A Comparative Assessment of iPSC Derived Cardiomyocytes with Heart Tissues in Humans and Chimpanzees

To study regulatory differences between species, the field of comparative primate genomics has used several approaches, including the use of post mortem frozen tissues, cell lines, and model organisms. However, there are limited quality cell lines from primates and post-mortem tissues cannot be staged, are not amenable to experimental perturbations and are often subject to high environmental variances. Inducible pluripotent stem cells (iPSCs) are an attractive system to study primate biology in a comparative context. However, the fidelity of iPSC derived cell types to primary tissues needs to be assayed in a comparative primate context before the utility of iPSCs can be fully realized for comparative genomics. In order to comprehensively benchmark the performance of iPSC model systems in a comparative framework, we collected RNA-sequencing from primary adult heart tissue and iPSC derived cardiomyocytes from multiple human and chimpanzee individuals. We identified the optimal parameters of iPSC differentiation into cardiomyocytes that minimized differences between each species and their respective adult tissue counterparts in a balanced manner across species. We found that iPSC derived cardiomyocytes are able to recapitulate 50% of the interspecies gene expression differences identified between human and chimpanzee in primary post mortem heart tissues. Furthermore, we determined that cultured cardiomyocytes appear more similar to adult hearts than any other single tissue in their ability to recapitulate differences in gene regulation between human and chimpanzee. Overall design: We differentiated multiple human (9) and chimpanzee (10) iPSC lines into cardiomyocytes (iPSC-CMs) for 15 days using a recently developed protocol (Burridge et al. 2014; Burridge et al. 2015). After replating at day 15, iPSC-CMs were cultured for 12 more days, resulting in a total differentiation time of 27 days. On days 20-27, iPSC-CMs were treated with T3 (methods), a subset of 5 human and 6 chimpanzee iPSC-CMs were cultured in parallel without T3 treatment. We harvested RNA from all source iPSC lines, iPSC-CMs (day 15), T3 treated and untreated iPSC-CMs (day 27) sample. We harvested RNA from an additional set of 5 human and 6 chimp T3 treated day 27 samples in a second batch that did not have a matched day 15 and (-) T3 set. Finally, we collected RNA from flash frozen primary heart tissues (21 chimps and 11 humans).