Multi-omics analysis in developmental bone biology

Abstract

Single-cell omics and multi-omics have revolutionized our understanding of molecular and cellular biological processes at a single-cell level. In bone biology, the combination of single-cell RNA-sequencing analyses and in vivo lineage-tracing approaches has successfully identified multi-cellular diversity and dynamics of skeletal cells. This established a new concept that bone growth and regeneration are regulated by concerted actions of multiple types of skeletal stem cells, which reside in spatiotemporally distinct niches. One important subtype is endosteal stem cells that are particularly abundant in young bone marrow. The discovery of this new skeletal stem cell type has been facilitated by single-cell multi-omics, which simultaneously measures gene expression and chromatin accessibility. Using single-cell omics, it is now possible to computationally predict the immediate future state of individual cells and their differentiation potential. In vivo validation using histological approaches is the key to interpret the computational prediction. The emerging spatial omics, such as spatial transcriptomics and epigenomics, have major advantage in retaining the location of individual cells within highly complex tissue architecture. Spatial omics can be integrated with other omics to further obtain in-depth insights. Single-cell multi-omics are now becoming an essential tool to unravel intricate multicellular dynamics and intercellular interactions of skeletal cells.

Keywords: Bone marrow stromal cells (BMSCs); In vivo lineage-tracing; Multi-omics; Single-cell RNA-sequencing (scRNA-seq); Single-nuclei ATAC-sequencing (snATAC-seq); Skeletal stem cells (SSCs).

Fig. 1

Representative strategy of single-cell multi-omics approach (scRNA-seq + snATAC-seq) in bone. FACS-isolated cre driver-marked tdTomato⁺ cells are analyzed by scRNA-seq and snATAC-seq, and then, the data are integrated by appropriate algorithms such as LIGER. Combined multi-omics analyses reveal not only cellular diversity but also the state and dynamics. Validation analyses using in vivo genetic lineage-tracing unveil cell fates of omics-identified cell types.

Fig. 2

Single-cell omics approach and subsequent validation analysis discover the new cell population in developing bone. a. scRNA-seq analysis using Prrx1-cre, which marks all mesenchymal cells in limb bud, at the condensation stage (E11.5 in mice) revealed the presence of peri-condensation cells expressing Hes1. b. scRNA-seq analysis using Col2a1-cre, which marks most skeletal cells, at the cartilage template stage (E13.5 in mice) elucidated the outer layers of perichondrial cells expressing Dlx5.