Mapping the Cellular Biogeography of Human Bone Marrow Niches Using Single-Cell Transcriptomics

Non-hematopoietic cells contribute essentially 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 one million single cells with a novel 53-antibody panel. We integrated scRNA-Seq and CODEX data to link cellular signaling and spatial proximity. Spatial analysis also revealed a hyperoxygenated arterio-endosteal niche for early myelopoiesis, and an adipocytic, but not endosteal or perivascular, localization for early hematopoietic stem and progenitor cells. We used our CODEX atlas to automatically annotate cell types in new bone marrow images and uncovered MSC expansion and leukemic blast/MSC-enriched spatial neighborhoods in AML patient samples. This comprehensive, spatially-resolved multiomic atlas of human bone marrow serve as a reference for future investigation of cellular interactions that drive hematopoiesis. We simultaneously profiled enriched mesenchymal, HSPC, and unenriched RBC depleted cells from fresh, enzymatically digested femoral head human bone marrow from hematologically healthy patients undergoing total hip arthroplasties and subjected to paired-end single-cell RNA sequencing using 10X Genomics Single Cell 3’ v3.1 and libraries were sequenced using an Illumina Nova Seq 6000.