Entrectinib in ROS1-positive advanced non-small cell lung cancer: the phase 2/3 BFAST trial

Abstract

Although comprehensive biomarker testing is recommended for all patients with advanced/metastatic non-small cell lung cancer (NSCLC) before initiation of first-line treatment, tissue availability can limit testing. Genomic testing in liquid biopsies can be utilized to overcome the inherent limitations of tissue sampling and identify the most appropriate biomarker-informed treatment option for patients. The Blood First Assay Screening Trial is a global, open-label, multicohort trial that evaluates the efficacy and safety of multiple therapies in patients with advanced/metastatic NSCLC and targetable alterations identified by liquid biopsy. We present data from Cohort D (ROS1-positive). Patients ≥18 years of age with stage IIIB/IV, ROS1-positive NSCLC detected by liquid biopsies received entrectinib 600 mg daily. At data cutoff (November 2021), 55 patients were enrolled and 54 had measurable disease. Cohort D met its primary endpoint: the confirmed objective response rate (ORR) by investigator was 81.5%, which was consistent with the ORR from the integrated analysis of entrectinib (investigator-assessed ORR, 73.4%; data cutoff May 2019, ≥12 months of follow-up). The safety profile of entrectinib was consistent with previous reports. These results demonstrate consistency with those from the integrated analysis of entrectinib in patients with ROS1-positive NSCLC identified by tissue-based testing, and support the clinical value of liquid biopsies to inform clinical decision-making. The integration of liquid biopsies into clinical practice provides patients with a less invasive diagnostic method than tissue-based testing and has faster turnaround times that may expedite the reaching of clinical decisions in the advanced/metastatic NSCLC setting. ClinicalTrials.gov registration: NCT03178552 .

Fig. 1. BFAST study design.

^aAll cohorts have additional, treatment-specific inclusion/exclusion criteria. ^bPlease see ClinicalTrials.gov for full treatment dosing information. Figure adapted with permission from Peled, N. et al. Higher dose alectinib for advanced RET+ NSCLC: results from the RET+ cohort of the Blood First Assay Screening Trial (BFAST), presented at the 2020 World Conference on Lung Cancer (28–31 January 2021, Singapore). bTMB, blood tumor mutational burden; FMI, Foundation Medicine, Inc.; IV, intravenous.

Fig. 2. Clinical outcomes of patients with ROS1-positive NSCLC who were identified by liquid biopsy and treated with entrectinib.

a–d, DoR (n = 44) (a), PFS (n = 55) (b), OS (n = 55) (c) and CNS progression (n = 54) (d) Kaplan–Meier curves for patients with ROS1-positive NSCLC who were identified via liquid biopsies and treated with entrectinib. BFAST Cohort D data cutoff, 26 November 2021. DoR, PFS and CNS progression were assessed by investigator. NE, not estimable; INV, investigator.

Fig. 3. Comutations identified in patients with ROS1-positive NSCLC at baseline and clinical outcomes of patients with mTP53 versus wtTP53.

a, Comutations and type of mutation identified in patients with ROS1-positive NSCLC via liquid biopsy at baseline; the most common comutation identified in patients from BFAST Cohort D was TP53. b,c, DoR (n = 44) (b) and PFS (n = 54) (c) Kaplan–Meier curves for patients from BFAST Cohort D with mTP53 (red) versus wtTP53 (blue). Patients with mTP53 had numerically shorter DoR and PFS compared with those with wtTP53 at baseline. CN, copy number.

Extended Data Fig. 1. Clinical outcomes of patients treated with entrectinib and who had CD74 as the ROS1 fusion partner and those with other (non-CD74) ROS1 fusion partners.

(A) DoR (n = 44) and (B) PFS (n = 55) Kaplan–Meier curves for patients who had CD74 as the ROS1 fusion partner (red) and those with other (non-CD74) ROS1 fusion partners (blue). There was no difference in median DoR and PFS between patients who had CD74 as the ROS1 fusion partner (n = 31) and those with other fusion partners (n = 24). One patient who had CD74 as the ROS1 fusion partner had non-measurable disease. CI, confidence intervals; DoR, duration of response; HR, hazard ratio; INV, investigator; PFS, progression-free survival; ROS1, ROS proto-oncogene 1.

Extended Data Fig. 2. PFS in patients treated with entrectinib who had EZR as the ROS1 fusion partner and those with other (non-EZR) ROS1 fusion partners.

Median PFS was similar between patients who had EZR as the ROS1 fusion partner (n = 13) and those with other fusion partners (n = 42). CI, confidence intervals; HR, hazard ratio; INV, investigator; NA, not available; PFS, progression-free survival; ROS1, ROS proto-oncogene.

Extended Data Fig. 3. Prevalence of ROS1 fusion co-mutations identified by liquid biopsy and tissue-based testing.

