The aim of The Stem Cell Genomics Project was to identify genetic factors involved in stem cell formation, self-renewal and differentiation.

For this project, investigators used both mouse- and human-derived stem cells, obtained from embryos and adult tissues. At the end of the project, approximately 1000 stem cell samples and 300 purified stem cell populations were isolated; some of the cells types included myoblasts, as well as embryonic, hematopoietic and neural stem cells. The investigators used global gene expression platforms, including Affymetrix GeneChips and SAGE (serial analysis of gene expression) to identify the genetic factors regulating stem cell maintenance and development. In addition, various protein analyses were performed to generate global profiles of protein activity and function. A comprehensive overview of the genetic factors that specify stem cell identity and regulate their ability to differentiate will allow the full exploitation of the potential of stem cells in a clinical setting.

Over the course of this project, a total of 1400 Affymetrix GeneChip hybridizations were performed and 11 SAGE libraries were generated. Expression profiles were complemented with protein profiling of phosphoproteins and cell surface proteins, thought to be important in stem cell maintenance and development. Among several new insights into stem cell development, the investigators produced a particularly notable report in the journal Cell (June 2003) linking the Wnt signaling pathway to muscle regeneration by adult stem cells —a finding with potential commercial use.

Other important outcomes included the development of a strong computational platform for handling the expression data and the creation of a public database called Stembase. Lastly, the work stimulated other commercial activities including the formation of the stem cell company Stempath, as well as several patents and licenses. Ultimately, this work may be used to develop new strategies for coaxing existing stem cells to replace damaged or diseased cells.