Mesenchymal stem/stromal cells (MSCs) are widely recognized for their ability to differentiate into bone, cartilage, and fat, making them attractive for tissue repair and cell therapy. However, tissue-derived MSCs (tMSCs) exhibit variability and limited expansion capacity, which restricts their clinical utility. iMSCs, generated from iPSCs, promise a more consistent and scalable alternative, yet the influence of developmental lineage on their characteristics has remained unclear.

To address this, the research team differentiated iMSCs from a single iPSC line through five lineage-specific pathways: cranial neural crest (cNCC), trunk neural crest (tNCC), paraxial mesoderm (somite), lateral plate mesoderm (LPM), and limb mesenchyme. All iMSC types met the International Society for Cellular Therapy's criteria for MSCs but displayed striking differences in morphology, proliferation, and differentiation potential. Somite-derived iMSCs (SM-iMSCs) exhibited the fastest proliferation and strongest osteogenic capacity, initiating mineralization earlier than other groups. Limb mesenchyme-derived iMSCs (Limb-iMSCs) demonstrated superior adipogenic potential, forming abundant lipid droplets and expressing high levels of adipogenic markers. In contrast, whereas cNCC-derived iMSCs showed stable chondrogenic differentiation without hypertrophy, making them promising candidates for cartilage repair, SM-iMSCs, despite robust chondrogenic activity, tended toward hypertrophy and calcification—a critical consideration for clinical applications.

Beyond differentiation, the study examined immunomodulatory properties. All iMSC subtypes upregulated PD-L1 and IDO1 in response to interferon-γ stimulation, confirming their potential for immune regulation. Interestingly, LPM-derived iMSCs expressed PD-L1 even at baseline, suggesting suitability for immunosuppressive therapies despite slower growth.

Transcriptomic analysis revealed distinct gene-expression clusters corresponding to embryonic origin. Principal component analysis showed three major clusters: one comprising cranial and trunk neural crest-derived cells, another including somite and limb mesenchyme-derived cells, and a third consisting of lateral plate mesoderm-derived cells. GO term enrichment confirmed pathways related to ossification, skeletal morphogenesis, and chondrogenesis, reinforcing therapeutic potential for bone and cartilage repair. While iMSCs shared high molecular similarity with tMSCs, they displayed enhanced proliferation and osteogenesis pathways. Importantly, these lineage-specific traits were consistently observed across two iPSC lines, demonstrating robustness and reproducibility.

These discoveries underscore the importance of considering embryonic origin when designing iMSC-based therapies. SM-iMSCs may be ideal for bone regeneration, cNCC-iMSCs for cartilage repair, Limb-iMSCs for adipose tissue engineering, and LPM-iMSCs for immunomodulation. The study also proposes strategies such as optimizing lineage-specific media and controlling hypertrophy during cartilage repair. Future research will focus on in vivo validation, single-cell transcriptomic profiling, and functional assays to further optimize iMSC applications and unlock their full therapeutic potential.

• doi: 10.1016/j.isci.2025.114482