Serial Cell-Free DNA Sequencing in <i>ROS1</i> Fusion-Positive Lung Cancers During Treatment With Entrectinib.

Abstract

Patients with metastatic <i>ROS1</i> fusion-positive non-small cell lung cancer (NSCLC) are effectively treated with entrectinib, a multikinase inhibitor. Whether serial targeted gene panel sequencing of cell-free DNA (cfDNA) can identify response and progression along with mechanisms of acquired resistance to entrectinib is underexplored. In patients with <i>ROS1</i> fusion-positive NSCLC, coclinical trial plasma samples were collected before treatment, after two cycles, and after progression on entrectinib (global phase II clinical trial, ClinicalTrials.gov identifier: NCT02568267). Samples underwent cfDNA analysis using MSK-ACCESS. Variant allele frequencies of detectable alterations were correlated with objective response per RECIST v1.1 criteria. Twelve patients were included, with best response as partial response (n = 9, 75%), stable disease (n = 2, 17%), and progressive disease (PD; n = 1, 8%). A <i>ROS1</i> fusion was variably detected in cfDNA; however, patients without a <i>ROS1</i> fusion in cfDNA had no other somatic alterations detected, indicative of possible low cfDNA shedding. Clearance of the enrolling <i>ROS1</i> fusion or concurrent non-<i>ROS1</i> alterations (<i>TP53</i>, <i>CDH1</i>, <i>NF1</i>, or <i>ARID1A</i> mutations) was observed in response to entrectinib therapy. Radiologic PD was accompanied by redemonstration of a <i>ROS1</i> fusion or non-<i>ROS1</i> alterations. On-target resistance was rare; only one patient acquired <i>ROS1</i> G2032R at the time of progression. Several patients acquired new off-target likely oncogenic alterations, including a truncating alteration in <i>NF1</i>. Serial cfDNA monitoring may complement radiographic assessments as determinants of response and resistance to entrectinib in <i>ROS1</i> fusion-positive lung cancers in addition to detecting putative resistance mechanisms on progression.