An integrated single-cell atlas of the skeleton from development through adulthood

Abstract

AbstractThe recent growth of single-cell transcriptomics has turned single-cell RNA sequencing (scRNA-seq) into a near-routine experiment. Breakthroughs in improving scalability have led to the creation of organism-wide transcriptomic datasets, aiming to comprehensively profile the cell types and states within an organism throughout its lifecycle. To date however, the skeleton remains a majorly underrepresented organ system in organism-wide atlases. Considering how the skeleton not only serves as the central framework of the vertebrate body but is also the home of the hematopoietic niche and a central player in major metabolic and homeostatic processes, this presents a major deficit in current reference atlas projects. To address this issue, we integrated seven separate scRNA-seq datasets containing skeletal cells and their developmental precursors, generating an atlas of over 800,000 cells. This skeletal cell atlas describes cells across the mesenchymal lineage from the induction of the limb field to adult bone, encompassing 50 different cell states. In addition, the original datasets were reannotated, enabling the discovery of novel, highly specific marker genes, some of which we have validated in vivo by whole-mount in situ hybridization. Furthermore, expanding the repertoire of available time points and cell types within a single dataset allowed for more complete analyses of cell-cell communication or in silico perturbation studies. Taken together, we present a missing piece in the current atlas mapping efforts, which will be of value to researchers in the fields of skeletal biology, hematopoiesis, metabolism and regenerative medicine.