BAP1 Immunostain and CDKN2A (p16) FISH Analysis: Clinical Applicability for the Diagnosis of Malignant Mesothelioma in Effusions

Our plain-English summary of BAP1 Immunostain and CDKN2A (p16) FISH Analysis: Clinical Applicability for the Diagnosis of Malignant Mesothelioma in Effusions, by A.E. Walts, K. Hiroshima, S.M. McGregor, et al (Diagnostic Cytopathology, 2016).

The study

• Authors: A.E. Walts, K. Hiroshima, S.M. McGregor, D. Wu, A.N. Husain, A.M. Marchevsky
• Journal: Diagnostic Cytopathology
• Published: 2016;44(7):599-606
• Cited by: 45 articles, as counted by NIH iCite
• Read it: PubMed · Publisher

Abstract

Background: Loss of BAP1 by immunohistochemistry (IHC) and CDKN2A(p16) deletion by fluorescence in situ hybridization (FISH) have been proposed to distinguish malignant mesothelioma (MM) from atypical reactive mesothelial proliferations (ARMP) in effusions but it is uncertain whether both tests are needed routinely.

Methods: Paraffin embedded blocks from 67 effusions (32 MM, 35 ARMP) were evaluated with BAP1 IHC. 38 of them (17 MM, 21 ARMP) were also analyzed with CDKN2A (p16) FISH. Criteria for MM were absence of BAP1 nuclear staining in >50% of atypical mesothelial cells in the presence of a positive internal control, and/or CDKN2A(p16) homozygous or hemizygous deletion pattern in >15% or >41.5% of atypical mesothelial cells, respectively. Sensitivity (SS), specificity (SP), positive, and negative predictive values (PPV, NPV) for MM were calculated.

Results: 17 of 32 MM were correctly diagnosed by IHC (SS 53.1%, SP 85.7%, PPV 77.3%, NPV 64.3% for MM). In the subset of 38 cases studied by IHC and FISH, the SS, SP, PPV, and NPV of IHC for MM were 41.2, 81.0, 63.6, and 63.0%, respectively. 7 of 17 MM were diagnosed by FISH (SS 41.2%, SP 100%, PPV 100%, NPV 67.7% for MM).

Conclusion: BAP1 IHC and CDKN2A(p16) FISH yield similar sensitivities for MM in paired samples but FISH has a higher specificity. To diagnose effusions with atypical mesothelial cells, use of both tests is optimal. However, BAP1 IHC alone may be sufficient to diagnose MM when clinical, imaging, and cytological findings strongly suggest MM. Diagn. Cytopathol. 2016. © 2016 Wiley Periodicals, Inc. Diagn. Cytopathol. 2016;44:599-606. © 2016 Wiley Periodicals, Inc.

© 2016 Wiley Periodicals, Inc.

In plain English

This study tested two laboratory methods for distinguishing malignant mesothelioma from reactive (non-cancerous) changes in fluid samples (effusions). Using archived Cedars-Sinai Medical Center samples, the authors stained 67 effusions (32 biopsy-confirmed mesothelioma, 35 reactive) for loss of the BAP1 protein. Under the study's cutoff, 17 of 32 mesothelioma samples (53.1%) were positive. Thirty of 35 reactive samples (85.7%) were correctly classified as negative, though every case showed a mix of stained and unstained cells. FISH testing for CDKN2A (p16) gene deletion in 38 samples found 7 of 17 mesotheliomas positive and all 21 reactive samples negative. Only 3 of those 17 mesotheliomas were positive on both tests, and 11 on at least one. Pooled with published studies, the weighted average share of mesotheliomas correctly identified was 59.2% (95% confidence interval 51.3 to 66.6%) for BAP1 and 71.8% (63.4 to 78.9%) for FISH. The authors concluded that both tests are preferable. Once other cancers are excluded, they found it reasonable to screen with BAP1 staining, confirming with FISH when clinical and imaging findings are not strongly suggestive of mesothelioma.

