Fluorescence in situ hybridization (FISH) provides estimates of minute and interstitial BAP1, CDKN2A, and NF2 gene deletions in peritoneal mesothelioma

Our plain-English summary of Fluorescence in situ hybridization (FISH) provides estimates of minute and interstitial BAP1, CDKN2A, and NF2 gene deletions in peritoneal mesothelioma, by S. Brich, F. Bozzi, F. Perrone, et al (Modern Pathology, 2020).

The study

• Authors: S. Brich, F. Bozzi, F. Perrone, E. Tamborini, A.D. Cabras, M. Deraco, S. Stacchiotti, G.P. Dagrada, S. Pilotti
• Journal: Modern Pathology
• Published: 2020;33(2):217-227
• Cited by: 21 articles, as counted by NIH iCite
• Read it: PubMed · Publisher

Abstract

The aim of this study was to assess the performance of fluorescence in situ hybridization (FISH) in identifying the copy number profiles of the three key peritoneal mesothelioma tumor suppressor genes BAP1, CDKN2A, and NF2, with particular emphasis on minute homozygous deletions, a copy number abnormality recently unveiled at the 3p21 (BAP1) chromosomal region using high-throughput methods. FISH was performed on 75 formalin-fixed-paraffin-embedded peritoneal mesotheliomas and recognized two types of monoallelic loss (monosomy, and hemizygous deletion) and two types of biallelic loss (canonical homozygous deletion with a complete loss of FISH signal and homozygous deletion with diminished signal). Diminished FISH signals revealed deletions occurring within the genomic region covered by the gene-specific probe and affected all three tumor suppressors. BAP1 homozygous deletions with diminished signal outnumbered canonical homozygous deletions (13 vs 3): conversely, canonical homozygous deletions were prevalent for CDKN2A (2 vs 14). Diminished signal homozygous deletion was the only pattern of biallelic loss observed for NF2 (2 cases). Hemizygous deletion mainly affected BAP1 (21 vs 6), while monosomy was prevalent for CDKN2A (14 vs 7) and particularly for NF2 where it accounts for all monoallelic losses. FISH/immunohistochemistry (BAP1, CDKN2A, and MTAP) correlation showed that all homozygous deletions, including those with diminished signals, resulted in a null BAP1 and CDKN2A immunophenotype but only canonical CDKN2A homozygous deletions resulted in MTAP loss of expression. BAP1 hemizygous deletion, but not monosomy, was also invariably associated with loss of protein expression whereas neither type of CDKN2A monoallelic loss correlated with p16 or MTAP immunohistochemistry. Array comparative genomic hybridization performed on a spontaneously emerging peritoneal mesothelioma cell line provided support for the interpretation of the FISH patterns and allowed us to extend the number of chromatin remodeling factors involved in mesothelioma to SETD7 and PCGF5, two previously unreported genes.

In plain English

Researchers at a cancer institute in Milan, Italy, tested how well a technique called fluorescence in situ hybridization (FISH) detects losses of three tumor suppressor genes, BAP1, CDKN2A and NF2, in peritoneal mesothelioma. They examined surgical tumor samples from 75 consecutive patients (42 male, 33 female) and a cell line grown from one patient's tumor. Asbestos exposure was not reported. FISH showed BAP1 loss in 43 cases (57%). Of 16 cases with BAP1 deleted from both chromosome copies, 13 showed only shrunken ("diminished") signals. All 37 cases with BAP1 homozygous or hemizygous deletions were negative for BAP1 on protein staining, compared with three of the six cases with monosomy. CDKN2A loss was found in 37 of 72 evaluated cases, and NF2 monosomy in 24 of 71. In the cell line, the authors found losses in two chromatin-related genes, SETD7 and PCGF5, which they described as previously unreported. BAP1 hemizygous deletion was more frequent in patients aged 58 or older. The authors concluded that FISH was highly specific but not very sensitive for BAP1, and that protein staining remains the best method for assessing BAP1.

