Identification of immunotherapy early treatment failure in non-small cell lung cancer (NSCLC) using a novel cell-free DNA (cfDNA) tissue-agnostic genome-wide methylome enrichment assay.

Abstract

8550 Background: Immune checkpoint inhibitor treatment failure constitutes a significant clinical challenge in non-small cell lung cancer (NSCLC). Molecular residual disease (MRD) detection in NSCLC may allow earlier detection of disease recurrence/progression and enable early treatment intensification or clinical trial enrolment. We have developed a novel tissue-agnostic genome-wide methylation enrichment platform based on cell free methylated DNA immunoprecipitation and high throughput sequencing (cfMeDIP-seq). Here, we present data on its application as an MRD assay to predict early recurrence or progression in patients (pts) with NSCLC receiving immunotherapy. Methods: The study population consists of pts with stage III/IV NSCLC at the Princess Margaret Cancer Centre, treated with definitive chemoradiation followed by consolidative durvalumab (stage III) or with PD-1 inhibitors +/- chemotherapy (stage IV). Pts underwent serial blood collection prior to initiation of treatment, 2-4 weeks after treatment initiation and approximately 6-8 weeks thereafter until progression. 5-10 ng of cfDNA was isolated from plasma. A classifier was trained on an independent set of lung and non-cancer samples to quantify relative circulating tumor DNA (ctDNA) content. The analysis considered multiple timepoints. Results were considered "positive” if there was a detected result at any follow-up timepoint. Results were considered "negative” if all follow-up timepoints were reported as not detected. Progression-free survival (PFS) was compared between groups using a log-rank test. Hazard ratio (HR) was estimated using Cox proportional hazards model. Results: A total of 187 samples from 63 unique pts (44% stage III and 56% stage IV) were analyzed and correlated with PFS. Pts with a positive MRD test showed significantly worse PFS than those who tested negative (HR 4.8; 95% CI, 2.1-10.8, P<0.0001), sensitivity 80%, specificity 91%. The lead time between MRD positivity and progression was up to 12.6 months, with a mean of 5.1 months. Secondary analysis of pts with stage III NSCLC revealed significantly worse PFS in MRD-positive pts compared to MRD-negative pts (HR 8; 95% CI, 1.4-46.7, P=0.007). Conclusions: MRD detection using genome-wide methylome enrichment correlates strongly with PFS in pts with advanced NSCLC receiving immunotherapy. This tissue agnostic assay shows promise for early identification of treatment failure, enabling timely selection of patients for treatment intensification or clinical trials.