Team Identifies Genetic Abnormalities in Stem Cell Lines

A multinational team of researchers led by stem cell scientists at The Scripps Research Institute and the University of California, San Diego (UCSD) School of Medicine has documented specific genetic abnormalities that occur in human embryonic (hESC) and induced pluripotent stem cell (iPSC) lines.

The team's study, published in the January 7, 2011 issue of the journal Cell Stem Cell, highlights the need for frequent genomic monitoring of pluripotent stem cells to assure their stability and clinical safety. The ability of human pluripotent stem cells to become every cell type in the body has made them potential sources for cell replacement therapies.

“We found that human pluripotent cells (hESCs and iPSCs) had higher frequencies of genomic aberrations than other cell types,” said Louise Laurent, assistant professor in the UCSD Department of Reproductive Medicine and first author of the study. “Most strikingly, we observed a higher frequency of genomic duplications in hESCs and deletions in iPSCs, when compared to non-pluripotent samples.”

“Since genetic aberrations are often associated with cancers, it is vital that cell lines destined for clinical use are free from cancer-associated genomic alternations,” said senior author Scripps Research Professor Jeanne F. Loring.

The team identified regions in the genome that had a greater tendency to become abnormal in pluripotent cell lines. With hESCs, the observed abnormalities were most often duplications near pluripotency-associated genes; in iPSC lines, there were duplications involving cell proliferation genes and deletions associated with tumor suppressor genes.

These changes could not have been detected by traditional microscopic techniques such as karyotyping. The team instead used a high-resolution molecular technique called “single nucleotide polymorphism” (SNP) analysis, which allowed them to look for genetic changes at more than a million sites in the human genome.

“We were surprised to see profound genetic changes occurring in some cultures over very short periods of time, such as during the process of reprogramming somatic cells into iPSCs and during differentiation of the cells in culture,” Laurent said. “We don’t know yet what effects, if any, these genetic abnormalities will have on the outcome of basic research studies or clinical applications, and we need to find out.”

“SNP analysis has not been a part of routine monitoring of hESC and iPSC cultures,” Loring concluded, “but our results suggest that perhaps it should be.”

In addition to Loring and Laurent, contributors to the paper, titled “Dynamic changes in the copy number of pluripotency and cell proliferation genes in human ESCs and iPSCs during reprogramming and time in culture,” include Ileana Slavin, Ha Tran, Candace Lynch, Sherman Ku, and Joel Gottesfeld of The Scripps Research Institute; Robert Morey of UC San Diego and The Scripps Research Institute; Franz-Josef Muller of Zentrum für Integrative Psychiatrie, Kiel, Germany and The Scripps Research Institute; Andrew Schork and Carolline M. Nievergelt of UC San Diego; Julie V. Harness and Hans S. Keirstead, UC Irvine; Sunray Lee and Hyun-Sook Park of Modern Cell & Tissue Technologies Inc., Seoul, South Korea; Maria J. Barrero and Juan Carlos Izpisua Balmonte of Salk Institute for Biological Studies and Centro de Medicina Regenerativa de Barcelona; Marina Martynova and Rusian Semechkin of International Stem Cell Corporation, Oceanside, CA; Vasiliy Galat of Northwestern University; Chuck Murry of University of Washington; Ulrich Schmidt of Sydney IVF Stem Cell Laboratory, Sydney, Australia; Andrew Laslett of Commonwealth Scientific and Industrial Research Organisation, Clayton, Australia and Monash University, Victoria, Australia; and Ron Shamir of Tel Aviv University.

The study was funded by the National Institutes of Health, the California Institute for Regenerative Medicine, the Hartwell Foundation, the Millipore Foundation, the Esther O’Keefe Foundation, the Edmond J. Safra foundation in Tel Aviv, the Legacy stem cell research fund, the PEW Charitable Trust, the South Korea Ministry of Education, Science and Technology, the Ministerio de Ciencia e Innovación of Spain, MICINN Fundacion Cellex, the G. Harold and Leila Y. Mathers Charitable Foundation and Sanofi-Aventis.

Send comments to: mikaono[at]scripps.edu

Detailed maps of the human genome reveal abnormalities in pluripotent stem cells.