Abstract 5068: Identification of key tumorigenic pathways in never-smoker lung adenocarcinoma using massively parallel DNA and RNA sequencing and methylation profiling
Authors: Whitsett Timothy G. , Cherni Irene , Inge Landon , Salhia Bodour , Fowler Aaron , Bremner Ross , Izatt Tyler , Aldrich Jessica , Kurdoglu Ahmet , Christoforides Alexis , Baker Angela S. , Phillips Lori , Liang Winnie S. , Sinari Shripad , Armstrong Brock , Selinski Cheryl , Betsou Fay , Phillips Robert , Trent Jeff R. , Von Hoff Daniel D. , Carpten John D. , Craig David W. , Weiss Glen J. , Tran Nhan L. 
Published: August 2012

Abstract
Considered independently, lung cancer in never-smokers would rank among the ten most common causes of cancer mortality. Driver pathways and potential therapeutics must be identified for this clinically relevant subpopulation. We hypothesize that novel mutations and pathways identified by whole genome sequencing (WGS), whole transcriptome sequencing (WTS), and methylation profiling drive tumorigenesis in adenocarcinomas (AC) of never-smoker (NS) patients, and represent potential therapeutic targets. We have completed WGS, WTS, and methylation profiling on two lung ACs from female, never-smokers, one early-stage and one stage IV, and one female smoker (S) patient with early-stage lung AC. Approximately 100 short nucleotide variants (SNV) were discerned from the early-stage and stage IV NS lung ACs. Of interest, these NS patients lacked alterations in common genes associated with lung cancer such as EGFR and KRAS. In comparison, the lung AC from a smoker contained 78 SNVs, including a well-characterized KRAS mutation. Mutations in MAGEC1, a tumor marker in melanoma, were observed in common between the early-stage NS tumor and the smoker lung AC. The early-stage NS tumor contained a mutation in PIK3C3 and CSNK1E, a casein kinase involved Wnt signaling. The stage IV NS tumor demonstrated mutations in tumor suppressor genes such as p53, LATS2, and ATM. With relatively few mutations discerned from NS lung ACs, WTS and methylation profiling were performed. WTS showed 1,083 genes differentially regulated in the early-stage NS and Ingenuity Pathway Analysis implicated G-protein coupled receptor signaling. 2,000 genes were differentially expressed in the stage IV NS lung AC with sonic hedgehog implicated as a significantly regulated pathway. Besides gene expression, methylation profiling revealed ∼3,100 differentially methylated genes in the early-stage NS lung AC compared to normal lung DNA, with 65% hypo-methylated, including genes involved in lung carcinogenesis such as RET and BCL2. In the stage IV NS lung AC, ∼35,000 genes were differentially methylated compared to normal lung DNA (10X the early-stage NS) with ∼62% hypo-methylated. Thus, while an early-stage smoker lung AC displayed a classic driver mutation in KRAS, lung ACs from never-smokers had relatively quiet genomes. Despite few mutations, thousands of genes were differentially regulated at the mRNA level or by methylation. We continue to validate the genes implicated in NS lung AC by mutation, differential expression, and differential methylation, as well as integrating the data across platforms to discern significantly regulated pathways. We believe that the genes and pathways implicated by WGS, WTS, and methylation profiling will lead to a better understanding of NS lung AC and identify possible therapeutic interventions.
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 5068. doi:1538-7445.AM2012-5068