Stem cell-based modeling and single-cell multiomics enable to identify gene regulatory networks that potentially regulate human endochondral ossification

Shinsuke Ohba, Department of Tissue and Developmental Biology, Graduate School of Dentistry

Prof. Shinsuke Ohba developed human pluripotent stem cell-based systems recapitulating endochondral ossification, a process of skeletal development, and identified gene regulatory networks that potentially contribute to the process, in collaboration with Dr. Shoichiro Tani (The University of Tokyo), Prof. Sakae Tanaka (The University of Tokyo), Prof. Hironori Hojo (The University of Tokyo), Prof. Ung-il Chung (The University of Tokyo), and Prof. David W. Rowe (University of Connecticut Health Center). This work was published in Cell Reports (Cell Press) on March 24, 2023 (


Mammalian skeletons are formed from three distinct origins (neural crest, lateral plate mesoderm, and paraxial mesoderm) through two distinct modes of ossification (intramembranous ossification and endochondral ossification). Most of skeletal elements in our bodies are derived from mesoderm and formed through endochondral ossification, in which cartilage models are gradually replaced by bones. Mouse genetic studies have revealed key transcription factors (TFs) to the sequential steps of bone formation; the key TFs have been shown to constitute gene regulatory networks that regulate cell-fate specification and cell differentiation during the process. However, cell-type-distinct TF interactions and networks remained to be elucidated especially in human ossification processes.

In this study, the research group first developed the protocol to induce endochondral ossification from human pluripotent stem cells (hPSCs). Next-generation sequencer (NGS)-based single-cell analyses and histological analyses revealed that the induced bone tissues recapitulate endochondral bones composed of human skeletal cells; an integrative analysis with a publicly available dataset of human embryos demonstrated the similarity of the induced tissues to human developing bones in terms of gene expression profiles. Single-cell multiome analyses (single-cell RNA-seq and single-cell ATAC-seq) of the hPSC-derived endochondral bones further clarified gene regulatory networks that potentially regulate differentiation and functions of multiple human skeletal cell types. Based on the networks, they also identified ZEB2 as a novel regulator of human skeletal development.


This study succeeded in recapitulating human endochondral ossification process, and thereby unraveled profiles of gene expression and epigenome in multiple human skeletal cell types. The datasets led to identification of gene regulatory networks that potentially regulate cell-fate specification during the process; this study also took a single-cell multiome approach toward characterization of hPSC-derived bone tissues. A series of NGS data obtained in this study is available on a public database. Thus, this study not only provides valuable resources for elucidating mechanisms of human skeletal development, but also contributes to a better understanding of pathogenesis of human skeletal disorders and identification of therapeutic targets for such disorders.

Information of the article

Shoichiro Tani*, Hiroyuki Okada, Shoko Onodera, Ryota Chijimatsu, Masahide Seki, Yutaka Suzuki, Xiaonan Xin, David W. Rowe, Taku Saito, Sakae Tanaka, Ung-il Chung, Shinsuke Ohba*, and Hironori Hojo*: Stem-cell-based modeling and single-cell multiomics reveal gene regulatory mechanisms underlying human skeletal development. Cell Rep, in press (*co-corresponding authors)

DOI: 10.1016/j.celrep.2023.112276