Deletions of CDKN2A and MTAP Detected by Copy-Number Variation Array Are Associated with Loss of p16 and MTAP Protein in Pleural Mesothelioma

Our plain-English summary of Deletions of CDKN2A and MTAP Detected by Copy-Number Variation Array Are Associated with Loss of p16 and MTAP Protein in Pleural Mesothelioma, by B. Vrugt, M.B. Kirschner, M. Meerang, et al (Cancers, 2023).

The study

• Authors: B. Vrugt, M.B. Kirschner, M. Meerang, K. Oehl, U. Wagner, A. Soltermann, H. Moch, I. Opitz, P.J. Wild
• Journal: Cancers
• Published: 2023;15(20)
• Cited by: 30 articles, as counted by NIH iCite
• Read it: PubMed · Publisher · Free full text

Abstract

CDKN2A deletion is a common alteration in pleural mesothelioma (PM) and frequently associated with co-deletion of MTAP. Since the standard detection method for CDKN2A deletion and FISH analysis is relatively expensive, we here investigated the suitability of inexpensive p16 and MTAP IHC by comparing concordance between IHC and OncoScan CNV arrays on samples from 52 PM patients. Concordance was determined using Cohen's kappa statistics. Loss of CDKN2A was associated with co-deletion of MTAP in 71% of cases. CDKN2A-MTAP copy-number normal cases were also IHC positive in 93% of cases for p16 and 100% for MTAP, while homozygous deletion of CDKN2A-MTAP was always associated with negative IHC for both proteins. In cases with heterozygous CDKN2A-MTAP loss, IHC expression of p16 and MTAP was negative in 100% and 71%, respectively. MTAP and p16 IHC showed high sensitivity (MTAP 86.5%, p16 100%) and specificity (MTAP 100%, p16 93.3%) for the detection of any gene loss. Loss of MTAP expression occurred exclusively in conjunction with loss of p16 labeling. Both p16 and MTAP IHC showed high concordance with Oncoscan CNV arrays (kappa = 0.952, p < 0.0001, and kappa = 0.787, p < 0.0001 respectively). We recommend combined MTAP and p16 immunohistochemistry to confirm the diagnosis of PM.

In plain English

This study compared two inexpensive tissue stains (immunohistochemistry for the proteins p16 and MTAP) with a genetic test (an OncoScan copy-number array) for deletions of the CDKN2A and MTAP genes. It used diagnostic tumor biopsies from 52 patients with pleural mesothelioma, dated 1999 to 2015. Asbestos exposure was not examined. The array found loss of both copies of both genes in 20 cases (38%), loss of one copy of both genes in 14 (27%), and loss of both CDKN2A copies with loss of one MTAP copy in 3 (6%). Fifteen cases (29%) had normal copy numbers of both genes. Compared with the array, p16 staining picked up 100% of gene losses, with a specificity of 93.3%. MTAP staining picked up 86.5%, with a specificity of 100%, but only 70.6% of single-copy MTAP losses. Nine tumors (17%) stained unevenly. The authors concluded that combined p16 and MTAP staining is a cost-effective stand-in (surrogate) for these gene changes, and that it can be reliably used to detect loss of both gene copies. They noted that the meaning of uneven staining in small samples remains unclear.

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-accuracy study on archived tumor tissue, comparing p16 and MTAP immunohistochemistry with OncoScan copy-number variation (CNV) arrays
• Who was studied: Diagnostic biopsies from 52 patients with pleural mesothelioma, dated 1999 to 2015, retrieved from the authors' pathology department archives (University Hospital Zurich). The tumors were 43 epithelioid, 6 biphasic and 3 sarcomatoid. Median age was 60 (range 35 to 73); 45 patients were male and 7 female.
• Exposure: Asbestos or other exposures were not studied. The study compared laboratory tests for CDKN2A and MTAP gene loss in tumor tissue: p16 and MTAP immunohistochemistry against OncoScan copy-number arrays, with FISH in six selected cases.
• Main results:
  • In all 52 cases, the CNV array found homozygous deletion of both CDKN2A and MTAP in 20 cases (38%), heterozygous deletion of both in 14 (27%), homozygous CDKN2A deletion with heterozygous MTAP loss in 3 (6%), and normal copy numbers of both genes in 15 (29%).
  • Loss of MTAP gene copies without CDKN2A deletion was not found in any case.
  • In the 15 cases with normal (wild-type) copy numbers of both genes, MTAP staining was retained in all, and p16 staining was positive in all but one.
  • In the 20 cases with homozygous loss of both genes, p16 and MTAP staining were lost in all cases.
  • In the 14 cases with heterozygous loss of both genes, p16 staining was negative in 100% and MTAP staining in 71%.
  • For detecting any gene loss (homozygous or heterozygous) compared with the CNV array, p16 staining had a sensitivity of 100% and a specificity of 93.3%. MTAP staining had a sensitivity of 86.5% and a specificity of 100%.
  • Agreement with the CNV array for any loss (Cohen's kappa) was 0.952 for p16 and 0.787 for MTAP, p less than 0.0001 for both.
  • MTAP staining detected homozygous MTAP loss with 100% sensitivity, but heterozygous MTAP loss with a sensitivity of 70.6%.
  • Loss of MTAP staining occurred only together with loss of p16 staining.
  • Nine mesotheliomas (17%) showed uneven (heterogeneous) p16 and MTAP staining. Six of these had wild-type copy numbers on the CNV array.
  • CDKN2A FISH, done in six selected cases, matched the CNV array results.
• The authors' conclusion: The authors concluded that combined p16 and MTAP immunohistochemistry is a cost-effective surrogate for CDKN2A-MTAP genetic alterations, and that it can be reliably used to detect homozygous deletions.
• Limitations the authors state:
  • The authors stated that FISH and CNV arrays are difficult to compare, and that FISH is still regarded as the gold standard.
  • The number of female patients was relatively low.
  • The diagnostic significance of uneven p16 and MTAP staining in small biopsies or cytology specimens remains unclear.
  • The authors could not rule out that the loss of p16 staining in the 14 heterozygous cases reflects uneven genetic make-up within the tumor.

Topics

Medical terms in this study, explained in our Lexicon: CDKN2A, MTAP, Pleural Mesothelioma, Fluorescence In Situ Hybridization (FISH), Homozygous Deletion, Immunohistochemistry.

Related studies

• Correlation of methylthioadenosine phosphorylase (MTAP) protein expression with MTAP and CDKN2A copy number in malignant pleural mesothelioma — D.B. Chapel, A.M. Dubuc, et al. (2021)
• CDKN2A and MTAP deletions in peritoneal mesotheliomas are correlated with loss of p16 protein expression and poor survival — A.M. Krasinskas, D.L. Bartlett, et al. (2010)
• Immunohistochemical Loss of MTAP as a Diagnostic and Prognostic Surrogate of CDKN2A/B Homozygous Deletion: A Narrative Review — S. Salzano, R. Caltabiano, et al. (2026)
• BAP1 Is Altered by Copy Number Loss, Mutation, and/or Loss of Protein Expression in More Than 70% of Malignant Peritoneal Mesotheliomas — N. Leblay, F. Leprêtre, et al. (2017)
• Genome-wide analysis of abdominal and pleural malignant mesothelioma with DNA arrays reveals both common and distinct regions of copy number alteration — A.C. Borczuk, J. Pei, et al. (2016)
• Genomic copy number alterations in 33 malignant peritoneal mesothelioma analyzed by comparative genomic hybridization array — P. Chirac, D. Maillet, et al. (2016)

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