DNA Methylation Profiling Discriminates between Malignant Pleural Mesothelioma and Neoplastic or Reactive Histologic Mimics

Our plain-English summary of DNA Methylation Profiling Discriminates between Malignant Pleural Mesothelioma and Neoplastic or Reactive Histologic Mimics, by L. Bertero, L. Righi, G. Collemi, et al (The Journal of Molecular Diagnostics, 2021).

The study

• Authors: L. Bertero, L. Righi, G. Collemi, C. Koelsche, Y. Hou, D. Stichel, D. Schrimpf, U. Flucke, I. Petersen, C. Vokuhl, S. Fröhling, P. Bironzo, G.V. Scagliotti, P. Cassoni, M. Papotti, A. von Deimling
• Journal: The Journal of Molecular Diagnostics
• Published: 2021;23(7):834-846
• Cited by: 16 articles, as counted by NIH iCite
• Read it: PubMed · Publisher

Abstract

The diagnosis of malignant pleural mesothelioma (MPM) is challenging because of its potential overlap with other neoplasms or even with reactive conditions. DNA methylation analysis is effective in diagnosing tumors. In the present study, this approach was tested for use in MPM diagnosis. The DNA methylation patterns of a discovery cohort and an independent-validation cohort of MPMs were compared to those of 202 cases representing malignant and benign diagnostic mimics (angiosarcoma, desmoid-type fibromatosis, epithelioid sarcoma, leiomyosarcoma, lung adenocarcinoma, lung squamous cell carcinoma, melanoma, nodular fasciitis, reactive mesothelial hyperplasia, sclerosing fibrous pleuritis, solitary fibrous tumor, and synovial sarcoma). By both unsupervised hierarchical clustering and t-distributed stochastic neighbor embedding analysis, MPM samples in the discovery cohort exhibited a DNA methylation profile different from those of other neoplastic and reactive mimics. These results were confirmed in the independent validation cohort and by in silico analysis of the MPM-The Cancer Genome Atlas data set. Copy number variation profiles were also inferred to identify molecular hallmarks of MPM, including CDKN2A and NF2 deletions. Methylation profiling was effective in the diagnosis of MPM, although caution is advised in samples with low tumor cell content.

Copyright © 2021 Association for Molecular Pathology and American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.

In plain English

This laboratory study from Turin, Italy, tested whether DNA methylation profiling (a pattern of chemical marks on DNA) of archived tissue could tell malignant pleural mesothelioma (MPM) apart from conditions that can look similar. The authors compared a discovery series of 34 MPMs and a separate validation series of 46 MPMs with reactive (non-cancer) pleural conditions and 180 other tumors from a Heidelberg databank. They also checked the results against 77 MPMs from The Cancer Genome Atlas. MPMs mostly formed their own distinct group. One sample first diagnosed as sclerosing fibrous pleuritis grouped with MPM, and a repeat biopsy 7 months later was diagnosed as sarcomatoid mesothelioma. A few MPMs grouped with other conditions, and the authors linked some of these to low tumor cell content or poor sample quality. Copy-number data suggested CDKN2A/B deletion in 59 of 73 assessable MPMs and NF2 deletion in 53 of 73. No pattern related to asbestos exposure was seen, but exposure data existed for only 24 of 79 samples. The authors concluded the method can distinguish MPM from these mimics, with caution for samples low in tumor cells.

