Variant Enrichment Analysis to Explore Pathways Disruption in a Necropsy Series of Asbestos-Exposed Shipyard Workers

Our plain-English summary of Variant Enrichment Analysis to Explore Pathways Disruption in a Necropsy Series of Asbestos-Exposed Shipyard Workers, by S. Crovella, R.R. Moura, L. Brandão, et al (International Journal of Molecular Sciences, 2022).

The study

• Authors: S. Crovella, R.R. Moura, L. Brandão, F. Vita, M. Schneider, F. Zanconati, L. Finotto, P. Zacchi, G. Zabucchi, V. Borelli
• Journal: International Journal of Molecular Sciences
• Published: 2022;23(21)
• Cited by: 2 articles, as counted by NIH iCite
• Read it: PubMed · Publisher · Free full text

Abstract

The variant enrichment analysis (VEA), a recently developed bioinformatic workflow, has been shown to be a valuable tool for whole-exome sequencing data analysis, allowing finding differences between the number of genetic variants in a given pathway compared to a reference dataset. In a previous study, using VEA, we identified different pathway signatures associated with the development of pulmonary toxicities in mesothelioma patients treated with radical hemithoracic radiation therapy. Here, we used VEA to discover novel pathways altered in individuals exposed to asbestos who developed or not asbestos-related diseases (lung cancer or mesothelioma). A population-based autopsy study was designed in which asbestos exposure was evaluated and quantitated by investigating objective signs of exposure. We selected patients with similar exposure to asbestos. Formalin-fixed paraffin-embedded (FFPE) tissues were used as a source of DNA and whole-exome sequencing analysis was performed, running VEA to identify potentially disrupted pathways in individuals who developed thoracic cancers induced by asbestos exposure. By using VEA analysis, we confirmed the involvement of pathways considered as the main culprits for asbestos-induced carcinogenesis: oxidative stress and chromosome instability. Furthermore, we identified protective genetic assets preserving genome stability and susceptibility assets predisposing to a worst outcome.

In plain English

This genetic study used autopsy tissue from men who had worked in the shipyards of Monfalcone, in northeastern Italy. All had objective signs of asbestos exposure. The authors compared 7 men who had pleural mesothelioma, 7 who had lung cancer, and 5 controls who died of cardiovascular disease after age 75 without asbestos-related cancer. Mineral analysis confirmed amphibole asbestos (over 80%) in all cancer cases. DNA from stored heart tissue was sequenced. A method called variant enrichment analysis then checked which biological pathways carried more genetic variants than a non-Finnish European reference dataset. None of the variants reported by earlier genome-wide studies of mesothelioma were found. One pathway was enriched only in controls, 5 only in the lung cancer group and 11 only in the mesothelioma group. Four were shared by the two cancer groups, including retinoid (vitamin A) metabolism. The authors concluded that the analysis confirmed the involvement of oxidative stress and chromosome instability, and proposed a possible protective role for the PACS-1 protein. They named the small number of subjects as a limitation.

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: Genetic study of archived autopsy tissue (population-based autopsy series): whole-exome sequencing analysed with variant enrichment analysis (VEA), comparing pathways with a reference dataset
• Who was studied: 19 male asbestos-exposed shipyard workers from a necropsy series (1983–2015) in the Monfalcone area, northeastern Italy: 7 with malignant pleural mesothelioma (2 epithelial, 2 biphasic, 3 sarcomatoid), 7 with lung cancer (2 small-cell, 5 non-small-cell), and 5 controls who died of other causes after 75 years of age without asbestos-related tumors
• Exposure: Occupational asbestos exposure in shipyard work. It was assessed at autopsy from pleural plaques and from lung counts of asbestos bodies and asbestos fibers. Mineralogical analysis confirmed amphibole asbestos (over 80%) in all lung cancer and mesothelioma cases. Fiber counts were not available for controls.
• Main results:
  • None of the variants described in previously published genome-wide association studies on mesothelioma and asbestos exposure were present in the sequencing data from this study.
  • Pathways enriched only in one group numbered 1 for controls, 11 for the mesothelioma group and 5 for the lung cancer group. 5 pathways were shared by all three groups.
  • The only pathway enriched exclusively in the controls (exposed men without asbestos-related cancer) was Nef-mediated downregulation of MHC class I complex cell surface expression. Table 2 gives an odds ratio of 5.59 (95% CI 2.75 to 10.40). The authors linked this pathway to the PACS-1 protein.
  • All five pathways enriched exclusively in the lung cancer group involve heparan sulphate glycosaminoglycan/proteoglycan biosynthesis and degradation.
  • Eleven pathways were enriched exclusively in the mesothelioma group, including:
• nuclear envelope reassembly (Table 2: odds ratio 4.25, 95% CI 2.38 to 7.19)
• scavenging of heme from plasma (odds ratio 3.66, 95% CI 2.06 to 6.14)
• degradation of the extracellular matrix
  • Four pathways were shared by the lung cancer and mesothelioma groups, including FGFR4 mutant receptor activation and retinoid metabolism and transport. Table 2 odds ratios for retinoid metabolism and transport were 2.46 (95% CI 1.67 to 3.52) in lung cancer and 2.08 (95% CI 1.53 to 2.77) in mesothelioma.
  • The five pathways shared by all three groups were judged by the authors not to be involved in cancer development and were not considered further.
• The authors' conclusion: The authors concluded that VEA confirmed the involvement of oxidative stress (heme) and chromosome instability in asbestos-induced carcinogenesis. They proposed a protective role of PACS-1 in maintaining genome stability. They named dysregulated extracellular matrix dynamics and EMT as factors predisposing to lung cancer and mesothelioma, and defective retinoid metabolism and transport as a possible risk factor.
• Limitations the authors state:
  • The strict selection based on objective signs of exposure limited the number of subjects analysed.
  • Formalin fixation of the stored tissue could create artificial mutations, which the authors said they took into account.

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: Autopsy, Mesothelioma, Lung Cancer, Asbestos Exposure, Carcinogenesis, Oxidative Stress.

Related studies

• Pleural mesothelioma and lung cancer: the role of asbestos exposure and genetic variants in selected iron metabolism and inflammation genes — F. Celsi, S. Crovella, et al. (2019)
• A genetic variant of NLRP1 gene is associated with asbestos body burden in patients with malignant pleural mesothelioma — S. Crovella, R.R. Moura, et al. (2018)
• Biological Pathways Associated With the Development of Pulmonary Toxicities in Mesothelioma Patients Treated With Radical Hemithoracic Radiation Therapy: A Preliminary Study — S. Crovella, A. Revelant, et al. (2021)
• Accuracy of pleural biopsy for the diagnosis of histologic subtype of malignant pleural mesothelioma: Necropsy-based study of 134 cases — P.G. Barbieri, D. Consonni, et al. (2022)
• Iron signature in asbestos-induced malignant pleural mesothelioma: A population-based autopsy study — S. Crovella, A.M. Bianco, et al. (2016)
• Pleural plaques and exposure to mineral fibres in a male urban necropsy population — A. Karjalainen, P.J. Karhunen, et al. (1994)

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