Circulating Tumor DNA Genomics Reveal Potential Mechanisms of Resistance to BRAF-Targeted Therapies in Patients withBRAF-Mutant Metastatic Non–Small Cell Lung Cancer

Abstract

Purpose: The limited knowledge on the molecular profile of BRAF-mutant non-small cell lung cancer (NSCLC) patients who progress under BRAF-targeted therapies (BRAF-TT) has hampered the development of subsequent therapeutic strategies for these patients. Here, we evaluated the clinical utility of ctDNA targeted sequencing to identify canonical BRAF mutations and genomic alterations potentially related to resistance to BRAF-TT, in a large cohort of BRAF-mutant NSCLC patients. Experimental Design: Prospective study of 78 advanced BRAF-mutant NSCLC patients, enrolled in 27 centers across France. Blood samples (n=208) were collected from BRAF-TT-naïve patients (n=47), non-progressive under treatment (n=115) or at disease progression (PD) to BRAF-TT (24/46 on BRAF-monotherapy; 22/46 on BRAF/MEK combination therapy). ctDNA sequencing was performed using InVisionFirst^®-Lung. In silico structural modeling was used to predict the potential functional effect of the alterations found in ctDNA. Results: BRAF^V600E ctDNA was detected in 74% of BRAF-TT-naïve patients, where alterations in genes related with the MAPK and PI3K pathways, signal transducers and protein kinases were identified in 29% samples. ctDNA positivity at the first-radiographic evaluation under treatment, as well as BRAF-mutant ctDNA positivity at PD were associated with poor survival. Potential drivers of resistance to either BRAF-TT monotherapy or BRAF/MEK combination were identified in 46% patients and included activating mutations in effectors of the MAPK and PI3K pathways, as well as alterations in U2AF1, IDH1 and CTNNB1. Conclusions: ctDNA sequencing is clinically relevant for the detection of BRAF-activating mutations and the identification of alterations potentially related to resistance to BRAF-TT in BRAF-mutant NSCLC.