Abstract LB-C009: Tumor methylation subtypes predict the clinical outcome to immunotherapy in pleural mesothelioma patients from the NIBIT-EPI-MESO study

Abstract Background: Pleural mesothelioma (PM) is an aggressive malignancy with a poor prognosis. The clinical efficacy of standard therapy with immune checkpoint inhibitors (ICI) is limited and heterogeneous across PM subtypes. Tumor-intrinsic characteristics (i.e., inflammatory phenotype, molecular features, DNA methylation) may influence immune responsiveness, but predictive biomarkers of ICI therapy efficacy in PM are still lacking. Methods: NIBIT-EPI-MESO is a retrospective, multicenter study, sponsored by the NIBIT Foundation, evaluating biological correlates of clinical outcomes in PM patients (pts) treated with ICI (i.e., anti-CTLA-4 plus anti-PD-1, anti-CTLA-4 plus anti-PD-L1, or anti-CTLA-4 monotherapy). Pre-ICI therapy FFPE tumor samples were analyzed by RRBS methylation (n=83 pts) and RNA-seq (n=82 pts), with methylation subtypes defined by consensus clustering of the top 1% most variable CpGs. Tumor microenvironment (TME) was characterized by multiplex immunofluorescence analysis of CD4, CD8, CD20, CD68, CD163 (n=35 pts). Integrated multi-omics analyses were used to associate tumor biology with clinical outcome of PM pts. Results. Unsupervised methylation profiling identified four PM subsets with increasingly global DNA methylation levels: demethylated (DEM), LOW, intermediate (INT), and CpG island methylator phenotype (CIMP). Methylation subtypes were significantly associated with response to ICI, with LOW/DEM enriched among responder (R) pts and INT/CIMP in non-R pts (p= 0.002); no association of response to ICI was found with PM histotype (p=0.33). The LOW subset exhibited the longest median overall survival (mOS) and the highest 3-year OS rate, expressed genes involved in pathways associated with innate and adaptive immune responses, and showed an “inflamed” TME (i.e., CD8+ T cells, CD20+ B cells). Conversely, the CIMP subtype had the shortest mOS and OS rate, was characterized by genes enriched in developmental, morphogenetic and cell cycle-related processes, along with a “desert” TME. Functional characterization of the identified methylation classes of PM was validated in the MESOMICS dataset. Accordingly, a PM methylation subtype classifier was developed to predict response to ICI therapy. Conclusions: Tumor DNA methylation defines biologically and clinically distinct immune phenotypes in PM and robustly predicts clinical response and long-term survival in ICI-treated PM patients, regardless of tumor histology. Citation Format: Luana Calabrò, Francesca Pia Caruso, Alessia Covre, Teresa Maria Rosaria Noviello, Maria Fortunata Lofiego, Rossella Tufano, Luigi Ferraro, Piera Grisolia, Antonio De Falco, Vincenzo Lagano, Francesco Sgambelluri, Giovanna Sabella, Giulia Rossi, Giulia Gibilisco, Francesco Marzani, Emma Bello, Elena Simonetti, Vincenzo D'Alonzo, Michele Caraglia, Sandra Coral, Antonina De Angelis, Luigi Cerbone, Sara Delfanti, Federica Grosso, Anna Maria Di Giacomo, Massimo Milione, Roberta Mortarini, Andrea Anichini, Michele Ceccarelli, Michele Maio. Tumor methylation subtypes predict the clinical outcome to immunotherapy in pleural mesothelioma patients from the NIBIT-EPI-MESO study [abstract]. In: Proceedings of the AACR Immuno-Oncology Conference (AACR IO): Discovery and Innovation in Cancer Immunology: Revolutionizing Treatment through Immunotherapy; 2026 Feb 18-21; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Immunol Res 2026;14(2 Suppl):Abstract nr LB-C009.