The molecular signature of gain-of-function (GOF) vs. non-GOF classification TP53 mutations in colorectal cancer.
Authors: Khushman Moh'd M. , Gandhi Nishant , Xiu Joanne , Manne Upender , Lou Emil , Shields Anthony F. , El-Deiry Wafik S. , Braxton David R. , Oberley Matthew James , Marshall John , Lenz Heinz-Josef , Seeber Andreas 
Published: June 2023

e15612

Background: The approach of collectively classifying TP53 mutations (m TP53) into gain-of-function (GOF) and non-GOF was proposed as a novel approach for prognostic stratification and incorporation in clinical trials design in colorectal cancer (CRC). We previously reported that the prognosis of CRC with m TP53 is independent of GOF. Here, we explored the underlying molecular signature of m TP53 in CRC based on GOF vs. non-GOF classification. Methods: CRC specimens (N = 13,976) were tested at Caris Life Sciences (Phoenix, AZ) with NextGen Sequencing (NGS) of DNA (592-gene panel or whole- exome sequencing). R175H, R248W, R248Q, R249S, R273H, R273L, and R282W were defined as GOF mTP53; all other mTP53 were defined as non-GOF. MSI-H/dMMR status was determined by immunohistochemistry of MMR protein and/or NGS. Statistical significance was determined using chi-square and Mann-Whitney U test with p-values adjusted for multiple comparisons (q < 0.05). Results: GOF mTP53 and non-GOF mTP53 were identified in 2,875 (21%) and 7,801 (56%) patients, respectively. Compared to patients with GOF mTP53, patients with non-GOF mTP53 had more prevalent tumor mutation burden-high (TMB > = 10mut/MB) (6.7% vs. 3.7%, q < 0.05) and MSI-H/dMMR (3.7% vs. 1.9%, q < 0.05). No difference in the prevalence of KRAS and BRAF mutations was observed. The expression of genes upregulated in tumors with mTP53 ( MYC, TERT, ASNS, E2FS, IGF1R, EFGR, ABCB1, BCL2L1, TIMM50, CDK1 and CDC25C) was higher in both GOF and non-GOF mTP53 compared to wildtype TP53 ( wtTP53, all q < 0.05). Apart from ABCB1 gene (1.14-fold GOF/nonGOF, q < 0.05), there was no difference in the expression of those genes between GOF and non-GOF mTP53. The expression of genes upregulated in tumors with wtTP53 ( CDKN1A, BAX, GADD45A and BBC3) was lower in both GOF and non-GOF mTP53 compared to wtTP53. The expression of BAX (0.96-fold) and BBC3(0.99-fold) was lower in GOF compared to non-GOF mTP53(both q < 0.05). Compared to wtTP53, higher expression of genes upregulated in tumors with mTP53 was demonstrated among several GOF mTP53 (except R273L and R249S) and all non-GOF mTP53 ( R273C, G245S, R213*, R196*, R306* and R342*; *indicating a stop codon). Compared to wtTP53, lower expression of genes upregulated in tumors with wtTP53 was demonstrated among several GOF mTP53 (except R273L). Similar results were also observed among missense, nonsense, frameshift and splicing mTP53. These results taken together suggest limited heterogeneity in transcriptional regulation among mTP53 regardless of their classification. Conclusions: In CRC, non-GOF mTP53 was prevalent in more than half of all cases. Compared to GOF mTP53, predictive biomarkers of response to immune checkpoint inhibitors (TMB and MSI-H/dMMR) were higher in this cohort albeit still relatively rare. Otherwise, differences in molecular signatures between GOF and non-GOF mTP53 did not contain clinically meaningful differences.