Mapping the cellular biogeography of human bone marrow niches using single-cell transcriptomics and proteomic imaging

Non-hematopoietic cells are essential contributors to hematopoiesis. However, heterogeneity and spatial organization of these cells in human bone marrow remain largely uncharacterized. We used single-cell RNA sequencing (scRNA-seq) to profile 29,325 non-hematopoietic cells and discovered nine transcriptionally distinct subtypes. We simultaneously profiled 53,417 hematopoietic cells and predicted their interactions with non-hematopoietic subsets. We employed co-detection by indexing (CODEX) to spatially profile over 1.2 million cells. We integrated scRNA-seq and CODEX data to link predicted cellular signaling with spatial proximity. Our analysis revealed a hyperoxygenated arterio-endosteal neighborhood for early myelopoiesis, and an adipocytic localization for early hematopoietic stem and progenitor cells (HSPCs). We used our CODEX atlas to annotate new images and uncovered mesenchymal stromal cell (MSC) expansion and spatial neighborhoods co-enriched for leukemic blasts and MSCs in acute myeloid leukemia (AML) patient samples. This spatially resolved, multiomic atlas of human bone marrow provides a reference for investigation of cellular interactions that drive hematopoiesis. [Display omitted] •scRNA-seq and CODEX reveal the composition and spatial architecture of human bone marrow•Human mesenchymal stromal cells are transcriptionally and functionally heterogeneous•Adult HSPCs exhibit a peri-adipocytic spatial localization•CODEX reference mapping to our healthy atlas reveals MSC expansion in AML This study employs scRNA-seq and CODEX multiplexed imaging to elucidate the cellular and spatial architecture of the human bone marrow microenvironment. Rare non-hematopoietic cells are enriched and profiled. Cellular neighborhoods and cell-cell interactions are revealed through integrative analysis of the multiomics data.