Mutational landscape of EGFR-, MYC-, and Kras-driven genetically engineered mouse models of lung adenocarcinoma

Genetically engineered mouse models (GEMMs) of cancer are increasingly being used to assess putative driver mutations identified by large-scale sequencing of human cancer genomes. To accurately interpret experiments that introduce additional mutations, an understanding of the somatic genetic profile and evolution of GEMM tumors is necessary. Here, we performed whole-exome sequencing of tumors from three GEMMs of lung adenocarcinoma driven by mutant epidermal growth factor receptor (EGFR), mutant Kirsten rat sarcoma viral oncogene homolog (Kras), or overexpression of MYC proto-oncogene. Tumors from EGFR- and Kras-driven models exhibited, respectively, 0.02 and 0.07 nonsynonymous mutations per megabase, a dramatically lower average mutational frequency than observed in human lung adenocarcinomas. Tumors from models driven by strong cancer drivers (mutant EGFR and Kras) harbored few mutations in known cancer genes, whereas tumors driven by MYC, a weaker initiating oncogene in the murine lung, acquired recurrent clonal oncogenic Kras mutations. In addition, although EGFR- and Kras-driven models both exhibited recurrent whole-chromosome DNA copy number alterations, the specific chromosomes altered by gain or loss were different in each model. These data demonstrate that GEMM tumors exhibit relatively simple somatic genotypes compared with human cancers of a similar type, making these autochthonous model systems useful for additive engineering approaches to assess the potential of novel mutations on tumorigenesis, cancer progression, and drug sensitivity

The genomic basis of adaptive evolution in threespine sticklebacks

Marine stickleback fish have colonized and adapted to thousands of streams and lakes formed since the last ice age, providing an exceptional opportunity to characterize genomic mechanisms underlying repeated ecological adaptation in nature. Here we develop a high-quality reference genome assembly for threespine sticklebacks. By sequencing the genomes of twenty additional individuals from a global set of marine and freshwater populations, we identify a genome-wide set of loci that are consistently associated with marine–freshwater divergence. Our results indicate that reuse of globally shared standing genetic variation, including chromosomal inversions, has an important role in repeated evolution of distinct marine and freshwater sticklebacks, and in the maintenance of divergent ecotypes during early stages of reproductive isolation. Both coding and regulatory changes occur in the set of loci underlying marine–freshwater evolution, but regulatory changes appear to predominate in this well known example of repeated adaptive evolution in nature.National Human Genome Research Institute (U.S.)National Human Genome Research Institute (U.S.) (NHGRI CEGS Grant P50-HG002568

Next-Generation Sequencing Suggests Complex, Heterogeneous Pathogenesis In Peripheral T-Cell Lymphoma Unspecified

Abstract Peripheral T-cell lymphoma (PTCL) makes up about 12 percent of non-Hodgkin lymphoma, comprising 18 diseases that are poorly understood and carry a generally worse prognosis than B-lymphomas. PTCL not otherwise specified (PTCL-NOS), a diagnosis of exclusion, is most common, making up 25-30 percent. Gene-expression studies suggest a heterogeneous origin of this diagnosis, with overlap to other PTCL types, but the genetic factors underlying its pathogenesis are undefined. Current therapy for PTCL-NOS is empiric and ultimately ineffective for most patients. Identification of specific therapeutic targets is therefore a high priority. We have sought better understanding of pathogenesis through next-generation sequencing of PTCL-NOS tumor DNA. Whole-exome sequencing revealed candidate genes but low availability of fresh-frozen samples limited our ability to draw conclusions by this method alone. We therefore sequenced the coding regions of 237 candidate genes in a collection formalin-fixed paraffin-embedded samples. We used Nimblegen Sequence Capture for PCR amplification of exons and Illumina hiSeq for raw sequence generation. Results were aligned to hg19 and compared to dbSNP and the 1,000 genomes data to exclude germline variants. Analysis, including comparison to the COSMIC database of cancer-specific mutations, revealed high-confidence mutations affecting more than 60 known cancer-related genes in 25 PTCL-NOS cases. Recurrent mutations pointed to frequent activation of three key signaling pathways: NF-kB (TNFAIP3), WNT/B-Catenin (APC, CHD8, CELSR2), and NOTCH (NOTCH1, FBXW7). Recurrent deregulation of epigenetic processes was indicated by mutations in genes affecting histone acetylation (EP300, CREBBP), histone methylation (MLL2, KDM6A), and DNA methylation (TET2, DNMT3A). In addition, components of core tumor suppressor pathways showed evidence of frequent inactivation (TP53, ATM, RB1, CUL9, PRKDC). In all, 22 of 25 cases had mutations in at least one of these 17 recurrently mutated genes. Multiple additional candidate disease mechanisms also were suggested by lower-confidence mutations but require confirmation studies, which are under way. In sum, analysis of the coding region of PTCL-NOS tumor DNA suggests a complex and heterogeneous pathogenesis, in line with gene-expression profiling. This work provides an opportunity to better sub-classify entities within the diagnosis of PTCL-NOS and identify specific therapeutic targets and their associated biomarkers. Disclosures: Horwitz: Seattle Genetics, Inc.: Consultancy, Research Funding; Millennium: Consultancy, Research Funding

The genomic basis of adaptive evolution in threespine sticklebacks.

Marine stickleback fish have colonized and adapted to thousands of streams and lakes formed since the last ice age, providing an exceptional opportunity to characterize genomic mechanisms underlying repeated ecological adaptation in nature. Here we develop a high-quality reference genome assembly for threespine sticklebacks. By sequencing the genomes of twenty additional individuals from a global set of marine and freshwater populations, we identify a genome-wide set of loci that are consistently associated with marine-freshwater divergence. Our results indicate that reuse of globally shared standing genetic variation, including chromosomal inversions, has an important role in repeated evolution of distinct marine and freshwater sticklebacks, and in the maintenance of divergent ecotypes during early stages of reproductive isolation. Both coding and regulatory changes occur in the set of loci underlying marine-freshwater evolution, but regulatory changes appear to predominate in this well known example of repeated adaptive evolution in nature