Genomic Landscape of Non-Small Cell Lung Cancer in Smokers and Never-Smokers

We report the results of whole-genome and transcriptome sequencing of tumor and adjacent normal tissue samples from 17 patients with non-small cell lung carcinoma (NSCLC). We identified 3,726 point mutations and more than 90 indels in the coding sequence, with an average mutation frequency more than 10-fold higher in smokers than in never-smokers. Novel alterations in genes involved in chromatin modification and DNA repair pathways were identified, along with DACH1, CFTR, RELN, ABCB5, and HGF. Deep digital sequencing revealed diverse clonality patterns in both never-smokers and smokers. All validated EFGR and KRAS mutations were present in the founder clones, suggesting possible roles in cancer initiation. Analysis revealed 14 fusions, including ROS1 and ALK, as well as novel metabolic enzymes. Cell-cycle and JAK-STAT pathways are significantly altered in lung cancer, along with perturbations in 54 genes that are potentially targetable with currently available drugs.

[1]  Laura A. Sullivan,et al.  Global Survey of Phosphotyrosine Signaling Identifies Oncogenic Kinases in Lung Cancer , 2007, Cell.

[2]  H. Aburatani,et al.  Identification of the transforming EML4–ALK fusion gene in non-small-cell lung cancer , 2007, Nature.

[3]  T. Sellers,et al.  Evidence for mendelian inheritance in the pathogenesis of lung cancer. , 1990, Journal of the National Cancer Institute.

[4]  P. A. Futreal,et al.  Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. , 2012, The New England journal of medicine.

[5]  Lior Pachter,et al.  Sequence Analysis , 2020, Definitions.

[6]  S. Lampel,et al.  The druggable genome: an update. , 2005, Drug discovery today.

[7]  Ales Cvekl,et al.  DACH1 Is a Cell Fate Determination Factor That Inhibits Cyclin D1 and Breast Tumor Growth , 2006, Molecular and Cellular Biology.

[8]  Ken Chen,et al.  SomaticSniper: identification of somatic point mutations in whole genome sequencing data , 2012, Bioinform..

[9]  Richard A. Moore,et al.  ARID1A mutations in endometriosis-associated ovarian carcinomas. , 2010, The New England journal of medicine.

[10]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[11]  S. Willsie.  A CFTR Potentiator in Patients with Cystic Fibrosis and the G551D Mutation , 2012 .

[12]  Süleyman Cenk Sahinalp,et al.  deFuse: An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data , 2011, PLoS Comput. Biol..

[13]  Elizabeth M. Smigielski,et al.  dbSNP: the NCBI database of genetic variation , 2001, Nucleic Acids Res..

[14]  Derek Y. Chiang,et al.  Characterizing the cancer genome in lung adenocarcinoma , 2007, Nature.

[15]  Ken Chen,et al.  Recurring mutations found by sequencing an acute myeloid leukemia genome. , 2009, The New England journal of medicine.

[16]  C. Mathers,et al.  Estimates of worldwide burden of cancer in 2008: GLOBOCAN 2008 , 2010, International journal of cancer.

[17]  Ling Lin,et al.  PathScan: a tool for discerning mutational significance in groups of putative cancer genes , 2011, Bioinform..

[18]  Lifeng Tian,et al.  The cell fate determination factor dachshund inhibits androgen receptor signaling and prostate cancer cellular growth. , 2009, Cancer research.

[19]  S. Ishikawa,et al.  Homozygously deleted gene DACH1 regulates tumor-initiating activity of glioma cells , 2011, Proceedings of the National Academy of Sciences.

[20]  Christopher A. Miller,et al.  VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. , 2012, Genome research.

[21]  R. Wilson,et al.  BreakDancer: An algorithm for high resolution mapping of genomic structural variation , 2009, Nature Methods.

[22]  A. Tsao,et al.  ROS1 Rearrangements Define a Unique Molecular Class of Lung Cancers , 2012 .

[23]  A. Hopkins,et al.  The druggable genome , 2002, Nature Reviews Drug Discovery.

[24]  Tom Royce,et al.  A comprehensive catalogue of somatic mutations from a human cancer genome , 2010, Nature.

[25]  Tian-Li Wang,et al.  Frequent Mutations of Chromatin Remodeling Gene ARID1A in Ovarian Clear Cell Carcinoma , 2010, Science.

[26]  Ng Tp.  Silica and lung cancer: a continuing controversy. , 1994 .

[27]  Doron Lipson,et al.  Identification of new ALK and RET gene fusions from colorectal and lung cancer biopsies , 2012, Nature Medicine.

[28]  Yasushi Totoki,et al.  KIF5B-RET fusions in lung adenocarcinoma , 2012, Nature Medicine.

