Abstract LB-383: Methylation profiles using 480,000 cytosine markers of early stage adenocarcinomas of the lung
Authors: Cote Michele L. , Colacino Justin A. , Sheng Shejie , Lonardo Fulvio , Stewart Mark , Dolinoy Dana C. , Jones Tamara R. , Schwartz Ann G. , Rozek Laura S. 
Published: August 2012

Abstract
Even detected in its earliest stages, lung cancer is a deadly disease, with fewer than 50% of cases surviving 5 years post-diagnosis. As surgical resection of the tumor is the extent of treatment for most early stage disease, ways to identify individuals who would benefit from additional therapy is critical to reduce the mortality in this population. Epigenetic changes are an important mechanism in carcinogenic progression, but their potential role in lung cancer progression is not yet understood. We identified formalin fixed, paraffin embedded (FFPE) tumors with high cellularity from 20 white women with early stage adenocarcinoma of the lung and two matched blood DNA samples from a previous population-based case-control study. These samples were profiled on the Infinium HumanMethylation450 BeadChip after processing with the Infinium HD FFPE Restore Kit in the University of Michigan Sequencing Core. The HumanMethylation450 BeadChip measures the methylation status at over 480,000 cytosines distributed over the genome. Excluding sites with missing values and high detection p-values, 466,807 sites were available for analysis. The Bioconductor package IMA was used for data processing and the R package limma was used to identify methylation differences based on survival (≥ 36 months, n = 14 vs &lt; 36 months, n=6) and somatic mutation status (2 samples each were either EGFR or KRAS positive) after adjustment for pack years of smoking and age at diagnosis. Comparing those who did and did not survive 36 months post-diagnosis, 2178 probes were differentially methylated after correction for multiple testing (adjusted q&lt;0.20). Of these, 270 (12.4%) were in CpG islands and 1040 (47.8%) were not located in a CpG island, shore or shelf. Comparing those with and without KRAS mutations, 1017 genes were differentially methylated. Of these, 596 (58.6%) were in CpG islands and 157 (15.4%) were not located in a CpG island, shore or shelf. There were fewer differences based on EGFR status, with only six methylation differences significant at q&lt;0.20. Ongoing validation analyses are underway to understand the extent and significance of differentially methylated sites. In this pilot study using a newly-designed, high density microarray for methylation analysis on FFPE samples, we identified a distinct epigenetic prognostic profile in lung cancer. We also note a potential epigenetic profile associated with KRAS mutations in lung adenocarcinomas, as has been noted in other tumor sites. Our initial results indicate specific epigenetic differences may correlate with survival in early stage adenocarcinoma of the lung and could provide insight into functional changes that affect disease progression, and ultimately survival.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr LB-383. doi:1538-7445.AM2012-LB-383