A gene expression profile of embryonic stem cells and embryonic stem cell-derived neurons

Embryonic stem (ES) cells have the ability to differentiate into a variety of cell lineages. We are examining ES cell differentiation in vitro by usin g cDNA microarrays to generate a molecular phenotype for each cell type. E1 4 ES cells induced by retinoic acid after forming embryoid bodies different iate almost exclusively to neurons. We obtained expression patterns for abo ut 8500 gene sequences by comparing mRNAs from undifferentiated ES cells an d their differentiated derivatives in a competitive hybridization. Our resu lts indicate that the genes expressed by ES cells change dramatically as th ey differentiate (58 gene sequences up-regulated, 34 down-regulated). Most notably, totipotent ES cells expressed high levels of a repressor of Hox ex pression (the polycomb homolog Mph1) and a co-repressor (CTBP2). Expression of these genes was undetectable in differentiated cells; the ES cell-deriv ed neurons expressed a different set of transcriptional regulators, as well as markers of neurogenesis. The gene expression profiles indicate that ES cells actively suppress differentiation by transcriptional repression; cell -cell contact in embryoid bodies and retinoic acid treatment may overcome t his suppression, allowing expression of Hox genes and inducing a suite of n euronal genes. Gene expression profiles will be a useful outcome measure fo r comparing in vitro treatments of differentiating ES cells and other stem cells. Also, knowing the molecular phenotype of transplantable cells will a llow correlation of phenotype with the success of the transplant.