Correlation of ten-year survival with cell-free DNA methylation of melanoma patients with asymptomatic brain metastases treated with nivolumab plus ipilimumab: The multicenter phase III NIBIT-M2 trial.

2008 Background: The NIBIT Foundation-sponsored phase III NIBIT-M2 study showed a 41% 7-y OS of melanoma patients (pts) with asymptomatic brain metastases (BM) treated with ipilimumab (I) plus nivolumab (N) (I+N) ( Di Giacomo AM, CCR 2021 and EJC 2024 ). Despite the significant efficacy of I+N therapy in this pts population, no biomarkers predictive of response have been identified yet also due to the accessibility of BM. We here report the 10-y survival and its correlation with cell-free (cf)DNA analyses on serial plasma samples collected from pts enrolled in the NIBIT-M2 study. Methods: The NIBIT-M2 study recruited melanoma pts with active, untreated, asymptomatic BM from 9 Italian Centers, randomized (1:1:1) to receive fotemustine (F) (Arm A), I+F (Arm B), or I+N (Arm C). Primary endpoint was OS. Exploratory analyses were conducted on cfDNA plasma samples collected at baseline and week (W) 12 on therapy. Tumor fraction (TF) was estimated from low pass WGS using IchorCNA. Tumor-specific methylation Score (T-meth Score) was computed as the ratio between the coverage over methylated regions analyzed by cf-methylated DNA immunoprecipitation and high-throughput sequencing (cfMeDIP-seq) and melanoma-specific methylated regions previously identified in the TCGA melanoma cohort. Results: From Jan 2013 to Sept 2018, 80 pts were enrolled: 76 received F (23), I+F (26), or I+N (27). As of December 1, 2025, with a median follow-up of 125 months (mo), median OS was 8.5 (95% CI: 4.8-12.2), 8.2 (95% CI: 2.1-14.3) and 29.2 (95% CI: 0-73.5) mo for Arm A, B, and C, respectively. The 10-y OS rate was 13.0% (95% CI: 0-26.7) in Arm A, 7.7% (95% CI: 0-17.9) in Arm B, and 31.2% (95% CI: 13.0-49.4) in Arm C. The 10-y melanoma specific survival was 13.0% (95% CI: 0-26.7), 7.7% (95% CI: 0-17.9), and 35.1% (95% CI: 16.3-53.9) in Arm A, B and C, respectively. Patients were stratified at baseline according to the median values of TF (n=57; median 0.022) and of T-meth Score (n=53; median 0.096): a significantly higher median OS was observed in pts with TF (22.3 vs 8.2 mo; p=0.033) and T-meth Score (26.3 vs 7.9 mo; p=0.002) below their median values. Of note, low TF and T-meth Score were enriched at baseline in pts from Arm C. Additionally, a decrease in TF (n=29) and T-meth Score (n=24) was observed at W12 in pts with an OS above the median (26.3 mo for TF and 24.0 mo for T-meth Score). Conclusions: The 10-y results of the NIBIT-M2 study, with the longest follow-up available to date in melanoma pts with asymptomatic BM treated with I+N, continue to show persistent long-term therapeutic efficacy of the combination. Plasma-derived TF and T-meth Score may predict long-term survival of melanoma pts with asymptomatic BM treated with I+N. Clinical trial information: NCT02460068 .