Characterization of the Human Mesenchymal Stromal Compartment in Normal Homeostasis and Acute Myeloid Leukemia at the Level of the Single Cell

Abstract

Mesenchymal stromal cells (MSCs) constitute a pivotal component of the bone marrow niche, providing key regulatory signals required for maintenance of normal hematopoietic stem cell (HSC) function. In recent years, there has been an increased appreciation of the role played by the bone marrow niche in leukemogenesis with increasing evidence pointing towards dysregulation of MSCs in acute myeloid leukemia (AML). However, studies to date have predominantly evaluated culture expanded MSCs which do not necessarily reflect the state of MSCs in their in situ milieu. This is further compounded by limitations inherent to bulk population measurements which fall short of capturing the underlying heterogeneity that may exist among seemingly identical cells. Leveraging the combined powers of single cell RNA sequencing (scRNA-seq) and mass cytometry (CyTOF), we provide here an in-depth characterization of the human bone marrow MSC compartment both in normal homeostasis and AML. We address the question of MSC heterogeneity, and through integrated analysis of our scRNA-seq data and recently published publicly available datasets, we show that MSCs in their native state are transcriptionally split into subsets of varying differentiation potential that exist along a continuum of cellular states. These subsets consist of a predominant cluster showing high expression of genes implicated in adipogenesis and a smaller cluster demonstrating upregulation of osteogenesis-related genes, suggesting that these cells are poised toward adipogenic and osteogenic differentiation respectively. In addition, we observe a much smaller population with a gene expression profile in keeping with that of more terminally differentiated osteoblasts, however this is not consistently observed across all samples. Furthermore, our comparative analysis of publicly available scRNA-seq datasets of murine stroma shows a high degree of conservation with similar patterns of cellular diversity. This pattern of cellular architecture is however lost in culture-expanded MSCs, underscoring the limitations associated with their use. In the context of AML, we show that native MSCs undergo transcriptional transformation, acquiring a distinct gene signature pattern distinguishing them from their normal counterparts. Among these changes are upregulation of genes implicated in inflammation indicating that deregulation of inflammatory signalling in AML is facilitated, at least in part, by cell-extrinsic mechanisms. In summary, our data reveal novels insights into the cellular architecture of the human MSC compartment in its native, unmanipulated state as well as unravel key transcriptional changes that characterize MSCs in AML, which can potentially be exploited for therapeutic targeting.