Distinct DNA methylation profiles in malignant mesothelioma, lung adenocarcinoma, and non-tumor lung

Our plain-English summary of Distinct DNA methylation profiles in malignant mesothelioma, lung adenocarcinoma, and non-tumor lung, by J.A. Tsou, L.Y. Shen, K.D. Siegmund, et al (Lung Cancer, 2005).

The study

• Authors: J.A. Tsou, L.Y. Shen, K.D. Siegmund, T.I. Long, P.W. Laird, C.K. Seneviratne, M.N. Koss, H.I. Pass, J.A. Hagen, I.A. Laird-Offringa
• Journal: Lung Cancer
• Published: 2005;47(2):193-204
• Cited by: 63 articles, as counted by NIH iCite
• Read it: PubMed · Publisher

Abstract

DNA methylation markers provide a powerful tool to make diagnoses based on genetic material obtained directly from tumors or from "remote" locations such as sputum, pleural fluid, or serum. In particular when limited cell numbers are available, amplifyable DNA markers can provide a very sensitive tool for cancer detection and classification. Malignant mesothelioma (MM), an aggressive cancer strongly associated with asbestos exposure, can be difficult to distinguish from adenocarcinoma of the lung when limited material is available. In an attempt to identify molecular markers for MM and adenocarcinoma, we examined the DNA methylation status of 14 loci. Analysis of methylation levels in 10 MM and 8 adenocarcinoma cell lines showed that methylation of APC was significantly elevated in adenocarcinoma compared to MM cell lines (P=0.0003), while methylation of CDH1 was higher in MM (P<0.02). Subsequent examination of the methylation status of the 14 loci in 6 MM and 7 adenocarcinoma primary tumors, which yielded similar methylation profiles, supported these observations. Comparison of methylation in MM cell lines and tumors versus non-tumor lung tissue indicated that APC exhibits less methylation in MM (P=0.003) while RASSF1, PGR1, ESR1, and CDH1 show more methylation in MM, the latter two showing the most significant difference between the two tissue types (P< or = 0.0001). Comparison of methylation in adenocarcinoma cell lines and tumors versus non-tumor lung tissue showed methylation of ESR1, PGR1 and RASSF1 to be significantly elevated in adenocarcinoma, with RASSF1 being most significant (P=0.0002). Thus, with the examination of 14 loci, we have identified 5 candidates that show potential for distinguishing between MM, adenocarcinoma and/or non-cancer lung. Our observations support the strong potential of methylation markers as tools for accurate diagnosis of neoplasms in and around the lung.

In plain English

This laboratory study looked for chemical marks on DNA, called methylation, that might help tell malignant mesothelioma (MM) apart from lung adenocarcinoma, a similar-looking lung cancer, and from non-tumor lung. The authors measured methylation at 14 gene sites in 10 MM and 8 adenocarcinoma cell lines. They then measured the same sites in 6 MM tumors, 7 adenocarcinoma tumors and 11 non-tumor lung samples. The article reports no asbestos exposure information for any sample. In the cell lines, APC was methylated in 7 of 8 adenocarcinoma lines but only 4 of 10 MM lines, and APC methylation levels differed significantly between the two groups (P = 0.0003). When cell lines and tumors were combined, APC (P less than 0.0001) and CDH1 (P = 0.0016) differed between MM and adenocarcinoma. Between MM and non-tumor lung, the most statistically significant differences were for CDH1 and ESR1; between adenocarcinoma and non-tumor lung, they were for RASSF1 (P = 0.0002). The authors concluded that they had identified 5 candidate markers with potential to distinguish these tissues. They noted that their sample size was small, that smoking histories for the non-tumor lung samples were unavailable, and that the gene regions tested might not be optimal.

