Mapping Human Pluripotent-to-Cardiomyocyte Differentiation: Methylomes, Transcriptomes, and Exon DNA Methylation “Memories”

• Published in: EBioMedicine 2016-02, Vol.4 (C), p.74-85
• Main Authors: Tompkins, Joshua D., Jung, Marc, Chen, Chang-yi, Lin, Ziguang, Ye, Jingjing, Godatha, Swetha, Lizhar, Elizabeth, Wu, Xiwei, Hsu, David, Couture, Larry A., Riggs, Arthur D.
• Format: Article
• Language: English
• Subjects: Cardiomyocytes; Cardiomyogenesis; Cell Differentiation; Cell Lineage; Cells, Cultured; Differentiation; DNA Methylation; Embryonic Stem Cells - cytology; Embryonic Stem Cells - metabolism; Epigenesis, Genetic; Epigenetic; Exons; Good manufacturing practice, GMP, epigenetic memory, WNT, hedgehog, transforming growth factor, ROR2, PDGFRα, demethylation, TET, TDG, HOX, TBOX; Human embryonic stem cells; Humans; lncRNA; Long non-coding RNA; Mesoderm; Methylome; Myocytes, Cardiac - cytology; Myocytes, Cardiac - metabolism; Pluripotent; Pluripotent Stem Cells - cytology; Pluripotent Stem Cells - metabolism; Research Paper; Transcriptome
• ISSN: 2352-3964; 2352-3964
• DOI: 10.1016/j.ebiom.2016.01.021

The directed differentiation of human cardiomyocytes (CMs) from pluripotent cells provides an invaluable model for understanding mechanisms of cell fate determination and offers considerable promise in cardiac regenerative medicine. Here, we utilize a human embryonic stem cell suspension bank, produced according to a good manufacturing practice, to generate CMs using a fully defined and small molecule-based differentiation strategy. Primitive and cardiac mesoderm purification was used to remove non-committing and multi-lineage populations and this significantly aided the identification of key transcription factors, lncRNAs, and essential signaling pathways that define cardiomyogenesis. Global methylation profiles reflect CM development and we report on CM exon DNA methylation “memories” persisting beyond transcription repression and marking the expression history of numerous developmentally regulated genes, especially transcription factors. •Pluripotent-derived-cardiomyocytes from scalable and defined cultures were used for transcriptome and methylome studies.•Mesoderm cell purification was conducted with ROR2 and PDGFRα surface markers removing heterogeneous cell contaminants.•Residual differentiation induced exon DNA methylation constitutes a developmental “memory” of transcription Human embryonic stem cells (hESCs) represent a theoretically unlimited cell replacement source in cardiac regenerative medicine. In this report, Tompkins et al. describe the derivation, differentiation stage-specific purification, and genome-wide analysis of cardiomyocytes derived from hESCs. Key features of the molecular programs that define human cardiac muscle cell differentiation are characterized and researchers observed that cells may harbor epigenetic DNA methylation “memories” that reflect the gene activation history of important developmental genes.