Multi-Layered Single-Cell Transcriptional Profiling of All Bone and Bone Marrow Populations Provides a Systems View of the Mesenchymal and Hematopoietic Stem Cell Niche

Coordinated interaction of many cell types is required to facilitate hematopoietic and mesenchymal stem cell maintenance and differentiation in the bone marrow. However, the molecular factors and cell types involved in this complex interplay are poorly understood. Here we performed large-scale single-cell transcriptional profiling in conjunction with a multi-layered sorting approach to generate a complete and evenly sampled transcriptional map of all major bone and bone marrow populations. Our dataset covers 30 cell types or differentiation trajectories involved in mesenchymal and hematopoietic stem cell differentiation, osteogenesis, adipogenesis, myelopoiesis, erythropoiesis, lymphopoiesis, memory T cell formation as well as bone marrow neural innervation and vascularization. Using this dataset, we derive fundamental properties of the described cell types, clarify the cellular source of signals affecting stem cell differentiation processes and provide a systems view on putative intercellular interactions, which we validate experimentally. Moreover, we identify novel niche cell subpopulations, characterize their molecular properties and determine their spatial localization in the bone marrow. Our analyses highlight the importance of pre-adipogenic Lepr+Vcam1+ CXCL12 abundant reticular cells as key niche cells for HSC stem cell maintenance, B cell differentiation, as well as memory T cell formation. Together, our data provide a holistic systems view of the molecular bone marrow niche architecture and the putative signaling interactions mediating bone marrow homeostasis.