Clinical impact of subclonal EGFR T790M mutations in advanced-stage EGFR-mutant non-small-cell lung cancers

Tereza Vaclova,Ryan Hartmaier,J Carl Barrett,Julian Downward,Aleksandra Markovets,Lewis Ward,Juliann Chmielecki,Paul D Smith,Daniel O’Neill,Kenneth S Thress,Xiangning Huang,Ursula Grazini,Elza C De Bruin

doi:10.1038/s41467-021-22057-8

Abstract

Advanced non-small-cell lung cancer (NSCLC) patients with EGFR T790M-positive tumours benefit from osimertinib, an epidermal growth factor receptor-tyrosine kinase inhibitor (EGFR-TKI). Here we show that the size of the EGFR T790M-positive clone impacts response to osimertinib. T790M subclonality, as assessed by a retrospective NGS analysis of 289 baseline plasma ctDNA samples from T790M‐positive advanced NSCLC patients from the AURA3 phase III trial, is associated with shorter progression-free survival (PFS), both in the osimertinib and the chemotherapy-treated patients. Both baseline and longitudinal ctDNA profiling indicate that the T790M subclonal tumours are enriched for PIK3CA alterations, which we demonstrate to confer resistance to osimertinib in vitro that can be partially reversed by PI3K pathway inhibitors. Overall, our results elucidate the impact of tumour heterogeneity on response to osimertinib in advanced stage NSCLC patients and could help define appropriate combination therapies in these patients.

Highlights

Advanced non-small-cell lung cancer (NSCLC) patients with EGFR T790M-positive tumours benefit from osimertinib, an epidermal growth factor receptor-tyrosine kinase inhibitor (EGFR-tyrosine kinase inhibitors (TKIs))
In order to identify AURA3 patients whose tumours harbour a subclonal T790M mutation, we first evaluated the prevalence and level of detection of the activating EGFR mutations, exon 19 deletion and L858R, and the TKI-resistant EGFR T790M in plasma collected at baseline using a clinically validated NGSbased cell-free DNA assay (Supplementary Table 1; details in ‘Methods')
Taking into account that EGFR ctDNA shedding status has been previously found to be associated with a baseline tumour target lesion size in AURA3 patients[13], our results indicate that AURA3 patients, who are not positive for both the activating and resistance EGFR mutations, may have smaller tumours

Summary

Introduction

Advanced non-small-cell lung cancer (NSCLC) patients with EGFR T790M-positive tumours benefit from osimertinib, an epidermal growth factor receptor-tyrosine kinase inhibitor (EGFR-TKI). T790M subclonality, as assessed by a retrospective NGS analysis of 289 baseline plasma ctDNA samples from T790M‐positive advanced NSCLC patients from the AURA3 phase III trial, is associated with shorter progression-free survival (PFS), both in the osimertinib and the chemotherapy-treated patients. Retrospective genotyping of matched tumour biopsy and plasma samples from patients enrolled in the osimertinib first-in-man study (AURA, NCT01802632) led to an identification of patients with T790M-negative tumours, but T790M-positive plasma, indicating that the mutation was only present in a fraction of tumour cells in these patients[9] This subset of patients showed the shortest PFS and a lower objective response rate. We retrospectively analyse baseline plasma from patients enrolled on the AURA3 clinical study to identify patients with subclonal T790M and show that subclonal T790M genotype is associated with shorter PFS in osimertinib-treated patients These samples were enriched for co-occurring activating PIK3CA mutations, which we demonstrate to reduce sensitivity to osimertinib in vitro in EGFR-mutant cell lines. Our results shed light on the implications of T790M subclonality in advanced-stage NSCLC patients and its link to resistance to osimertinib and could help define appropriate combination therapies in these patients

Objectives

Methods

Results