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

TP53 functions as a central regulator in response to DNA damage and other cell stressors by inducing the expression of many protective pathways such as cell cycle arrest and apoptosis. Consequently, this gene is often found disrupted in human cancers. Elephants are a particularly interesting species for the study of cancer, by virtue of their large number of cell divisions and long lives yet low incidence of cancer. Elephants also possess multiple retrogene copies of TP53, which have previously been shown to induce strong cellular responses to DNA damage. However, most previous studies have largely focused only on African elephant TP53 retrogenes and often in non-native backgrounds. Here we generated CRISPR-Cas9 knockouts of TP53, all 29 TP53 retrogenes, or both in combination in Asian elephant fibroblasts. 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 large role in the tumor microenvironment and mitigating metastatic growth. We also find that only a small fraction of these 29 retrogenes appear to be expressed across a variety of tissues and identify three loci that are likely driving this response. This work shows for the first time the transcriptomic effect of these retrogenes within their native background and establishes a foundation for future research into the relative contributions of these genes.