Monitoring immune checkpoint inhibition in advanced solid tumors using genome-wide cfDNA fragmentomes

The rapid identification of disease progression in patients receiving immune checkpoint inhibitors (ICIs) is challenging using methods that rely on imaging assessments. Here, we investigated genome-wide cell-free DNA (cfDNA) fragmentation profiles to molecularly detect disease progression in the phase I study of entinostat and nivolumab +/- ipilimumab in advanced solid tumors (ETCTN-9844, NCT02453620). Patients with metastatic or unresectable solid tumors received an entinostat run-in 2 weeks prior to the addition of anti-PD-1 and anti-CTLA-4 ICIs. Blood was collected at baseline (50/50 patients) and at 10 weeks after treatment initiation (27/50 patients). Low-coverage (1-2x) whole genome sequencing was performed on cfDNA from plasma samples. Genome-wide cfDNA fragmentation features were included in a Bayesian model to approximate a tumor fraction as compared to best response by RECIST v1.1. Molecular response was defined as reduction (≥ 30%) of the fragmentation based tumor fraction between the baseline and 10-week time point. 50 patients with breast (n = 28), salivary gland (n = 7), gastrointestinal (n = 6), gynecological (n = 4), sarcoma (n = 3), and lung cancer (n = 2) received a median of 4 prior lines of therapy (0-14). Response assessment using molecular analyses and best overall response by RECIST were reported at a mean of 9.3 (5-10.7) and 14.3 weeks (5-73). Molecular responders and non-responders at week 10 experienced a median PFS that was not reached (NR) and 4.5 months (HR = 5.4; 95% CI 1.7-17; p = 0.004) while patients with RECIST response and non-response at week 10 had similar PFS (median 6.4 vs. 6.7 months; HR = 1.7; 95% CI 0.54-5.3; p = 0.36). Among the subgroup of radiographic non-responders with stable disease, PFS for molecular responders was NR while for molecular non-responders it was 5.2 months (p = 0.021). There is a clinical need for non-invasive tests to identify primary or acquired resistance to ICIs, sparing patients from ineffective treatments associated with immune-related adverse events. Here, we demonstrate a cfDNA fragmentation based approach for molecular detection of disease progression that could guide future trials with ICIs.