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 pathology study of tumor tissue: FISH gene-deletion testing compared with immunohistochemistry (protein staining), plus array comparative genomic hybridization and karyotyping of a cell line grown from one patient's tumor
• Who was studied: 75 consecutive formalin-fixed, paraffin-embedded surgical specimens from patients with peritoneal mesothelioma: 42 males and 33 females, median age 58 (range 22 to 77); 71 epithelioid, 2 sarcomatoid, 2 biphasic. The authors are based in Milan, Italy. Study dates are not given.
• Exposure: Not addressed. The study examined gene losses (BAP1, CDKN2A, NF2) in tumor tissue and reports no asbestos or other exposure data.
• Main results:
  • BAP1 homozygous deletion was found in 16 cases (21%). In 13 of these the FISH signals were diminished rather than absent (one diminished signal in 8 cases, more than one in 5 cases).
  • BAP1 hemizygous deletion was found in 21 cases (28%).
  • All 37 cases with BAP1 homozygous deletions (including diminished-signal cases) or hemizygous deletions were negative for BAP1 on immunohistochemistry. Only 3 of the 6 (50%) cases with BAP1 monosomy were negative.
  • CDKN2A loss was found in 37 of the 72 cases (51%) that could be evaluated. Three cases failed FISH.
  • CDKN2A homozygous deletion was found in 16 cases (22%). In 14 of these, the FISH signal was completely lost (the canonical pattern).
  • Loss of MTAP protein expression was seen only in cases with canonical CDKN2A homozygous deletion (13 cases).
  • Taking CDKN2A FISH as the gold standard, p16 immunohistochemistry had sensitivity of 100% and specificity of 42%. MTAP immunohistochemistry had specificity of 100% and sensitivity of 86.6%.
  • NF2 monosomy was found in 24 of the 71 cases tested (34%).
  • Two cases (3%) showed NF2 homozygous loss with a single diminished NF2 signal.
  • In the cell line, single-copy losses were found in four chromatin remodeling/oncosuppressor genes, including SETD7 and PCGF5. The authors described SETD7 and PCGF5 as previously unreported.
  • No FISH or immunohistochemistry feature was associated with sex or age, except BAP1 hemizygous deletion. That deletion was more frequent in patients aged 58 or older (p less than 0.03).
• The authors' conclusion: The authors concluded that FISH was highly specific but not very sensitive for detecting BAP1 alterations, and that immunohistochemistry remains the best method for assessing BAP1 in mesothelioma.
• Limitations the authors state:
  • The authors stated that FISH, like every other molecular technique, cannot reveal all the possible ways the BAP1 gene can be inactivated.
  • The authors noted that correctly reading diminished-signal deletions required comparing tumor cells with the surrounding non-tumor cells.

Topics

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

Medical terms in this study, explained in our Lexicon: Fluorescence In Situ Hybridization (FISH), Interstitial, BAP1, CDKN2A, Peritoneal Mesothelioma, Tumor Suppressor Gene, Homozygous Deletion, Immunohistochemistry.

Related studies

• Hemizygous loss of NF2 detected by fluorescence in situ hybridization is useful for the diagnosis of malignant pleural mesothelioma — Y. Kinoshita, M. Hamasaki, et al. (2020)
• 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)
• Sarcomatoid Mesothelioma: A CDKN2A molecular analysis of 53 cases with immunohistochemical correlation with BAP1 — M. Zaleski, N. Kalhor, et al. (2020)
• MTAP immunohistochemistry is an accurate and reproducible surrogate for CDKN2A fluorescence in situ hybridization in diagnosis of malignant pleural mesothelioma — D.B. Chapel, J.J. Schulte, et al. (2020)
• 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)
• Utility of Methylthioadenosine Phosphorylase Compared With BAP1 Immunohistochemistry, and CDKN2A and NF2 Fluorescence In Situ Hybridization in Separating Reactive Mesothelial Proliferations From Epithelioid Malignant Mesotheliomas — K.B. Berg, S. Dacic, et al. (2018)

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