Engineering Asian elephant TP53: TP53 retrogene knockouts activate common and unique cancer-relevant pathways

Throughout their evolution, proboscideans have gotten larger and spread to occupy novel environments throughout the world. These phenotypic changes have been accompanied by a suite of genetic changes including those responsible for tumor suppression and environmental adaptation. Here we examine a handful of woolly mammoth-specific deletions, and their potential contributions to arctic adaptation, as well as the expanded TP53 genetic repertoire in elephants. We use CRISPR-Cas9 to introduce mammoth-specific noncoding deletions as well as knockouts of TP53, all 29 TP53 retrogenes, or both in combination in Asian elephant cell lines, and examine the transcriptomic response. We find that many of the mammoth-specific deletions likely contribute to various arctic phenotypes including vascular development, metabolism and thermogenesis, and hair and skin adaptations. Additionally, we find that while there is considerable overlap in the DNA damage responses of the TP53 and retrogene knockouts, there are also many unique pathways enriched in both. In particular, the retrogene knockouts exhibit strong enrichment of many extracellular pathways suggesting they may play a role in the tumor microenvironment and mitigating metastatic growth. This highlights the usability of cell culture models to disentangle the effects of regulatory mutations or complex genetic systems, especially in non-model species where the generation of animal models is not possible.