Digital PCR for Detecting Loss of BAP1 and MTAP in Pleural Fluids of Mesothelioma Patients: Perspectives in the Diagnosis

Our plain-English summary of Digital PCR for Detecting Loss of BAP1 and MTAP in Pleural Fluids of Mesothelioma Patients: Perspectives in the Diagnosis, by G. Rosini, G. Alì, R. Bruno, et al (Pathology International, 2026).

The study

• Authors: G. Rosini, G. Alì, R. Bruno, M. Cipollini, R. Foddis, A. Celi, R. Silvestri, F. Rea, V. Aprile, M. Lucchi, F. Gemignani, S. Landi
• Journal: Pathology International
• Published: 2026;76(9):e70172
• Read it: PubMed · Publisher · Free full text

Abstract

Pleural mesothelioma (PM) often presents loss of BAP1 and MTAP genes. Digital PCR (dPCR) can accurately measure gene copy numbers (CNs). We hypothesized that cell-free DNA (cfDNA) extracted from the supernatant of pleural fluids (SPFs) could allow an efficient detection of these genetic events. BAP1/MTAP CN was measured with dPCR in SPFs and in solid tumor biopsies (STBs) of 37 PM patients. Results were compared with immunohistochemistry (IHC) carried out in STBs. IHC alone detected BAP1/MTAP-losses in 32/37 (86.5%). However, the sensitivity improved to 34/37 (91.9%) when low CN of BAP1/MTAP was included. Among 20 patients presenting SPFs, dPCR alone detected a low CN in 18 samples (sensitivity = 90%). Finally, this two-gene signature was applied on SPFs in a prospective series of six consecutive patients presenting an undefined diagnosis (negative for PM) and two showed reduced CN. After 7 months of follow-up, these subjects were further re-evaluated for the persistence/worsening of the symptoms and were diagnosed for PM. We highlighted dPCR's potential for detecting subtle BAP1/MTAP losses in SPFs of PM patients. This appears as a complementary approach for a more accurate diagnosis in specific contexts, when high-risk patients receive negative results after IHC analysis.

© 2026 The Author(s). Pathology International published by Japanese Society of Pathology and John Wiley & Sons Australia, Ltd.

In plain English

This Italian study tested whether digital PCR, which counts gene copies, detects BAP1 and MTAP losses in pleural mesothelioma. It studied 37 such patients who had thoracoscopy in Pisa from February 2021 to June 2023. Fourteen had ascertained asbestos exposure, 8 likely, 2 none and 13 uncertain. Protein staining (immunohistochemistry) of biopsies showed BAP1 or MTAP loss in 32 of 37 (86.5%; 95% confidence interval 72.0 to 94.1). Biopsy digital PCR found reduced copies in 27 of 37 (73.0%; 95% CI 57.0 to 84.6). Pleural-fluid digital PCR found reduced copies in 18 of 20 with fluid samples (90.0%; 95% CI 69.9 to 97.2). Combining staining with biopsy digital PCR raised detection to 34 of 37 (91.9%; 95% CI 78.7 to 97.2). Six people with past asbestos exposure initially had thoracoscopy negative for mesothelioma. Two of them had reduced copies in their pleural fluid and were diagnosed with mesothelioma 6 to 7 months later. The authors called this preliminary proof-of-concept evidence that the test may complement tissue staining. They cautioned that reduced copies alone are not direct evidence of malignancy.

We wrote this plain-English summary from the full article with the help of AI, and a second AI model checked each sentence against the article. It is not the authors' wording; the abstract and the article are their own account.

