A systematic characterization of fibroblast subtypes and heterogeneity

Fibroblasts are essential components in development, disease, and treatment response, yet their diversity and function remain incompletely understood. Here, we constructed a comprehensive fibroblast landscape by integrating large-scale single-cell and single-nucleus RNA sequencing datasets spanning 60 major human organs and tissues across various developmental stages and biological conditions. We identified 16 fibroblast subtypes and systematically characterized their tissue specificities, transcriptional heterogeneity, and cell states. Further analyses revealed distinct fibroblast subtypes associated with pluripotency and senescence across tissues. Leveraging the well-defined fibroblast atlas, we demonstrated that different fibroblast subtypes were associated with various complex traits such as anthropometric and immune diseases. Furthermore, analysis using the subtype-specific gene activities in bulk cancer data revealed that myoCAF was a risk factor for patient survival. Collectively, our study provides a comprehensive fibroblast atlas, offering insights into the functions, heterogeneity, and clinical applications of fibroblast subtypes.