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 study measuring DNA methylation at 14 gene sites (loci) in cancer cell lines and tissue samples, using a real-time PCR test called MethyLight
• Who was studied: 10 MM cell lines and 8 lung adenocarcinoma cell lines. Also 6 frozen primary MM tumors, 5 of which came from the same tumors as 5 of the MM cell lines. Also 7 adenocarcinoma primary tumors and 11 non-tumor lung samples from Los Angeles County Hospital; the non-tumor samples came from patients operated on for non-cancer reasons such as trauma and pneumothorax. Collection dates are not given.
• Exposure: Not studied. The article reports no asbestos or other exposure data for the patients or cell lines. What was measured was methylation at 14 gene sites (APC, CALCA, CDH1, CDKN2A, ESR1, ESR2, GSTP1, MGMT, MTHFR, MYOD1, PGR, PTGS2, RASSF1, TIMP3).
• Main results:
  • Cell lines: APC was methylated in 88% (7/8) of adenocarcinoma cell lines but in 4/10 MM cell lines, at a very low level. After correction for multiple comparisons, APC was the only gene whose methylation levels differed significantly between the two kinds of cell lines (P = 0.0003). This P-value comes from a test comparing methylation levels, not from a test of the counts of methylated lines.
  • Cell lines: CDH1 methylation was higher in MM (P < 0.02). This was not statistically significant once the multiple-comparisons correction was applied.
  • Methylation patterns in tumors were similar to those in cell lines of the same type. The only significant difference was that PTGS2 methylation was higher in adenocarcinoma tumors than in adenocarcinoma cell lines (P = 0.0031).
  • Tumor samples: CDH1 was methylated in 83% (5/6) of MM tumors and 29% (2/7) of adenocarcinoma tumors. APC was methylated in 100% of adenocarcinoma tumors and 50% (3/6) of MM tumors.
  • Tumor samples only, pairwise comparisons: APC and PTGS2 methylation differed significantly between MM and adenocarcinoma tumors (P = 0.002 and 0.005, respectively).
  • Cell lines and tumors combined (MM n = 11, adenocarcinoma n = 15, non-tumor lung n = 11): all five markers (CDH1, APC, RASSF1, ESR1, PGR) differed significantly between MM and non-tumor lung. For APC, MM showed little to no methylation, while most non-tumor lung samples showed moderate methylation. ESR1, CDH1, RASSF1 and PGR were more methylated in MM. CDH1 and ESR1 (P less than or equal to 0.0001) showed little to no methylation in normal lung.
  • Combined data, adenocarcinoma versus non-tumor lung: RASSF1, ESR1 and PGR differed significantly (P < 0.003). RASSF1 was the most informative (P = 0.0002).
  • Combined data, MM versus adenocarcinoma: APC differed (P < 0.0001), and CDH1 also differed significantly (P = 0.0016).
  • In a clustering analysis based on the five markers, all but one non-cancer lung sample grouped together. Most adenocarcinoma cell lines and tumors formed a second group. MM cell lines and tumors grouped in two separate subclusters.
• The authors' conclusion: The authors concluded that, of the 14 loci examined, they had identified 5 candidate markers that show potential for distinguishing between MM, adenocarcinoma and/or non-cancer lung.
• Limitations the authors state:
  • The sample size was small.
  • The clustering results were based on a small sample size and only five loci.
  • Smoking history was not available for the patients who provided the non-tumor lung samples, so the origin of methylation found in non-tumor lung is unknown.
  • Results depend on the test method and on where the primers sit on the gene; the gene region sampled might not be optimal.
  • Cell lines represent only the subset of tumors that can be grown in the laboratory.
  • APC methylation data may be harder to interpret than data for other genes because the gene has multiple promoters and transcription start sites.

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, Lung Adenocarcinoma, Sputum, Asbestos Exposure, Adenocarcinoma, Neoplasm.

Related studies

• DNA methylation profile of 28 potential marker loci in malignant mesothelioma — J.A. Tsou, J.S. Galler, et al. (2007)
• Aberrant DNA methylation profile in pleural fluid for differential diagnosis of malignant pleural mesothelioma — M. Fujii, N. Fujimoto, et al. (2012)
• Aberrant methylation profile of human malignant mesotheliomas and its relationship to SV40 infection — M. Suzuki, S. Toyooka, et al. (2005)
• CpG island methylation and expression of tumour-associated genes in lung carcinoma — R. Dammann, M. Strunnikova, et al. (2005)
• Aberrant methylation of the CDKN2a/p16INK4a gene promoter region in preinvasive bronchial lesions: a prospective study in high-risk patients without invasive cancer — A. Lamy, R. Sesboüé, et al. (2002)
• Methylation profile landscape in mesothelioma: possible implications in early detection, disease progression, and therapeutic options — X. Zhang, N. Tang, et al. (2015)

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