A cellular taxonomy of the bone marrow stroma in homeostasis and leukemia demonstrates cancer-crosstalk with stroma to impair normal tissue function

Here, we use single-cell RNA-seq to define a cellular taxonomy of the mouse bone marrow stroma and its perturbation by malignancy. We identified stromal subsets expressing distinct hematopoietic regulatory genes, spanning new fibroblastic, and osteoblastic subpopulations. Emerging acute myeloid leukemia resulted in impaired osteogenic differentiation and reduced production of hematopoietic regulatory molecules necessary for normal hematopoiesis. Thus, cancer can affect tissue stroma in which they reside to disadvantage normal parenchymal cells. Our taxonomy of the regulatory stromal compartment provides experimental support for a model where malignant cells are more an architect than a destroyer of normal tissue, remodeling tissue stroma to enable emergent cancer. Overall design: We profiled non-hematopoietic bone and bone marrow cells from Mouse by scRNA-seq. We enriched stroma cells from eight mice C57Bl/6 mice at the age of 8-10 weeks by FACS through selective depletion of hematopoietic cells and immune lineage cells as labeled by CD45, lineage and Ter119, profiled them by droplet-based scRNA-seq. To study changes under leukemia, we profiled by scRNA-seq 12,456 bone marrow stromal cells from MLL-AF9 (MLL) mice (n=4) and 10,548 cells from matched control transplanted mice (n=5). Finally, we profiled additional separate samples of bone and flushed bone marrow cells (~21,000 cells) to establish contribution of each component in the original cluster map of bone marrow stroma.