The role of DNA methylation in chondrogenesis of human iPSCs as a stable marker of cartilage quality

Abstract

Lack of insight into factors that determine purity and quality of human iPSC (hiPSC)- derived neo-cartilage precludes applications of this powerful technology towards regenerative solutions in the clinical setting. Here we set out to generate methylome-wide landscapes of hiPSC derived neo-cartilages from different tissues-of-origin and integrated transcriptome-wide data to identify dissimilarities in set-points of methylation with associated transcription and the respective pathways in which these genes act.

Methylome-wide landscapes of neo-cartilages of hiPSCs reprogrammed from two different somatic tissues were 85% similar to that of hPACs. By integration of transcriptome-wide data, differences in transcriptionally active CpGs between hCiC relative to hPAC were prioritized. Among the CpG-gene pairs lower expressed in hCiCs relative to hPACs, we identified genes such as MGP, GDF5, and CHAD enriched in closely related pathways and involved in cartilage development that likely mark phenotypic differences in chondrocyte states. Vice versa, among the CpG-gene pairs higher expressed, we identified genes such as KIF1A or NKX2-2 enriched in neurogenic pathways and likely reflecting off target differentiation.

We did not find significant variation between the neo-cartilages derived from hiPSCs of different tissue sources, suggesting that application of a robust differentiation protocol such as we applied here is more important as compared to the epigenetic memory of the cells of origin. Results of our study could be further exploited to improve quality, purity, and maturity of hiPSC derived neo-cartilage matrix, ultimately to realize introduction of sustainable, hiPSC derived neo-cartilage implantation into clinical practice.

Full publication

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Authors: Ghazaleh Hajmousa, Rodrigo Coutinho de Almeida, Niek Bloks, Alejandro Rodríguez Ruiz, Marga Bouma, Roderick Slieker, Thomas B Kuipers, Rob GHH Nelissen, Keita Ito, Christian Freund, Yolande FM Ramos, Ingrid Meulenbelt.