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Aberrant integration of Hepatitis B virus DNA promotes major restructuring of human hepatocellular carcinoma genome architecture

Eva G. Álvarez, Jonas Demeulemeester, Clemency Jolly, Daniel García-Souto, Paula Otero, Ana Pequeño, Jorge Zamora, Marta Tojo, Javier Temes, Adrian Baez-Ortega, Bernardo Rodríguez-Martín, Yilong Li, Ana Oitaben, Alicia L. Bruzos, Mónica Martínez-Fernández, Kerstin Haase, Martin Santamarina, Sonia Zumalave, Rosanna Abal, Jorge Rodríguez-Castro, Aitor Rodriguez-Casanova, Angel Diaz-Lagares, Keiran Raine, Adam P. Butler, Atsuhi Ono, Hiroshi Aikata, Kazuaki Chayama, Masaki Ueno, Shinya Hayami, Hiroki Yamaue, Miguel G. Blanco, Xavier Forns, Carmen Rivas, Sofía Pérez-del-Pulgar, Raúl Torres-Ruiz, Sandra Rodríguez Perales, Urtzi Garaigorta, Hidewaki Nakagawa, Peter J. Campbell, Peter Van Loo, Jose M. C. Tubio
doi: https://doi.org/10.1101/2021.04.19.440412
Eva G. Álvarez
1Molecular Medicine and Chronic Diseases Research Centre (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela 15706, Spain
2Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela 15706, Spain
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Jonas Demeulemeester
3The Francis Crick Institute, London NW1 1AT, UK
4Department of Human Genetics, University of Leuven, Leuven B-3000, Belgium
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Clemency Jolly
3The Francis Crick Institute, London NW1 1AT, UK
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Daniel García-Souto
1Molecular Medicine and Chronic Diseases Research Centre (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela 15706, Spain
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Paula Otero
1Molecular Medicine and Chronic Diseases Research Centre (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela 15706, Spain
2Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela 15706, Spain
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Ana Pequeño
1Molecular Medicine and Chronic Diseases Research Centre (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela 15706, Spain
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Jorge Zamora
1Molecular Medicine and Chronic Diseases Research Centre (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela 15706, Spain
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Marta Tojo
5The Biomedical Research Centre (CINBIO), Universidade de Vigo, Vigo 36310, Spain
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Javier Temes
1Molecular Medicine and Chronic Diseases Research Centre (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela 15706, Spain
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Adrian Baez-Ortega
6Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
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Bernardo Rodríguez-Martín
1Molecular Medicine and Chronic Diseases Research Centre (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela 15706, Spain
2Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela 15706, Spain
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Yilong Li
7Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
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Ana Oitaben
1Molecular Medicine and Chronic Diseases Research Centre (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela 15706, Spain
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Alicia L. Bruzos
1Molecular Medicine and Chronic Diseases Research Centre (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela 15706, Spain
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Mónica Martínez-Fernández
1Molecular Medicine and Chronic Diseases Research Centre (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela 15706, Spain
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Kerstin Haase
3The Francis Crick Institute, London NW1 1AT, UK
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Martin Santamarina
1Molecular Medicine and Chronic Diseases Research Centre (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela 15706, Spain
2Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela 15706, Spain
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Sonia Zumalave
1Molecular Medicine and Chronic Diseases Research Centre (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela 15706, Spain
2Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela 15706, Spain
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Rosanna Abal
1Molecular Medicine and Chronic Diseases Research Centre (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela 15706, Spain
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Jorge Rodríguez-Castro
1Molecular Medicine and Chronic Diseases Research Centre (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela 15706, Spain
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Aitor Rodriguez-Casanova
8Cancer Epigenomics, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), 15760 Santiago de Compostela, Spain
9Roche-Chus Joint Unit, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), 15760 Santiago de Compostela, Spain
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Angel Diaz-Lagares
8Cancer Epigenomics, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), 15760 Santiago de Compostela, Spain
10Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029 Madrid, Spain
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Keiran Raine
7Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
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Adam P. Butler
7Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
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Atsuhi Ono
11Department of Gastroenterology and Metabolism, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
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Hiroshi Aikata
11Department of Gastroenterology and Metabolism, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
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Kazuaki Chayama
11Department of Gastroenterology and Metabolism, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
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Masaki Ueno
12Department of Surgery, Wakayama Medical University, Wakayama, Japan
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Shinya Hayami
12Department of Surgery, Wakayama Medical University, Wakayama, Japan
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Hiroki Yamaue
12Department of Surgery, Wakayama Medical University, Wakayama, Japan
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Miguel G. Blanco
1Molecular Medicine and Chronic Diseases Research Centre (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela 15706, Spain
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Xavier Forns
13Liver Unit, Hospital Clínic, University of Barcelona, IDIBAPS, CIBERehd, Barcelona, Spain
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Carmen Rivas
1Molecular Medicine and Chronic Diseases Research Centre (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela 15706, Spain
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Sofía Pérez-del-Pulgar
13Liver Unit, Hospital Clínic, University of Barcelona, IDIBAPS, CIBERehd, Barcelona, Spain
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Raúl Torres-Ruiz
14Molecular Cytogenetics and Genome Engineering Group, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain
15Division of Hematopoietic Innovative Therapies, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain
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Sandra Rodríguez Perales
14Molecular Cytogenetics and Genome Engineering Group, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain
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Urtzi Garaigorta
16Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología – Consejo Superior de Investigaciones Científicas (CNB – CSIC), Madrid 28049, Spain
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Hidewaki Nakagawa
17RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
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Peter J. Campbell
7Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
18Department of Haematology, University of Cambridge, Cambridge CB2 2XY, UK
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Peter Van Loo
3The Francis Crick Institute, London NW1 1AT, UK
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Jose M. C. Tubio
1Molecular Medicine and Chronic Diseases Research Centre (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela 15706, Spain
2Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela 15706, Spain
7Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
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  • For correspondence: jmctubio@gmail.com
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Abstract

