Malignant cells from pleural fluids in malignant mesothelioma patients reveal novel mutations

Our plain-English summary of Malignant cells from pleural fluids in malignant mesothelioma patients reveal novel mutations, by S. Sneddon, I. Dick, Y.C.G. Lee, et al (Lung Cancer, 2018).

The study

• Authors: S. Sneddon, I. Dick, Y.C.G. Lee, A.W.B. Musk, A.M. Patch, J.V. Pearson, N. Waddell, R.J.N. Allcock, R.A. Holt, B.W.S. Robinson, J. Creaney
• Journal: Lung Cancer
• Published: 2018;119:64-70
• Cited by: 22 articles, as counted by NIH iCite
• Read it: PubMed · Publisher

Abstract

Objectives: Malignant mesothelioma (MM) is an asbestos related tumour affecting cells of serosal cavities. More than 70% of MM patients develop pleural effusions which contain tumour cells, representing a readily accessible source of malignant cells for genetic analysis. Although common somatic mutations and losses have been identified in solid MM tumours, the characterization of tumour cells within pleural effusions could provide novel insights but is little studied.

Materials And Methods: DNA and RNA were extracted from cells from short term cultures of 27 human MM pleural effusion samples. Whole exome and transcriptome sequencing was performed using the Ion Torrent platform. Somatic mutations were identified using VarScan2 and SomaticSniper. Copy number alterations were identified using ExomeCNV in R. Significant copy number alterations were identified across all samples using GISTIC2.0. The association between tumour intrinsic properties and survival was analyzed using the Cox proportional hazards regression model.

Results: We identified BAP1, CDKN2A and NF2 alterations in the cells from MM pleural effusions at a higher frequency than what is typically seen in MM tumours from surgical series. The median mutation rate was 1.09 mutations/Mb. TRAF7 and LATS2 alterations were also identified at a high frequency (66% and 59% respectively). Novel regions of interest were identified, including alterations in FGFR3, and the regions 19p13.3, 8p23.1 and 1p36.32.

Conclusion: Short term cultures of tumour cells from MM pleural effusions offer an accessible alternative to surgical tumour biopsies in the study of MM genomics and reveal novel mutations of interest. Pleural effusion tumour cells provide an opportunity for the monitoring of tumour dynamics, treatment response and the clonal evolution of MM tumours.

Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

In plain English

This laboratory study sequenced tumour cells from pleural effusions (chest fluid) of 27 people with malignant mesothelioma, collected before treatment and briefly cultured. All but one had documented asbestos exposure. The median mutation rate was 1.09 mutations per million bases. In 26 of 27 samples, both copies of all or part of the region containing CDKN2A were lost. Loss of the chromosome arm carrying NF2 was seen in 18 of 27 samples, TRAF7 loss in 18, LATS2 changes in 16 and BAP1 mutations in 8. The authors reported that alterations in CDKN2A, BAP1 and NF2 (mutations and losses together), and in TRAF7 and LATS2, were found more often than in earlier surgical-sample studies. FGFR3, a gene not previously linked to mesothelioma, was affected in 12 of 27. Losses at 19p13.3, 8p23.1 and 1p36.32 were highly significant, though such regions were altered in some earlier cases. Non-epithelioid tumour type and no treatment were linked to worse survival. The authors concluded that cultured effusion cells are an attractive tool for studying mesothelioma. No matching surgical samples were available, and the group was small.

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 genetic study: whole exome and transcriptome sequencing of short-term cultures of tumour cells from pleural effusions, compared with each patient's blood DNA, with a survival analysis (Cox regression)
• Who was studied: 27 malignant mesothelioma patients with pleural effusions. Pre-treatment effusion samples were collected between 2002 and 2014, and the study was approved by ethics committees in Perth, Western Australia. Tumour histology was epithelioid in 22, biphasic in 2 and sarcomatoid in 3. Mean age at diagnosis was 65 years (range 45 to 88), and 23 (85%) were male.
• Exposure: Asbestos exposure was documented for all but one patient. No fiber types, jobs or doses are given. The study itself examined tumour genetic changes, not exposure.
• Main results:
  • The median mutation rate across the 27 samples was 1.09 mutations per million bases (range 0.38 to 3.50).
  • CDKN2A: 26 of 27 samples showed homozygous loss (both copies lost) of all or part of the region (locus) containing the gene.
  • BAP1: somatic mutations or indels were found in 8 of 27 samples, and only eight samples had wild-type BAP1.
  • NF2: loss of the 22q chromosome arm, which contains NF2, was found in 18 of 27 samples.
  • TRAF7 loss was found in 18 of 27 samples, and LATS2 was affected in 16 of 27 samples.
  • The authors reported that genetic alterations (mutations and losses together) in CDKN2A, BAP1 and NF2 were found in a higher proportion of samples than previously reported for surgical samples.
  • The authors reported finding lesions in TRAF7 and LATS2 at a higher frequency than an earlier large study of surgical samples.
  • FGFR3, a gene not previously associated with mesothelioma, was affected in 12 of 27 samples.
  • Significant losses were found in regions 19p13.3, 8p23.1 and 1p36.32. The results section describes these regions as not previously reported in mesothelioma. The discussion notes that alterations in 8p23.1, 1p36 and 19p13 had been seen in some earlier mesothelioma cases, and that this study identified them with high statistical significance.
  • In univariate survival analysis, non-epithelial compared with epithelial histology had a hazard ratio of 6.14 (95% CI 1.79 to 21.09). Not treated compared with treated had a hazard ratio of 5.81 (95% CI 2.13 to 15.88).
  • BAP1 mutation status or loss was not associated with survival, and total number of SNVs was not associated with survival.
  • Patients with low TP53 expression had significantly better survival than those with high TP53 expression after adjustment (printed as HR 1.14, 95% CI 1.09 to 9.01, p = 0.03).
• The authors' conclusion: The authors concluded that short-term cultures of tumour cells from pleural effusions are an attractive tool for studying malignant mesothelioma. In their view, these cells share the molecular features reported in solid tumours, add mutational information, and can be sampled repeatedly to follow the tumour over time.
• Limitations the authors state:
  • No matched surgical or biopsy samples from the same tumours were available for comparison.
  • The culture process may introduce selection bias.
  • The cohort was small and mostly epithelioid, which may have affected the survival and mutation-count findings.
  • Because nearly all patients were asbestos-exposed, the authors could not test whether asbestos exposure was related to survival or to the number of mutations.
  • Only exome and transcriptome sequencing was done, so disruption of BAP1 protein function was not assessed.

Topics

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

Medical terms in this study, explained in our Lexicon: Malignant Mesothelioma, Pleural Effusion, Somatic Mutation, BAP1, CDKN2A.

Related studies

• Whole-exome sequencing reveals frequent genetic alterations in BAP1, NF2, CDKN2A, and CUL1 in malignant pleural mesothelioma — G. Guo, J. Chmielecki, et al. (2015)
• 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)
• 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)
• 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)
• BAP1 mutation is a frequent somatic event in peritoneal malignant mesothelioma — H. Alakus, S.E. Yost, et al. (2015)
• Recent insights emerging from malignant mesothelioma genome sequencing — M. Carbone, G. Gaudino, et al. (2015)

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