The Mechanism of Phenotypic Drift in hES Cells

Funding agency: University of Connecticut Research Foundation
Amount: $50,000
PI: : R.J. O’Neill, Co-PIs: B. Graveley, I. Mandoiu, T. Rasmussen, and Y. Wu
Period: 01/2009 – 12/2009

Human embryonic stem cells (hESCs) have tremendous thearapeutic potential due to their ability to give rise to all possible cell types in the human body. Moreover, the recent ability to reprogram somatic cells into induced pluripotent stem (iPS) cells sets the stage for generating patient-specific stem cells that could potentially treat a wide variety of diseases. Unfortunately, one hallmark of hESCs (and perhaps iPS cells) is that they are unstable, and change over time. However, any therapeutic use of stem cells, whether hESCs or iPS, will require that the cells are both genetically stable and homogenous. Therefore, it is necessary to obtain a thorough understanding of the mechanistic basis of phenotypic variation. The goal of this project is to investigate the mechanistic nature of variability between distinct hESC lines as well as between hESC subcultures that have phenotypically drifted. Specifically, we will use Illumina and 454 sequencing to determine and compare the mRNA and small RNA repertoires of these cell lines and to identify structural alterations in the genomes of each cell line. A combined analysis of these three datasets will allow us to identify the differences in gene expression, epigenetic states, and genome integrity that underlie phenotypic drift in hESCs which may provide insight into ways to more carefully control hESCs.