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      Transmissible Dog Cancer Genome Reveals the Origin and History of an Ancient Cell Lineage

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          Abstract

          Canine transmissible venereal tumor (CTVT) is the oldest known somatic cell lineage. It is a transmissible cancer that propagates naturally in dogs. We sequenced the genomes of two CTVT tumors and found that CTVT has acquired 1.9 million somatic substitution mutations and bears evidence of exposure to ultraviolet light. CTVT is remarkably stable and lacks subclonal heterogeneity despite thousands of rearrangements, copy-number changes, and retrotransposon insertions. More than 10,000 genes carry nonsynonymous variants, and 646 genes have been lost. CTVT first arose in a dog with low genomic heterozygosity that may have lived about 11,000 years ago. The cancer spawned by this individual dispersed across continents about 500 years ago. Our results provide a genetic identikit of an ancient dog and demonstrate the robustness of mammalian somatic cells to survive for millennia despite a massive mutation burden.

          Abstract

          An unusual tumor in dogs arose more than 10,000 years ago, and despite a huge mutational burden, its genome has remained stable. [Also see Perspective by [Related article:]Parker and Ostrander ]

          Breaking Tumor Dogma

          Canine transmissible venereal tumor (CTVT) is an unusual form of cancer because the infectious agent is not a virus or bacterium but the tumor cells themselves, which are passed from one dog to another during coitus. To explore the molecular features of the tumor and its possible origins, Murchison et al. (p. [Related article:]437 ; see the Perspective by [Related article:] Parker and Ostrander ) sequenced the genomes of two CTVTs and their host dogs, one from Australia and one from Brazil. Although CTVT has acquired a massive number of genomic alterations, including hundreds of times more somatic mutations than are normally found in human cancers, the tumor cell genome has remained diploid and stable. Indeed, CTVT may first have arisen in a dog that lived more than 10,000 years ago.

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          Most cited references37

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          Fast and accurate short read alignment with Burrows–Wheeler transform

          Motivation: The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A first generation of hash table-based methods has been developed, including MAQ, which is accurate, feature rich and fast enough to align short reads from a single individual. However, MAQ does not support gapped alignment for single-end reads, which makes it unsuitable for alignment of longer reads where indels may occur frequently. The speed of MAQ is also a concern when the alignment is scaled up to the resequencing of hundreds of individuals. Results: We implemented Burrows-Wheeler Alignment tool (BWA), a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps. BWA supports both base space reads, e.g. from Illumina sequencing machines, and color space reads from AB SOLiD machines. Evaluations on both simulated and real data suggest that BWA is ∼10–20× faster than MAQ, while achieving similar accuracy. In addition, BWA outputs alignment in the new standard SAM (Sequence Alignment/Map) format. Variant calling and other downstream analyses after the alignment can be achieved with the open source SAMtools software package. Availability: http://maq.sourceforge.net Contact: rd@sanger.ac.uk
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            Signatures of mutational processes in human cancer

            All cancers are caused by somatic mutations. However, understanding of the biological processes generating these mutations is limited. The catalogue of somatic mutations from a cancer genome bears the signatures of the mutational processes that have been operative. Here, we analysed 4,938,362 mutations from 7,042 cancers and extracted more than 20 distinct mutational signatures. Some are present in many cancer types, notably a signature attributed to the APOBEC family of cytidine deaminases, whereas others are confined to a single class. Certain signatures are associated with age of the patient at cancer diagnosis, known mutagenic exposures or defects in DNA maintenance, but many are of cryptic origin. In addition to these genome-wide mutational signatures, hypermutation localized to small genomic regions, kataegis, is found in many cancer types. The results reveal the diversity of mutational processes underlying the development of cancer with potential implications for understanding of cancer etiology, prevention and therapy.
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              Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing

              Intratumor heterogeneity may foster tumor evolution and adaptation and hinder personalized-medicine strategies that depend on results from single tumor-biopsy samples. To examine intratumor heterogeneity, we performed exome sequencing, chromosome aberration analysis, and ploidy profiling on multiple spatially separated samples obtained from primary renal carcinomas and associated metastatic sites. We characterized the consequences of intratumor heterogeneity using immunohistochemical analysis, mutation functional analysis, and profiling of messenger RNA expression. Phylogenetic reconstruction revealed branched evolutionary tumor growth, with 63 to 69% of all somatic mutations not detectable across every tumor region. Intratumor heterogeneity was observed for a mutation within an autoinhibitory domain of the mammalian target of rapamycin (mTOR) kinase, correlating with S6 and 4EBP phosphorylation in vivo and constitutive activation of mTOR kinase activity in vitro. Mutational intratumor heterogeneity was seen for multiple tumor-suppressor genes converging on loss of function; SETD2, PTEN, and KDM5C underwent multiple distinct and spatially separated inactivating mutations within a single tumor, suggesting convergent phenotypic evolution. Gene-expression signatures of good and poor prognosis were detected in different regions of the same tumor. Allelic composition and ploidy profiling analysis revealed extensive intratumor heterogeneity, with 26 of 30 tumor samples from four tumors harboring divergent allelic-imbalance profiles and with ploidy heterogeneity in two of four tumors. Intratumor heterogeneity can lead to underestimation of the tumor genomics landscape portrayed from single tumor-biopsy samples and may present major challenges to personalized-medicine and biomarker development. Intratumor heterogeneity, associated with heterogeneous protein function, may foster tumor adaptation and therapeutic failure through Darwinian selection. (Funded by the Medical Research Council and others.).
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                Author and article information

                Journal
                Science
                Science
                American Association for the Advancement of Science (AAAS)
                0036-8075
                1095-9203
                January 24 2014
                January 24 2014
                : 343
                : 6169
                : 437-440
                Affiliations
                [1 ]Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK.
                [2 ]Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK.
                [3 ]Animal Management in Rural and Remote Indigenous Communities (AMRRIC), Post Office Box 1464, Nightcliff, NT 0814, Australia.
                [4 ]Department of Clinical and Veterinary Surgery, São Paulo State University (UNESP), Via de Acesso Prof. Paulo Donato Castellane, s/n. CEP: 14884-900, Jaboticabal, São Paulo, Brazil.
                [5 ]Department of Veterinary Sciences, University of Messina, 98168 Messina, Italy.
                [6 ]Wohl Virion Centre and Medical Research Council Centre for Medical and Molecular Virology, Division of Infection and Immunity, University College London, Gower Street, London WC1E 6BT, UK.
                [7 ]Department of Life Sciences, Imperial College London, Silwood Park, Ascot, Berks. SL5 7PY, UK.
                Article
                10.1126/science.1247167
                3918581
                24458646
                21979df6-15d8-4930-aeeb-de7ddf136178
                © 2014
                History

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