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Your search keyword '"Tubio, Jose MC [0000-0003-3540-2459]"' showing total 3 results
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3 results on '"Tubio, Jose MC [0000-0003-3540-2459]"'

1. Mitochondrial genome sequencing of marine leukaemias reveals cancer contagion between clam species in the Seas of Southern Europe

Author

European Commission, Ministerio de Economía y Competitividad (España), Xunta de Galicia, Centro de Estudos do Ambiente e do Mar (Portugal), Garcia-Souto, Daniel [0000-0002-0997-8799], Bruzos, Alicia L [0000-0003-4362-545X], Diaz, Seila [0000-0002-6607-290X], Rocha, Sara [0000-0002-9705-1511], Pequeño-Valtierra, Ana [0000-0002-0049-5707], Roman-Lewis, Camila F [0000-0002-8571-8331], Costas, Damian [0000-0002-9415-0362], Rodriguez-Castro, Jorge [0000-0003-2912-9601], Valencia, José María [0000-0002-1912-1975], Annona, Giovanni [0000-0001-7806-6761], Tarallo, Andrea [0000-0002-2749-8588], Bratoš Cetinić, Ana [0000-0002-2928-4858], Posada, David [0000-0003-1407-3406], Pasantes, Juan Jose [0000-0001-6515-3946], Tubio, Jose Mc [0000-0003-3540-2459], Garcia-Souto, Daniel, Bruzos, Alicia L., Diaz, Seila, Rocha, Sara, Pequeño-Valtierra, Ana, Roman-Lewis, Camila F, Alonso, Juana, Rodriguez, Rosana, Costas, Damian, Rodriguez-Castro, Jorge, Villanueva, Antonio, Valencia, José María, Annona, Giovanni, Tarallo, Andrea, Ricardo, Fernando, Bratoš Cetinić, Ana, Posada, David, Pasantes, Juan Jose, Tubio, Jose Mc, Silva, Luis, European Commission, Ministerio de Economía y Competitividad (España), Xunta de Galicia, Centro de Estudos do Ambiente e do Mar (Portugal), Garcia-Souto, Daniel [0000-0002-0997-8799], Bruzos, Alicia L [0000-0003-4362-545X], Diaz, Seila [0000-0002-6607-290X], Rocha, Sara [0000-0002-9705-1511], Pequeño-Valtierra, Ana [0000-0002-0049-5707], Roman-Lewis, Camila F [0000-0002-8571-8331], Costas, Damian [0000-0002-9415-0362], Rodriguez-Castro, Jorge [0000-0003-2912-9601], Valencia, José María [0000-0002-1912-1975], Annona, Giovanni [0000-0001-7806-6761], Tarallo, Andrea [0000-0002-2749-8588], Bratoš Cetinić, Ana [0000-0002-2928-4858], Posada, David [0000-0003-1407-3406], Pasantes, Juan Jose [0000-0001-6515-3946], Tubio, Jose Mc [0000-0003-3540-2459], Garcia-Souto, Daniel, Bruzos, Alicia L., Diaz, Seila, Rocha, Sara, Pequeño-Valtierra, Ana, Roman-Lewis, Camila F, Alonso, Juana, Rodriguez, Rosana, Costas, Damian, Rodriguez-Castro, Jorge, Villanueva, Antonio, Valencia, José María, Annona, Giovanni, Tarallo, Andrea, Ricardo, Fernando, Bratoš Cetinić, Ana, Posada, David, Pasantes, Juan Jose, Tubio, Jose Mc, and Silva, Luis

Abstract

Clonally transmissible cancers are tumour lineages that are transmitted between individuals via the transfer of living cancer cells. In marine bivalves, leukaemia-like transmissible cancers, called hemic neoplasia (HN), have demonstrated the ability to infect individuals from different species. We performed whole-genome sequencing in eight warty venus clams that were diagnosed with HN, from two sampling points located more than 1000 nautical miles away in the Atlantic Ocean and the Mediterranean Sea Coasts of Spain. Mitochondrial genome sequencing analysis from neoplastic animals revealed the coexistence of haplotypes from two different clam species. Phylogenies estimated from mitochondrial and nuclear markers confirmed this leukaemia originated in striped venus clams and later transmitted to clams of the species warty venus, in which it survives as a contagious cancer. The analysis of mitochondrial and nuclear gene sequences supports all studied tumours belong to a single neoplastic lineage that spreads in the Seas of Southern Europe.

Published
2022

2. 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

3. 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

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