Most cancers are characterized by the somatic acquisition of genomic rearrangements during tumour evolution that eventually drive the oncogenesis. There are different mutational mechanisms causing structural variation, some of which are specific to particular cancer types. Here, using multiplatform sequencing technologies, we identify and characterize a remarkable mutational mechanism in human hepatocellular carcinoma caused by Hepatitis B virus, by which DNA molecules from the virus are inserted into the tumour genome causing dramatic changes in its configuration, including non-homologous chromosomal fusions and megabase-size telomeric deletions. This aberrant mutational process, present in at least 8% of all HCC tumours, is active early during liver cancer evolution and can provide the driver rearrangements that a cancer clone requires to survive and grow.

Competing Interest Statement

The authors have declared no competing interest.

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Aberrant integration of Hepatitis B virus DNA promotes major restructuring of human hepatocellular carcinoma genome architecture
Eva G. Álvarez, Jonas Demeulemeester, Clemency Jolly, Daniel García-Souto, Paula Otero, Ana Pequeño, Jorge Zamora, Marta Tojo, Javier Temes, Adrian Baez-Ortega, Bernardo Rodríguez-Martín, Yilong Li, Ana Oitaben, Alicia L. Bruzos, Mónica Martínez-Fernández, Kerstin Haase, Martin Santamarina, Sonia Zumalave, Rosanna Abal, Jorge Rodríguez-Castro, Aitor Rodriguez-Casanova, Angel Diaz-Lagares, Keiran Raine, Adam P. Butler, Atsuhi Ono, Hiroshi Aikata, Kazuaki Chayama, Masaki Ueno, Shinya Hayami, Hiroki Yamaue, Miguel G. Blanco, Xavier Forns, Carmen Rivas, Sofía Pérez-del-Pulgar, Raúl Torres-Ruiz, Sandra Rodríguez Perales, Urtzi Garaigorta, Hidewaki Nakagawa, Peter J. Campbell, Peter Van Loo, Jose M. C. Tubio
bioRxiv 2021.04.19.440412; doi: https://doi.org/10.1101/2021.04.19.440412
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Aberrant integration of Hepatitis B virus DNA promotes major restructuring of human hepatocellular carcinoma genome architecture
Eva G. Álvarez, Jonas Demeulemeester, Clemency Jolly, Daniel García-Souto, Paula Otero, Ana Pequeño, Jorge Zamora, Marta Tojo, Javier Temes, Adrian Baez-Ortega, Bernardo Rodríguez-Martín, Yilong Li, Ana Oitaben, Alicia L. Bruzos, Mónica Martínez-Fernández, Kerstin Haase, Martin Santamarina, Sonia Zumalave, Rosanna Abal, Jorge Rodríguez-Castro, Aitor Rodriguez-Casanova, Angel Diaz-Lagares, Keiran Raine, Adam P. Butler, Atsuhi Ono, Hiroshi Aikata, Kazuaki Chayama, Masaki Ueno, Shinya Hayami, Hiroki Yamaue, Miguel G. Blanco, Xavier Forns, Carmen Rivas, Sofía Pérez-del-Pulgar, Raúl Torres-Ruiz, Sandra Rodríguez Perales, Urtzi Garaigorta, Hidewaki Nakagawa, Peter J. Campbell, Peter Van Loo, Jose M. C. Tubio
bioRxiv 2021.04.19.440412; doi: https://doi.org/10.1101/2021.04.19.440412

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