Single-cell transcriptomics identifies chondrocyte differentiation dynamics in vivo and in vitro
Developing in vitro chondrocytes that replicate in vivo development would benefit musculoskeletal disease modeling and regenerative medicine. Although current methodologies have made progress, challenges such as off-target differentiation can result in heterogeneous cell states. Furthermore, the lack of comparison with human embryonic tissue precludes detailed evaluation of in vitro cells. Here, we perform single-cell RNA sequencing (scRNA-seq) of embryonic long bones and combine this with public data to form an atlas of endochondral ossification. We use this to evaluate published in vitro chondrogenesis protocols that use human cell lines, finding variability in cells produced by each. We apply single-nuclear RNA sequencing (snRNA-seq) to our human embryonic stem cell chondrogenesis protocol and perform trajectory alignment with in vivo data to shed light on off-target differentiation in vitro. Using this information, we inhibit FOXO1, a transcription factor active in embryonic osteoblasts and in vitro cells, to increase chondrocyte transcripts in vitro. This work offers a framework for improving in vitro chondrogenesis using developmental data.
Authors
- Simone Webb (ORCID: https://orcid.org/0000-0003-3058-8952)
- Susan J. Kimber (ORCID: https://orcid.org/0000-0002-0568-6342)
- Omer Ali Bayraktar (ORCID: https://orcid.org/0000-0001-6055-277X)
- Dinithi Sumanaweera (ORCID: https://orcid.org/0000-0003-4515-0988)
- John E. Lawrence (ORCID: https://orcid.org/0000-0002-7951-915X)
- Lira Mamanova (ORCID: https://orcid.org/0000-0003-1463-8622)
- Steven Paul Woods (ORCID: https://orcid.org/0000-0001-6873-5722)
- Sarah Amalia Teichmann (ORCID: https://orcid.org/0000-0002-6294-6366)
- Elena Prigmore (ORCID: https://orcid.org/0000-0001-8870-0316)
- Tong Li
- Adrienne M. Flanagan (ORCID: https://orcid.org/0000-0002-2832-1303)
- Kenny S. Roberts (ORCID: https://orcid.org/0000-0001-6155-0821)
- Alexander V. Predeus (ORCID: https://orcid.org/0000-0002-2750-1599)
- Petra Balogh
- Matthew J. Young (ORCID: https://orcid.org/0000-0002-5109-4719)
- Muzlifah A. Haniffa (ORCID: https://orcid.org/0000-0002-3927-2084)
- Sam Behjati (ORCID: https://orcid.org/0000-0002-6600-7665)
- Laura Jardine (ORCID: https://orcid.org/0000-0003-4495-8205)
- Xiaoling He (ORCID: https://orcid.org/0009-0004-1002-8418)
- Roger A. Barker (ORCID: https://orcid.org/0000-0001-8843-7730)
- Di Zhou (ORCID: https://orcid.org/0000-0003-0851-7269)
- Krzysztof Polański (ORCID: https://orcid.org/0000-0002-2586-9576)
- Elizabeth J. Tuck (ORCID: https://orcid.org/0000-0002-1837-7549)
- Peng He (ORCID: https://orcid.org/0000-0002-2457-3554)
Institutions
- European Bioinformatics Institute (GB)
- Wellcome/MRC Cambridge Stem Cell Institute (GB)
- University of Cambridge (GB)
- Wellcome Centre for Cell-Matrix Research (GB)
- Wellcome Sanger Institute (GB)
- Royal National Orthopaedic Hospital (GB)
- University of Manchester (GB)
- Henry Royce Institute (GB)
- University College London (GB)
- Newcastle University (GB)
Publication Details
- Journal
- Developmental Cell
- Published
- 2025-07-24
- DOI
- https://doi.org/10.1016/j.devcel.2025.06.031
- Citations
- 5
- Primary Topic
- Immune cells in cancer
- Type
- article
- Field-Weighted Citation Impact
- 3.99
Funders
- Wellcome Trust
- Medical Research Council