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Identifying the Gene Regulatory Networks Controlling Efficient Human iPSC Chondrogenesis

Review of Single cell transcriptomic analysis of human pluripotent stem cell chondrogenesisfrom Nature Communications by Stuart P. Atkinson

In the hope of taking a step closer to an effective stem cell-based treatment for osteoarthritis [1], researchers led by Farshid Guilak (Washington University in Saint Louis, St. Louis, MO, USA) recently described a step-wise protocol that coupled inductive and repressive signals required for mesoderm specification in embryonic development [2] to prompt the efficient chondrogenic differentiation of human induced pluripotent stem cells (iPSCs) [3].

In their recently published follow-up study, the authors sought to elucidate the gene regulatory networks controlling the efficiency of iPSC chondrogenesis through both bulk and single-cell RNA sequencing in the hope of identifying means to improve efficiency [4]. Encouragingly, Wu et al. now report that inhibiting the expression of specific WNTs and melanocyte-inducing TF (MITF) during the chondrogenic differentiation of iPSCs can significantly increase chondrocyte homogeneity in a study that may aid the clinical translation of this therapeutic approach for osteoarthritis.

Their in-depth analysis revealed that WNTs and MITF function as “hub genes” that govern the generation of off-target differentiation into neural cells and melanocytes, respectively, during the differentiation of various human iPSC lines into distinct subtypes of chondrocytes. With this knowledge in hand, the study targeted WNTs and MITF for inhibition, which helped to eliminate off-target cell lineages and significantly enhanced the yield and homogeneity of iPSC-derived chondrocytes. The authors also employed heterocellular signaling models to establish off-target cell-mediated canonical and non-canonical WNT signaling as the culprit behind the induction of chondrocyte hypertrophic differentiation. Meanwhile, the authors also identified hub genes governing chondrogenic differentiation, such as the conventional master transcription factor SOX9 and the novel complement C1q like 1 (C1QL1) secreted protein with Ca2+ binding sites that regulate synaptogenesis in neuronal cells [5]. 

Overall, the evaluation of those mechanisms regulating the heterogeneous differentiation during the chondrogenesis of human iPSCs has fostered the development of a more robust and efficient protocol that may circumvent the need for prospective sorting and expansion of isolated progenitor cells and promote the application of cartilage regenerative medicine in human osteoarthritis patients.

For more on how gene regulatory network analysis may enhance differentiation protocols and bring iPSC-derived cells closer to the clinic, stay tuned to the Stem Cells Portal!


  1. Adkar SS, Brunger JM, Willard VP, et al., Genome Engineering for Personalized Arthritis Therapeutics. Trends in Molecular Medicine 2017;23:917-931.
  2. Loh KM, Chen A, Koh PW, et al., Mapping the Pairwise Choices Leading from Pluripotency to Human Bone, Heart, and Other Mesoderm Cell Types. Cell 2016;166:451-467.
  3. Adkar SS, Wu C-L, Willard VP, et al., Step-Wise Chondrogenesis of Human Induced Pluripotent Stem Cells and Purification Via a Reporter Allele Generated by CRISPR-Cas9 Genome Editing. STEM CELLS 2019;37:65-76.
  4. Wu C-L, Dicks A, Steward N, et al., Single cell transcriptomic analysis of human pluripotent stem cell chondrogenesis. Nature Communications 2021;12:362.
  5. Ressl S, Vu Brandon K, Vivona S, et al., Structures of C1q-like Proteins Reveal Unique Features among the C1q/TNF Superfamily. Structure 2015;23:688-699.