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      Processed pseudogenes acquired somatically during cancer development

      research-article
      1 , 1 , 1 , 2 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 ,   1 , 3 , 1 , 1 , 1 , 3 , 1 , 1 , 2 , 1 , 1 , 1 , 1 , 1 , 4 , 5 , 6 , 7 , 8 , 9 , 2 , 10 , 11 , 1 , 12 , 13 , 11 , 14 , 15 , 16 , 2 , 1 , 1 , 1 , 5 , a , 1 , 3 , 5 , ICGC Breast Cancer Group
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          Abstract

          Cancer evolves by mutation, with somatic reactivation of retrotransposons being one such mutational process. Germline retrotransposition can cause processed pseudogenes, but whether this occurs somatically has not been evaluated. Here we screen sequencing data from 660 cancer samples for somatically acquired pseudogenes. We find 42 events in 17 samples, especially non-small cell lung cancer (5/27) and colorectal cancer (2/11). Genomic features mirror those of germline LINE element retrotranspositions, with frequent target-site duplications (67%), consensus TTTTAA sites at insertion points, inverted rearrangements (21%), 5′ truncation (74%) and polyA tails (88%). Transcriptional consequences include expression of pseudogenes from UTRs or introns of target genes. In addition, a somatic pseudogene that integrated into the promoter and first exon of the tumour suppressor gene, MGA, abrogated expression from that allele. Thus, formation of processed pseudogenes represents a new class of mutation occurring during cancer development, with potentially diverse functional consequences depending on genomic context.

          Abstract

          Germline pseudogenes have an important role in human evolution. Here, the authors analyse sequencing data from 660 cancer samples and find evidence for the formation of somatically acquired pseudogenes, a new class of mutation, which may contribute to cancer development.

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          Most cited references42

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          Fast and accurate long-read alignment with Burrows–Wheeler transform

          Motivation: Many programs for aligning short sequencing reads to a reference genome have been developed in the last 2 years. Most of them are very efficient for short reads but inefficient or not applicable for reads >200 bp because the algorithms are heavily and specifically tuned for short queries with low sequencing error rate. However, some sequencing platforms already produce longer reads and others are expected to become available soon. For longer reads, hashing-based software such as BLAT and SSAHA2 remain the only choices. Nonetheless, these methods are substantially slower than short-read aligners in terms of aligned bases per unit time. Results: We designed and implemented a new algorithm, Burrows-Wheeler Aligner's Smith-Waterman Alignment (BWA-SW), to align long sequences up to 1 Mb against a large sequence database (e.g. the human genome) with a few gigabytes of memory. The algorithm is as accurate as SSAHA2, more accurate than BLAT, and is several to tens of times faster than both. Availability: http://bio-bwa.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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              A coding-independent function of gene and pseudogene mRNAs regulates tumour biology

              The canonical role of messenger RNA (mRNA) is to deliver protein-coding information to sites of protein synthesis. However, given that microRNAs bind to RNAs, we hypothesized that RNAs possess a biological role in cancer cells that relies upon their ability to compete for microRNA binding and is independent of their protein-coding function. As a paradigm for the protein-coding-independent role of RNAs, we describe the functional relationship between the mRNAs produced by the PTEN tumour suppressor gene and its pseudogene (PTENP1) and the critical consequences of this interaction. We find that PTENP1 is biologically active as determined by its ability to regulate cellular levels of PTEN, and that it can exert a growth-suppressive role. We also show that PTENP1 locus is selectively lost in human cancer. We extend our analysis to other cancer-related genes that possess pseudogenes, such as oncogenic KRAS. Further, we demonstrate that the transcripts of protein coding genes such as PTEN are also biologically active. Together, these findings attribute a novel biological role to expressed pseudogenes, as they can regulate coding gene expression, and reveal a non-coding function for mRNAs.
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                Author and article information

