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

Emil Karpinski, Nikil Badey, Esther Mintzer, Asaf Ashkenazy-Titelman, George M Church
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Abstract

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.
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亚洲象TP53工程:TP53逆转录基因敲除激活常见和独特的癌症相关途径
TP53 通过诱导细胞周期停滞和细胞凋亡等多种保护性途径的表达,在应对 DNA 损伤和其他细胞应激源时发挥核心调节作用。因此,在人类癌症中,该基因经常被破坏。大象细胞分裂次数多,寿命长,但癌症发病率低,因此是研究癌症的一个特别有趣的物种。大象还拥有多个 TP53 的逆转录基因拷贝,以前的研究表明,TP53 能诱导细胞对 DNA 损伤做出强烈反应。然而,以前的研究大多只关注非洲象的 TP53 逆基因,而且往往是在非本地背景下进行的。在这里,我们在亚洲象成纤维细胞中产生了TP53的CRISPR-Cas9基因敲除、全部29个TP53逆源基因敲除或两者结合的基因敲除。我们发现,虽然TP53基因敲除和逆转录基因敲除的DNA损伤反应有相当多的重叠,但两者也有许多独特的途径。特别是,逆转录基因敲除子在许多细胞外通路中表现出很强的富集性,这表明它们可能在肿瘤微环境和减轻转移性生长中发挥了很大作用。我们还发现,这 29 个逆转录基因中只有一小部分似乎在各种组织中表达,并确定了可能驱动这种反应的三个位点。这项工作首次显示了这些逆源基因在其原生背景下的转录组效应,并为今后研究这些基因的相对贡献奠定了基础。
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