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4 results on '"Demeulemeester, Jonas [0000-0002-2660-2478]"'

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

Author

Hidewaki Nakagawa, Hiroshi Aikata, Mónica Martínez-Fernández, Atsushi Ono, Marta Tojo, Peter J. Campbell, Adrian Baez-Ortega, Kerstin Haase, Jonas Demeulemeester, Adam Butler, Xavier Forns, Rosanna Abal, Keiran Raine, Javier Temes, Urtzi Garaigorta, Daniel García-Souto, Carmen Rivas, Aitor Rodriguez-Casanova, Eva G. Alvarez, Sonia Zumalave, Jorge Zamora, Hiroki Yamaue, Clemency Jolly, Yang Li, Peter Van Loo, Jose M. C. Tubio, Kazuaki Chayama, Iago Otero, Sofía Pérez-del-Pulgar, Masaki Ueno, Miguel Blanco, Shinya Hayami, Sandra Rodriguez-Perales, Kazuhiro Maejima, Jorge Rodríguez-Castro, Angel Diaz-Lagares, Raúl Torres-Ruiz, Ana Pequeño-Valtierra, Juan Ruiz-Bañobre, Ana Oitaben, Bernardo Rodriguez-Martin, Paula Otero, Alicia L. Bruzos, Álvarez, Eva G [0000-0002-3522-5088], Demeulemeester, Jonas [0000-0002-2660-2478], Otero, Paula [0000-0001-5614-1468], García-Souto, Daniel [0000-0002-0997-8799], Temes, Javier [0000-0003-3370-4728], Rodriguez-Martin, Bernardo [0000-0003-4693-3140], Oitaben, Ana [0000-0002-4877-6145], Bruzos, Alicia L [0000-0003-4362-545X], Haase, Kerstin [0000-0002-0944-5618], Zumalave, Sonia [0000-0002-2108-1861], Rodríguez-Castro, Jorge [0000-0003-2912-9601], Rodriguez-Casanova, Aitor [0000-0002-9828-3613], Raine, Keiran M [0000-0002-5634-1539], Otero, Iago [0000-0002-7924-693X], Blanco, Miguel G [0000-0002-2883-7326], Ruiz-Bañobre, Juan [0000-0003-0755-4295], Pérez-Del-Pulgar, Sofía [0000-0002-9890-300X], Torres-Ruiz, Raúl [0000-0001-9606-0398], Rodriguez-Perales, Sandra [0000-0001-7221-3636], Garaigorta, Urtzi [0000-0002-0683-5725], Campbell, Peter J [0000-0002-3921-0510], Van Loo, Peter [0000-0003-0292-1949], Tubio, Jose MC [0000-0003-3540-2459], and Apollo - University of Cambridge Repository

Subjects
LIVER, Hepatocellular carcinoma, General Physics and Astronomy, medicine.disease_cause, Genome, 631/67/1858, Ecology,Evolution & Ethology, Cancer genomics, Tumour virus infections, 631/208/69, Human Biology & Physiology, Multidisciplinary, Liver Neoplasms, ASSOCIATION, READ ALIGNMENT, TRANSLOCATION, Multidisciplinary Sciences, Gene Expression Regulation, Neoplastic, Science & Technology - Other Topics, Liver cancer, Genetics & Genomics, Hepatitis B virus, Carcinoma, Hepatocellular, Science, Virus Integration, 631/67/1504/1610/4029, 45/23, Biology, General Biochemistry, Genetics and Molecular Biology, Virus, Article, 14/32, CHROMOSOMES, medicine, Humans, Gene, Computational & Systems Biology, Science & Technology, Whole Genome Sequencing, MUTATIONS, Genome, Human, Cancer, General Chemistry, Tumour Biology, medicine.disease, digestive system diseases, DNA, Viral, Cancer research, Carcinogenesis
Abstract

Most cancers are characterized by the somatic acquisition of genomic rearrangements during tumour evolution that eventually drive the oncogenesis. 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, dicentric chromosomes and megabase-size telomeric deletions. This aberrant mutational mechanism, present in at least 8% of all HCC tumours, can provide the driver rearrangements that a cancer clone requires to survive and grow, including loss of relevant tumour suppressor genes. Most of these events are clonal and occur early during liver cancer evolution. Real-time timing estimation reveals some HBV-mediated rearrangements occur as early as two decades before cancer diagnosis. Overall, these data underscore the importance of characterising liver cancer genomes for patterns of HBV integration., Hepatitis B virus (HBV) infection and DNA integration is a frequent cause of hepatocellular carcinoma (HCC), but the consequences of this process are not fully understood. Here the authors use whole-genome and long-read sequencing data from HCC patient samples to study the timing and alterations induced by HBV insertions.

