Asbestos-associated genome-wide DNA methylation changes in lung cancer

Our plain-English summary of Asbestos-associated genome-wide DNA methylation changes in lung cancer, by E. Kettunen, H. Hernandez-Vargas, M.P. Cros, et al (International Journal of Cancer, 2017).

The study

• Authors: E. Kettunen, H. Hernandez-Vargas, M.P. Cros, G. Durand, F. Le Calvez-Kelm, K. Stuopelyte, S. Jarmalaite, K. Salmenkivi, S. Anttila, H. Wolff, Z. Herceg, K. Husgafvel-Pursiainen
• Journal: International Journal of Cancer
• Published: 2017;141(10):2014-2029
• Cited by: 41 articles, as counted by NIH iCite
• Read it: PubMed · Publisher

Abstract

Previous studies have revealed a robust association between exposure to asbestos and human lung cancer. Accumulating evidence has highlighted the role of epigenome deregulation in the mechanism of carcinogen-induced malignancies. We examined the impact of asbestos on DNA methylation. Our genome-wide studies (using Illumina HumanMethylation450K BeadChip) of lung cancer tissue and paired normal lung from 28 asbestos-exposed or non-exposed patients, mostly smokers, revealed distinctive DNA methylation changes. We identified a number of differentially methylated regions (DMR) and differentially variable, differentially methylated CpGs (DVMC), with individual CpGs further validated by pyrosequencing in an independent series of 91 non-small cell lung cancer and paired normal lung. We discovered and validated BEND4, ZSCAN31 and GPR135 as significantly hypermethylated in lung cancer. DMRs in genes such as RARB (FDR 1.1 × 10-19 , mean change in beta [Δ] -0.09), GPR135 (FDR 1.87 × 10-8 , mean Δ -0.09) and TPO (FDR 8.58 × 10-5 , mean Δ -0.11), and DVMCs in NPTN, NRG2, GLT25D2 and TRPC3 (all with p <0.05, t-test) were significantly associated with asbestos exposure status in exposed versus non-exposed lung tumors. Hypomethylation was characteristic to DVMCs in lung cancer tissue from asbestos-exposed subjects. When DVMCs related to asbestos or smoking were analyzed, 96% of the elements were unique to either of the exposures, consistent with the concept that the methylation changes in tumors may be specific for risk factors. In conclusion, we identified novel DNA methylation changes associated with lung tumors and asbestos exposure, suggesting that changes may be present in causal pathway from asbestos exposure to lung cancer.

© 2017 UICC.

In plain English

This laboratory study measured DNA methylation (chemical tags that help switch genes on and off) in lung cancer. The authors tested tumors and paired normal peripheral lung from 28 Caucasian male surgery patients in Helsinki, 1989-1995. Lung fiber counts defined the groups: 14 asbestos-exposed patients had 5.9 million to 145 million fibers per gram of dry lung tissue, and 14 were non-exposed. Work histories were also reviewed. All but one had smoked. At sites that differed by exposure, tumors from exposed patients mostly showed lower methylation. The most statistically significant exposure-linked region was in the gene RARB; the largest average difference was in RPTOR. In exposed patients' lung tissue, 96% of elements linked to asbestos or smoking were unique to one exposure. In a second series of 91 patients, the authors confirmed higher methylation in tumor than normal lung at BEND4 (77 pairs), GPR135 (67 pairs) and ZSCAN31 (72 pairs). That check compared tumor with normal lung, not exposed with non-exposed patients. The authors concluded their data suggest an association between asbestos exposure status and abnormal methylation. They called for larger studies.

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: Genome-wide DNA methylation array study (Illumina HumanMethylation450K) comparing lung tumors with paired normal lung, and asbestos-exposed with non-exposed patients, followed by pyrosequencing validation in an independent case series
• Who was studied: Discovery series: tumor and paired microscopically normal peripheral lung from 28 Caucasian male lung surgery patients, Helsinki University Central Hospital, 1989-1995 (14 asbestos-exposed, 14 non-exposed). It also included normal lung from six non-cancer male patients. Validation series: 91 tumor and peripheral normal lung pairs from Caucasian males from different Central Hospitals in Finland. All lung cancer cases were current or former smokers, except one life-long non-smoker in each series.
• Exposure: Asbestos exposure groups were defined by lung fiber counts (scanning electron microscopy). Interview-based work histories were also evaluated by an industrial hygienist. Fiber types are not named. Exposed discovery patients had 5.9 x10^6 to 145 x10^6 fibers per gram of dry lung tissue (median 11.7 x10^6); non-exposed had 0 to 0.5 x10^6. Cigarette smoking was also analyzed as pack-years.
• Main results:
  • In the discovery series, genome-wide mean methylation was lower in both tumor and normal lung tissue of asbestos-exposed patients than in non-exposed patients.
  • Comparing tumors only, 529 differentially methylated regions were associated with asbestos exposure status (FDR less than 0.05). By FDR, the most significant was in the promoter of RARB, with lower methylation in tumors from asbestos-exposed patients.
  • Among those tumor regions, the largest mean methylation change (mean change in beta -0.2091) was in RPTOR. It showed lower methylation in asbestos-exposed tumors.
  • The 999 asbestos exposure status-related variable sites found in tumors mostly showed low methylation in exposed patients. The highest methylation levels were in tumors of non-exposed patients.
  • Pyrosequencing found more pronounced loss of methylation in TPO in lung tumors of asbestos-exposed patients than in non-exposed patients (P=0.014).
  • In asbestos-exposed patients' lung tissue, 96% of the elements linked to smoking pack-years or to asbestos exposure status were unique to one exposure.
  • In the validation series, tumors showed higher methylation than paired normal lung. The difference in mean methylation was 11.1% for BEND4 (77 pairs), 6.6% for GPR135 (67 pairs) and 23.4% for ZSCAN31 (72 pairs). These comparisons were tumor versus normal, not by asbestos exposure.
  • For one site in NPTN, methylation variation in tumors was 29.8% in non-exposed and 0.5% in exposed discovery patients. In the validation series it was 26.5% in non-exposed (n=29) and 24.0% in exposed patients (n=24).
• The authors' conclusion: The authors concluded that their data suggest an association between asbestos exposure status in lung cancer and abnormal methylation at distinct regions and sites. They added that these changes may lie on a pathway from asbestos exposure to lung cancer.
• Limitations the authors state:
  • The functional effects of the small methylation changes need clarification in larger studies, particularly of smokers with occupational asbestos exposure.
  • The exposed group in the validation series had a broader fiber count range than in the discovery series, which prevented direct comparison of the two series.
  • The method used cannot tell ordinary methylation from its oxidized form, so some patterns may reflect 5-hydroxymethylcytosine.
  • Smoking-related methylation changes were minor, possibly because two groups of smokers were compared.
  • Gene expression studies are needed to clarify the molecular pathways involved.

Topics

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

Medical terms in this study, explained in our Lexicon: Lung Cancer, Non-Small Cell Lung Cancer, Asbestos Exposure.

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