Cross-species transcriptional profiles establish a functional portrait of embryonic stem cells

Abstract

An understanding of the regulatory mechanisms responsible for pluripotency in embryonic stem cells (ESCs) is critical for realizing their potential in medicine and science. Significant similarities exist among ESCs harvested from different species, yet major differences have also been observed. Here, by cross-species analysis of a large set of functional categories and all transcription factors and growth factors, we reveal conserved and divergent functional landscapes underlining fundamental and species-specific mechanisms that regulate ESC development. Global transcriptional trends derived from all expressed genes, instead of differentially expressed genes alone, were examined, allowing for a higher discriminating power in the functional portrait. We demonstrate that cross-species correlation of transcriptional changes that occur upon ESC differentiation is a powerful predictor of ESC-important biological pathways and functional cores within a pathway. Hundreds of functional modules, as defined by Gene Ontology, were associated with conserved expression patterns but bear no overt relationship to ESC development, suggestive of new mechanisms critical to ESC pluripotency. Yet other functional modules were not conserved; instead, they were significantly up-regulated in ESCs of either species, suggestive of species-specific regulation. The comparisons of ESCs across species and between human ESCs and embryonal carcinoma stem cells suggest that while pluripotency as an essential function in multicellular organisms is conserved throughout evolution, mechanisms primed for differentiation are less conserved and contribute substantially to the differences among stem cells derived from different tissues or species. Our findings establish a basis for defining the "stemness" properties of ESCs from the perspective of functional conservation and variation. The data and analyses resulting from this study provide a framework for new hypotheses and research directions and a public resource for functional genomics of ESCs.

Figure 1

Expression patterns of selected converged (a) and divergent (b) biological processes and pathways. On the headmap of each module, the column represents an orthologous gene expressed in hESC (top row) and in mESC (bottom row). The expression fold change of the gene is represented by different colors (green: down-regulated in ESC, red: up-regulated in ESC, black: no change). For conserved modules (a; with high r values), many orthologous genes showed expression in the same direction (e.g. either up-regulated in both species or down-regulation in both) with similar expression fold changes between human and mouse. For divergent modules (b; low or negative r values), most orthologous genes showed expression in opposite directions (e.g. up-regulated in one species and down-regulated in another) with dissimilar expression fold changes between human and mouse. Details of the genes shown in each module along with the expression values and fold changes are provided in Supplementary Table S3.

Figure 2

Summary of conserved biological processes showing correlated expression patterns between human and mouse ESCs.