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  1. Article ; Online: Molecular pathogenesis of CLL and its evolution.

    Rodríguez, David / Bretones, Gabriel / Arango, Javier R / Valdespino, Víctor / Campo, Elías / Quesada, Víctor / López-Otín, Carlos

    International journal of hematology

    2015  Volume 101, Issue 3, Page(s) 219–228

    Abstract: In spite of being the most prevalent adult leukemia in Western countries, the molecular mechanisms driving the establishment and progression of chronic lymphocytic leukemia (CLL) remain largely unknown. In recent years, the use of next-generation ... ...

    Abstract In spite of being the most prevalent adult leukemia in Western countries, the molecular mechanisms driving the establishment and progression of chronic lymphocytic leukemia (CLL) remain largely unknown. In recent years, the use of next-generation sequencing techniques has uncovered new and, in some cases, unexpected driver genes with prognostic and therapeutic value. The mutational landscape of CLL is characterized by high-genetic and epigenetic heterogeneity, low mutation recurrence and a long tail of cases with undefined driver genes. On the other hand, the use of deep sequencing has also revealed high intra-tumor heterogeneity and provided a detailed picture of clonal evolution processes. This phenomenon, in which aberrant DNA methylation can also participate, appears to be tightly associated to poor outcomes and chemo-refractoriness, thus providing a new subject for therapeutic intervention. Hence, and having in mind the limitations derived from the CLL complexity thus described, the application of massively parallel sequencing studies has unveiled a wealth of information that is expected to substantially improve patient staging schemes and CLL clinical management.
    MeSH term(s) Animals ; Chromosome Aberrations ; Clonal Evolution ; DNA Methylation ; Epigenesis, Genetic ; High-Throughput Nucleotide Sequencing ; Humans ; Leukemia, Lymphocytic, Chronic, B-Cell/diagnosis ; Leukemia, Lymphocytic, Chronic, B-Cell/genetics ; Leukemia, Lymphocytic, Chronic, B-Cell/pathology ; Mutation
    Language English
    Publishing date 2015-03
    Publishing country Japan
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 1076875-0
    ISSN 1865-3774 ; 0917-1258 ; 0925-5710
    ISSN (online) 1865-3774
    ISSN 0917-1258 ; 0925-5710
    DOI 10.1007/s12185-015-1733-0
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 269: Show issues Location:
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    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  2. Article ; Online: Altered patterns of global protein synthesis and translational fidelity in RPS15-mutated chronic lymphocytic leukemia.

    Bretones, Gabriel / Álvarez, Miguel G / Arango, Javier R / Rodríguez, David / Nadeu, Ferran / Prado, Miguel A / Valdés-Mas, Rafael / Puente, Diana A / Paulo, Joao A / Delgado, Julio / Villamor, Neus / López-Guillermo, Armando / Finley, Daniel J / Gygi, Steven P / Campo, Elías / Quesada, Víctor / López-Otín, Carlos

    Blood

    2018  Volume 132, Issue 22, Page(s) 2375–2388

    Abstract: Genomic studies have recently ... ...

    Abstract Genomic studies have recently identified
    MeSH term(s) Cell Line, Tumor ; Cohort Studies ; HEK293 Cells ; Humans ; Leukemia, Lymphocytic, Chronic, B-Cell/genetics ; Leukemia, Lymphocytic, Chronic, B-Cell/pathology ; Mutation ; Mutation Rate ; Point Mutation ; Protein Biosynthesis ; Protein Domains ; Ribosomal Proteins/chemistry ; Ribosomal Proteins/genetics ; Ribosomes/genetics ; Ribosomes/pathology
    Chemical Substances Ribosomal Proteins ; ribosomal protein S15
    Language English
    Publishing date 2018-09-04
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 80069-7
    ISSN 1528-0020 ; 0006-4971
    ISSN (online) 1528-0020
    ISSN 0006-4971
    DOI 10.1182/blood-2017-09-804401
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.MO 364: Show issues

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  3. Article ; Online: Mutations in CHD2 cause defective association with active chromatin in chronic lymphocytic leukemia.