What the study did and found

• Design: Laboratory diagnostic study comparing digital PCR gene copy number measurement with immunohistochemistry in pleural mesothelioma patients, plus a small prospective series
• Who was studied: 37 patients with pleural mesothelioma (32 men, 5 women, aged 60 to 87) who had thoracoscopy at the University Hospital of Pisa between February 2021 and June 2023; 20 of them had pleural fluid samples. Also six men aged 70 to 83 initially diagnosed with phlogosis (inflammation), and 24 healthy volunteers used for probe testing.
• Exposure: The study measured BAP1 and MTAP gene copy number and protein loss. Asbestos exposure among the 37 patients was recorded as ascertained (14), likely (8), unexposed (2) or uncertain (13). No fiber types are named.
• Main results:
  • Immunohistochemistry on tumor biopsies showed loss of BAP1 in 26 of 37 patients (70.3%) and loss of MTAP in 16 of 37 patients (43.2%).
  • Immunohistochemistry on tumor biopsies showed loss of at least one of the two proteins in 32 of 37 patients (86.5%; 95% CI 72.0 to 94.1).
  • Digital PCR on tumor biopsies found reduced copy number of at least one gene in 27 of 37 patients (73.0%; 95% CI 57.0 to 84.6).
  • Among 20 patients with pleural fluid samples, digital PCR on the fluid found reduced copy number in 18 of 20 (90.0%; 95% CI 69.9 to 97.2). Immunohistochemistry on biopsies in the same subgroup detected loss in 17 of 20 (85.0%).
  • The authors found no statistically significant difference between the two-protein immunohistochemistry signature and their integrated copy number analysis.
  • Combining immunohistochemistry with digital PCR on tumor biopsies increased detection among the 37 patients from 32 to 34 (91.9%; 95% CI 78.7 to 97.2).
  • Combining immunohistochemistry with integrated copy number analysis (biopsy and/or fluid) showed at least one alteration in 36 of 37 patients (97.3%).
  • In tumor biopsies, digital PCR and immunohistochemistry agreed for BAP1 in 25 of 37 patients (67.6%, p = 0.0159) and for MTAP in 29 of 37 patients (78.4%, p = 5 × 10^-4).
  • Six people with past asbestos exposure had an initial thoracoscopy that did not find mesothelioma. Two of them were diagnosed with pleural mesothelioma 6 to 7 months later, and both had reduced copy number of at least one gene in the pleural fluid collected at the first thoracoscopy.
• The authors' conclusion: The authors concluded that their findings provide preliminary proof-of-concept evidence that digital PCR copy number analysis of DNA from pleural fluid may complement tissue-based immunohistochemistry in selected high-risk or unresolved cases. They said validation in larger cohorts is required.
• Limitations the authors state:
  • Pleural fluid samples from people without cancer were not systematically available, so no normal reference range could be set for that specimen type.
  • Probe testing and the threshold were based on DNA from blood cells, but the assay was then applied to cell-free DNA from pleural fluid.
  • DNA was not taken from the same tissue sections used for immunohistochemistry, which may have contributed to disagreement between the methods.
  • The conservative copy number threshold may have favored specificity over sensitivity.
  • Only two genes were analyzed.
  • The sample size was small and statistical power limited, and analyses by histological subtype could not be done.
  • The six-patient series is only hypothesis-generating and does not establish predictive performance.
  • Reduced copy number alone should not be regarded as direct evidence of malignancy or as a definitive marker of pleural mesothelioma.

Topics

The National Library of Medicine indexes this study under subjects our site covers: Mesothelioma.

Medical terms in this study, explained in our Lexicon: BAP1, MTAP, Mesothelioma, Pleural Mesothelioma, Immunohistochemistry.

Related studies

• HEG1, BAP1, and MTAP are useful in cytologic diagnosis of malignant mesothelioma with effusion — K. Hiroshima, D. Wu, et al. (2021)
• A combination of MTAP and BAP1 immunohistochemistry in pleural effusion cytology for the diagnosis of mesothelioma — Y. Kinoshita, T. Hida, et al. (2018)
• A combination of MTAP and BAP1 immunohistochemistry is effective for distinguishing sarcomatoid mesothelioma from fibrous pleuritis — Y. Kinoshita, M. Hamasaki, et al. (2018)
• Usefulness of methylthioadenosine phosphorylase and BRCA-associated protein 1 immunohistochemistry in the diagnosis of malignant mesothelioma in effusion cytology specimens — K.B. Berg, A.M. Churg, et al. (2020)
• Loss of expression of BAP1 is a useful adjunct, which strongly supports the diagnosis of mesothelioma in effusion cytology — J. Andrici, A. Sheen, et al. (2015)
• Loss of BAP1 expression is very rare in peritoneal and gynecologic serous adenocarcinomas and can be useful in the differential diagnosis with abdominal mesothelioma — J. Andrici, J. Jung, et al. (2016)

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