Single cell transcriptomic analysis of human pluripotent stem cell chondrogenesis

  • Nat Commun. 2021 Jan 13;12(1):362. doi: 10.1038/s41467-020-20598-y.
Chia-Lung Wu  1  2  3 ,  Amanda Dicks  1  2  4 ,  Nancy Steward  1  2 ,  Ruhang Tang  1  2 ,  Dakota B Katz  1  2  4 ,  Yun-Rak Choi  1  2  5 ,  Farshid Guilak  6  7  8
Affiliations
  • 1. Dept. of Orthopaedic Surgery, Washington University in Saint Louis, St. Louis, MO, 63110, USA.
  • 2. Shriners Hospitals for Children-St. Louis, St. Louis, MO, 63110, USA.
  • 3. Department of Orthopaedics and Rehabilitation, Center for Musculoskeletal Research, University of Rochester, Rochester, NY, 14627, USA.
  • 4. Dept. of Biomedical Engineering, Washington University in Saint Louis, St. Louis, MO, 63110, USA.
  • 5. Dept. of Orthopaedic Surgery, Yonsei University, Seoul, South Korea.
  • 6. Dept. of Orthopaedic Surgery, Washington University in Saint Louis, St. Louis, MO, 63110, USA. [email protected].
  • 7. Shriners Hospitals for Children-St. Louis, St. Louis, MO, 63110, USA. [email protected].
  • 8. Dept. of Biomedical Engineering, Washington University in Saint Louis, St. Louis, MO, 63110, USA. [email protected].
PMID: 33441552 DOI: 10.1038/s41467-020-20598-y
Abstract

The therapeutic application of human induced pluripotent stem cells (hiPSCs) for cartilage regeneration is largely hindered by the low yield of chondrocytes accompanied by unpredictable and heterogeneous off-target differentiation of cells during chondrogenesis. Here, we combine bulk RNA Sequencing, single cell RNA Sequencing, and bioinformatic analyses, including weighted gene co-expression analysis (WGCNA), to investigate the gene regulatory networks regulating hiPSC differentiation under chondrogenic conditions. We identify specific WNTs and MITF as hub genes governing the generation of off-target differentiation into neural cells and melanocytes during hiPSC chondrogenesis. With heterocellular signaling models, we further show that Wnt signaling produced by off-target cells is responsible for inducing chondrocyte hypertrophy. By targeting WNTs and MITF, we eliminate these cell lineages, significantly enhancing the yield and homogeneity of hiPSC-derived chondrocytes. Collectively, our findings identify the trajectories and molecular mechanisms governing cell fate decision in hiPSC chondrogenesis, as well as dynamic transcriptome profiles orchestrating chondrocyte proliferation and differentiation.

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