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. 2012 Jun 1;7(6):559-66.
doi: 10.4161/epi.20219. Epub 2012 Jun 1.

Key epigenetic changes associated with lung cancer development: results from dense methylation array profiling

Heather H Nelson  1 , Carmen J Marsit, Brock C Christensen, E Andres Houseman, Milica Kontic, Joseph L Wiemels, Margaret R Karagas, Margaret R Wrensch, Shichun Zheng, John K Wiencke, Karl T Kelsey
Affiliations

Key epigenetic changes associated with lung cancer development: results from dense methylation array profiling

Heather H Nelson et al. Epigenetics. .

Abstract

Epigenetic alterations are a common event in lung cancer and their identification can serve to inform on the carcinogenic process and provide clinically relevant biomarkers. Using paired tumor and non-tumor lung tissues from 146 individuals from three independent populations we sought to identify common changes in DNA methylation associated with the development of non-small cell lung cancer. Pathologically normal lung tissue taken at the time of cancer resection was matched to tumorous lung tissue and together were probed for methylation using Illumina GoldenGate arrays in the discovery set (n = 47 pairs) followed by bisulfite pyrosequencing for validation sets (n = 99 pairs). For each matched pair the change in methylation at each CpG was calculated (the odds ratio), and these ratios were averaged across individuals and ranked by magnitude to identify the CpGs with the greatest change in methylation associated with tumor development. We identified the top gene-loci representing an increase in methylation (HOXA9, 10.3-fold and SOX1, 5.9-fold) and decrease in methylation (DDR1, 8.1-fold). In replication testing sets, methylation was higher in tumors for HOXA9 (p < 2.2 × 10 (-16) ) and SOX1 (p < 2.2 × 10 (-16) ) and lower for DDR1 (p < 2.2 × 10 (-16) ). The magnitude and strength of these changes were consistent across squamous cell and adenocarcinoma tumors. Our data indicate that the identified genes consistently have altered methylation in lung tumors. Our identified genes should be included in translational studies that aim to develop screening for early disease detection.

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Figures

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Figure 1. Mean fold change in methylation between tumor and normal for 47 matched tissue pairs and all 1413 autosomal CpGs by chromosome. Positive fold change values indicate increased methylation in tumor relative to normal tissue and negative fold change values indicate decreased methylation in tumor relative to normal tissue. Horizontal dotted lines indicate 2-fold and 5-fold changes in mean methylation between tumor and normal lung. Genes with CpG loci chosen for replication in independent populations (HOXA9, SOX1, DDR1) are shown.
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