Monkeys in a dish: Standardizing primate iPSCs to study the evolution of pluripotency networks

• Applicants: Professor Dr. Wolfgang Enard; Privatdozentin Dr. Ines Hellmann
• Subject Area: General Genetics and Functional Genome Biology ; Bioinformatics and Theoretical Biology
• Term: since 2026
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 573973867

An evolutionary dimension is fundamental for understanding biology and humans are no exception. Comparative approaches provide unique information to understand how the human genome functions in health and disease and primates, as our closest relatives, are particularly important in this context. However, experimental access to molecular and cellular phenotypes of primates is difficult or impossible for ethical and practical reasons. The emergence of induced pluripotent stem cells (iPSCs) and their derivatives has revolutionized how we study and manipulate otherwise inaccessible cell types in humans. More recently, it has become apparent that standardized quality controls and a sufficient number of replicates are often central to making robust inferences. iPSCs from non-human primates (NHPs) have started to revolutionize comparative approaches, but standardizations have not been adapted for NHP-iPSCs as they are available from only a few species and a few individuals per species. Here, we propose to begin tackling this using the cynomolgus macaque (Macaca fascicularis) as it is an established primate model for early development and as an Old World monkey (OWM) has a well-suited phylogenetic distance for comparative studies of gene regulation. We will optimize conditions for comparative iPSC generation and maintenance and will adapt the newly established human ISSCR standards to NHPs. For this we will leverage efficient RNA-seq assays and will develop and implement an user-friendly computational analysis pipeline. As proof of principle, we are going to extend our approach to another OWM species (M. sylvanus) as well as a New World Monkey species (Saimiri boliviensis), which will also serve as an outgroup in our evolutionary analyses. Finally, we will create the first large panel of comparable human and NHP-iPSCs, which in turn allows us to analyze the evolution of pluripotency networks in primates using RNA-seq and ATAC-seq data. This is relevant, as it has become clear in recent years that these regulatory networks get extensively rewired during evolution despite their conserved property of pluripotency. Our large data set will provide unique insights into the logic of this rewiring and hence into the evolution and function of gene regulatory networks of pluripotent stem cells. In summary, our proposal will advance comparative genomic approaches based on NHP-iPSCs by providing a generalized, efficient pipeline to characterize them according to established standards and by providing the largest panel of cynomolgus iPSCs matched to human counterparts. Furthermore, the ensuing comprehensive omics-dataset will allow us to make inferences about the evolution of gene regulatory networks active in iPSCs, which will provide unique insights into the workings of pluripotency networks.

• DFG Programme: Research Grants