Single-cell transcriptional profiling reveals a novel RAB13 ⁺ endothelial subpopulation and profibrotic mesenchymal cells in the aged human bone marrow

The bone marrow (BM) microenvironment plays a crucial role in regulating hematopoiesis, yet the molecular and functional changes associated with aging in humans remain poorly understood. Using single-cell RNA sequencing (scRNA-seq), we uncovered transcriptional shifts in BM endothelial cells (EC) and mesenchymal stem cells (MSC) during aging. Our analysis revealed that aged sinusoidal EC adopt a prothrombotic, exhibit mitochondrial dysfunction, and have compromised vascular function. Additionally, we identified a unique arterial EC subset, present only in aged individuals, associated with transcriptional elongation and senescence processes and characterized by RAB13 expression. MSC from aged subjects displayed an impaired matrix remodeling and epithelial-mesenchymal transition, driven partly by a subpopulation of THY1 ⁺ profibrotic stromal cells absent in young subjects. Aged MSC were also characterized by an increased ATP-oxidative metabolism and reduced protein folding capacity. Finally, using immunofluorescent imaging and spatial transcriptomics, we confirmed the presence of RAB13 ⁺ senescent EC in aged samples and revealed significant age-related changes in cell-cell communication within the BM niche. In summary, this work provides a comprehensive view of the molecular diversity, cellular interactions, and spatial organization of aged EC and MSC, offering novel insights and potential targets that could be exploited for preventing aged-associated changes in humans.