[29]  David T. W. Jones,et al.  Genome Sequencing of Pediatric Medulloblastoma Links Catastrophic DNA Rearrangements with TP53 Mutations , 2012, Cell.

[30]  Brian H. Dunford-Shore,et al.  Somatic mutations affect key pathways in lung adenocarcinoma , 2008, Nature.

[31]  Joshua F. McMichael,et al.  Clonal evolution in relapsed acute myeloid leukemia revealed by whole genome sequencing , 2011, Nature.

[32]  A. Sparks,et al.  The mutation spectrum revealed by paired genome sequences from a lung cancer patient , 2010, Nature.

[33]  G. Simon,et al.  Molecular targeted agents and biologic therapies for lung cancer. , 2011, Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer.

[34]  E. Birney,et al.  A small cell lung cancer genome reports complex tobacco exposure signatures , 2009, Nature.

[35]  Kiran C. Bobba,et al.  The genetic basis of early T-cell precursor acute lymphoblastic leukaemia , 2012, Nature.

[36]  Steven J. M. Jones,et al.  Comprehensive genomic characterization of squamous cell lung cancers , 2012, Nature.

[37]  N. Carter,et al.  Massive Genomic Rearrangement Acquired in a Single Catastrophic Event during Cancer Development , 2011, Cell.

[38]  Lior Pachter,et al.  Identification of novel transcripts in annotated genomes using RNA-Seq , 2011, Bioinform..

[39]  Jian Yu,et al.  Survey of Tyrosine Kinase Signaling Reveals ROS Kinase Fusions in Human Cholangiocarcinoma , 2011, PloS one.

[40]  Matthew B. Callaway,et al.  MuSiC: Identifying mutational significance in cancer genomes , 2012, Genome research.

[41]  Hiroyuki Ogata,et al.  KEGG: Kyoto Encyclopedia of Genes and Genomes , 1999, Nucleic Acids Res..

[42]  Christopher A. Maher,et al.  ChimeraScan: a tool for identifying chimeric transcription in sequencing data , 2011, Bioinform..

[43]  Yuki Togashi,et al.  RET, ROS1 and ALK fusions in lung cancer , 2012, Nature Medicine.

[44]  E Helene Sage,et al.  Enhanced expression of SPARC/osteonectin in the tumor-associated stroma of non-small cell lung cancer is correlated with markers of hypoxia/acidity and with poor prognosis of patients. , 2003, Cancer research.

[45]  Mario Cazzola,et al.  A gain-of-function mutation of JAK2 in myeloproliferative disorders. , 2005, The New England journal of medicine.

[46]  Amy E. Hawkins,et al.  DNA sequencing of a cytogenetically normal acute myeloid leukemia genome , 2008, Nature.

[47]  Michael A Choti,et al.  Inactivating mutations of the chromatin remodeling gene ARID2 in hepatocellular carcinoma , 2011, Nature Genetics.

[48]  Silica and lung cancer: a continuing controversy. , 1994, Annals of the Academy of Medicine, Singapore.

[49]  M. DePristo,et al.  A framework for variation discovery and genotyping using next-generation DNA sequencing data , 2011, Nature Genetics.

[50]  Steven J. M. Jones,et al.  BreakFusion: targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data , 2012, Bioinform..

[51]  M. DePristo,et al.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.

[52]  Patricia L. Harris,et al.  Activating mutations in the epidermal growth factor receptor underlying responsiveness of non-small-cell lung cancer to gefitinib. , 2004, The New England journal of medicine.

[53]  David R. Kelley,et al.  Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks , 2012, Nature Protocols.

[54]  Helga Thorvaldsdóttir,et al.  Integrative Genomics Viewer , 2011, Nature Biotechnology.

[55]  Sébastien Couraud,et al.  Lung cancer in never smokers--a review. , 2012, European journal of cancer.

[56]  Steven J. M. Jones,et al.  Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors , 2010, Genome Biology.

[57]  R. Schreiber,et al.  Disruption of the Jak1 Gene Demonstrates Obligatory and Nonredundant Roles of the Jaks in Cytokine-Induced Biologic Responses , 1998, Cell.

[58]  G. Swanson,et al.  Lung cancer risk in families of nonsmoking probands: Heterogeneity by age at diagnosis , 1999, Genetic epidemiology.

[59]  Susumu Goto,et al.  KEGG for integration and interpretation of large-scale molecular data sets , 2011, Nucleic Acids Res..

[60]  Richard D. Wood,et al.  Human DNA Repair Genes , 2001, Science.

[61]  Jude Kendall,et al.  Oncogenic cooperation and coamplification of developmental transcription factor genes in lung cancer , 2007, Proceedings of the National Academy of Sciences.

[62]  Kai Ye,et al.  Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads , 2009, Bioinform..