Comparison of Cytoplasmic and Nuclear MTAP Loss in Pleural Effusion Cytology: Correlation With Homozygous p16/ CDKN2A Deletion

Objective Pleural mesothelioma (PM) is an aggressive malignancy in which pleural effusion cytology is often the first diagnostic material. MTAP immunohistochemistry, while not a stand‐alone diagnostic tool, may serve as a useful adjunct when combined with other markers in the evaluation of pleural mesothelioma. However, the diagnostic relevance of nuclear versus cytoplasmic MTAP loss in cytology specimens remains unclear. Methods We retrospectively analysed pleural effusion cytology samples from 48 histologically confirmed PM cases (2017–2022). Dual‐colour fluorescence in situ hybridization (FISH) was performed for p16/CDKN2A, while MTAP immunohistochemistry (Proteintech 2B1G6 clone) was assessed for nuclear and cytoplasmic loss, further subclassified as focal or diffuse. Associations between MTAP loss and p16/CDKN2A deletion were evaluated using Fisher's exact test. Results MTAP loss was observed in 21 cases (43.8%), while homozygous p16/CDKN2A deletion was detected in 33 cases (68.8%). Concurrent MTAP loss and p16/CDKN2A deletion occurred in 15 cases (31.3%). Nuclear and cytoplasmic MTAP loss were perfectly concordant in terms of presence ( p < 0.001), although their staining patterns differed: diffuse nuclear loss often corresponded to focal rather than diffuse cytoplasmic loss. No significant association was observed between MTAP staining patterns and p16/CDKN2A deletion ( p > 0.05). Conclusions Our findings demonstrate that while nuclear and cytoplasmic MTAP loss are concordant in presence, staining patterns and antibody clone selection affect correlation with p16/CDKN2A deletion. Given that pleural effusion cytology is often the initial diagnostic step in PM, standardised MTAP testing protocols are needed to ensure reproducibility and minimise false‐negative interpretations, rather than implying improved diagnostic accuracy.