SUMMARY Lung adenocarcinoma, the most common subtype of non-small cell lung cancer, is responsible for over 500,000 deaths per year worldwide. Here, we report exome and genome sequences of 183 lung adenocarcinoma tumor/normal DNA pairs. These analyses revealed a mean exonic somatic mutation rate of 12.0 events/megabase and identified the majority of genes previously reported as significantly mutated in lung adenocarcinoma. In addition, we identified statistically recurrent somatic mutations in the splicing factor gene U2AF1 and truncating mutations affecting RBM10 and ARID1A. Analysis of nucleotide context-specific mutation signatures grouped the sample set into distinct clusters that correlated with smoking history and alterations of reported lung adenocarcinoma genes. Whole genome sequence analysis revealed frequent structural re-arrangements, including in-frame exonic alterations within EGFR and SIK2 kinases. The candidate genes identified in this study are attractive targets for biological characterization and therapeutic targeting of lung adenocarcinoma.

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While genomically targeted therapies have improved outcomes for patients with lung adenocarcinoma, little is known about the genomic alterations which drive squamous cell lung cancer. Sanger sequencing of the tyrosine kinome identified mutations in the DDR2 kinase gene in 3.8% of squamous cell lung cancers and cell lines. Squamous lung cancer cell lines harboring DDR2 mutations were selectively killed by knock-down of DDR2 by RNAi or by treatment with the multi-targeted kinase inhibitor dasatinib. Tumors established from a DDR2 mutant cell line were sensitive to dasatinib in xenograft models. Expression of mutated DDR2 led to cellular transformation which was blocked by dasatinib. A squamous cell lung cancer patient with a response to dasatinib and erlotinib treatment harbored a DDR2 kinase domain mutation. These data suggest that gain-of-function mutations in DDR2 are important oncogenic events and are amenable to therapy with dasatinib. As dasatinib is already approved for use, these findings could be rapidly translated into clinical trials.

BackgroundSquamous cell lung carcinomas account for approximately 25% of new lung carcinoma cases and 40,000 deaths per year in the United States. Although there are multiple genomically targeted therapies for lung adenocarcinoma, none has yet been reported in squamous cell lung carcinoma.Methodology/Principal FindingsUsing SNP array analysis, we found that a region of chromosome segment 8p11-12 containing three genes–WHSC1L1, LETM2, and FGFR1–is amplified in 3% of lung adenocarcinomas and 21% of squamous cell lung carcinomas. Furthermore, we demonstrated that a non-small cell lung carcinoma cell line harboring focal amplification of FGFR1 is dependent on FGFR1 activity for cell growth, as treatment of this cell line either with FGFR1-specific shRNAs or with FGFR small molecule enzymatic inhibitors leads to cell growth inhibition.Conclusions/SignificanceThese studies show that FGFR1 amplification is common in squamous cell lung cancer, and that FGFR1 may represent a promising therapeutic target in non-small cell lung cancer.

We assessed somatic alleles of six receptor tyrosine kinase genes mutated in lung adenocarcinoma for oncogenic activity. Five of these genes failed to score in transformation assays; however, novel recurring extracellular domain mutations of the receptor tyrosine kinase gene ERBB2 were potently oncogenic. These ERBB2 extracellular domain mutants were activated by two distinct mechanisms, characterized by elevated C-terminal tail phosphorylation or by covalent dimerization mediated by intermolecular disulfide bond formation. These distinct mechanisms of receptor activation converged upon tyrosine phosphorylation of cellular proteins, impacting cell motility. Survival of Ba/F3 cells transformed to IL-3 independence by the ERBB2 extracellular domain mutants was abrogated by treatment with small-molecule inhibitors of ERBB2, raising the possibility that patients harboring such mutations could benefit from ERBB2-directed therapy.HER2 | breast cancer | bladder cancer L ung cancer is the leading cause of cancer death, accounting for over 150,000 deaths annually in the United States alone (1). Current treatment options are thus inadequate for the majority of patients and additional therapies are needed. Mutationally activated oncogenes that promote tumorigenesis represent potential drug targets due to frequent dependency of tumor cells on such oncogenes (2, 3), and somatically altered receptor tyrosine kinases in particular have been successfully exploited as therapeutic targets in several cancers.The prototypical therapy targeted to a somatically activated tyrosine kinase oncogene is imatinib mesylate, which targets the BCR-ABL fusion protein in chronic myelogenous leukemia (4). Targeted therapies developed for lung cancer include gefitinib and erlotinib, small-molecule inhibitors of mutationally activated EGFR in lung adenocarcinoma (5-8), and crizotinib, a smallmolecule inhibitor of the EML4-ALK translocation product in lung adenocarcinoma (9). Trastuzumab, a monoclonal antibody inhibitor targeting ERBB2, and the small-molecule EGFR/ ERBB2 inhibitor lapatinib are effective in ERBB2-amplified patients with breast cancer (10, 11).The advent of next-generation sequencing technologies has enabled compilation of large somatic mutation datasets from cancer sequencing studies. Statistical methods that examine differences in gene mutation frequency can reveal evidence of positive selection; however, demonstration of the contribution of a mutated gene to tumorigenesis additionally requires functional validation. To identify new lung cancer oncogenes, we systematically assessed somatic alleles of significantly mutated receptor tyrosine kinase genes reported in patients with lung adenocarcinoma (12) for activity in cellular transformation assays.Although most receptor tyrosine kinase mutations tested failed to score, novel extracellular domain mutations of ERBB2 were oncogenic. Our results indicate a unique therapeutic opportunity for patients with lung and breast cancer who harbor extracellular domain mutations of ERBB2. Resul...

Macrophage activation by bacterial lipopolysaccharide (LPS) promotes the secretion of proin¯ammatory cytokines, such as tumor necrosis factor-a (TNF-a) and interleukin-1b (IL-1b), and of secondary mediators, such as leukotrienes and prostaglandins (PGs). Mice lacking the gene encoding the serine/threonine protein kinase Tpl2/Cot produce low levels of TNF-a in response to LPS because of an ERK-dependent post-transcriptional defect, and they are resistant to LPS/D-galactosamine-induced endotoxin shock. In this study we demonstrate that prostaglandin E2 and its regulatory enzyme, COX-2, are also targets of Tpl2-transduced LPS signals in bone marrow-derived mouse macrophages. Thus, LPS-stimulated Tpl2 ±/± macrophages express low levels of COX-2 and PGE2, compared with wild-type Tpl2 +/+ cells. The ability of Tpl2 to regulate COX-2 expression depends on ERK signals that activate p90Rsk and Msk1, which in turn phosphorylate CREB, a key regulator of COX-2 transcription. These data identify physiological targets of Tpl2 signaling downstream of ERK and further implicate Tpl2 in the pathophysiology of in¯ammation.

Macrophages and B-cells from

Kinase domain mutations of the epidermal growth factor receptor (EGFR) are common oncogenic events in lung adenocarcinoma. Here we explore the dependency upon asymmetric dimerization of the kinase domain for activation of lung cancer-derived EGFR mutants. We show that while wild-type EGFR and the L858R mutant require dimerization for activation and oncogenic transformation, the exon 19 deletion, exon 20 insertion, and L858R/T790M EGFR mutants do not require dimerization. In addition, treatment with the monoclonal antibody, cetuximab, shrinks mouse lung tumors induced by the dimerization-dependent L858R mutant, but exerts only a modest effect on tumors driven by dimerization-independent EGFR mutants. These data imply that different EGFR mutants show differential requirements for dimerization, and that disruption of dimerization may be among the antitumor mechanisms of cetuximab.