DNA methylation of microRNA-coding genes in non-small-cell lung cancer patients

Gerwin Heller, Corinna Altenberger, Irene Steiner, Thais Topakian, Barbara Ziegler, Erwin Tomasich, György Lang, Adelheid End-Pfützenreuter, Sonja Zehetmayer, B. Döme, Britt Madeleine Arns, Walter Klepetko, Christoph C. Zielinski, Sabine Zöchbauer-Müller

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14 Citations (Scopus)

Abstract

Deregulated DNA methylation leading to transcriptional inactivation of certain genes occurs frequently in non-small-cell lung cancers (NSCLCs). As well as protein-coding genes, microRNA (miRNA)-coding genes may be targets for methylation in NSCLCs; however, the number of known methylated miRNA genes is still small. Thus, we investigated methylation of miRNA genes in primary tumour (TU) samples and corresponding non-malignant lung tissue (NL) samples of 50 NSCLC patients by using methylated DNA immunoprecipitation followed by custom-designed tiling microarray analyses (MeDIP-chip), and 252 differentially methylated probes between TU samples and NL samples were identified. These probes were annotated, which resulted in the identification of 34 miRNA genes with increased methylation in TU samples. Some of these miRNA genes were already known to be methylated in NSCLCs (e.g. those encoding miR-9-3 and miR-124), but methylation of the vast majority of them was previously unknown. We selected six miRNA genes (those encoding miR-10b, miR-1179, miR-137, miR-572, miR-3150b, and miR-129-2) for gene-specific methylation analyses in TU samples and corresponding NL samples of 104 NSCLC patients, and observed a statistically significant increase in methylation of these genes in TU samples (p < 0.0001). In silico target prediction of the six miRNAs identified several oncogenic/cell proliferation-promoting factors (e.g. CCNE1 as an miR-1179 target). To investigate whether miR-1179 indeed targets CCNE1, we transfected miR-1179 gene mimics into CCNE1-expressing NSCLC cells, and observed downregulated CCNE1 mRNA expression in these cells as compared with control cells. Similar effects on cyclin E1 expression were seen in western blot analyses. In addition, we found a statistically significant reduction in the growth of NSCLC cells transfected with miR-1179 mimics as compared with control cells. In conclusion, we identified many methylated miRNA genes in NSCLC patients, and found that the miR-1179 gene is a potential tumour cell growth suppressor in NSCLCs. Overall, our findings emphasize the impact of miRNA gene methylation on the pathogenesis of NSCLCs.

Original languageEnglish
Pages (from-to)387-398
Number of pages12
JournalJournal of Pathology
Volume245
Issue number4
DOIs
Publication statusPublished - Aug 1 2018

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Keywords

  • CpG island methylation
  • MeDIP-chip
  • miRNA
  • MS-HRM analysis
  • non-small-cell lung cancer

ASJC Scopus subject areas

  • Pathology and Forensic Medicine

Cite this

Heller, G., Altenberger, C., Steiner, I., Topakian, T., Ziegler, B., Tomasich, E., Lang, G., End-Pfützenreuter, A., Zehetmayer, S., Döme, B., Arns, B. M., Klepetko, W., Zielinski, C. C., & Zöchbauer-Müller, S. (2018). DNA methylation of microRNA-coding genes in non-small-cell lung cancer patients. Journal of Pathology, 245(4), 387-398. https://doi.org/10.1002/path.5079