    Rodríguez, David / Bretones, Gabriel / Quesada, Víctor / Villamor, Neus / Arango, Javier R / López-Guillermo, Armando / Ramsay, Andrew J / Baumann, Tycho / Quirós, Pedro M / Navarro, Alba / Royo, Cristina / Martín-Subero, José I / Campo, Elías / López-Otín, Carlos

    Blood

    2015  Volume 126, Issue 2, Page(s) 195–202

    Abstract: Great progress has recently been achieved in the understanding of the genomic alterations driving chronic lymphocytic leukemia (CLL). Nevertheless, the specific molecular mechanisms governing chromatin remodeling in CLL are unknown. Here we report the ... ...

    Abstract Great progress has recently been achieved in the understanding of the genomic alterations driving chronic lymphocytic leukemia (CLL). Nevertheless, the specific molecular mechanisms governing chromatin remodeling in CLL are unknown. Here we report the genetic and functional characterization of somatic mutations affecting the chromatin remodeler CHD2, one of the most frequently mutated genes in CLL (5.3%) and in monoclonal B lymphocytosis (MBL, 7%), a B-cell expansion that can evolve to CLL. Most of the mutations affecting CHD2, identified by whole-exome sequencing of 456 CLL and 43 MBL patients, are either truncating or affect conserved residues in functional domains, thus supporting a putative role for CHD2 as a tumor suppressor gene. CHD2 mutants show altered nuclear distribution, and a chromodomain helicase DNA binding protein 2 (CHD2) mutant affected in its DNA-binding domain exhibits defective association with active chromatin. Clinicobiological analyses show that most CLL patients carrying CHD2 mutations also present mutated immunoglobulin heavy chain variable region genes (IGHVs), being the most frequently mutated gene in this prognostic subgroup. This is the first study providing functional evidence supporting CHD2 as a cancer driver and opens the way to further studies of the role of this chromatin remodeler in CLL.
    MeSH term(s) Amino Acid Sequence ; Animals ; COS Cells ; Cells, Cultured ; Chlorocebus aethiops ; Chromatin/metabolism ; Chromatin Assembly and Disassembly/genetics ; Cohort Studies ; DNA-Binding Proteins/genetics ; HEK293 Cells ; Humans ; Leukemia, Lymphocytic, Chronic, B-Cell/genetics ; Leukemia, Lymphocytic, Chronic, B-Cell/metabolism ; Molecular Sequence Data ; Mutation ; Sequence Homology, Amino Acid
    Chemical Substances CHD2 protein, human ; Chromatin ; DNA-Binding Proteins
    Language English
    Publishing date 2015-06-01
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 80069-7
    ISSN 1528-0020 ; 0006-4971
    ISSN (online) 1528-0020
    ISSN 0006-4971
    DOI 10.1182/blood-2014-10-604959
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Uh III Zs.140: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
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    ab Jg. 2022: Lesesaal (EG)
    Zs.MO 364: Show issues

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  4. Article ; Online: Giant tortoise genomes provide insights into longevity and age-related disease.

    Quesada, Víctor / Freitas-Rodríguez, Sandra / Miller, Joshua / Pérez-Silva, José G / Jiang, Zi-Feng / Tapia, Washington / Santiago-Fernández, Olaya / Campos-Iglesias, Diana / Kuderna, Lukas F K / Quinzin, Maud / Álvarez, Miguel G / Carrero, Dido / Beheregaray, Luciano B / Gibbs, James P / Chiari, Ylenia / Glaberman, Scott / Ciofi, Claudio / Araujo-Voces, Miguel / Mayoral, Pablo /
    Arango, Javier R / Tamargo-Gómez, Isaac / Roiz-Valle, David / Pascual-Torner, María / Evans, Benjamin R / Edwards, Danielle L / Garrick, Ryan C / Russello, Michael A / Poulakakis, Nikos / Gaughran, Stephen J / Rueda, Danny O / Bretones, Gabriel / Marquès-Bonet, Tomàs / White, Kevin P / Caccone, Adalgisa / López-Otín, Carlos

    Nature ecology & evolution

    2018  Volume 3, Issue 1, Page(s) 87–95

    Abstract: Giant tortoises are among the longest-lived vertebrate animals and, as such, provide an excellent model to study traits like longevity and age-related diseases. However, genomic and molecular evolutionary information on giant tortoises is scarce. Here, ... ...

