Whole-genome sequencing of human malignant mesothelioma tumours and cell lines

Our plain-English summary of Whole-genome sequencing of human malignant mesothelioma tumours and cell lines, by H. Oey, M. Daniels, V. Relan, et al (Carcinogenesis, 2019).

The study

• Authors: H. Oey, M. Daniels, V. Relan, T.M. Chee, M.R. Davidson, I.A. Yang, J.J. Ellis, K.M. Fong, L. Krause, R.V. Bowman
• Journal: Carcinogenesis
• Published: 2019;40(6):724-734
• Cited by: 27 articles, as counted by NIH iCite
• Read it: PubMed · Publisher

Abstract

Pleural mesothelioma is a cancer of serosal surfaces caused by environmental exposure to asbestos. Clinical outcome remains poor and while trials of new treatments are ongoing it remains an understudied cancer. Mesothelioma cell lines can readily be grown from primary tumour and from tumour cells shed into pleural effusion with the latter representing a particularly valuable source of DNA in clinical settings, procurable without the need for additional invasive procedures. However, it is not well understood how accurately patient-derived cultured tumour cells represent the molecular characteristics of their primary tumour. We used whole-genome sequencing of primary tumour and matched cultured cells to comprehensively characterize mutations and structural alterations. Most cases had complex rearranged genomes with evidence of chromoanagenesis and rearrangements reminiscent of chromoplexy. Many of the identified driver mutations were structural, indicating that mesothelioma is often caused by structural alterations and catastrophic genomic events, rather than point mutations. Because the majority of genomic changes detected in tumours were also displayed by the genomes of cultured tumour cells, we conclude that low-passage cultured tumour cells are generally suitable for molecular characterization of mesothelioma and may be particularly useful where tissue samples with high tumour cell content are not available. However, the subclonal compositions of the cell lines did not fully recapitulate the subclonal diversity of the primary tumours. Furthermore, longitudinal acquisition of major alterations in subclonal cell populations was observed after long-term passaging. These two factors define limitations of tumour-derived cell lines as genomic substrate for clinical purposes.

© The Author(s) 2019. Published by Oxford University Press. All rights reserved. For Permissions, please email: [email protected].

In plain English

This laboratory study used whole-genome sequencing to compare the DNA of mesothelioma tumours with cells grown in culture from the same patients. The goal was to see whether cultured cells could stand in for tumour tissue in genetic testing. It covered nine patients with malignant mesothelioma at The Prince Charles Hospital in Queensland, Australia. The article text does not describe the patients' asbestos exposure. Primary tumours carried relatively few point mutations (1667 to 4323 per genome) but many large structural changes in their chromosomes. Most mutations and structural changes found in tumours were also present in the matched cell lines. In one case (MM10), no point mutations were shared. All cases except MM10 had structural changes involving the gene CDKN2A. Four cases had BAP1 mutations predicted to be disruptive. The cell lines held only part of each tumour's mix of cell populations, and that mix changed over time in culture. The authors concluded that low-passage cultured tumour cells are generally suitable for genetic characterization of mesothelioma, but that these shifts must be taken into account.

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 genomic study: whole-genome sequencing of primary tumours, cell lines grown from them, and blood from the same patients
• Who was studied: Nine patients with pathologically confirmed malignant mesothelioma attending The Prince Charles Hospital, Queensland, Australia. Case MM9 had only primary tumour sequenced and case MM4 had only cell lines sequenced. Study dates are not given in the text.
• Exposure: Asbestos exposure was not measured or reported in the article text. The study compared tumour tissue with cultured tumour cells, including cells grown from pleural effusion fluid.
• Main results:
  • Primary tumours had a low number of point mutations: 1667 to 4323 per genome, about 1.2 mutations per megabase.
  • Most point mutations found in primary tumours were also found in the cell lines derived from them. The exception was MM10, where no variants were shared between tumour and cell line.
  • In case MM1, 12% (937/7549) of variants were found only in the primary tumour.
  • In case MM1, 7% (526/7549) of variants were found only in cell lines from resected tumour, and 30% (2348/7549) only in cell lines from pleural effusion.
  • Structural changes (large rearrangements) showed a high level of agreement between primary tumours and the cell lines derived from them.
  • Most cases showed rearrangement patterns resembling chromoplexy. MM4 had a chain of 100 breakpoints. All other cases except MM8 had chains ranging from 22 to 64 breakpoints.
  • All cases except MM10 had structural alterations involving CDKN2A, all predicted to cause complete loss of the gene.
  • BAP1 had point mutations predicted to be disruptive in four cases. These four cases also tested negative for BAP1 on tissue staining.
  • Except for MM9 and MM10, no case was judged likely to produce fully functional NF2 protein.
  • Many of the driver mutations found were structural. The authors read this as indicating that mesothelioma is often caused by structural alterations and catastrophic genomic events rather than point mutations.
  • Cell lines carried only a subset of the cell populations (subclones) found in the primary tumour. Their composition could differ from the tumour and changed over time in culture. In MM1, both cell lines were dominated by a subclone that made up only 5% of the sequenced tumour.
  • Cell lines from case MM4 changed at later passage, becoming tetraploid with large deletions.
  • Mutational signatures 3, 5 and 8 were the most prevalent.
• The authors' conclusion: The authors concluded that low-passage cultured tumour cells are generally suitable for molecular characterization of mesothelioma. They wrote that such cells may be particularly useful where tissue samples with high tumour cell content are not available. They added that subclonal populations, and shifts in them over time, must be taken into account when using cell lines to represent a patient's tumour.
• Limitations the authors state:
  • Some variants may have been missed because of low tumour cell content in tumour samples or insufficient sequencing coverage.
  • Methods for judging sample suitability fell short. Microscopy estimated 90% tumour content for MM2, but genetic analysis found only 18%, which compromised variant calls in that tumour.
  • The MM10 cell line may have consisted of premalignant cells or fibroblasts rather than tumour cells.
  • Growing cultures to sufficient purity and quantity takes time, usually a few weeks.

Topics

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

Medical terms in this study, explained in our Lexicon: Mesothelioma, Pleural Mesothelioma, Serosal Surface, Environmental Exposure, Pleural Effusion.

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• Germline and somatic variant identification using BGISEQ-500 and HiSeq X Ten whole genome sequencing — A.M. Patch, K. Nones, et al. (2018)
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