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  1. AU="Temes, Javier"
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  1. Article ; Online: Author Correction: Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition.

    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 C P / 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 / Campbell, Peter J / Tubio, Jose M C

    Nature genetics

    2023  Volume 55, Issue 6, Page(s) 1080

    Language English
    Publishing date 2023-03-22
    Publishing country United States
    Document type Published Erratum
    ZDB-ID 1108734-1
    ISSN 1546-1718 ; 1061-4036
    ISSN (online) 1546-1718
    ISSN 1061-4036
    DOI 10.1038/s41588-023-01319-9
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Somatic evolution of marine transmissible leukemias in the common cockle, Cerastoderma edule.

    Bruzos, Alicia L / Santamarina, Martín / García-Souto, Daniel / Díaz, Seila / Rocha, Sara / Zamora, Jorge / Lee, Yunah / Viña-Feás, Alejandro / Quail, Michael A / Otero, Iago / Pequeño-Valtierra, Ana / Temes, Javier / Rodriguez-Castro, Jorge / Aramburu, Leyre / Vidal-Capón, André / Villanueva, Antonio / Costas, Damián / Rodríguez, Rosana / Prieto, Tamara /
    Tomás, Laura / Alvariño, Pilar / Alonso, Juana / Cao, Asunción / Iglesias, David / Carballal, María J / Amaral, Ana M / Balseiro, Pablo / Calado, Ricardo / El Khalfi, Bouchra / Izagirre, Urtzi / de Montaudouin, Xavier / Pade, Nicolas G / Probert, Ian / Ricardo, Fernando / Ruiz, Pamela / Skazina, Maria / Smolarz, Katarzyna / Pasantes, Juan J / Villalba, Antonio / Ning, Zemin / Ju, Young Seok / Posada, David / Demeulemeester, Jonas / Baez-Ortega, Adrian / Tubio, Jose M C

    Nature cancer

    2023  Volume 4, Issue 11, Page(s) 1575–1591

    Abstract: Transmissible cancers are malignant cell lineages that spread clonally between individuals. Several such cancers, termed bivalve transmissible neoplasia (BTN), induce leukemia-like disease in marine bivalves. This is the case of BTN lineages affecting ... ...

    Abstract Transmissible cancers are malignant cell lineages that spread clonally between individuals. Several such cancers, termed bivalve transmissible neoplasia (BTN), induce leukemia-like disease in marine bivalves. This is the case of BTN lineages affecting the common cockle, Cerastoderma edule, which inhabits the Atlantic coasts of Europe and northwest Africa. To investigate the evolution of cockle BTN, we collected 6,854 cockles, diagnosed 390 BTN tumors, generated a reference genome and assessed genomic variation across 61 tumors. Our analyses confirmed the existence of two BTN lineages with hemocytic origins. Mitochondrial variation revealed mitochondrial capture and host co-infection events. Mutational analyses identified lineage-specific signatures, one of which likely reflects DNA alkylation. Cytogenetic and copy number analyses uncovered pervasive genomic instability, with whole-genome duplication, oncogene amplification and alkylation-repair suppression as likely drivers. Satellite DNA distributions suggested ancient clonal origins. Our study illuminates long-term cancer evolution under the sea and reveals tolerance of extreme instability in neoplastic genomes.
    MeSH term(s) Animals ; Humans ; Cardiidae/genetics ; Bivalvia ; Leukemia ; Neoplasms ; Clonal Evolution
    Language English
    Publishing date 2023-10-02
    Publishing country England
    Document type Journal Article
    ISSN 2662-1347
    ISSN (online) 2662-1347
    DOI 10.1038/s43018-023-00641-9
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Aberrant integration of Hepatitis B virus DNA promotes major restructuring of human hepatocellular carcinoma genome architecture.

    Álvarez, Eva G / Demeulemeester, Jonas / Otero, Paula / Jolly, Clemency / García-Souto, Daniel / Pequeño-Valtierra, Ana / Zamora, Jorge / Tojo, Marta / Temes, Javier / Baez-Ortega, Adrian / Rodriguez-Martin, Bernardo / Oitaben, Ana / Bruzos, Alicia L / Martínez-Fernández, Mónica / Haase, Kerstin / Zumalave, Sonia / Abal, Rosanna / Rodríguez-Castro, Jorge / Rodriguez-Casanova, Aitor /
    Diaz-Lagares, Angel / Li, Yilong / Raine, Keiran M / Butler, Adam P / Otero, Iago / Ono, Atsushi / Aikata, Hiroshi / Chayama, Kazuaki / Ueno, Masaki / Hayami, Shinya / Yamaue, Hiroki / Maejima, Kazuhiro / Blanco, Miguel G / Forns, Xavier / Rivas, Carmen / Ruiz-Bañobre, Juan / Pérez-Del-Pulgar, Sofía / Torres-Ruiz, Raúl / Rodriguez-Perales, Sandra / Garaigorta, Urtzi / Campbell, Peter J / Nakagawa, Hidewaki / Van Loo, Peter / Tubio, Jose M C

    Nature communications

    2021  Volume 12, Issue 1, Page(s) 6910

    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 ... ...

    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.
    MeSH term(s) Carcinoma, Hepatocellular/genetics ; Carcinoma, Hepatocellular/virology ; DNA, Viral ; Gene Expression Regulation, Neoplastic ; Genome, Human ; Hepatitis B virus/genetics ; Humans ; Liver Neoplasms/genetics ; Virus Integration ; Whole Genome Sequencing
    Chemical Substances DNA, Viral
    Language English
    Publishing date 2021-11-25
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-021-26805-8
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition.

    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 C P / 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 / Campbell, Peter J / Tubio, Jose M C

    Nature genetics

    2020  Volume 52, Issue 3, Page(s) 306–319

    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 ... ...

    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.
    MeSH term(s) Carcinogenesis/genetics ; Gene Rearrangement/genetics ; Genome, Human/genetics ; Humans ; Long Interspersed Nucleotide Elements/genetics ; Neoplasms/genetics ; Neoplasms/pathology ; Retroelements/genetics
    Chemical Substances Retroelements
    Language English
    Publishing date 2020-02-05
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 1108734-1
    ISSN 1546-1718 ; 1061-4036
    ISSN (online) 1546-1718
    ISSN 1061-4036
    DOI 10.1038/s41588-019-0562-0
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 3613: Show issues Location:
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    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)
    Zs.MG 46: Show issues

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