Functional plasticity of putative TP53 gain of function mutations in human gastrointestinal tract adenocarcinomas.
Authors: Braxton David R. , Xiu Joanne , El-Deiry Wafik S. , Darabi Sourat , Korn Wolfgang Michael , Demeure Michael J. , Eisenberg Burton Larry ,   Precision Oncology Alliance-Translational Research Group
Published: June 2021

e15530 Background: The TP53 gene product is a multifunctional protein and prototypical tumor suppressor. Certain missense mutations occurring in hotspots in the TP53 gene may confer gain of function (GOF) oncogenic properties. A recent mouse model (Kadosh et. al., Nature, 2020) demonstrated that secreted factors in the gut microbiome permit GOF p53 to be oncogenic in lower GI tract cancers (LT). By contrast, the GOF p53 mutants in the upper tract cancers (UT) retained tumor suppressor functions. We aimed to provide evidence of the plasticity of TP53 GOF mutants in human GI cancers. We hypothesized that UT should have a lower rate of TP53 GOF than the LT, and UT cancers with putative GOF TP53 mutations should display a higher degree of co-occurring oncogenic alterations such as dysregulation of CCND1, MYCS, or WNT. We also explored outcome differences for TP53 GOF variants. Methods: Tumors of UT (stomach, esophagus, small intestine) and LT (colorectum, anus) were tested at Caris Life Sciences (Phoenix, AZ) by NGS (NextSeq, 592 or NovoSeq, whole exome). MSI/MMRP status was determined by IHC and NGS. Real-world overall survival (OS) was obtained from payor claims data and Kaplan-Meier estimates were calculated. P values adjusted for multiple correction (q) of < 0.05 was considered significant. Six p53 variants were classified as GOF (p.R175, p.G245, p.R248, p.R249, p.R273, and p.R282). Results: Of the 5311 UT and 14810 LT tumors sequenced, 4799 harbored a TP53 GOF variant. UT had TP53 GOF in 22.9% of cases compared to 27.0% of LT (q < 0.05). 67 genes were enriched for amplification (q < 0.05) in the UT TP53 GOF cancers compared to the LT TP53 GOF, including cell cycle regulators( CCND1, CCNE1, CDK6, CDK12), and oncogenes ( KRAS, ERBB2, EGFR). LT TP53 GOF cancers were enriched for eight gene amplifications, including CDX2, FLT3, and SRC. Differences in SNV/InDel patterns were not remarkable. OS analysis revealed TP53 GOF in UT had shorter OS when compared to TP53 wild-type (WT) (Median OS: 418 vs 515 days; HR: 0.864; 95%CI [0.772-0.966]; p = 0.011), but not when MSI/MMRP status was considered separately. LT TP53 GOF did not show OS difference in aggregate, however, MSI-High TP53 GOF cancers showed a shorter OS (Median OS: 762 vs 1479 days; HR: 1.522; [1.068 - 2.171]; p = 0.019). Sub-analysis of LT MSI-High cancers treated by immune checkpoint blockade showed a non-significant trend toward shorter OS of TP53 GOF versus TP53 wild type cancers (HR: 2.55; [0.90-7.19], p: 0.067), but no such trend was seen in UT (HR: 1.434; [0.304-6.758], p:0.646). Conclusions: Our study is the first to compare putative TP53 GOF variants across UT and LT GI adenocarcinoma. TP53 GOF variants are associated with decreased OS in both UT cancers and MSI-High LT cancers. Our findings support the functional plasticity of TP53 GOF variants in human GI cancers. Therefore, the purported effects of secreted microbiome factors on TP53 GOF variants cannot be ruled out.