NicheScribe: consistent and generalizable annotation of stromal cells in the murine bone marrow niche.

UNLABELLED: Hematopoietic stem and progenitor cells (HSPC) depend on interactions with nearby stromal cells to support their homeostatic functions and mount responses to perturbations. The murine bone marrow (BM) niche can be profiled using single-cell RNA sequencing (scRNA-seq), but there is considerable inconsistency in cell type identification, and uncertainty over how populations can be isolated prospectively by flow cytometry. Here, we produced new scRNA-seq reference datasets using purified populations of murine BM stromal cells, which we used to create a bespoke classifier for stromal cells. Our NicheScribe approach is consistent, accurate, and generalizable to query datasets irrespective of methods used for cell isolation. Moreover, consistent annotation permits comparative analyses of the same stromal cells across different bone types and perturbations like inflammation, neoplasia, and aging. Our work provides new tools for consistent cell type annotation in the murine BM niche and new insights for combined molecular and functional analyses.

HIGHLIGHTS: New NicheScribe approach for annotation of stromal cells in scRNA-seq datasetsNicheScribe links molecular state to prospective isolation by flow cytometryDifferent bones have distinct complements of stromal cells LepR + mesenchymal stromal cells adopt diverse transcriptional programs upon stimulation.

ETOC BLURB: Swann et al. develop a computational approach for consistent annotation of stromal cells in murine bone marrow niche, which is applicable to single-cell and spatial transcriptomics. They find that stromal cell frequencies vary in different bones, and that leptin receptor-expressing mesenchymal stromal cells exhibit diverse transcriptional responses to different perturbations.