    Abstract Giant tortoises are among the longest-lived vertebrate animals and, as such, provide an excellent model to study traits like longevity and age-related diseases. However, genomic and molecular evolutionary information on giant tortoises is scarce. Here, we describe a global analysis of the genomes of Lonesome George-the iconic last member of Chelonoidis abingdonii-and the Aldabra giant tortoise (Aldabrachelys gigantea). Comparison of these genomes with those of related species, using both unsupervised and supervised analyses, led us to detect lineage-specific variants affecting DNA repair genes, inflammatory mediators and genes related to cancer development. Our study also hints at specific evolutionary strategies linked to increased lifespan, and expands our understanding of the genomic determinants of ageing. These new genome sequences also provide important resources to help the efforts for restoration of giant tortoise populations.
    MeSH term(s) Aging/genetics ; Animals ; DNA Repair/genetics ; Evolution, Molecular ; Genome ; HEK293 Cells ; Humans ; Inflammation Mediators ; Male ; Neoplasms/genetics ; Phylogeny ; Population Density ; Turtles/genetics
    Chemical Substances Inflammation Mediators
    Language English
    Publishing date 2018-12-03
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 2397-334X
    ISSN (online) 2397-334X
    DOI 10.1038/s41559-018-0733-x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx.

    Abascal, Federico / Corvelo, André / Cruz, Fernando / Villanueva-Cañas, José L / Vlasova, Anna / Marcet-Houben, Marina / Martínez-Cruz, Begoña / Cheng, Jade Yu / Prieto, Pablo / Quesada, Víctor / Quilez, Javier / Li, Gang / García, Francisca / Rubio-Camarillo, Miriam / Frias, Leonor / Ribeca, Paolo / Capella-Gutiérrez, Salvador / Rodríguez, José M / Câmara, Francisco /
    Lowy, Ernesto / Cozzuto, Luca / Erb, Ionas / Tress, Michael L / Rodriguez-Ales, Jose L / Ruiz-Orera, Jorge / Reverter, Ferran / Casas-Marce, Mireia / Soriano, Laura / Arango, Javier R / Derdak, Sophia / Galán, Beatriz / Blanc, Julie / Gut, Marta / Lorente-Galdos, Belen / Andrés-Nieto, Marta / López-Otín, Carlos / Valencia, Alfonso / Gut, Ivo / García, José L / Guigó, Roderic / Murphy, William J / Ruiz-Herrera, Aurora / Marques-Bonet, Tomas / Roma, Guglielmo / Notredame, Cedric / Mailund, Thomas / Albà, M Mar / Gabaldón, Toni / Alioto, Tyler / Godoy, José A

    Genome biology

    2016  Volume 17, Issue 1, Page(s) 251

    Abstract: Background: Genomic studies of endangered species provide insights into their evolution and demographic history, reveal patterns of genomic erosion that might limit their viability, and offer tools for their effective conservation. The Iberian lynx ( ... ...

    Abstract Background: Genomic studies of endangered species provide insights into their evolution and demographic history, reveal patterns of genomic erosion that might limit their viability, and offer tools for their effective conservation. The Iberian lynx (Lynx pardinus) is the most endangered felid and a unique example of a species on the brink of extinction.
    Results: We generate the first annotated draft of the Iberian lynx genome and carry out genome-based analyses of lynx demography, evolution, and population genetics. We identify a series of severe population bottlenecks in the history of the Iberian lynx that predate its known demographic decline during the 20th century and have greatly impacted its genome evolution. We observe drastically reduced rates of weak-to-strong substitutions associated with GC-biased gene conversion and increased rates of fixation of transposable elements. We also find multiple signatures of genetic erosion in the two remnant Iberian lynx populations, including a high frequency of potentially deleterious variants and substitutions, as well as the lowest genome-wide genetic diversity reported so far in any species.
    Conclusions: The genomic features observed in the Iberian lynx genome may hamper short- and long-term viability through reduced fitness and adaptive potential. The knowledge and resources developed in this study will boost the research on felid evolution and conservation genomics and will benefit the ongoing conservation and management of this emblematic species.
    MeSH term(s) Animals ; Endangered Species ; Genetic Variation ; Genetics, Population ; Genome ; High-Throughput Nucleotide Sequencing ; Lynx/genetics ; Molecular Sequence Annotation ; Sequence Analysis, DNA
    Language English
    Publishing date 2016-12-14
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2040529-7
    ISSN 1474-760X ; 1474-760X
    ISSN (online) 1474-760X
    ISSN 1474-760X
    DOI 10.1186/s13059-016-1090-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx

