Single‐cell transcriptomes of murine bone marrow stromal cells reveal niche‐associated heterogeneity

Bone marrow (BM) stromal cells are important in the development and maintenance of cells of the immune system. Using single cell RNA sequencing, we here explore the functional and phenotypic heterogeneity of individual transcriptomes of 1167 murine BM mesenchymal stromal cells. These cells exhibit a tremendous heterogeneity of gene expression, which precludes the identification of defined subpopulations. However, according to the expression of 108 genes involved in the communication of stromal cells with hematopoietic cells, we have identified 14 non‐overlapping subpopulations, with distinct cytokine or chemokine gene expression signatures. With respect to the maintenance of subsets of immune memory cells by stromal cells, we identified distinct subpopulations expressing Il7, Il15 and Tnfsf13b. Together, this study provides a comprehensive dissection of the BM stromal heterogeneity at the single cell transcriptome level and provides a basis to understand their lifestyle and their role as organizers of niches for the long‐term maintenance of immune cells. We have developed an optimized isolation protocol in order to dissect the heterogeneity of VCAM‐1+ BM derived stromal cells. The droplet single cell RNA‐sequencing analysis of BM stromal cells reveals heterogeneity regarding to the expression of cytokines and chemokines. These unique stromal cell subsets could be important for the organization of survival niche for various hematopoietic as well as immune cells.