Analyzing the genomic integrity of stem cells

Prolonged culture of pluripotent and multipotent stem cells exposes the cells to strong selection pressures, often resulting in genomic alterations.Any genetic manipulation of the cells may further jeopardize their genomic stability.Genomic aberrations affect the differentiation capacity of stem cells, their stem cell identity and their tumorigenicity, and should thus be routinely evaluated for their proper use in basic research and in clinical trials.Here we review the common methods currently available to analyze the genomic integrity of stem cells, and present a recently developed method for the evaluation of the genomic integrity of stem cells by their gene expression profiles.We describe the principles of this method, provide guidelines for its implementation, and discuss its advantages and limitations compared to other available methods. Introduction: Genomic instability in stem cellsStem cells grown in culture are exposed to strong selection pressures that often results in genomic alterations, varying in size from point mutations, through copy number changes in small genomic elements (e.g.amplification of repetitive sequences and retroelement mobility), to large chromosomal aberrations, trisomies and monosomies (Lefort et al., 2009).While these aberrations are assumed to occur randomly, only those that confer a selective advantage would prevail and ultimately take over the culture.Different culturing conditions, such as media composition, cell passaging techniques, and freeze-thaw cycles, may affect the nature and the frequency of the acquired aberrations; however, no culturing technique is immune to genomic instability, and it is thus considered, for most practical purposes, a "necessary evil" that does not seriously compromise the utility of aberrant cells in basic science.Stem cells acquire genomic changes throughout their expansion in culture.Much attention has been drawn in recent years to the genomic aberrations acquired by human embryonic stem cells (hESCs) and human induced pluripotent stem cells (hiPSCs), from the resolution of point mutations to the resolution of whole-chromosome trisomies (Baker et al., 2007; Ben-David et al., 2011;Gore et al., 2011;Hussein et al., 2011;Laurent et al., 2011;Mayshar et al., 2010).More recently, we have shown that human adult stem cells that are expanded in culture are also prone to acquire chromosomal aberrations (Ben-David et al., 2011).In both pluripotent and multipotent stem cells, the genomic aberrations are eventually acquired in a large portion of the cell lines, and the aberrant cells can take over the population within very few passages (Ben-David et al., 2011;Mayshar et al., 2010), making the genomic instability of human stem cells a prevalent phenomenon in need of proper evaluation and consideration.