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: Retrospective diagnostic accuracy study of archived cell blocks, with sensitivity, specificity and predictive values calculated for each test. It was combined with a literature review and meta-analysis of published effusion studies.
• Who was studied: 67 effusions from Cedars-Sinai Medical Center archives: 63 pleural and 4 peritoneal fluids. 32 came from patients with biopsy-confirmed malignant mesothelioma (22 males, 10 females; median age 69; 25 epithelioid, 6 biphasic, 1 well differentiated papillary). 35 were reactive pleural effusions with atypical mesothelial cells (19 males, 16 females; median age 69). The reactive patients were followed for a median of 36 months, and none developed mesothelioma. No collection dates are given.
• Exposure: No asbestos or other exposure was studied. The study evaluated two diagnostic tests. The first was BAP1 immunostaining, judged positive when more than 50% of atypical mesothelial cells lacked nuclear staining. It was done on all 67 cases. The second was CDKN2A (p16) FISH, judged positive for homozygous deletion in more than 15% of cells or hemizygous deletion in more than 41.5% of cells. It was done on 38 cases.
• Main results:
  • BAP1 immunostaining, all 67 cases: 17 of 32 mesotheliomas were positive under the study's cutoff (sensitivity 53.1%), and 30 of 35 reactive effusions were classified as negative (specificity 85.7%). The positive predictive value was 77.3% and the negative predictive value 64.3%.
  • Reactive effusions on BAP1 immunostaining: 30 of 35 were negative and 5 were positive. Four of those 5 were negative by FISH, and FISH was not done on the fifth.
  • In every case, the BAP1-stained slide showed a mix of stained and unstained atypical mesothelial cells. Negative and positive results therefore reflect the study's cutoff, not uniform staining.
  • CDKN2A (p16) FISH in the 38-case subset: 7 of 17 mesotheliomas were positive. The table gives this as sensitivity 41.2%; the text prints 42.1%. All 21 reactive effusions were negative (specificity 100%). The positive predictive value was 100% and the negative predictive value 67.7%.
  • BAP1 immunostaining in the same 38-case subset: 7 of 17 mesotheliomas were correctly identified (41.2%), and 17 of 21 reactive effusions were correctly identified (81.0%). The positive predictive value was 63.6% and the negative predictive value 63.0%.
  • In the 38-case subset, only 3 of 17 mesotheliomas (17.6%) were positive on both tests. 11 of 17 (64.7%) were positive on at least one test, with all 21 reactive effusions negative under that approach.
  • Meta-analysis of this study and published studies, weighted average percentage of mesotheliomas correctly diagnosed: 59.2% (95% CI 51.3 to 66.6%) with BAP1 immunostaining alone and 71.8% (95% CI 63.4 to 78.9%) with FISH alone. The figure was 70.8% with a positive result on either test, and 30.4% when both tests had to be positive.
  • In the meta-analysis, FISH was slightly more specific than BAP1 immunostaining, but the difference was not statistically significant. Doing both tests did not significantly increase the number of mesotheliomas correctly detected.
• The authors' conclusion: The authors concluded that their data and the literature support using BAP1 immunostaining and CDKN2A (p16) FISH to evaluate atypical mesothelial cells in effusions. In their view, performing both tests is preferable. Because FISH may not be available in many laboratories, they found it reasonable to screen with BAP1 immunostaining and confirm with FISH in selected cases where clinical and imaging findings are not strongly suggestive of mesothelioma. This applies after carcinoma and other malignancies have been excluded.
• Limitations the authors state:
  • The relatively low sensitivity of FISH may be partly due to the low number of atypical mesothelial cells in some samples.
  • Variable BAP1 staining, and disagreement between the two observers over which cells were atypical, made precise cutoffs hard to apply consistently. The authors chose a strict cutoff of more than 50% of cells, deliberately giving up sensitivity in favor of specificity.
  • Several of the 95% confidence intervals in the meta-analysis are quite broad.
  • FISH results varied significantly between studies, possibly because of different interpretation criteria or technical difficulties inherent in the test.
  • The authors stress that carcinoma and other malignancies must first be excluded before BAP1 staining is useful for mesothelioma. Alterations in BAP1 and CDKN2A (p16) are also reported in other cancers.

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, CDKN2A, Fluorescence In Situ Hybridization (FISH), Malignant Mesothelioma, Immunohistochemistry, Mesothelial Cells.

Related studies

• Utility of BAP1 Immunohistochemistry and p16 (CDKN2A) FISH in the Diagnosis of Malignant Mesothelioma in Effusion Cytology Specimens — H.C. Hwang, B.S. Sheffield, et al. (2016)
• 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)
• Usefulness of p16/CDKN2A fluorescence in situ hybridization and BAP1 immunohistochemistry for the diagnosis of biphasic mesothelioma — D. Wu, K. Hiroshima, et al. (2017)
• Fluorescence in situ hybridization (FISH) provides estimates of minute and interstitial BAP1, CDKN2A, and NF2 gene deletions in peritoneal mesothelioma — S. Brich, F. Bozzi, et al. (2020)
• Cytologic Differential Diagnosis of Malignant Mesothelioma and Reactive Mesothelial Cells With FISH Analysis of p16 — K. Hiroshima, D. Wu, et al. (2016)
• BAP1 immunohistochemistry has limited prognostic utility as a complement of CDKN2A (p16) fluorescence in situ hybridization in malignant pleural mesothelioma — S.M. McGregor, J. McElherne, et al. (2017)

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