Published
2021

2. Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition

Author

Rodriguez-Martin, Bernardo, Alvarez, Eva G, Baez-Ortega, Adrian, Zamora, Jorge, Supek, Fran, Demeulemeester, Jonas, Santamarina, Martin, Ju, Young Seok, Temes, Javier, Garcia-Souto, Daniel, Detering, Harald, Li, Yilong, Rodriguez-Castro, Jorge, Dueso-Barroso, Ana, Bruzos, Alicia L, Dentro, Stefan C, Blanco, Miguel G, Contino, Gianmarco, Ardeljan, Daniel, Tojo, Marta, Roberts, Nicola D, Zumalave, Sonia, Edwards, Paul A, Weischenfeldt, Joachim, Puiggròs, Montserrat, Chong, Zechen, Chen, Ken, Lee, Eunjung Alice, Wala, Jeremiah A, Raine, Keiran M, Butler, Adam, Waszak, Sebastian M, Navarro, Fabio CP, Schumacher, Steven E, Monlong, Jean, Maura, Francesco, Bolli, Niccolo, Bourque, Guillaume, Gerstein, Mark, Park, Peter J, Wedge, David C, Beroukhim, Rameen, Torrents, David, Korbel, Jan O, Martincorena, Iñigo, Fitzgerald, Rebecca C, Van Loo, Peter, Kazazian, Haig H, Burns, Kathleen H, PCAWG Structural Variation Working Group, Campbell, Peter J, Tubio, Jose MC, PCAWG Consortium, Rodriguez-Martin, Bernardo [0000-0003-4693-3140], Supek, Fran [0000-0002-7811-6711], Demeulemeester, Jonas [0000-0002-2660-2478], Ju, Young Seok [0000-0002-5514-4189], Temes, Javier [0000-0003-3370-4728], Garcia-Souto, Daniel [0000-0002-0997-8799], Blanco, Miguel G [0000-0002-2883-7326], Ardeljan, Daniel [0000-0002-5593-421X], Roberts, Nicola D [0000-0002-0469-1043], Zumalave, Sonia [0000-0002-2108-1861], Edwards, Paul A [0000-0002-4789-3374], Weischenfeldt, Joachim [0000-0002-3917-5524], Chen, Ken [0000-0003-4013-5279], Wala, Jeremiah A [0000-0001-6591-1620], Raine, Keiran M [0000-0002-5634-1539], Waszak, Sebastian M [0000-0003-3042-9521], Navarro, Fabio CP [0000-0002-5640-9070], Monlong, Jean [0000-0002-9737-5516], Bourque, Guillaume [0000-0002-3933-9656], Park, Peter J [0000-0001-9378-960X], Korbel, Jan O [0000-0002-2798-3794], Fitzgerald, Rebecca C [0000-0002-3434-3568], Van Loo, Peter [0000-0003-0292-1949], Burns, Kathleen H [0000-0003-1620-3761], Campbell, Peter J [0000-0002-3921-0510], Tubio, Jose MC [0000-0003-3540-2459], and Apollo - University of Cambridge Repository

Subjects
Gene Rearrangement, Genome, Retroelements, Genome, Human, Carcinogenesis, Human Genome, PCAWG Consortium, Biological Sciences, Medical and Health Sciences, Rare Diseases, Long Interspersed Nucleotide Elements, Neoplasms, PCAWG Structural Variation Working Group, Genetics, Humans, Digestive Diseases, Cancer, Human, Developmental Biology
Abstract

About half of all cancers have somatic integrations of retrotransposons. Here, to characterize their role in oncogenesis, we analyzed the patterns and mechanisms of somatic retrotransposition in 2,954 cancer genomes from 38 histological cancer subtypes within the framework of the Pan-Cancer Analysis of Whole Genomes (PCAWG) project. We identified 19,166 somatically acquired retrotransposition events, which affected 35% of samples and spanned a range of event types. Long interspersed nuclear element (LINE-1; L1 hereafter) insertions emerged as the first most frequent type of somatic structural variation in esophageal adenocarcinoma, and the second most frequent in head-and-neck and colorectal cancers. Aberrant L1 integrations can delete megabase-scale regions of a chromosome, which sometimes leads to the removal of tumor-suppressor genes, and can induce complex translocations and large-scale duplications. Somatic retrotranspositions can also initiate breakage-fusion-bridge cycles, leading to high-level amplification of oncogenes. These observations illuminate a relevant role of L1 retrotransposition in remodeling the cancer genome, with potential implications for the development of human tumors.