    Abascal, Federico / Albà, M. Mar / Alioto, Tyler / Andrés-Nieto, Marta / Arango, Javier R / Blanc, Julie / Câmara, Francisco / Capella-Gutiérrez, Salvador / Casas-Marce, Mireia / Cheng, Jade Yu / Corvelo, André / Cozzuto, Luca / Cruz, Fernando / Derdak, Sophia / Erb, Ionas / Frias, Leonor / Gabaldón, Toni / Galán, Beatriz / García, Francisca /
    García, José L / Godoy, José A / Guigó, Roderic / Gut, Ivo / Gut, Marta / Li, Gang / López-Otín, Carlos / Lorente-Galdos, Belen / Lowy, Ernesto / Mailund, Thomas / Marcet-Houben, Marina / Marques-Bonet, Tomas / Martínez-Cruz, Begoña / Murphy, William J / Notredame, Cedric / Prieto, Pablo / Quesada, Víctor / Quilez, Javier / Reverter, Ferran / Ribeca, Paolo / Rodríguez, José M / Rodriguez-Ales, Jose L / Roma, Guglielmo / Rubio-Camarillo, Miriam / Ruiz-Herrera, Aurora / Ruiz-Orera, Jorge / Soriano, Laura / Tress, Michael L / Valencia, Alfonso / Villanueva-Cañas, José L / Vlasova, Anna

    Genome biology. 2016 Dec., v. 17, no. 1

    2016  

    Abstract: BACKGROUND: Genomic studies of endangered species provide insights into their evolution and demographic history, reveal patterns of genomic erosion that might limit their viability, and offer tools for their effective conservation. The Iberian lynx (Lynx ...

    Abstract BACKGROUND: Genomic studies of endangered species provide insights into their evolution and demographic history, reveal patterns of genomic erosion that might limit their viability, and offer tools for their effective conservation. The Iberian lynx (Lynx pardinus) is the most endangered felid and a unique example of a species on the brink of extinction. RESULTS: We generate the first annotated draft of the Iberian lynx genome and carry out genome-based analyses of lynx demography, evolution, and population genetics. We identify a series of severe population bottlenecks in the history of the Iberian lynx that predate its known demographic decline during the 20th century and have greatly impacted its genome evolution. We observe drastically reduced rates of weak-to-strong substitutions associated with GC-biased gene conversion and increased rates of fixation of transposable elements. We also find multiple signatures of genetic erosion in the two remnant Iberian lynx populations, including a high frequency of potentially deleterious variants and substitutions, as well as the lowest genome-wide genetic diversity reported so far in any species. CONCLUSIONS: The genomic features observed in the Iberian lynx genome may hamper short- and long-term viability through reduced fitness and adaptive potential. The knowledge and resources developed in this study will boost the research on felid evolution and conservation genomics and will benefit the ongoing conservation and management of this emblematic species.
    Keywords demography ; endangered species ; extinction ; gene conversion ; genetic variation ; genome ; genomics ; Lynx pardinus ; population dynamics ; population genetics ; transposons ; viability
    Language English
    Dates of publication 2016-12
    Size p. 251.
    Publishing place BioMed Central
    Document type Article
    ZDB-ID 2040529-7
    ISSN 1474-760X ; 1465-6914 ; 1465-6906
    ISSN (online) 1474-760X ; 1465-6914
    ISSN 1465-6906
    DOI 10.1186/s13059-016-1090-1
    Database NAL-Catalogue (AGRICOLA)

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