Single-Cell Functional Genomics

Description (provided by applicant): In this proposal we wish to assess as to how far human stem cells suffer from random accumulating changes in the genome, epigenome and transcriptome, measured by comparative, integrated analysis of single cells. This question is relevant not only for aging-related functional decline of organs and tissues, but especially for the validity of using human embryonic or adult stem cells in regenerative medicine. While there is ample evidence for genomic and epigenomic changes in cell populations, including embryonic stem cells during sub-culture, the functional impact of such changes is unclear. This is due to a virtual lack of methods to study cells not as averages across entire populations, but at the level of individual cells, in assays that integrate changes in the transcriptome with genomic and epigenomic changes. Here we propose to use integrative assays for assessing alterations in the genome, epigenome and transcriptome in the same individual cells. This approach requires technology sensitive and precise enough to manipulate individual cells and interrogate them sequentially for various experimental end points. The main question we wish to address here is whether human embryonic stem (hES) cells are capable of withstanding the genetic and epigenetic erosion that occurs in normal, differentiated somatic cells. Since it is hoped that hES cells can be used to replenish organs and tissues, it is extremely important to know whether such cells experience genetic drift and if so the rate and magnitude of spontaneous alterations. Such an approach has never been attempted before and lends itself well to the EUREKA mechanism because it addresses an extremely difficult problem, is unsuitable for regular NIH support due to the high risk involved and the relative lack of preliminary data, is highly innovative with ample use of novel technologies and can be completed within a 4-year time frame.