Skeletal Cell Atlas – A resource to facilitate accessibility of genomics data

Single-cell RNA sequencing (scRNA-seq) is a next-generation sequencing method that examines the transcriptomes of individual cells. It allows to determine, at the single-cell level, which genes are expressed, in what quantities, and how their expression varies among thousands of cells within a sample.

Ultra-high throughput scRNA-seq platforms and the concomitant development of computational algorithms required to analyze the data 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 these atlases, often with insufficiently detailed annotation of the skeletal lineage. Considering how the skeleton not only serves as the 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, our ULIEGE partners (in collaboration with KU Leuven) have integrated seven separate scRNA-seq datasets containing skeletal cells and their developmental precursors, generating an atlas of over 800000 cells.

This Skeletal Cell Atlas encompasses 50 different cell states – characterizing the most known cell populations in the skeleton – from the induction of the limb field to the adult bone. In addition, the original datasets were reannotated, enabling the discovery of novel, highly specific marker genes, some of which were validated in vivo. Furthermore, expanding the repertoire of available time points and cell types within a single dataset allowed for more complete analyses of the cell-cell communication or in silico perturbation studies.

Taken together, this atlas, provides a missing piece in the current atlas mapping efforts, with an initial reference of the musculoskeletal system which will be of value to researchers in the fields of skeletal biology, hematopoiesis, metabolism, and regenerative medicine.

In future work, this first version will serve as the basis of a collaborative effort to complete the atlas. The release on bioRxiv of the single-cell atlas of the skeleton developed by the ULIEGE/KU Leuven teams also comes with an accompanying web app where the Skeletal Cell Atlas can be explored or downloaded here.

In the particular context of the In Silico World project and the OcDefects solution, this skeletal single-cell atlas serves as the biological benchmark – a standard/reference against which the regulatory network (intracellular model) may be compared – for the development of the intracellular part of the OcDefects multiscale model of the knee joint.