Single-Cell Transcriptomic and Spatial Characterization of Multipotent Stromal Cells in Homeostatic,Remodeled, and In Vitro Expanded Human Bone Marrow

Bone marrow multipotent stromal cells (BM-MSCs) are important constituents of the bone marrow microenvironment, both in homeostasis and hematopoietic malignancies. These cells have the capacity to differentiate into adipocytic, osteogenic, and chondrogenic lineages and are essential in providing structural and physiological support for hematopoiesis and bone remodeling. Single-cell transcriptomics (scRNA-seq) techniques revealed the heterogeneous nature of BM-MSCs in mice, allowing the identification and characterization of relevant stromal cellular subpopulations important in the context of hematopoiesis. On the other hand, extensive investigation of human BM-MSCs has only started (Bandyopadhyay et al., 2024) leaving gaps in the fundamental understanding of their hierarchical organization, functional roles, and spatial relationships with other components of the bone marrow niche.

In this study, we performed a comprehensive characterization of the total non-hematopoietic compartment of the human bone marrow microenvironment through scRNA-seq. To capture maximum stromal heterogeneity, which we had observed with multiplex immunofluorescence methods, we employed a negative selection strategy relying on the depletion of mature hematopoietic (CD45⁺) and mature erythroid (CD235⁺) lineages. BM-MSCs were sourced from the femoral head of five control donors (median age = 62) and three stressed-state donors with active leukemia or recent chemotherapy (median age = 60), all undergoing elective hip replacement surgery for osteoarthritis. Our stromal-enriched, freshly-isolated scRNA-seq dataset contains 28,673 cells, consisting of major hematopoietic clusters including myeloid & erythroid progenitors (MEPs), immature B-cells, megakaryocytes & monocytes, and natural killer (NK) and T-cells. We focused our attention on the non-hematopoietic compartment consisting of 6,459 cells, where we successfully identified endothelial cells, osteo-lineage stromal cells (CD56⁺), fibroblastic BM-MSCs (PDPN⁺), and CXCL12-abundant reticular (CAR) cells. We found that CAR cells display four distinct transcriptional polarizations: inflammatory, peri-arteriolar, peri-sinusoidal, and adipocytic. These findings were substantiated via flow cytometry and spatially resolved via RNA in situ hybridization on control histological bone marrow biopsies. Furthermore, the transcriptional profiles of these stromal subpopulations were compared against our scRNA-seq dataset of minimally (P1) versus extensively (P4-6) in vitro expanded primary BM-MSCs, where we found a transcriptomic convergence resulting in a loss of heterogeneity upon cell culture. Additional functional capacities of our stromal subpopulations were assessed bioinformatically where we found distinct ligand-receptor interactions with the hematopoietic progenitor constituents of the dataset via CellChat and CellPhone DB. Experimentally, the subpopulations were evaluated for Colony Forming Unit-Fibroblastic (CFU-F) potential, trilineage differentiation capabilities, and hematopoietic support through co-culture with hematopoietic stem and progenitor cells (HSPCs). Notably, the predicted stromal hierarchical organization was determined through RNAVelocity, identifying the fibroblastic PDPN⁺BM-MSCs at the pinnacle of the progenitor/differentiation axis. Our dataset further identified the enrichment of these PDPN⁺ BM-MSCs and endothelial cells, coupled with the upregulation of angiogenic pathways, in the remodeled bone marrow of our stressed-state donors. Our study provides key insights into the complexity of the homeostatic and remodeled human bone marrow microenvironment and induces further considerations in investigating in vitro expanded BM-MSCs for regenerative medicine.