Validation of a Gene Expression Approach for the Cytological Diagnosis of Epithelioid and Biphasic Pleural Mesothelioma on a Consecutive Series

Our plain-English summary of Validation of a Gene Expression Approach for the Cytological Diagnosis of Epithelioid and Biphasic Pleural Mesothelioma on a Consecutive Series, by R. Bruno, A.M. Poma, G. Alì, et al (Cancers, 2023).

The study

• Authors: R. Bruno, A.M. Poma, G. Alì, A. Proietti, A. Ribechini, A. Chella, G. Fontanini
• Journal: Cancers
• Published: 2023;15(23)
• Read it: PubMed · Publisher · Free full text

Abstract

Cytological diagnosis of pleural mesothelioma (PM) is controversial, even using ancillary markers (BAP1, MTAP and CDKN2A). Here, we aimed to prospectively validate a previously developed 117-gene expression panel for the differential cytological diagnosis of epithelioid, biphasic PM and mesothelial hyperplasia. Seventy-seven pleural effusions were classified using the 117-gene expression levels (NanoString system). Sixty-eight cases were also screened for ancillary markers. The performance of both gene panel and ancillary markers was evaluated using ROC metrics. A score using the top consistently deregulated genes between epithelioid and biphasic PM was built to subtype malignant effusions. The panel alone reached a diagnostic accuracy (0.89) comparable to the best marker combination (BAP1 plus MTAP: 0.88). Ancillary tests missed 8 PMs, 7 of which were correctly classified by the panel. The score built by averaging the expression levels of MSLN, CLDN15 and CFB showed an accuracy of 0.80 in subtyping epithelioid and biphasic effusions. The 117-gene panel is effective for PM cytological diagnosis of epithelioid and biphasic PM. This tool can be complementary to ancillary markers, reducing invasive procedures and allowing an earlier diagnosis. Finally, the possibility to subtype PM on effusions strengthens the panel's role in PM diagnosis and management.

In plain English

This Italian study tested whether a panel measuring the activity of 117 genes could diagnose pleural mesothelioma from fluid around the lungs (pleural effusions). From 2019 to 2021, the University Hospital of Pisa consecutively enrolled 85 patients with epithelioid or biphasic pleural mesothelioma or with benign reactive mesothelial hyperplasia, and samples from 77 could be analyzed. The article did not report the patients' asbestos exposure. Across the 77 samples, the panel's accuracy was 0.91 (95% confidence interval 0.83 to 0.96). It correctly classified 27 of 30 epithelioid and 13 of 15 biphasic mesotheliomas as malignant. In 65 samples tested by all methods, its accuracy of 0.89 (0.83 to 0.95) was similar to that of the BAP1 and MTAP stains combined, 0.88 (0.80 to 0.94). Of eight mesotheliomas with no BAP1, MTAP or p16 changes, the panel correctly classified 7. A three-gene score distinguished epithelioid from biphasic mesothelioma with an accuracy of 0.80 (0.63 to 0.90). The authors concluded the panel was effective. They noted that it misclassified some benign samples and that their series probably had a higher share of malignant cases than most consecutive series.

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: Prospective validation of a diagnostic gene expression test on a consecutive series of pleural effusion samples, compared with standard ancillary tests
• Who was studied: 85 patients consecutively enrolled from 2019 to 2021 at the University Hospital of Pisa, Italy: 36 with epithelioid pleural mesothelioma, 15 with biphasic pleural mesothelioma and 34 with reactive mesothelial hyperplasia. 8 samples were inadequate, so 77 underwent gene expression analysis. 68 of these were cell blocks also tested for BAP1, MTAP and p16, and 65 had complete results for all methods.
• Exposure: Not an exposure study. Asbestos is mentioned only as background in the introduction, and the patients' asbestos exposure is not reported. The study evaluated a 117-gene expression panel (NanoString system) and compared it with BAP1 and MTAP immunohistochemistry and p16 (CDKN2A) FISH testing.
• Main results:
  • Across all 77 samples, the gene panel model had a sensitivity of 0.84 (95% CI 0.71–0.93), a specificity of 1 (95% CI 0.94–1) and an accuracy of 0.91 (95% CI 0.83–0.96)
  • 27 of 30 epithelioid pleural mesothelioma cases were correctly classified as malignant
  • 13 of 15 biphasic pleural mesothelioma cases were correctly classified
  • In the 65 samples analyzed by all methods, the gene panel alone had an accuracy of 0.89 (95% CI 0.83–0.95) and a sensitivity of 0.80. The combination of BAP1 plus MTAP had an accuracy of 0.88 (95% CI 0.80–0.94) and a sensitivity of 0.77. The authors described these as comparable.
  • 8 of 35 mesothelioma cell blocks (22.8%) would not have been correctly diagnosed by the ancillary tests (BAP1, MTAP, p16)
  • Of the 8 mesothelioma cases with neither BAP1 nor MTAP/p16 alterations, 7 were correctly classified as malignant by the gene panel
  • In a two-step approach (BAP1 and MTAP first, then the gene panel for cases that kept BAP1 and MTAP expression), Table 1 reports a sensitivity of 0.97, a specificity of 0.87 and an accuracy of 0.92 in the 65 samples
  • In this series, the p16 FISH test did not improve diagnostic performance. Used alone, it had a sensitivity of 0.36 in the 65 samples.
  • A score averaging the expression of three genes (MSLN, CLDN15, CFB) distinguished epithelioid from biphasic mesothelioma on pleural effusions with an accuracy of 0.80 (95% CI 0.63–0.90)
• The authors' conclusion: The authors concluded that the study confirmed the effectiveness of the 117-gene panel for distinguishing epithelioid and biphasic pleural mesothelioma from benign effusions on cytology. They added that the ability to subtype mesothelioma on effusions strengthens its diagnostic role.
• Limitations the authors state:
  • Specificity may be slightly reduced because the gene panel misclassified some reactive mesothelial hyperplasia samples
  • The proportion of malignant cases was probably higher than in most consecutive series
  • Not all routine laboratories have a NanoString system
  • Gene selection and the classification algorithm could still be improved

Topics

Medical terms in this study, explained in our Lexicon: Epithelioid, Biphasic Mesothelioma, Pleural Mesothelioma, BAP1, MTAP, CDKN2A, Reactive Mesothelial Hyperplasia, Pleural Effusion.

Related studies

• Gene Expression Analysis of Biphasic Pleural Mesothelioma: New Potential Diagnostic and Prognostic Markers — R. Bruno, A.M. Poma, et al. (2022)
• Differential Diagnosis of Malignant Pleural Mesothelioma on Cytology: A Gene Expression Panel versus BRCA1-Associated Protein 1 and p16 Tests — R. Bruno, G. Alì, et al. (2020)
• Membranous HEG1 expression is a useful marker in the differential diagnosis of epithelioid and biphasic malignant mesothelioma versus carcinomas — K. Hiroshima, D. Wu, et al. (2021)
• Comparative Gene Expression Analysis of Epithelioid Pleural and Peritoneal Mesothelioma — R. Sparavelli, A.M. Poma, et al. (2026)
• Clinical validation of a 90-gene expression test for tumor tissue of origin diagnosis: a large-scale multicenter study of 1417 patients — W. Sun, W. Wu, et al. (2022)
• Cytological Diagnosis of Malignant Mesothelioma: A Case Series — S. Dahiya, M. Singh, et al. (2022)

Browse more research in Cancers, or return to medical research.