Research Project

Summary
Stem cells have extraordinary potential to help in the treatment of some of the most intractable diseases - for example, arthritis, diabetes, neurological conditions such as Parkinson's and Alzheimer’s, and stroke. They are not yet available for this purpose because of lack of basic knowledge about stem cells. Full exploitation of their potential requires understanding of the genetic factors that make them what they are and of how they specify different kinds of cells and tissues in the body.

Researchers on this project endeavoured to determine which genes are active in stem cells using DNA micro-arraying, protein studies (proteomics), and serial analysis of gene expression (SAGE). They studied stem cells from the embryos of humans and mice and from bone-marrow, brain, and muscle tissues in adults. They took cells from laboratory mice and from human biopsy samples and maintained them as laboratory cell-cultures for use in experiments.

The team carried out 1,400 DNA micro-array and 11 SAGE experiments and analysed protein from almost 140 protein samples. In addition, it set up a data bank that it called StemBase, complete with new methods of graphical display and analysis. This material is available publicly to stem cell researchers all over the world. All together, twenty-five investigators from across Canada participated in this project.

Fast Facts

• Highlighted outcome: StemBase, the largest stem-cell gene-expression database in the world.
• Number of research personnel: 45.
• Number of peer-reviewed publications: 11 plus two book chapters and 33 invited presentations.
• Number of patents in process or obtained: 3 plus 2 commercial licenses and 1 company.
• Resources generated: StemBase database (six libraries of gene-expression products and 62 DNA micro-array experiments consisting of 188 samples and 997 files deposited).
• Number of public outreach events: 8 technical seminars, 4 public lectures, 7 newspaper, magazine, and TV articles, and 24 public laboratory tours.

Notable Publications
Polesskaya A, Seale P, and Rudnicki MA 2003. Wnt signaling induces the myogenic specification of resident CD45+ adult stem cells during muscle regeneration. Cell 113:841-52.

Perez-Iratxeta C, Palidwor G, Porter CJ, Sanche NA, Huska MR, Suomela BP, Muro EM, Krzyzanowski PM, Hughes E, Campbell PA, Rudnicki MA, and Andrade MA. 2005. Study of stem cell function using microarray experiments. FEBS Letters. 579:1795-1801.

Fernando P, Deng W, De Repentigny Y, Kothary R, Kelly JF, and Megeney LA. 2005. Active kinase proteome screening reveals novel signal complexity in cardiomyopathy. Mol. Cell. Proteomics 4:673-82.

Muro EM, Perez-Iratxeta C, and Andrade-Navarro MA. 2006. Amplification of the Gene Ontology annotation of Affymetrix probe sets. BMC Bioinformatics 7:159.

Puente LG, Borris DJ, Carriere JF, Kelly JF, and Megeney LA. 2006. Identification of candidate regulators of embryonic stem cell differentiation by comparative phosphoprotein-affinity profiling. Mol. Cell. Proteomics 5:57-67.