Abstract A43: Identification of key tumorigenic pathways in never-smoker lung adenocarcinoma patients using massively parallel DNA and RNA sequencing
Authors: Timothy G. Whitsett, Shripad Sinari, Kelly W. Sheff, Phillip Y. Cheung, Julianna Ross, Brock Armstrong, Landon Inge, Ross Bremner, Cheryl Selinsky, Fay Betsou, Robert Phillips, Irene Cherni, Jeff M. Trent, Daniel D. Von Hoff, John D. Carpten, David W. Craig, Glen J. Weiss, Nhan L. Tran, Tyler Izatt, Jessica Aldrich, Ahmet Kurdoglu, Alexis Christoforides, Angela S. Baker, Lori Phillips, Winnie S. Liang
Journal: Clinical Cancer Research (2012)

Abstract Lung cancer remains the leading cause of cancer deaths in the US and throughout the world. Never-smokers with lung cancer constitute an understudied subset of these patients, though recent estimates show that ∼10% of men and women with lung cancer in the US are never-smokers. Independently, lung cancer in never-smokers ranks among the ten most common causes of cancer mortality, and thus the causes, driver pathways, and potential therapeutics must be investigated for this clinically relevant subpopulation. We hypothesize that novel mutations and pathways identified by whole genome sequencing (WGS) and whole transcriptome sequencing (WTS) drive tumorigenesis in adenocarcinomas of never-smoker patients, and represent potential therapeutic targets. We have completed WGS and WTS on two lung adenocarcinomas from female, never-smokers, one early-stage and one advanced-stage (metastatic), and one female smoker patient with early-stage lung adenocarcinoma. Approximately 100 short nucleotide variants (SNV) causing non-synonymous DNA sequence changes were discerned from the early- and advanced-stage adenocarcinomas from never-smokers. Of interest, these never-smoker patients lacked alterations in common genes associated with lung cancer such as EGFR, KRAS, and EML/ALK translocations, making them ideal cases for the discovery of new mutations that may drive lung adenocarcinomas in never-smokers. In comparison, the adenocarcinoma from a smoker patient contained 78 SNVs, including a well-characterized KRAS mutation. Mutations in MAGEC1, a tumor marker in melanoma and multiple myeloma, were observed in common between the early-stage, never-smoker tumor and the smoker tumor. The mutations observed in the never-smoker cases included genes suspected to play a role in lung carcinogenesis. The early-stage, never-smoker patient contained a mutation in PIK3C3 and DOCK10, known to play a role in cancer cell migration, and CSNK1E, a casein kinase involved Wnt signaling and in beta catenin-induced cancer cell proliferation. The late-stage never-smoker patient demonstrated a p53 mutation, a mutation in the tumor suppressor LATS2, and a mutation in the DNA damage checkpoint gene, ATM. The mutations discovered in known tumor suppressor genes tended to be in the late-stage, never-smoke patient. Ingenuity Pathway Analysis implicated G-protein coupled receptor signaling for the early-stage never-smoker, Hif1α signaling for the smoker, and Sonic Hedgehog Signaling for the late-stage, never-smoker in both WGS and WTS. Currently, we are validating the identified mutations discovered by WGS using Sanger sequencing and surveying their frequency in ∼30 and ∼60 additional cases of lung adenocarcinoma from never-smokers and clinically matched smokers, respectively. Validation of these mutations and pathways will lead to a better understanding of tumorigenesis and tumor progression in never-smokers and identify nodes for therapeutic vulnerability.