Authors: Heather H. Nelson, 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 and Karl T. Kelsey

Heather H. Nelson

Corresponding author: hhnelson@umn.edu
Masonic Cancer Center, Division of Epidemiology and Community Health; University of Minnesota; Minneapolis, MN USA

Carmen J. Marsit

Department of Pathology and Laboratory Medicine; Brown University; Providence, RI USA

Brock C. Christensen

Department of Pathology and Laboratory Medicine; Brown University; Providence, RI USA; Department of Community Health; Center for Environmental Health and Technology, Brown University; Providence, RI USA

E. Andres Houseman

Department of Community Health; Center for Environmental Health and Technology, Brown University; Providence, RI USA

Milica Kontic

Department of Oncology; Institute for Lung Diseases and TB; Belgrade University; Belgrade, Serbia

Joseph L. Wiemels

Department of Epidemiology and Biostatistics; University of California at San Francisco; San Francisco, CA USA

Margaret R. Karagas

Section of Biostatistics and Epidemiology; Department of Community and Family Medicine; Dartmouth-Hitchcock Medical Center; Lebanon, NH USA

Margaret R. Wrensch

Department of Neurological Surgery; University of California at San Francisco; San Francisco, CA USA

Shichun Zheng

Department of Neurological Surgery; University of California at San Francisco; San Francisco, CA USA

John K. Wiencke

Department of Neurological Surgery; University of California at San Francisco; San Francisco, CA USA

Karl T. Kelsey

Department of Pathology and Laboratory Medicine; Brown University; Providence, RI USA; Department of Community Health; Center for Environmental Health and Technology, Brown University; Providence, RI USA

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.

Received: December 5, 2011; Accepted: March 30, 2012

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