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

Abstract

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.

Single-cell RNA-sequence analysis of human bone marrow reveals new targets for isolation of skeletal stem cells using spherical nucleic acids

“…Pseudotime inference analysis can be employed to map the developmental trajectory of cells, which in the case of SSCs can support the characterisation of subtypes within enriched or expanded SSC populations. 104,105 Unfortunately, we were unable to perform these workflows in the current study due to the low frequency of bone marrow SSCs, warranting scRNA-seq of bone marrow from an increased numbers of donors in future studies. Limited cell numbers also restrict current methods of in vitro analysis as we were unable to obtain sufficient cell numbers to perform quantitative analysis of tri-lineage differentiation in vitro (RT-qPCR).…”

Secretion encoded single-cell sequencing (SEC-seq) uncovers gene expression signatures associated with high VEGF-A secretion in mesenchymal stromal cells

“…MSCs have been extensively studied for cell therapy applications, leveraging an array of antiinflammatory and pro-regenerative secreted products; yet, successful translation has been hindered by clinical outcome inconsistency attributed to functional differences that stem from the cell source and single cell level heterogeneity. Using scRNA-seq or morphological profiling, subpopulations of MSCs with various functional genotypes have been recently discovered and examined to mitigate this heterogeneity [42][43][44] . The primary mechanism of action for MSC therapies is thought to be through the secretion of bioactive factors that promote immunomodulation and regeneration of resident cells, such as the growth factor VEGF-A.…”

Renal osteodystrophy: something old, something new, something needed

“…Only by identifying the genes and pathways involved in ROD, can we develop targeted therapies that address the underlying causes of the disease, rather than just treating the symptoms or the end-organ effects of disease, such as hyperparathyroidism-induced high turnover or increased cortical porosity [49]. These novel methods are only now being applied to bone [50 ▪ ] and more recently to ROD [45 ▪▪ ], and only a few studies have investigated transcriptomic and epigenetic changes in ROD. Not only do we need further research using RNA-seq in large patient cohorts to fully understand the complex molecular mechanisms underlying ROD and to develop effective treatments, but the fundamental infrastructure to develop patient-centered clinically relevant research is lacking, impeding the development of strategies that will improve the lives of patients living with CKD.…”