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New study reveals dynamic changes in gene regulation of human pluripotent stem cells
by Amy Swinderman  |  Email the author


LA JOLLA, Calif.—In what they are calling "the most comprehensive study of human pluripotent stem cell variation to date," a team of researchers from the Scripps Research Institute and the University of California, San Diego, has discovered dynamic changes in gene regulation in these cells, a finding that may have important implications for using them for basic and clinical research.  
Human pluripotent stem cells (hPSCs) can give rise to virtually every type of cell in the body, and thus hold huge potential for cell replacement therapies and drug development. But there is still much to be learned about how these cells behave in the lab, says Prof. Jeanne Loring of Scripps Research, a lead author on a study recently published in the journal Cell Stem Cell.  
Loring's lab focuses on basic and translational research approaches to understanding stem cells at a molecular level, and its scientists are working to apply that knowledge in the field of regenerative medicine. Last year, the team reported recurrent changes in the genomes of hPSCs as they are expanded in culture, and their development of a technique for purifying cell mixtures.  
"One of the big issues about using human pluripotent stem cells for any kind of clinical application—including disease studies and drug development—is that these cells are unlike cells anyone has ever studied before, and we must learn more about them. The first thing that came to mind for us is that these cells are like cancer cells in some ways. If one cell has a slight survival advantage over others, as it grows and divides, this cell will take over the culture. The same thing happens in cancers, especially blood cancers."  
The team used tiny beads to attach lectin to stem cells. The cells that washed past were almost all non-stem cells, and the scientists observed that both cell types could be collected separately for use in research or in treatments. This work presented a new way to solve purification and safety problems in stem cell research, says Loring.  
"But we didn't answer the question of whether these changes are close to the genes involved in maintaining those cells as being pluripotent," she notes. "The changes that occurred in culture were enhancing that cell type. That may or may not be a problem, but what is important is that we pointed out that it happened."  
Now, in a follow-up study that appears in the May 4 issue of Cell Stem Cell, Loring's lab is reporting that these cells can also change their epigenomes, the patterns of DNA modifications that regulate the activity of specific genes. These changes may influence the cells' abilities to serve as models of human disease and development.  
Specifically, the team assessed the state of both DNA methylation and gene expression in more than 200 hPSC samples from more than 100 cell lines, along with 80 adult cell samples representing 17 distinct tissue types. Both DNA methylation and demethylation are important regulatory processes in cellular differentiation.
Key to the research was a new global DNA methylation array developed in collaboration with Illumina Inc. that detects the methylation state of 450,000 sites in the human genome. The results showed surprising changes in patterns of DNA methylation in the stem cells. Because of the unprecedented breadth of the study, the researchers were able to determine the frequency of different types of changes.  
The team observed that pluripotent cells differ from somatic cells at sites in the genome that are generally considered to be epigenetically stable—the inactivated X chromosome in female cells and imprinted loci. X chromosome inactivation (XCI) was not erased following the reprogramming of human fibroblasts, but was lost over time, leading to a loss of dosage compensation of subsets of X chromosome genes. This includes a large number of X- linked disease genes, which may complicate a large number of hPSC-based models of X-linked disease. Aberrations in genomic imprints are frequent in hPSCs, and all of the hPSCs analyzed in this study had abberant DNA methylation of at least one imprinted gene.  
"There are whole families of diseases associated with abnormal imprinting," says Loring. "We're probably going to find that in a lot of cases, neurodevelopmental diseases will have abnormalities in methylation that we can trace to a mutated gene, and then use that as leverage to try to figure out how they are controlled."  
Some diseases or conditions Loring specifically mentions are Rett's syndrome, Fragile X syndrome and even autism.
"In the autistic brain, this would be a handy way to explain why you have certain characteristics," she adds.  
The team is now working on controlling the imprinting and which genes are turned on or off when cells differentiate.  
"These are not small questions, but now we know that we need to ask them," says Loring.  
The results presented by her team are interesting from a developmental biology perspective because "it places us on the edge of understanding the development of some diseases," Loring points out.  
"When you think about embryonic development, it all goes so well, and it is hard for us to understand how all of these things can fall into place," she says. "This research will give us insight into how that happens. This is the kind of thing we couldn't have done a year ago because we didn't have the tools. I feel like we are in an exciting place right now because we're getting really good at culturing cells and doing bioinformatic analysis. The combination of these things is leading to interesting kinds of insights that wouldn't have been possible before."
The study, "Recurrent Variations in DNA Methylation in Human Pluripotent Stem Cells and their Differentiated Derivatives," was supported by the California Institute for Regenerative Medicine and the U.S. National Institutes of Health. Loring's colleagues on the multi-site project included Gulsah Altun, Candace Lynch, Ha Tran, Ileana Slavin, Ibon Garitaonandia, Franz-Josef Müller, Yu-Chieh Wang, Francesca S. Boscolo and Eyitayo Fakunle from Scripps Research; Julie V. Harness and Hans S. Keirstead from the University of California at Irvine; Mana M. Parast from the University of California San Diego; Tsaiwei Olee and Darryl D. D'Lima from Scripps Health; Biljana Dumevska and Andrew L. Laslett from the Commonwealth Scientific and Industrial Research Organization in Australia; Uli Schmidt from the Stem Cell Laboratory in Sydney, Australia; Hyun Sook Park and Sunray Lee from the Laboratory of Stem Cell Niche in Seoul, South Korea; Ruslan Semechkin from International Stem Cell Corp.; and Vasiliy Galat from Children 's Memorial Research Center in Chicago.  

Code: E07111203



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