Cross-Species Comparative Transcriptomic Analysis of Embryonic Stem Cells (ESCs)

Embryonic stem cells (ESCs), with their unique capacity for pluripotency and differentiation, are powerful for studying cell fate determination. However, molecular mechanisms governing pluripotency, particularly those conserved across species, are poorly understood. In this study, we conducted a comprehensive transcriptomic comparison of ESCs from nine mammalian species—human, mouse, rat, cattle, pig, horses, sheep, crab-eating macaque, and marmoset—to identify both conserved and species-specific mechanisms of pluripotency regulation. Principal component analysis (PCA) revealed a conserved trajectory underlying the naïve-to-primed state transition across species. Differential expression analysis further identified evolutionarily conserved genes, such as ZBTB10 and IHO1. Gene Ontology analysis highlighted that pathways related to embryonic development and cell-cell communication were enriched among the conserved genes. Weighted Gene Co-expression Network Analysis (WGCNA) identified a primed state-associated module, which was significantly preserved across species. Key hub genes within this co-expression network were potential critical regulators of pluripotency. Moreover, among the four pluripotency states, the primed state emerged as the most evolutionarily conserved, exhibiting lower dN/dS ratios and phylogenetic clustering consistent with traditional species relationships, suggesting it may serve as a developmental “checkpoint” across species. These findings provide strong evidence for the evolutionary conservation of pluripotency regulation, particularly in the primed state. These insights lay the groundwork for future research in both basic biology and translational applications.