Nuclear Factor I genes drive chondrogenic cell-fate commitment

bioRxiv (Cold Spring Harbor Laboratory)

Abstract

Abstract Human induced pluripotent stem cells (hiPSCs) offer a powerful platform to model chondrogenesis and enable regenerative strategies, yet regulation of cell-fate commitment remains elusive. Here, we systematically mapped cell-fate trajectories from 7 time points during a 49-day chondrogenic hiPSC differentiation protocol using single-nucleus multimodal transcriptomic and chromatin accessibility profiling (scRNA-seq and scATAC-seq). Integrative analysis of dynamics revealed branching differentiation trajectories with clear bifurcation points and distinct cell-fates. Notably, the chondrogenic trajectory originated at day 6 as a neurogenic development and branched off at day 21 to a chondrogenic cell-fate. Through transcription factor activity analysis (TFAA) and cis-co-accessibility networks, we found that NFIA and NFIB drove chondrogenic distinction, exhibited in both modalities as directly targeting chondrogenic genes such as COMP , FIBIN , VIM. This was then confirmed by experimental validation as modulation of NFIA expression at this point further enhanced chondrocyte formation. Together, our study provides a high-resolution multimodal atlas of chondrogenic differentiation and identified critical transcriptional regulators that can now be leveraged to implement regenerative cartilage therapies from hiPSCs.

Authors 9

1. Rick Mulders Aachen Department of Biomedical Data Sciences Section Molecular Epidemiology

   Leiden University Medical Center

   Affiliation as printed

   Dept. of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands

2. Mathew Nickel-Maunu Aachen Department of Biomedical Data Sciences Section Molecular Epidemiology

   Leiden University Medical Center

   Affiliation as printed

   Dept. of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands

3. Marcella van Hoolwerff Aachen Department of Biomedical Data Sciences Section Molecular Epidemiology

   Leiden University Medical Center

   Affiliation as printed

   Dept. of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands

4. Giorgia Mazzini Aachen Department of Biomedical Data Sciences Section Molecular Epidemiology

   Leiden University Medical Center

   Affiliation as printed

   Dept. of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands

5. Lucas Jansen Klomp Aachen Department of Biomedical Data Sciences Section Molecular Epidemiology

   Leiden University Medical Center

   Affiliation as printed

   Dept. of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands

6. Hil Meijer Aachen Department of Biomedical Data Sciences Section Molecular Epidemiology

   Leiden University Medical Center

   Affiliation as printed

   Dept. of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands

7. Janine N. Post Aachen Department of Biomedical Data Sciences Section Molecular Epidemiology

   Leiden University Medical Center

   Affiliation as printed

   Dept. of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands

8. Y.F. Ramos Aachen Department of Biomedical Data Sciences Section Molecular Epidemiology

   Leiden University Medical Center

   Affiliation as printed

   Dept. of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands

9. Ingrid Meulenbelt corresponding Aachen Department of Biomedical Data Sciences Section Molecular Epidemiology

   Leiden University Medical Center

   Affiliation as printed

   Dept. of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands