Inflammation perturbs hematopoiesis by remodeling specific compartments of the bone marrow niche.

Hematopoietic stem and progenitor cells are regulated by interactions with stromal cells in the bone marrow (BM) cavity, which can be segregated into 2 spatially defined central marrow (CM) and endosteal (Endo) compartments. However, the importance of this spatial compartmentalization for BM responses to complex conditions such as inflammation remains largely unknown. Here, we extensively validate a combination of single-cell RNA sequencing profiling and matching flow cytometry isolation that reproducibly identifies 7 key CM and Endo populations and accurately surveys both niche locations. We demonstrate that inflammatory perturbations exert specific effects on different cellular compartments, with type I interferon responses causing leptin receptor-expressing mesenchymal stromal cells to abandon their normal stromal functions and instead adopt an inflammatory phenotype associated with overproduction of chemokines that modulate local monocyte dynamics in the surrounding microenvironment. Our results provide a comprehensive method for molecular and functional stromal characterization and highlight the importance of altered stomal cell activity in regulating hematopoietic responses to inflammatory challenges.