Decoding Mesenchymal Stem Cell Heterogeneity by Single-Cell Transcriptomics: From Molecular Insights to Harnessing Heterogeneity for Precision Therapy of Musculoskeletal Degenerative Diseases

Mesenchymal stem/stromal cells (MSCs) hold great promise for treating musculoskeletal degenerative diseases such as osteoarthritis, sarcopenia, and osteoporosis, yet their clinical translation is severely hindered by cellular heterogeneity. This review systematically examines the multidimensional origins of MSCs heterogeneity, including donor background, tissue source, in vitro culture conditions, and intra-population functional diversity and highlights how single-cell RNA sequencing (scRNA-seq) has revolutionized our ability to decode this complexity. We summarize recent advances in constructing single-cell transcriptomic maps of MSCs from bone marrow, adipose tissue, umbilical cord, placenta, and discuss how different culture systems (serum-free vs. serum-containing, normoxia vs. hypoxia, 2D vs. 3D, and serial passaging) dynamically shape MSCs heterogeneity. Importantly, we present the homogeneity advantage of induced pluripotent stem cells (iPSCs)-derived MSCs (iMSCs), which exhibit higher transcriptomic consistency and rejuvenation features, making them attractive for standardized "off-the-shelf" cell therapies. Despite challenges such as epigenetic memory, tumorigenicity risk, and long-term genetic stability, iMSCs have entered Phase I/II clinical trials for multiple system atrophy and spinal cord injury. This review provides a complete perspective from "decoding heterogeneity" to "harnessing heterogeneity", offering theoretical and practical guidance for developing safer, more effective, and more predictable MSCs-based therapies for musculoskeletal degeneration.