Comprehensive classification of TP53 somatic missense variants based on their impact on p53 structural stability

Somatic variation is a major type of genetic variation contributing to human diseases, including cancer. The functional impact of many somatic variants including missense variants remains unclear, hindering the translation of such variation information into clinical applications. We previously developed a protein structural-based method, Ramachandran plot-molecular dynamics simulations (RP-MDS), to predict the function of germline missense variants based on their effects on protein structure stability, which produced successful predictions of the deleterious germline missense variants in multiple cancer-related genes. We reasoned that somatic missense variants and germline missense variants should have similar effects on the stability of the protein structure. In this study, we applied our protein structural-based approach, RP-MDS, to provide a comprehensive classification of the somatic missense variants in TP53. We analyzed 397 somatic missense variants and showed that 195 (49.1%) variants were deleterious due to their disruptions to p53 structure. The results were furthered validated by using a p53 - p21 promoter - green fluorescent protein (GFP) reporter gene assay. Our study demonstrated that deleterious somatic missense variants can be identified by referring to their effects on protein structural stability.

体细胞变异（somatic variation）是一类关键的遗传变异类型，与包括癌症在内的多种人类疾病的发生发展密切相关。目前包括错义变异（missense variants）在内的多数体细胞变异的功能效应仍不明确，这极大阻碍了此类变异信息向临床应用的转化。
本团队此前开发了一种基于蛋白质结构的分析方法——拉马昌德兰绘图-分子动力学模拟（RP-MDS），通过分析变异对蛋白质结构稳定性的影响来预测生殖系错义变异（germline missense variants）的功能，该方法已成功在多个癌症相关基因中鉴定出具有有害效应的生殖系错义变异。我们推测，体细胞错义变异与生殖系错义变异对蛋白质结构稳定性的影响机制应具有相似性。
本研究将上述基于蛋白质结构的RP-MDS方法应用于TP53基因的体细胞错义变异的全面分类分析。本研究共分析了397个体细胞错义变异，结果显示其中195个（占比49.1%）变异因破坏p53蛋白结构而具有有害效应。本研究通过p53-p21启动子-绿色荧光蛋白（GFP）报告基因实验对上述结果进行了验证。本研究证实，可通过分析变异对蛋白质结构稳定性的影响来精准鉴定具有有害效应的体细胞错义变异。