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PLoS One. 2015 Feb 25;10(2):e0118307. doi: 10.1371/journal.pone.0118307. eCollection 2015.

Increased risk of genetic and epigenetic instability in human embryonic stem cells associated with specific culture conditions.

Author information

1
Center for Regenerative Medicine, Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States of America.
2
Department of Reproductive Medicine, UCSD Healthcare, 9500 Gilman Drive, Mail Code 0695, San Diego, CA 92093, United States of America.
3
Center for Regenerative Medicine, Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States of America; Department of Reproductive Medicine, UCSD Healthcare, 9500 Gilman Drive, Mail Code 0695, San Diego, CA 92093, United States of America.
4
Department of Pathology, UCSD Healthcare, 9500 Gilman Drive, Mail Code 0695, La Jolla, CA 92093-0612, United States of America.
5
Department of Human Genetics, University of Chicago, 920 E 58th St, CLSC 317, Chicago, IL, 60637, United States of America.
6
Department of Biochemistry and Molecular Biology, Center for Molecular Medicine, Paul D. Coverdell Center for Biomedical and Health Sciences, University of Georgia, Athens, GA, 30602, United States of America.

Abstract

The self-renewal and differentiation capacities of human pluripotent stem cells (hPSCs) make them a promising source of material for cell transplantation therapy, drug development, and studies of cellular differentiation and development. However, the large numbers of cells necessary for many of these applications require extensive expansion of hPSC cultures, a process that has been associated with genetic and epigenetic alterations. We have performed a combinatorial study on both hESCs and hiPSCs to compare the effects of enzymatic vs. mechanical passaging, and feeder-free vs. mouse embryonic fibroblast feeder substrate, on the genetic and epigenetic stability and the phenotypic characteristics of hPSCs. In extensive experiments involving over 100 continuous passages, we observed that both enzymatic passaging and feeder-free culture were associated with genetic instability, higher rates of cell proliferation, and persistence of OCT4/POU5F1-positive cells in teratomas, with enzymatic passaging having the stronger effect. In all combinations of culture conditions except for mechanical passaging on feeder layers, we noted recurrent deletions in the genomic region containing the tumor suppressor gene TP53, which was associated with decreased mRNA expression of TP53, as well as alterations in the expression of several downstream genes consistent with a decrease in the activity of the TP53 pathway. Among the hESC cultures, we also observed culture-associated variations in global gene expression and DNA methylation. The effects of enzymatic passaging and feeder-free conditions were also observed in hiPSC cultures. Our results highlight the need for careful assessment of the effects of culture conditions on cells intended for clinical therapies.

PMID:
25714340
PMCID:
PMC4340884
DOI:
10.1371/journal.pone.0118307
[Indexed for MEDLINE]
Free PMC Article

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