CpG island methylation and expression of tumour-associated genes in lung carcinoma

Our plain-English summary of CpG island methylation and expression of tumour-associated genes in lung carcinoma, by R. Dammann, M. Strunnikova, U. Schagdarsurengin, et al (European Journal of Cancer, 2005).

The study

• Authors: R. Dammann, M. Strunnikova, U. Schagdarsurengin, M. Rastetter, M. Papritz, U.E. Hattenhorst, H.S. Hofmann, R.E. Silber, S. Burdach, G. Hansen
• Journal: European Journal of Cancer
• Published: 2005;41(8):1223-36
• Cited by: 123 articles, as counted by NIH iCite
• Read it: PubMed · Publisher

Abstract

In this study, microarray analysis was used to identify tumour-related genes that were down regulated in lung carcinoma. The promoter sequences of the identified genes were analysed for methylation patterns. In lung cancer cell lines, CpG island methylation was frequently detected for TIMP4 (64%), SOX18 (73%), EGF-like domain 7 (56%), CD105 (71%), SEMA2 (55%), RASSF1A (71%), p16 (56%) SLIT2 (100%) and TIMP3 (29%). Methylation was however rarely observed in cell lines for SLIT3 (18%) and DLC1 (18%). In primary lung tumours, methylation of TIMP4 (94%), SOX18 (100%), EGF-like domain 7 (100%), CD105 (69%), SEMA2 (93%), DLC1 (61%), RASSF1A (44%), p16 (47%), SLIT2 (100%) and TIMP3 (13%) was also detected. Methylation of several CpG islands was frequently found in normal lung tissue of cancer patients and this may have been attributed to epigenetic field defect and/or infiltrating tumour cells. Interestingly, inactivation of RASSF1A and p16 correlated well with an extended smoking habit (P=0.02), and exposure to asbestos (P=0.017) or squamous cell carcinoma (P=0.011), respectively. These results have identified genes whose aberrant promoter methylation could play a crucial role in the malignancy of lung carcinoma.

In plain English

This was a laboratory study of lung cancer tissue and cell lines. The authors used microarray gene-activity testing on tissue from 89 patients with non-small cell lung cancer who had lung surgery between 1999 and 2001. They looked for genes less active in tumours than in normal lung. They then tested 11 genes for a chemical mark called methylation, using up to 15 cell lines, 18 tumours and 8 matching normal lung samples; not every gene was tested in every sample. TIMP4 methylation was found in 17 of 18 tumours but also in 7 of 8 normal samples. RASSF1A methylation was found in 7 of 16 tumours and in none of 7 matching normal samples tested. p16 methylation was found in 8 of 17 tumours. Comparing methylation with patient features, the authors found p16 methylation in all four patients exposed to asbestos (P = 0.017). The article does not describe what that asbestos exposure was. Patients with RASSF1A methylation had smoked longer (P = 0.02). The authors concluded that several of these genes may be new targets in lung cancer development.

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 of gene activity (microarray, real-time RT-PCR) and DNA methylation in lung tumour tissue, matching normal lung and cancer cell lines, with methylation compared against patients' clinical features
• Who was studied: 89 consecutive patients with non-small cell lung cancer (squamous cell carcinoma or adenocarcinoma) who had lung resection surgery between 1999 and 2001. The authors worked at Martin-Luther-University Halle-Wittenberg, Germany. Methylation was tested in up to 15 lung cancer cell lines, 18 primary tumours and 8 matching normal lung samples. The number tested varied by gene, for example SLIT2 in 3 cell lines, 16 tumours and 7 normal samples. The clinical comparisons involved about 22 to 24 patients per gene (Table 6).
• Exposure: Asbestos exposure, recorded for 4 patients in the comparison of methylation with clinical features. The article gives no fiber type, job, product or dose. Years of smoking was also compared.
• Main results:
  • The microarray analysis found 388 ESTs (gene fragments) that were less active in tumours than in matching normal lung tissue.
  • TIMP4 methylation was found in 64% (9/14) of cell lines, 94% (17/18) of lung tumours and 88% (7/8) of matching normal lung samples.
  • RASSF1A methylation was found in 10 of 14 (71%) cell lines and 7 of 16 (44%) primary tumours. It was found in none of the 7 matching normal lung samples tested (0/7, Table 5).
  • p16 methylation was found in 5 of 9 (56%) cell lines and 8 of 17 (47%) primary tumours. Table 5 also lists 14% (1/7) of matching normal lung.
  • p16 methylation was found in all 4 asbestos-exposed patients: 4 were in the p16-methylated group and 0 in the unmethylated group (P = 0.017, Fisher exact test). The asbestos association was reported for p16, not for RASSF1A, where the exposed patients were split 2 and 2.
  • Patients with RASSF1A methylation had smoked longer than those without it (33 plus or minus 11 years versus 19 plus or minus 13 years; P = 0.02).
  • p16 methylation was associated with squamous cell carcinoma: among p16-methylated patients, 8 had squamous cell carcinoma and 1 had adenocarcinoma (P = 0.011). DLC1 methylation was associated with distant metastasis; no P value was printed for this.
• The authors' conclusion: The authors concluded that silencing of SLIT3, SOX18, EGF-like domain 7, CD105, SEMA2, DLC1 and TIMP4 may represent new targets in the development of lung cancer. They said these genes should be studied further in growth assays.
• Limitations the authors state:
  • Several genes were methylated in histologically normal lung from cancer patients. The authors said this could reflect infiltrating tumour cells, a field defect, imprinting or tissue-specific methylation.
  • For genes methylated about as often in normal tissue as in tumours, the authors said no link to lung cancer development can reasonably be assumed.
  • The authors noted that methylation differences were more pronounced in cell lines than in primary tumours, possibly because of how cell lines are propagated.

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: Carcinoma, Lung Cancer, Habit, Squamous Cell Carcinoma.

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• Aberrant methylation profile of human malignant mesotheliomas and its relationship to SV40 infection — M. Suzuki, S. Toyooka, et al. (2005)
• Distinct DNA methylation profiles in malignant mesothelioma, lung adenocarcinoma, and non-tumor lung — J.A. Tsou, L.Y. Shen, et al. (2005)
• DNA methylation status of REIC/Dkk-3 gene in human malignancies — T. Hayashi, H. Asano, et al. (2012)
• Mesothelin (MSLN) promoter is hypomethylated in malignant mesothelioma, but its expression is not associated with methylation status of the promoter — K. Tan, K. Kajino, et al. (2010)

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