentiation (Fig. 1F, G), and was defined as MPCs. Cluster 3 cells express a number of genes related to the regulation of adipocyte differentiation and are defined as preadipocytes. Cluster 4 cells highly expressed cartilage-specific genes and extracellular matrix remodeling genes (Fig. 1G) and were defined as pre-COs. Cluster 5 overexpressed genes involved in chondrogenic, immunomodulatory and secretory signaling pathways (Fig. 1F) and were defined as prechondrocytes. Cluster 6 was enriched for genes necessary for smooth muscle contraction (Fig. 1F,G) and was defined as pre-SMCs. To explore the relationships and developmental hierarchies among the various subpopulations, pseudotime analysis was performed using Monocle2. Define stem-like APCs as the starting state, followed by MPCs. The MPCs then derived two branching paths: one leading to pre-Cos and prechondrocytes, the other leading to preadipocytes (Figure 1H). These findings reveal that MSCs were composed of heterogeneous and continually developing cell populations.

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Figure 1. Characteristics and single-cell transcriptome profiling of BMMSCs and WJMSCs.

2.Cluster 1 has stem transcriptional features

The study compared single-cell transcriptomic data between cluster 1 cells and NG2+ periarteriolar cells, LEPR+ peri-sinusoidal cells, and paraxial mesoderm cells. Cluster 1 was closely associated with NG2+ periarteriole cells (Fig. 2C) and paraxial mesoderm cells (Fig. 2D). Notch signaling-related stemness genes (E2F1, EZH2, and TFDP1), apoptosis negative regulator genes (HMGB2, BRCA1, PAK4, and MAZ), and the polycomb groups (PCGF6 and PHC1) were strongly co-expressed in Cluster 1 (Figure 2C). , D). These observations suggest that cluster 1 cells resemble mesodermal progenitors with the ability to self-renew and differentiate into multiple mesodermal cell lineages.

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Figure 2. Identification of specialized stem-like cells (Cluster 1) with high proliferative capacity.

3.Cluster 2 can be subdivided into three directions

Cells in Cluster 2 were defined as pluripotent MPCs, and researchers subdivided the MPCs (Fig. 3B), with three subpopulations showing distinct expression patterns. Subgroup 1 expressed genes related to osteoblast differentiation and osteoblastic progenitor proliferation (Fig. 3C). Therefore, cells in subgroup 1 are called osteo-primed MPCs. Subgroup 2 expressed genes related to fatty acid metabolism and lipid accumulation, termed adipo-primed MPCs (Figure 3C). Subgroup 3 expresses chondrogenesis-related genes and is termed chondro-primed MPCs. Pseudotime analysis were performed on stem-like APCs (Cluster 1), osteo-primed MPCs, adipo-primed MPCs, chondro-primed MPCs (Fig. 3D). From the initial differentiation of stem-like APCs into three MPC subpopulations, researchers identified two major differentiation routes, each associated with multiple MPC subpopulations (Fig. 3E).

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Figure 3. Cluster 2 MPCs are primed towards trilineage orientations.

4.Cluster 5 has specific immunomodulatory capacity

Cluster 5 enriched genes involved in chondrogenesis, immunogenicity, complement system activation or inhibition, myeloid lymphoid activation, and anti-inflammatory properties (Fig. 4B,C). These results suggest that cluster 5 has immunomodulatory potential. In addition to their immunomodulatory properties, Cluster 5 overexpressed genes are involved in endoplasmic reticulum protein processing, protein folding, post-translational protein modification, and extracellular secretion regulation. Taken together, these results suggest that the immunomodulatory role of cluster 5 may be due to their production of exosomes or secretion of soluble factors. To examine the ability of cluster 5 cells to fight inflammation, cluster 5 was purified by the surface marker CD106 (Figure 4E) and co-cultured with activated CD3+ T cells. CD106+ WJMSCs and BMMSCs reduced the proliferation of CD3+ T cells more significantly than CD106- cells (Fig. 4F), indicating that CD106+ cluster 5 exhibited stronger anti-inflammatory capacity than other MSC subsets. In summary, these observations suggest that Cluster 5 has pro- and anti-inflammatory potential mediated in a paracrine manner.

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Figure 4. BMMSC-dominant prechondrocytes (Cluster 5) specifically harbor immunoregulatory capacity.

5.The characteristics of primary MSCs and passaged MSCs are different

To explore the similarities and differences between cultured MSCs and primary MSCs, this data was further compared with published scRNA-seq data from human primary umbilical cord MSCs (UCMSCs) and BMMSCs, as well as cultured endometrial MSCs, an integrated analysis was performed. The results showed that MSCs from different tissue cultures had similar subpopulation composition. The primary BMMSC-specific cell population (cluster 7) highly expresses hematopoietic stem cell-niche factor genes, including CXCL12 and ANGPT1, and is therefore called the HSC-niche support cluster. Primary BMMSCs may have lost gene expression activity associated with HSC-niche support after in vitro culture, which is consistent with previous findings that MSCs lost HSC-niche function during culture. In addition, the expression levels and expression ratios of MSCs markers CD73/NT5E, CD90/THY1 and CD44 were higher in cultured cells than in primary MSCs. This suggests that these properties of MSCs may increase during culture. In summary, this study not only reveal the molecular and functional heterogeneity of cultured MSCs, but also provide a foundation for exploring their unique heterogeneity.

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