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

Autor: Hajmousa G; Department of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden University Medical Center, Post-zone S-05-P, P.O. Box 9600, 2300 RC, Leiden, The Netherlands., de Almeida RC; Department of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden University Medical Center, Post-zone S-05-P, P.O. Box 9600, 2300 RC, Leiden, The Netherlands., Bloks N; Department of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden University Medical Center, Post-zone S-05-P, P.O. Box 9600, 2300 RC, Leiden, The Netherlands., Ruiz AR; Department of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden University Medical Center, Post-zone S-05-P, P.O. Box 9600, 2300 RC, Leiden, The Netherlands., Bouma M; Department of Anatomy and Embryology and Human iPSC Hotel, 2333 ZA, Leiden, The Netherlands., Slieker R; Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands., Kuipers TB; Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands., Nelissen RGHH; Department of Orthopedics, Leiden University Medical Center, Leiden, The Netherlands., Ito K; Orthopaedic Biomechanics, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands., Freund C; Department of Anatomy and Embryology and Human iPSC Hotel, 2333 ZA, Leiden, The Netherlands., Ramos YFM; Department of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden University Medical Center, Post-zone S-05-P, P.O. Box 9600, 2300 RC, Leiden, The Netherlands., Meulenbelt I; Department of Biomedical Data Sciences, Section Molecular Epidemiology, Leiden University Medical Center, Post-zone S-05-P, P.O. Box 9600, 2300 RC, Leiden, The Netherlands. I.Meulenbelt@lumc.nl.
Jazyk: angličtina
Zdroj: Clinical epigenetics [Clin Epigenetics] 2024 Oct 15; Vol. 16 (1), pp. 141. Date of Electronic Publication: 2024 Oct 15.
DOI: 10.1186/s13148-024-01759-y
Abstrakt: Background: Lack of insight into factors that determine purity and quality of human iPSC (hiPSC)-derived neo-cartilage precludes applications of this powerful technology toward 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.
Methods: We applied in vitro chondrogenesis using hiPSCs generated from two different tissue sources: skin fibroblasts and articular cartilage. Upon differentiation toward chondrocytes, these are referred to as hFiCs and hCiC, respectively. Genome-wide DNA methylation and RNA sequencing datasets were generated of the hiPSC-derived neo-cartilages, and the epigenetically regulated transcriptome was compared to that of neo-cartilage deposited by human primary articular cartilage (hPAC).
Results: 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.
Conclusions: 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.
(© 2024. The Author(s).)
Databáze: MEDLINE
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