Loss of MTAP expression is not an accurate surrogate for CDKN2A homozygous deletions in peritoneal mesothelioma

Aims: Mesothelioma is a malignant neoplasm of the serosal membranes originating from mesothelial cells. Peritoneal mesothelioma is the second most common mesothelial neoplasm after pleural mesothelioma, accounting for approximately 6%–15% of cases. Due to its high morphological variability, often mimicking other lesions, mesothelioma remains a diagnostic challenge. CDKN2A homozygous deletion has been established as a highly accurate biomarker for differentiating mesothelioma from benign mesothelial proliferations. MTAP immunohistochemistry (IHC) has been proposed as a cheaper and more reproducible surrogate for CDKN2A homozygous deletion (HD) detected by FISH in pleural mesothelioma. The aim of our study was to evaluate the reliability of MTAP IHC as a surrogate marker for CDKN2A HD in peritoneal mesothelioma. Methods and results: Thirty-nine FFPE tissue samples of PeM were analysed for CDKN2A copy number status by FISH. MTAP IHC was performed using antibody clone 2G4, and cytoplasmic positivity was evaluated using two different cut-offs (1% and 30%). Agreement between IHC and FISH was assessed using Cohen's Kappa. A ROC curve analysis was performed to evaluate the overall diagnostic performance of MTAP IHC. McNemar's test was used to identify statistically significant discordance between the techniques, and a power analysis was conducted to confirm the adequacy of the sample size. Additionally, 14 benign peritoneal lesions were included as external controls and underwent both FISH and IHC. All control samples showed preserved MTAP expression and no CDKN2A deletion. CDKN2A HD was detected in 27/39 cases. MTAP loss was observed in 13 cases, while the remaining 26 cases showed variable levels of MTAP positivity (15%–100%; mean: 36.4%; median: 25%). Cohen's Kappa revealed a low, non-significant concordance between MTAP IHC and CDKN2A HD (cut-off 1%: Kappa = 0.091, P = 0.462; cut-off 30%: Kappa = 0.083, P = 0.326). ROC curve analysis (AUC = 0.569) confirmed the poor discriminatory performance of MTAP IHC. McNemar's test showed a statistically significant discordance between MTAP IHC and CDKN2A FISH results. Power analysis confirmed that the sample size (n = 39) was adequate. Conclusions: These findings may reflect biological and pathogenetic differences between pleural and peritoneal mesotheliomas. Larger, multicentric studies are needed to validate the diagnostic role of MTAP IHC in peritoneal mesothelioma.