Selection Via Pluripotency-Related Transcriptional Screen Minimizes the Influence of Somatic Origin on iPSC Differentiation Propensity

Authors

  • Katherine A. Hartjes,

    1. Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA
    2. Center for Regenerative Medicine, Mayo Clinic, Rochester, Minnesota, USA
    Search for more papers by this author
  • Xing Li,

    1. Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
    2. Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, USA
    Search for more papers by this author
  • Almudena Martinez-Fernandez,

    1. Center for Regenerative Medicine, Mayo Clinic, Rochester, Minnesota, USA
    2. Division of Cardiovascular Diseases, Mayo Clinic, Rochester, Minnesota, USA
    Search for more papers by this author
  • Alexa J. Roemmich,

    1. Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA
    Search for more papers by this author
  • Brandon T. Larsen,

    1. Division of Anatomic Pathology, Mayo Clinic, Rochester, Minnesota, USA
    Search for more papers by this author
  • Andre Terzic,

    1. Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA
    2. Center for Regenerative Medicine, Mayo Clinic, Rochester, Minnesota, USA
    3. Division of Cardiovascular Diseases, Mayo Clinic, Rochester, Minnesota, USA
    4. Department of Medical Genetics, Mayo Clinic, Rochester, Minnesota, USA
    Search for more papers by this author
  • Timothy J. Nelson

    Corresponding author
    1. Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA
    2. Center for Regenerative Medicine, Mayo Clinic, Rochester, Minnesota, USA
    3. Division of General Internal Medicine, Mayo Clinic, Rochester, Minnesota, USA
    4. Transplant Center, Mayo Clinic, Rochester, Minnesota, USA
    • Correspondence: Timothy J. Nelson, M.D., Ph.D., Mayo Clinic, 200 First Street SW, Rochester, Minnesota 55905, USA. Telephone: 507-538-4891; Fax: 507-266-9936; e-mail: nelson.timothy@mayo.edu

    Search for more papers by this author

Abstract

The value of induced pluripotent stem cells (iPSCs) within regenerative medicine is contingent on predictable and consistent iPSC differentiation. However, residual influence of the somatic origin or reprogramming technique may variegate differentiation propensity and confound comparative genotype/phenotype analyses. The objective of this study was to define quality control measures to select iPSC clones that minimize the influence of somatic origin on differentiation propensity independent of the reprogramming strategy. More than 60 murine iPSC lines were derived from different fibroblast origins (embryonic, cardiac, and tail tip) via lentiviral integration and doxycycline-induced transgene expression. Despite apparent equivalency according to established iPSC histologic and cytomorphologic criteria, clustering of clonal variability in pluripotency-related gene expression identified transcriptional outliers that highlighted cell lines with unpredictable cardiogenic propensity. Following selection according to a standardized gene expression profile calibrated by embryonic stem cells, the influence of somatic origin on iPSC methylation and transcriptional patterns was negated. Furthermore, doxycycline-induced iPSCs consistently demonstrated earlier differentiation than lentiviral-reprogrammed lines using contractile cardiac tissue as a measure of functional differentiation. Moreover, delayed cardiac differentiation was predominately associated with upregulation in pluripotency-related gene expression upon differentiation. Starting from a standardized pool of iPSCs, relative expression levels of two pluripotency genes, Oct4 and Zfp42, statistically correlated with enhanced cardiogenicity independent of somatic origin or reprogramming strategy (R2 = 0.85). These studies demonstrate that predictable iPSC differentiation is independent of somatic origin with standardized gene expression selection criteria, while the residual impact of reprogramming strategy greatly influences predictable output of tissue-specification required for comparative genotype/phenotype analyses. Stem Cells 2014;32:2350–2359

Ancillary