The prevalence of comutations that were identified by liquid biopsies in BFAST Cohort D were comparable with those identified by tissue-based testing from the FMCore database. A low prevalence of rearrangements were identified in the tissue-based testing data; these were identified in the following genes: CDKN2A (n = 8), NF1 (n = 3), APC (n = 1), ARID1A (n = 1), CREBBP (n = 1), CTNNB1 (n = 1), and TP53 (n = 1). *Patients who had liquid biopsies were enrolled in BFAST Cohort D (n = 54) and testing was conducted using FoundationOne®Liquid CDx clinical trial assay or FoundationACT™ (Foundation Medicine, Inc., Cambridge, MA). ^†Patients with NSCLC from the FMCore database (N = 612) who were ROS1-positive by tissue-based NGS testing with FoundationOne®CDx (Data cut-off: April 2023)30. ^‡Copy number deletions are not accurately detected in liquid biopsies due to limited sensitivity, which may in part explain the high prevalence of CDKN2A deletions identified in the tissue-based assay. Amp, copy number amplification; Del, copy number deletion; FoundationACT™, Foundation Medicine Assay for Circulating Tumor DNA; NGS, next generation sequencing; NSCLC, non-small cell lung cancer; ROS1, ROS proto-oncogene 1; SNV/indel, short variant.

Extended Data Fig. 4. Clinical outcomes of patients treated with entrectinib and had low ( < 1%) and those with high ( ≥ 1%) baseline ctDNA fraction.

(A) DoR (n = 44) and (B) PFS (n = 55) Kaplan–Meier curves for patients who had low ( < 1%, blue) and those with high ( ≥ 1%, red) baseline ctDNA fraction. There was no difference in median DoR or median PFS between patients with a baseline cTF <1% and those with a baseline cTF ≥1%. CI, confidence intervals; cTF, ctDNA fraction; DoR, duration of response; HR, hazard ratio; INV, investigator; NA, not available; PFS, progression-free survival.

Extended Data Fig. 5. Correlation of baseline cTF with tumor size as measured by SLD.

cTF was derived from patients who have been screened via FoundationACT™ or FoundationOne® Liquid CDx assays and individual values have been plotted (n = 52*). A linear regression was conducted using the stat_smooth() R function with method set to “lm” and 95% CI bands are shown. Pearson’s correlation coefficient testing (two-sided) identified a weak but positive association between baseline cTF and tumor burden. *Three patients had missing SLD. cTF, ctDNA fraction; FoundationACT™, Foundation Medicine Assay for Circulating Tumor DNA; SLD, sum of the longest diameters.

Extended Data Fig. 6. Clinical outcomes of patients treated with entrectinib and cleared ROS1 from the ctDNA by C3D1 and those who did not.

(A) DoR (n = 29) and (B) PFS (n = 36) Kaplan–Meier curves for patients who cleared ROS1 from the ctDNA by C3D1 (blue) and those who did not (red). ROS1 clearance was associated with longer median DoR and median PFS compared with lack of clearance. 36 patients had plasma samples from C3D1, one of these patients had non-measurable disease. CI, confidence interval; ctDNA, circulating tumor DNA; DoR, duration of response; HR, hazard ratio; INV, investigator; NA, not available; PFS, progression-free survival; ROS1, ROS proto-oncogene 1.

Extended Data Fig. 7. Patient cases assessing the relationship between ctDNA levels and tumor response over the duration of entrectinib treatment.

Treatment started at t0. Empty data points represent when ctDNA was not detected. Patient 3 (A–B) had consistent levels of ctDNA throughout the duration of treatment (A) and levels of ctDNA were not associated with tumor response (B). Clinical presentation for Patient 3: 51-year-old male with one target lesion in the lung and one non-target lesion in the lymph node. Disease progression was due to a small increase in the target lesion in the lung; non-target lesion stayed stable. After disease progression, the patient continued treatment with entrectinib and received five subsequent lines of therapy. As of April 2023, the patient was still alive. Patient 3 had two ROS1 fusion proteins (ROS1-FAM91A1 and ROS1-SDC4), indicative of two cell populations and an AKT2 resistance mutation was identified at treatment discontinuation. Patient 14 (C–D) responded to treatment with entrectinib cleared ctDNA by day 59 (C) and ctDNA levels rebounded before radiological progression (D). Clinical presentation for Patient 14: 37-year-old male with three target lesions (one in the lung and two in the lymph nodes) and one non-target lesion. Disease progression was due to progression in the target lesions in the lymph nodes and the presence of two new lesions in the lymph nodes. There was no disease progression in the primary target lesion (lung) and non-target lesions were stable. After disease progression, the patient continued treatment with entrectinib and received seven subsequent lines of therapy. As of October 2023, the patient was still alive. cTF, circulating tumor fraction; PR, partial response; PD, progressive disease; SD, stable disease; SLD, sum of the longest diameters.