Single-cell RNA sequencing analysis of human bone-marrow-derived mesenchymal stem cells and functional subpopulation identification

Mesenchymal stem cells (MSCs) are a common kind of multipotent cell in vivo, but their heterogeneity limits their further applications. To identify MSC subpopulations and clarify their relationships, we performed cell mapping of bone-marrow-derived MSCs through single-cell RNA (scRNA) sequencing. In our study, three main subpopulations, namely, the stemness subpopulation, functional subpopulation, and proliferative subpopulation, were identified using marker genes and further bioinformatic analyses. Developmental trajectory analysis showed that the stemness subpopulation was the root and then became either the functional subpopulation or the proliferative subpopulation. The functional subpopulation showed stronger immunoregulatory and osteogenic differentiation abilities but lower proliferation and adipogenic differentiation. MSCs at different passages or isolated from different donors exhibited distinct cell mapping profiles, which accounted for their corresponding different functions. This study provides new insight into the biological features and clinical use of MSCs at the single-cell level, which may contribute to expanding their application in the clinic. Stem cells: Three subpopulations found in bone marrow Stem cells in the bone marrow are not all the same: a team led by Huiyong Shen and Yanfeng Wu from Sun Yat-sen University in Shenzhen, China, have identified three main subpopulations of adult stem cells in human marrow, a finding that could lead to more consistent and purer populations of cells for use in in clinical applications. The researchers analyzed gene expression profiles of mesenchymal stem cells (MSCs) using single-cell RNA sequencing methods. The genetic patterns pointed to three distinct cell subpopulations: one that maintained its stem-like capacity for self-renewal; a second “functional” group with strong bone- and blood-forming potential; and a third characterized by active proliferation and cell cycle progression. The authors propose that protocols that isolate only the functional subpopulation of cells could help reduce a source of variation that has limited the therapeutic efficacy of MSC-based therapies.