Human ES Cells Evolve in Culture

Researchers identify common genetic changes in cultured human embryonic stem cells, including one that confers a growth advantage.

Nov 28, 2011
Ruth Williams


A worldwide effort to screen the genomes of more than a hundred human embryonic stem cell (hESC) lines has revealed a number of consistent genetic differences that appear after the cells are cultured for a period of time. About 20 percent of the lines, for example, contained an amplification of a short region on chromosome 20, which appears to confer a growth advantage to the cells. The report was published online yesterday (November 27) in Nature Biotechnology.

A few years ago, a group of scientists decided to launch the global project, which was run by the International Stem Cell Initiative (ISCI), because they were concerned about the occurrence of genetic changes in cultured hESCs, which could spell trouble for the their use in cell replacement therapies. Specifically, reports of consistent genomic alterations were appearing from a number of separate labs, explained project organizer Peter Andrews of the University of Sheffield. “What sparked our interest was that these changes were not random,”  suggesting that particular genes might be under selective pressure when hESCs are exposed to culture conditions. Scientists are culturing hESCs in a way that encourages continuous self-renewal, he said, so if the cells acquire mutations that improve replication and division, for example, they will be selected for.

To identify such candidate genes, Andrews and his colleagues organized a worldwide collaborative effort to compare the genomes of as many hESC cell lines as possible. “Individual studies are generally not big enough to have enough power,” said Louise Laurent of the University of California, San Diego, School of Medicine, who was not involved in the study. The new study, she said, “is an example of what the ISCI is good at—bringing together a lot of collaborators and putting together a large-scale project.”

In total, the genomes of 125 independent hESC lines from 38 laboratories in 19 different countries were analyzed. A number of commonly amplified and deleted regions were identified, but only one—an amplification on the long arm of chromosome 20—occurred with sufficient frequency and was of a small enough size to identify a single candidate gene.

The gene, BCL2L1, encodes a protein that inhibits cell death. Cell lines with the amplified BCL2L1 region had a growth advantage in culture, as did cells in which BCL2L1 itself was artificially overexpressed—suggesting BCL2L1 is under selective pressure in hESCs in culture.

Such genetic changes to hESCs might appear to put the kibosh on plans for their use in patients. However, Andrews insisted that the finding was “not a disaster.” For one thing, the amplification of BCL2L1, like other changes, was more common in hESC that had been cultured for a long time, indicating that younger cultured cells may contain fewer genetic differences. Furthermore, the majority of the cell lines analyzed remained at least karyotypically normal—that is, they did not have large-scale changes.

“What it says from a safety and application point of view is that we can grow cells and we can expect them to remain genetically normal, but we have to monitor them,” Andrews said. “Because if you grow the cells for sufficient time there is a likelihood that they will acquire changes, and that these changes will be non-random.” Should an hESC cell line develop the BCL2L1 region amplification, for example, it might be time to discard them. “It is a phenomenon that will happen, but it is manageable,” he said.

Laurent’s view was equally tempered. “These sorts of studies are really valuable because people need to go into potential stem cell therapies with their eyes open,” she said. “However, the caveat is that for none of these [abnormal genetic sites] has a direct functional role been shown. It’s going to take a lot more work before we can definitively say whether they are a bad sign or not.”

The International Stem Cell Initiative, “Screening ethnically diverse human embryonic stem cells identifies a chromosome 20 minimal amplicon conferring growth advantage,” Nature Biotechnology, doi:10.1038/nbt.2051, 2011.