Concurrent TP53 Mutations Facilitate Resistance Evolution in EGFR-Mutant Lung Adenocarcinoma

Abstract

Introduction: Patients with EGFR-mutant NSCLC experience variable duration of benefit on EGFR tyrosine kinase inhibitors. The effect of concurrent genomic alterations on outcome has been incompletely described.

Methods: In this retrospective study, targeted next-generation sequencing data were collected from patients with EGFR-mutant lung cancer treated at the Dana-Farber Cancer Institute. Clinical data were collected and correlated with somatic mutation data. Associations between TP53 mutation status, genomic features, and mutational processes were analyzed.

Results: A total of 269 patients were identified for inclusion in the cohort. Among 185 response-assessable patients with pretreatment specimens, TP53 alterations were the most common event associated with decreased first-line progression-free survival and decreased overall survival, along with DNMT3A, KEAP1, and ASXL1 alterations. Reduced progression-free survival on later-line osimertinib in 33 patients was associated with MET, APC, and ERBB4 alterations. Further investigation of the effect of TP53 alterations revealed an association with worse outcomes even in patients with good initial radiographic response, and faster acquisition of T790M and other resistance mechanisms. TP53-mutated tumors had higher mutational burdens and increased mutagenesis with exposure to therapy and tobacco. Cell cycle alterations were not independently predictive, but portended worse OS in conjunction with TP53 alterations.

Conclusions: TP53 alterations associate with faster resistance evolution independent of mechanism in EGFR-mutant NSCLC and may cooperate with other genomic events to mediate acquisition of resistance mutations to EGFR tyrosine kinase inhibitors.

Keywords: EGFR; Genomics; Non–small cell lung cancer; Resistance.

Figure 1.. Genomic and clinical predictors of outcome to EGFR TKI therapy.

Association between co-occurring alterations and A. Progression-free survival (PFS) on first-line EGFR TKI (PFS1)(n=184), B. PFS on subsequent osimertinib (PFS-Osi)(n=37), and C. Overall survival (OS)(n=269). Hazard ratio is shown on the x-axis, -log10(p-value) from univariate cox-proportional hazards model is shown on the y-axis. Points are colored by the observed genetic events as indicated. Only genes altered in 5 or more samples are included in A & C, and in 2 or more samples in B. D. Forest plots of clinicogenomic variables and PFS1 (left), PFS-Osi (middle), and OS (right). CNA: copy number alteration; SCLC: small cell lung cancer; TKI: tyrosine kinase inhibitor; TMB: tumor mutational burden.

Figure 2.. Association between TP53 alteration, outcome, and resistance mechanism.

Association between TP53 alteration detected at any time point and A. First TKI progression-free survival (PFS1), B. PFS on subsequent osimertinib (PFS-Osi), and C. Overall survival (OS). D. Distribution of radiographic responses in patients with (MT) and without (WT) pre-treatment TP53 alteration (Fisher’s p-value=0.7541). E. Distribution of resistance mechanisms in pre-treatment TP53 MT vs WT patients (Fisher’s p-value=0.6483). F. Proportion of patients with pre-treatment Rb1 alterations in patients with and without small cell transformation at any time point. G. PFS1 and H. OS stratified by pre-treatment Rb1 and TP53 mutation status. TKI: tyrosine kinase inhibitor

Figure 3.. TP53 alterations, mutation load, chromosomal instability and mutagenesis.

A. Tumor mutational burden (TMB) in TP53 wild type (WT) vs altered (MT) tumors (Wilcoxon p-value=0.00051). B. Proportion copy number altered (CNA) in TP53 WT vs MT (Wilcoxon p-value=0.0014). C. TMB in TP53 WT vs MT tumors stratified by treatment context (TP53 WT, pre vs post-treatment, p-value=0.042; TP53 MT, pre vs post-treatment, p-value=5.228e-05; pre-treatment, TP53 MT vs WT, p=0.02239; post-treatment, TP53 MT vs WT, p=0.01113). D. CNA load in TP53 WT vs MT tumors stratified by treatment context (TP53 WT, pre vs post-treatment, p-value=0.11; TP53 MT, pre vs post-treatment, p-value=0.45; pre-treatment, TP53 MT vs WT, p-value=0.00126). E. Proportion of mutations attributable to each signature in TP53 MT vs WT (Signature 4, p=0.0012; Signature 5, p=0.0282). F. Proportion of mutations attributable to each signature in pre vs post-treatment samples, TP53 WT samples (Signature 1, p=0.020. G. Proportion of mutations attributable each signature in pre vs post-treatment samples, TP53 MT samples; Signature 1, p=0.0024). All other comparisons, p > 0.05. *p<0.05; **p<0.01, ***p<0.001. N=311 samples, 212 with TP53 alterations, 99 without.

Figure 4.. TP53 alterations and smoking-associated mutagenesis.

A. Proportion of ever vs never smokers in TP53 WT vs MT patients (Chi-square p-value=0.3646). B. TMB in TP53 WT vs MT patients in ever (left) and never (right) smokers (Ever smoker, Wilcoxon p-value=0.006424; Never smoker, Wilcoxon p-value=0.0216). C. Proportion signature 4 mutations in ever vs never smokers, stratified by TP53 WT vs MT; TP53 WT, Wilcoxon p-value=0.46; TP53 MT, Wilcoxon p-value=0.0001. *p<0.05; **p<0.01, ***p<0.001. MT: altered; WT: wild type. N=269; 106 ever smokers, 163 never smokers.

Figure 5.. Cell cycle alterations and outcome.

A. First TKI progression-free survival (PFS1) and B. overall survival (OS) stratified by CDK4/6 and TP53 co-alteration status. Cox-proportional hazards for outcome relative to TP53 wild type/CDK4/6 wild type shown below. C. PFS1 and D. OS stratified by cell cycle and TP53 co-alteration status. Cox-proportional hazards for outcome relative to TP53 wild type/cell cycle wild type shown below. The most frequently altered cell cycle genes were considered and were: MDM2, CDK4, CDK6, CCND1, CCNE1, CDKN2A, CDKN2B, and EP300. MT: altered; TKI: tyrosine kinase inhibitor; WT: wild type.