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Epigenetic Signatures to Standardize Manufacture of Induced Pluripotent Stem Cells

The method allows for generating stem cells to good manufacturing practice (GMP) quality for clinical-grade cells.  

INVENTION: The reprogramming process, by which mature somatic cells acquire pluripotent cellular properties resembling those of embryonic stem cells, requires complete reversion of the somatic epigenome into an ESC-like state. Investigators at the Salk Institute used whole-genome profiling of the DNA methylomes of multiple ESC, iPSC and somatic progenitor lines, to identify epigenomic signatures in human iPSCs that differ from human ESCs. These differentially methylated regions in the human iPSC genome are useful for identifying iPSCs and can be used as diagnostic markers for incomplete iPSC reprogramming. In addition, these genomic signatures are helpful for the characterization of the efficacy of different reprogramming techniques, identification of the factors that enable reprogramming, and standardizing the manufacture of stem cells for applications in cell therapy and drug development screening.


  • Identification of iPSCs
  • Diagnostic marker for incomplete reprogramming
  • Characterization of the efficacy of different reprogramming methods
  • Identification of reprogramming factors
  • Cell purity analysis
  • Standardization of iPSCs across multiple reprogramming methods
  • Generation of stem cells to GMP standards
  • Monitor stem cell integrity


  • Based on whole-genome profiles of DNA methylation at single-base resolution in five human iPSC lines
  • Provide loci information for differentially methylated regions in iPSCs
  • Well characterized stem cells for partner demands
  • Scale up for integration with clinical GMP facilities


BACKGROUND: Generation of iPSCs from somatic cells offers tremendous potential for therapeutics, the study of disease states and elucidation of development processes, without the controversy of using embryos. Understanding the full range of epigenomic variability and the factors that enable complete reprogramming to occur is invaluable for the progression of stem cell research and the development of cell regeneration therapies using iPSCs.

INVENTORS: Joseph R. Ecker
PATENT STATUS: US Provisional Application Filed; Nature 2011 Mar 3;471(7336):68-73. Cell 2013 May 23: 153(5): 1134-48.
CONTACT: Michelle A. Booden, Ph.D., 858.453.4100 x1612,
Patent Information:
For Information, Contact:
Michelle Booden
Director, Licensing and Intellectual Property
Salk Institute
DNA methylation
Good manufacturing practice
Induced pluripotent stem cells
Regenerative Medicine
Stem cell quality control
Stem Cells
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