Quantitative Multicolored Deep Imaging of Human Bones Reveals a Composite Osteo-Sinusoidal Niche for Mesenchymal Stromal Cells

Abstract Human bone marrow mesenchymal stromal/stem cells (BM-MSCs) are widely utilized in clinical trials and tissue engineering; however, their native microenvironment remains poorly understood. Here, we introduced a tissue-clearing protocol for human bones and integrated it with simultaneous mRNA and protein detection. Using this protocol, named DeepBone, we spatially mapped BM-MSCs relative to key bone microenvironment components, including human blood capillaries, adipocytes, sinusoids, and bony trabeculae. Quantitative analysis revealed that the native microenvironment of human BM-MSCs in young bone is enriched in vasculature, sinusoids, bone matrix, and adipocytes. In contrast, in aged bone, BM-MSCs showed no preferential association with bone or adipocytes. Proliferative BM-MSCs were predominantly found along blood vessels. Moreover, we identified a specialized microenvironment for BM-MCs in young bone, characterized by sinusoids coiled around trabeculae and enriched by R-type vessels. These findings provide novel insights into the native niches of BM-MSCs, offering a foundation for the development of tissue-engineering strategies that mimic their physiological context.