Published
2020

3. Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition

Author

Alvarez, Eva G., Baez-Ortega, Adrian, Zamora, Jorge, Supek, Fran, Demeulemeester, Jonas, Santamarina, Martin, Temes, Javier, Garcia-Souto, Daniel, Detering, Harald, Li, Yilong, Rodriguez-Castro, Jorge, Dueso-Barroso, Ana, Bruzos, Alicia L., Dentro, Stefan C., Blanco, Miguel G., Contino, Gianmarco, Ardeljan, Daniel, Tojo, Marta, Zumalave, Sonia, Edwards, Paul A. W., Puiggròs, Montserrat, Chong, Zechen, Lee, Eunjung Alice, Raine, Keiran, Butler, Adam, Waszak, Sebastian M., Schumacher, Steven E., Monlong, Jean, Maura, Francesco, Bolli, Niccolo, Bourque, Guillaume, Gerstein, Mark, Wedge, David C., Beroukhim, Rameen, Torrents, David, Martincorena, Inigo, Fitzgerald, Rebecca C., Van Loo, Peter, Kazazian, Haig H., Tubio, Jose M. C., Akdemir, Kadir C., Boutros, Paul C., Bowtell, David D. L., Brors, Benedikt, Burns, Kathleen H., Campbell, Peter J., Chan, Kin, Chen, Ken, Cortés-Ciriano, Isidro, Dunford, Andrew J., Edwards, Paul A., Estivill, Xavier, Etemadmoghadam, Dariush, Feuerbach, Lars, Fink, J. Lynn, Frenkel-Morgenstern, Milana, Garsed, Dale W., Gordenin, Dmitry A., Haan, David, Haber, James E., Hess, Julian M., Hutter, Barbara, Imielinski, Marcin, Jones, David T. W., Ju, Young Seok, Kazanov, Marat D., Klimczak, Leszek J., Koh, Youngil, Korbel, Jan O., Kumar, Kiran, Lee, Jake June-Koo, Lynch, Andy G., Macintyre, Geoff, Markowetz, Florian, Martincorena, Iñigo, Martinez-Fundichely, Alexander, Meyerson, Matthew, Miyano, Satoru, Nakagawa, Hidewaki, Navarro, Fabio C. P., Ossowski, Stephan, Park, Peter J., Pearson, John V., Rippe, Karsten, Roberts, Nicola D., Roberts, Steven A., Rodriguez-Martin, Bernardo, Scully, Ralph, Shackleton, Mark, Sidiropoulos, Nikos, Sieverling, Lina, Stewart, Chip, Villasante, Izar, Waddell, Nicola, Wala, Jeremiah A., Weischenfeldt, Joachim, Yang, Lixing, Yao, Xiaotong, Yoon, Sung-Soo, Zhang, Cheng-Zhong, Rodriguez-Martin, Bernardo [0000-0003-4693-3140], Supek, Fran [0000-0002-7811-6711], Demeulemeester, Jonas [0000-0002-2660-2478], Ju, Young Seok [0000-0002-5514-4189], Temes, Javier [0000-0003-3370-4728], Garcia-Souto, Daniel [0000-0002-0997-8799], Blanco, Miguel G. [0000-0002-2883-7326], Ardeljan, Daniel [0000-0002-5593-421X], Roberts, Nicola D. [0000-0002-0469-1043], Zumalave, Sonia [0000-0002-2108-1861], Edwards, Paul A. W. [0000-0002-4789-3374], Weischenfeldt, Joachim [0000-0002-3917-5524], Chen, Ken [0000-0003-4013-5279], Wala, Jeremiah A. [0000-0001-6591-1620], Raine, Keiran [0000-0002-5634-1539], Waszak, Sebastian M. [0000-0003-3042-9521], Navarro, Fabio C. P. [0000-0002-5640-9070], Monlong, Jean [0000-0002-9737-5516], Bourque, Guillaume [0000-0002-3933-9656], Park, Peter J. [0000-0001-9378-960X], Korbel, Jan O. [0000-0002-2798-3794], Fitzgerald, Rebecca C. [0000-0002-3434-3568], Van Loo, Peter [0000-0003-0292-1949], Burns, Kathleen H. [0000-0003-1620-3761], Campbell, Peter J. [0000-0002-3921-0510], Tubio, Jose M. C. [0000-0003-3540-2459], and Apollo - University of Cambridge Repository

