Molecular characterization of heterogeneous mesenchymal stem cells with single-cell transcriptomes

Mesenchymal stem cells (MSC) are heterogeneous cell populations with promising therapeutic potentials in regenerative medicine. The therapeutic values of MSC in various clinical situations have been reported. Clonal assays (expansion of MSC from a single cell) demonstrated that multiple types of cells with different developmental potential exist in a MSC population. Due to the heterogeneous nature of MSC, molecular characterization of MSC in the absence of known biomarkers is a challenge for cell therapy with MSC. Here, we review potential therapeutic applications of MSC and discuss a systematic approach for molecular characterization of heterogeneous cell population using single-cell transcriptome analysis. Differentiation/maturation of cells is orchestrated by sequential expression of a series of genes within a cell. Therefore, single-cell mRNA expression (transcriptome) profiles from consecutive developmental stages are more similar than those from disparate stages. Bioinformatic analysis can cluster single-cell transcriptome profiles from consecutive developmental stages into a dendrogram based on the similarity matrix of these profiles.Because a single-cell is an ultimately “pure” sample in expression profiling, these dendrograms can be used to classify individual cells into molecular subpopulations within a heterogeneous cell population without known biomarkers. This approach is especially powerful in studying cell populations with little molecular information and few known biomarkers, for example the MSC populations. The molecular understanding will provide novel targets for manipulating MSC differentiation with small molecules and other drugs to enable safer and more effective therapeutic applications of MSC.