                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Pub. Group
                2041-1723
                09 April 2014
                : 5
                : 3644
                Affiliations
                [1 ]Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton , Cambridgeshire CB10 1SA, UK
                [2 ]Lungs for Living Research Centre, Rayne Institute, University College London , London WC1E 6JF, UK
                [3 ]University of Cambridge , Cambridge CB2 0XY, UK
                [4 ]Departments of Pathology and Oncology, Johns Hopkins Medical Institutions , Baltimore, Maryland 21205, USA
                [5 ]Addenbrooke’s NHS Foundation Trust , Cambridge CB2 0QQ, UK
                [6 ]Children’s Brain Tumour Research Centre, University of Nottingham , Nottingham NG7 2UH, UK
                [7 ]Department of Pediatrics, Hospital for Sick Children, University of Toronto , Toronto, Ontario, Canada M5G 1X8
                [8 ]Institute for Cancer Research, Sutton , London SM2 5NG, UK
                [9 ]Dana-Farber Cancer Institute , Boston, Massachusetts 02215, USA
                [10 ]Royal National Orthopaedic Hospital , Middlesex HA7 4LP, UK
                [11 ]Peter MacCallum Cancer Centre , Melbourne, Victoria 3002, Australia
                [12 ]Department of Pathology, Jules Bordet Institute, 1000 Brussels, Belgium
                [13 ]Department of Pathology, Memorial-Sloan-Kettering Cancer Center , New York, New York 10065, USA
                [14 ]Department of Gastroenterology, Royal Melbourne Hospital, University of Melbourne , Parkville, Victoria 3050, Australia
                [15 ]National Institute of Environmental Health Sciences, Research Triangle Park , North Carolina 27713, USA
                [16 ]UNC Lineberger Comprehensive Cancer Center, University of North Carolina , Chapel Hill, North Carolina 27599, USA
                [17 ]Cambridge Breast Unit, Addenbrooke’s Hospital, Cambridge University Hospital NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre , Cambridge CB2 0QQ, UK
                [18 ]Department of Pathology, Academic Medical Center , Meibergdreef 9, 1105 Amsterdam, AZ, The Netherlands
                [19 ]Department of Cancer Biology, Dana-Farber Cancer Institute , 450 Brookline Avenue, Boston, Massachusetts 02215, USA
                [20 ]Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School , 75 Francis Street, Boston, Massachusetts 02115, USA
                [21 ]East of Scotland Breast Service, Ninewells Hospital , Dundee DD1 9SY, UK
                [22 ]Department of Research Oncology, Guy’s Hospital, King’s Health Partners AHSC, King’s College London School of Medicine , London SE1 9RT, UK
                [23 ]Institut Bergonié , 229 cours de l’Argone, 33076 Bordeaux, France
                [24 ]Institut Curie, Department of Tumor Biology , 26 rue d’Ulm, 75248 Paris cédex 05, France
                [25 ]Institut Curie, INSERM Unit 830 , 26 rue d’Ulm, 75248 Paris cédex 05, France
                [26 ]Department of Pathology, Jules Bordet Institute , 1000 Brussels, Belgium
                [27 ]Department of Pathology, Skåne University Hospital, Lund University , SE-221 85 Lund, Sweden
                [28 ]Department of Pathology, Oslo University Hospital Ulleval and University of Oslo, Faculty of Medicine and Institute of Clinical Medicine , 0450 Oslo, Norway
                [29 ]Lund University, Division of Oncology, Department of Clinical Sciences, Lund University Cancer Center at Medicon Village , Lund SE-223 81, Sweden
                [30 ]Blekinge Hospital, Department of Pathology and Cytology , SE-371 85 Karlskrona, Sweden
                [31 ]Translational Cancer Research Unit , GZA Hospitals St Augustinus, 2610 Antwerp, Belgium
                [32 ]Department of Pathology, Erasmus Medical Center , 3015 Rotterdam, The Netherlands
                [33 ]The University of Queensland, School of Medicine, Herston, Brisbane, Queensland 4006, Australia
                [34 ]Pathology Queensland: The Royal Brisbane & Women’s Hospital , Brisbane, Queensland 4029, Australia
                [35 ]The University of Queensland, UQ Centre for Clinical Research, Herston , Brisbane, Queensland 4029, Australia
                [36 ]Department of Pathology, Memorial Sloan-Kettering Cancer Center , New York, New York 10065, USA
                [37 ]Centre Georges-François Leclerc , 1 rue du Professeur Marion, 21079 Dijon, France
                [38 ]0nstitut Paoli Calmettes, Department of Biopathology , 232 Boulevard Sainte Marguerite, 13009 Marseille, France
                [39 ]Centre Léon Bérard, Lyon, France; Université Claude Bernard Lyon1—Université de Lyon, 69008 Lyon, France
                [40 ]Department of Oncology, University of Cambridge and Cancer Research UK Cambridge Research Institute, Li Ka Shin Centre , Cambridge CB2 0RE, UK
                [41 ]Dundee Cancer Centre, Ninewells Hospital , Dundee DD1 9SY, UK
                [42 ]Erasmus MC Cancer Institute, Erasmus University Medical Center , 3015 Rotterdam, The Netherlands
                [43 ]Radboud University, Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences , 6500 HB Nijmegen, The Netherlands
                [44 ]Department of Radiation Oncology, Radboud University Medical Centre , 6500 Nijmegen, The Netherlands
                [45 ]Department of Laboratory Medicine, Radboud University Medical Centre , 6500 Nijmegen, The Netherlands
                [46 ]Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Université Libre de Bruxelles , 1000 Brussels, Belgium
                [47 ]Universite Lyon1, INCa-Synergie, Centre Leon Berard , 28 rue Laennec, 69008 Lyon, France
                [48 ]Department Experimental Therapy, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
                [49 ]Department of Genetics, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital , O310 Oslo, Norway
                [50 ]Department of Molecular Oncology, BC Cancer Agency , 675 W10th Avenue, Vancouver, British Columbia, Canada V5Z 1L3
                [51 ]The Netherlands Cancer Institute, Division of Molecular Carcinogenesis , 1066 Amsterdam, The Netherlands
                [52 ]Department of Surgery, University of California, San Francisco , San Francisco, California 94143, USA
                [53 ]Cancer Research Laboratory, Faculty of Medicine, University of Iceland , 101 Reykjavik, Iceland
                [54 ]Department of Pathology, University Hospital , 101 Reykjavik, Iceland
                [55 ]Icelandic Cancer Registry, Icelandic Cancer Society , Skogarhlid 8, P.O. Box 5420, 125 Reykjavik, Iceland
                [56 ]Institute for Clinical Medicine, Faculty of Medicine, University of Oslo , 0450 Oslo, Norway
                [57 ]National Genotyping Center, Institute of Biomedical Sciences, Academia Sinica , 128 Academia Road, Sec 2, Nankang, Taipei 115, Taiwan, China
                [58 ]NCCS-VARI Translational Research Laboratory, National Cancer Centre Singapore , 11 Hospital Drive, 169610 Singapore, Singapore
                [59 ]Department of General Surgery, Singapore General Hospital , 169608 Singapore, Singapore
                Author notes
                [*]

                A full list of Participants in ICGC Breast Cancer Group who supplied or verified samples for this project and their affiliations appears at the end of the paper.

                Article
                ncomms4644
                10.1038/ncomms4644
                3996531
                24714652
                79653772-bde1-435f-a66b-043826cf3bdc
                Copyright © 2014, Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.

                This work is licensed under a Creative Commons Attribution 3.0 Unported License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/3.0/

                History
                : 06 February 2014
                : 13 March 2014
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