Concurrent RB1 and TP53 Alterations Define a Subset of EGFR-Mutant Lung Cancers at risk for Histologic Transformation and Inferior Clinical Outcomes

Abstract

Introduction: EGFR-mutant lung cancers are clinically and genomically heterogeneous with concurrent RB transcriptional corepressor 1 (RB1)/tumor protein p53 (TP53) alterations identifying a subset at increased risk for small cell transformation. The genomic alterations that induce lineage plasticity are unknown.

Methods: Patients with EGFR/RB1/TP53-mutant lung cancers, identified by next-generation sequencing from 2014 to 2018, were compared to patients with untreated, metastatic EGFR-mutant lung cancers without both RB1 and TP53 alterations. Time to EGFR-tyrosine kinase inhibitor discontinuation, overall survival, SCLC transformation rate, and genomic alterations were evaluated.

Results: Patients with EGFR/RB1/TP53-mutant lung cancers represented 5% (43 of 863) of EGFR-mutant lung cancers but were uniquely at risk for transformation (7 of 39, 18%), with no transformations in EGFR-mutant lung cancers without baseline TP53 and RB1 alterations. Irrespective of transformation, patients with EGFR/TP53/RB1-mutant lung cancers had a shorter time to discontinuation than EGFR/TP53- and EGFR-mutant -only cancers (9.5 versus 12.3 versus 36.6 months, respectively, p = 2 × 10^-9). The triple-mutant population had a higher incidence of whole-genome doubling compared to NSCLC and SCLC at large (80% versus 34%, p < 5 × 10^-9 versus 51%, p < 0.002, respectively) and further enrichment in triple-mutant cancers with eventual small cell histology (seven of seven pre-transformed plus four of four baseline SCLC versus 23 of 32 never transformed, respectively, p = 0.05). Activation-induced cytidine deaminase/apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like mutation signature was also enriched in triple-mutant lung cancers that transformed (false discovery rate = 0.03).

Conclusions: EGFR/TP53/RB1-mutant lung cancers are at unique risk of histologic transformation, with 25% presenting with de novo SCLC or eventual small cell transformation. Triple-mutant lung cancers are enriched in whole-genome doubling and Activation-induced cytidine deaminase/apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like hypermutation which may represent early genomic determinants of lineage plasticity.

Keywords: EGFR-mutation; RB1; Small cell histologic transformation; TP53; Whole genome doubling.

Figure 1.

Time to treatment discontinuation (TTD) and overall survival (OS) of patients with EGFR/RB1/TP53-mutant lung cancers: patients with EGFR/RB1/TP53-mutant lung cancer without baseline small cell lung cancer (SCLC) who were EGFR-TKI naïve at the time of next-generation sequencing (NGS) (n = 20) versus patients with EGFR/TP53-mutant RB1-wildtype (n = 79) and EGFR-mutant RB1/TP53-wild type lung cancer who were EGFR-TKI naïve at the time of NGS (A) The median TTD for patients with EGFR/RB1/TP53-mutant lung cancer was 9.5 months versus 12.3 months for EGFR/TP53-mutant RB1-wildtype (HR 2.0, 95% CI 1.1 – 3.6) versus 36.6 months in EGFR-mutant RB1/TP53-wiltype groups (HR 7.7, 95% CI 3.6 – 14.2; log-rank for trend p = 2e⁻⁹). (B) The median OS of patients with EGFR/RB1/TP53-altered lung cancer was 29.1 months as compared to 40.8 months in EGFR/TP53-mutant RB1-wildtype and 56.4 months in patients with EGFR-mutant RB1/TP53-wildtype (HR 1.0 95% CI 0.4 – 2.4, HR 1.8 95% CI 0.7 – 4.3, respectively; log-rank for trend p = 0.16).

Figure 2.

Genomic landscape of lung cancer with concurrent EGFR/RB1/TP53 mutations. The type of genetic alteration (missense, in-frame, truncating, amplification, deep (homozygous) deletion, fusion/intragenic alteration) is described in the legend. The frequency of mutations is noted on the right. Mutations present in at least 5% of cases were included in the figure, as well as PIK3CA, MYC, and CREBBP mutations given their known relevance in small cell lung cancer.

Figure 3.

Enrichment analysis of genomic alterations. (A) Enrichment of mutations in EGFR-mutant lung cancer with concurrent TP53/RB1 mutations versus without concurrent TP53/RB1 mutations. (B) Within EGFR/RB1/TP53-mutant lung cancer, enrichment of mutations in cases with eventual SCLC transformation. Level of enrichment is represented as a volcano plot with the log ratio in frequency between the two states (x-axis) and its significance -log(p-value) (y-axis). The type of alteration is represented by color. The dashed line represents p-value = 0.05.

Figure 4.

AID/APOBEC mutation signature and whole genome doubling (WGD) in EGFR/RB1/TP53-mutant lung cancers. (A) Mutation signature analysis identified significant enrichment of AID/APOBEC in pre-transformed SCLC compared to never transformed. Heatmap is calculated based on weights [0,1] measuring how strongly a mutation signature is represented in a given sample. Top annotation plots significance as -log(FDR) for enrichment of a mutation signature in pre-transformed SCLC. The dashed red line corresponds to an FDR of 0.05. (B) The frequency of WGD in lung cancer with concurrent EGFR/RB1/TP53 mutations is higher compared to all NSCLC and SCLC. Plots show the distribution of the proportion of autosomal genes with major copy number of at least 2 in lung cancers with concurrent EGFR/RB1/TP53 mutations, NSCLC, and SCLC respectively. Using a cutoff of 50%, the proportion of samples with WGD is colored in red, corresponding to a WGD frequency of 80% in lung cancer with concurrent EGFR/RB1/TP53 vs 34% in NSCLC (p < 5×10⁻⁹) vs 51% in SCLC (p < 0.002).