Subjects
692/699/67, 45, 631/208/212, article, 45/23, humanities
Abstract

Funder: Consellería de Cultura, Educación e Ordenación Universitaria, Xunta de Galicia (Ministry of Culture, Education and University Planning, Government of Galicia); doi: https://doi.org/10.13039/501100008425, Funder: Ministerio de Educación, Cultura y Deporte (Ministry of Education, Culture and Sports, Spain); doi: https://doi.org/10.13039/501100003176, Funder: EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council); doi: https://doi.org/10.13039/100010663, Funder: Ministerio de Economía y Competitividad (Ministry of Economy and Competitiveness); doi: https://doi.org/10.13039/501100003329, Funder: Korea Health Industry Development Institute (KHIDI); doi: https://doi.org/10.13039/501100003710, Funder: Danish Medical Research Council, Funder: NIH, Funder: Associazione Italiana Contro le Leucemie-Linfomi e Mieloma, Funder: Cancer Research UK (CRUK); doi: https://doi.org/10.13039/501100000289, About half of all cancers have somatic integrations of retrotransposons. Here, to characterize their role in oncogenesis, we analyzed the patterns and mechanisms of somatic retrotransposition in 2,954 cancer genomes from 38 histological cancer subtypes within the framework of the Pan-Cancer Analysis of Whole Genomes (PCAWG) project. We identified 19,166 somatically acquired retrotransposition events, which affected 35% of samples and spanned a range of event types. Long interspersed nuclear element (LINE-1; L1 hereafter) insertions emerged as the first most frequent type of somatic structural variation in esophageal adenocarcinoma, and the second most frequent in head-and-neck and colorectal cancers. Aberrant L1 integrations can delete megabase-scale regions of a chromosome, which sometimes leads to the removal of tumor-suppressor genes, and can induce complex translocations and large-scale duplications. Somatic retrotranspositions can also initiate breakage–fusion–bridge cycles, leading to high-level amplification of oncogenes. These observations illuminate a relevant role of L1 retrotransposition in remodeling the cancer genome, with potential implications for the development of human tumors.

Published
2020

4. Recurrent rearrangements of FOS and FOSB define osteoblastoma

Author

Nischalan Pillay, Michael R. Stratton, Lei Zhang, William Mifsud, Matthew Fittall, Roberto Tirabosco, Patrick S. Tarpey, Hongtao Ye, Elena Miranda, Sam Behjati, Jonas Demeulemeester, Cristina R. Antonescu, Fernanda Amary, Peter Van Loo, Annelien Verfaillie, Peter J. Campbell, Anna Christina Strobl, Agamemnon E. Grigoriadis, Maxime Tarabichi, Fitim Berisha, Matthew D. Young, Adrienne M. Flanagan, Fittall, Matthew W [0000-0002-5172-4100], Pillay, Nischalan [0000-0003-0579-4105], Demeulemeester, Jonas [0000-0002-2660-2478], Van Loo, Peter [0000-0003-0292-1949], and Apollo - University of Cambridge Repository

Subjects
0301 basic medicine, Male, General Physics and Astronomy, medicine.disease_cause, Pathogenesis, Mice, 0302 clinical medicine, Osteoblastoma, PSEUDOMYOGENIC HEMANGIOENDOTHELIOMA, DOMAIN, lcsh:Science, Child, Gene Rearrangement, Mutation, Multidisciplinary, Middle Aged, 3. Good health, Multidisciplinary Sciences, 030220 oncology & carcinogenesis, Child, Preschool, Science & Technology - Other Topics, Osteosarcoma, Immunohistochemistry, Female, Proto-Oncogene Proteins c-fos, FOSB, musculoskeletal diseases, Osteoid osteoma, Adult, Adolescent, Science, Bone Neoplasms, Biology, General Biochemistry, Genetics and Molecular Biology, Article, 03 medical and health sciences, Young Adult, medicine, Animals, Humans, Amino Acid Sequence, Science & Technology, Base Sequence, Whole Genome Sequencing, General Chemistry, Gene rearrangement, medicine.disease, TRANSFORMATION, 030104 developmental biology, Cancer research, lcsh:Q, EPITHELIOID HEMANGIOMA
Abstract

The transcription factor FOS has long been implicated in the pathogenesis of bone tumours, following the discovery that the viral homologue, v-fos, caused osteosarcoma in laboratory mice. However, mutations of FOS have not been found in human bone-forming tumours. Here, we report recurrent rearrangement of FOS and its paralogue, FOSB, in the most common benign tumours of bone, osteoblastoma and osteoid osteoma. Combining whole-genome DNA and RNA sequences, we find rearrangement of FOS in five tumours and of FOSB in one tumour. Extending our findings into a cohort of 55 cases, using FISH and immunohistochemistry, provide evidence of ubiquitous mutation of FOS or FOSB in osteoblastoma and osteoid osteoma. Overall, our findings reveal a human bone tumour defined by mutations of FOS and FOSB., FOS has been linked to bone tumour pathogenesis, and viral homologue v-fos causes osteosarcoma in mice. Here, the authors report rearrangement of FOS and its paralogue FOSB in osteoblastoma and osteoid osteoma, revealing human bone tumours that are defined by mutations of FOS and FOSB.

Published
2018

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