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 laboratory study of archived tissue samples. It compared genome-wide DNA methylation profiles (and copy-number profiles inferred from the same data) of MPMs with those of tumor and non-tumor mimics, using a discovery series, a validation series and an external public data set.
• Who was studied: Discovery series of 34 MPMs (10 epithelioid, 12 biphasic, 12 sarcomatoid) from two university hospitals in Turin, Italy. Most of these patients were men (27/34) and their median age was 70 years. One sarcomatoid case was excluded because it yielded too little DNA. Validation series of 46 MPMs (22 epithelioid, 12 biphasic, 12 sarcomatoid) from the same institutions. Reactive comparison cases were sclerosing fibrous pleuritis and reactive mesothelial hyperplasia (12 cases). Reference profiles came from 180 tumors in the Heidelberg databank (synovial sarcoma, angiosarcoma, epithelioid sarcoma, leiomyosarcoma, melanoma, solitary fibrous tumor, lung adenocarcinoma, lung squamous cell carcinoma, desmoid-type fibromatosis, nodular fasciitis). The external data set was 77 MPMs from The Cancer Genome Atlas. MPM specimens had been sampled 1 to 21 years before analysis.
• Exposure: This was not an asbestos exposure study; it tested a diagnostic laboratory method. The authors looked for links between methylation profiles and asbestos exposure, but exposure information was available for only 24 of 79 MPM samples (30%). No fiber types or doses are reported.
• Main results:
  • Discovery MPM series compared with other tumors: by t-SNE analysis all MPM cases grouped together, apart from the other tumor types. By hierarchical clustering, one biphasic MPM clustered with the epithelioid sarcoma group.
  • Compared with reactive pleural conditions, one case first diagnosed as sclerosing pleuritis fell into the MPM methylation class and showed CDKN2A and NF2 deletions. A pleural biopsy repeated 7 months later was diagnosed as sarcomatoid mesothelioma. One epithelioid MPM clustered with the reactive cases; the authors attributed this to technical flaws, as its tumor cell content was 30%.
  • Validation series of 46 MPMs: MPM again showed a distinct profile, with partial overlap with lung squamous carcinoma and epithelioid sarcoma. On t-SNE analysis three MPM cases grouped only with other entities. One of these had 20% tumor cell content. The other two had only focal or negative expression of mesothelial markers.
  • The 77 MPMs from The Cancer Genome Atlas gave similar results. The MPM samples were more scattered, and there was partial overlap between MPM and epithelioid sarcomas, mainly involving the TCGA cases.
  • Copy-number profiles were assessable in 73 MPMs; 7 cases were excluded. Among these 73, the profiles suggested CDKN2A/B deletion in 59 of 73 (81%) and NF2 deletion in 53 of 73 (73%).
  • Epithelioid and biphasic MPMs could not be clearly told apart, but most sarcomatoid MPMs clustered together.
  • No patterns were detected linking methylation profiles to age at diagnosis, overall survival or asbestos exposure. Asbestos exposure data were available for only 24 of 79 samples.
• The authors' conclusion: The authors concluded that DNA methylation profiling can distinguish MPM from both neoplastic and reactive histologic mimics and may help refine MPM diagnosis in biopsy and surgical specimens. They advised caution in samples with low tumor cell content.
• Limitations the authors state:
  • The t-SNE plots were assessed by visual inspection, which the authors said involves some subjectivity.
  • The method can fail when samples are poor, for example with low tumor cell content or unsatisfactory DNA quality.
  • The authors named sampling error as the most significant potential limitation.
  • The reference cohort did not include rarer lung cancer mimics such as pleomorphic and spindle cell carcinomas.
  • No diagnostic classifier was built. The authors said one should be developed and tested on a larger series of samples.

Topics

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

Medical terms in this study, explained in our Lexicon: Pleural Mesothelioma, Neoplasm, Discovery, Epithelioid, Sarcoma, Lung Adenocarcinoma, Squamous Cell Carcinoma, Reactive Mesothelial Hyperplasia.

Related studies

• DNA methylation profiling of asbestos-treated MeT5A cell line reveals novel pathways implicated in asbestos response — E. Casalone, A. Allione, et al. (2018)
• Aberrant promoter methylation of WIF-1 and SFRP1, 2, 4 genes in mesothelioma — H. Kohno, V.J. Amatya, et al. (2010)
• Aberrant DNA methylation profile in pleural fluid for differential diagnosis of malignant pleural mesothelioma — M. Fujii, N. Fujimoto, et al. (2012)
• Targeted next-generation sequencing of cancer genes in advanced stage malignant pleural mesothelioma: a retrospective study — M. Lo Iacono, V. Monica, et al. (2015)
• The relationship between tumor MSLN methylation and serum mesothelin (SMRP) in mesothelioma — H.H. Nelson, L.M. Almquist, et al. (2011)
• The panoramic picture of pepsinogen gene family with pan-cancer — S. Shen, H. Li, et al. (2020)

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