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1.
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20 p, 3.2 MB |
The HDAC7-TET2 epigenetic axis is essential during early B lymphocyte development
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Azagra, Alba (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Meler, Ainara (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
de Barrios, Oriol (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Tomás Daza, Laureano (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Collazo, Olga (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Monterde, B. (Instituto de Biomedicina y Biotecnología de Cantabria. Universidad de Cantabria-CSIC) ;
Obiols, Mireia (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Rovirosa Mulet, Llorenç (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Vila-Casadesús, M. (Centre de Regulació Genòmica) ;
Cabrera Pasadas, Mònica (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Gusi Vives, Mar (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Graf, T. (Universitat Pompeu Fabra) ;
Varela, I. (Instituto de Biomedicina y Biotecnología de Cantabria. Universidad de Cantabria-CSIC) ;
Sardina, José Luis (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Javierre, B. M (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Parra, Maribel (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras)
Correct B cell identity at each stage of cellular differentiation during B lymphocyte development is critically dependent on a tightly controlled epigenomic landscape. We previously identified HDAC7 as an essential regulator of early B cell development and its absence leads to a drastic block at the pro-B to pre-B cell transition. [...]
2022 -  10.1093/nar/gkac619
Nucleic acids research, Vol. 50 Núm. 15 (26 2022) , p. 8471-8490
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2.
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16 p, 3.4 MB |
Low input capture Hi-C (liCHi-C) identifies promoter-enhancer interactions at high-resolution
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Tomás Daza, Laureano (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Rovirosa, Llorenç (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
López-Martí, Paula (Barcelona Supercomputing Center) ;
Nieto-Aliseda, Andrea (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Serra, François (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Planas-Riverola, Ainhoa (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Molina, Oscar (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
McDonald, Rebecca (Wellcome-MRC Cambridge Stem Cell Institute) ;
Ghevaert, Cedric (NHS Blood and Transplant) ;
Cuatrecasas, Esther (Hospital Sant Joan de Déu (Manresa)) ;
Costa, Dolors (Cancer Network Biomedical Research Center) ;
Camós, Mireia (Instituto de Salud Carlos III) ;
Bueno, Clara (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Menéndez, Pablo (Institució Catalana de Recerca i Estudis Avançats) ;
Valencia, Alonso (Institució Catalana de Recerca i Estudis Avançats) ;
Javierre, B. M (Institut Germans Trias i Pujol)
Long-range interactions between regulatory elements and promoters are key in gene transcriptional control; however, their study requires large amounts of starting material, which is not compatible with clinical scenarios nor the study of rare cell populations. [...]
2023 - 10.1038/s41467-023-35911-8
Nature communications, Vol. 14 Núm. 1 (december 2023) , p. 268
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3.
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13 p, 5.7 MB |
High-resolution simulations of chromatin folding at genomic rearrangements in malignant B cells provide mechanistic insights into proto-oncogene deregulation
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Rico, Daniel (Newcastle University) ;
Kent, Daniel (Newcastle University) ;
Karataraki, Nefeli (Newcastle University) ;
Mikulasova, Aneta (Newcastle University) ;
Berlinguer-Palmini, Ronaldo (Newcastle University) ;
Walker, Brian A. (Indiana University) ;
Javierre, B. M (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Russell, Lisa J. (Newcastle University) ;
Brackley, Chris A. (University of Edinburgh)
Genomic rearrangements are known to result in proto-oncogene deregulation in many cancers, but the link to 3D genome structure remains poorly understood. Here, we used the highly predictive heteromorphic polymer (HiP-HoP) model to predict chromatin conformations at the proto-oncogene CCND1 in healthy and malignant B cells. [...]
2022 - 10.1101/gr.276028.121
Genome research, Vol. 32 Núm. 8 (july 2022) , p. 1355-1366
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4.
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44 p, 10.1 MB |
Intra- and interchromosomal contact mapping reveals the Igh locus has extensive conformational heterogeneity and interacts with B-lineage genes
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Mielczarek, O. (Nuclear Dynamics Programme. Babraham Institute. Babraham Research Campus) ;
Rogers, C.H. (Immunology Programme. Babraham Institute. Babraham Research Campus) ;
Zhan, Y. (Friedrich Miescher Institute for Biomedical Research) ;
Matheson, L.S. (Immunology Programme. Babraham Institute. Babraham Research Campus) ;
Stubbington, M.J.T. (Nuclear Dynamics Programme. Babraham Institute. Babraham Research Campus) ;
Schoenfelder, S. (Nuclear Dynamics Programme. Babraham Institute. Babraham Research Campus) ;
Bolland, D.J. (Immunology Programme. Babraham Institute. Babraham Research Campus) ;
Javierre, B. M (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Wingett, S.W. (Bioinformatics Group. Babraham Institute. Babraham Research Campus) ;
Várnai, C. (Nuclear Dynamics Programme. Babraham Institute. Babraham Research Campus) ;
Segonds-Pichon, A. (Bioinformatics Group. Babraham Institute. Babraham Research Campus) ;
Conn, S.J. (Flinders Health and Medical Research Institute. College of Medicine and Public Health. Flinders University) ;
Krueger, F. (Babraham Institute) ;
Andrews, S. (Babraham Institute) ;
Fraser, P. (Nuclear Dynamics Programme. Babraham Institute. Babraham Research Campus) ;
Giorgetti, L. (Friedrich Miescher Institute for Biomedical Research) ;
Corcoran, A.E. (Immunology Programme. Babraham Institute. Babraham Research Campus)
To produce a diverse antibody repertoire, immunoglobulin heavy-chain (Igh) loci undergo large-scale alterations in structure to facilitate juxtaposition and recombination of spatially separated variable (V), diversity (D), and joining (J) genes. [...]
2023 - 10.1016/j.celrep.2023.113074
Cell reports, Vol. 42 Núm. 9 (26 2023) , p. 113074
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5.
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12 p, 1.9 MB |
Genetic perturbation of PU.1 binding and chromatin looping at neutrophil enhancers associates with autoimmune disease
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Watt, Stephen (Human Genetics. Wellcome Sanger Institute. Genome Campus) ;
Vasquez, Louella (Human Genetics. Wellcome Sanger Institute. Genome Campus) ;
Walter, Klaudia (Human Genetics. Wellcome Sanger Institute. Genome Campus) ;
Mann, Alice L. (Human Genetics. Wellcome Sanger Institute. Genome Campus) ;
Kundu, Kousik (School of Clinical Medicine. University of Cambridge) ;
Chen, Lu (Sichuan University) ;
Sims, Ying (Human Genetics. Wellcome Sanger Institute. Genome Campus) ;
Ecker, Simone (UCL Cancer Institute) ;
Burden, Frances (National Health Service Blood and Transplant) ;
Farrow, Samantha (National Health Service Blood and Transplant) ;
Farr, Ben (Human Genetics. Wellcome Sanger Institute. Genome Campus) ;
Iotchkova, Valentina (University of Oxford) ;
Elding, Heather (Human Genetics. Wellcome Sanger Institute. Genome Campus) ;
Mead, Daniel (Human Genetics. Wellcome Sanger Institute. Genome Campus) ;
Tardaguila, Manuel (Human Genetics. Wellcome Sanger Institute. Genome Campus) ;
Ponstingl, Hannes (Human Genetics. Wellcome Sanger Institute. Genome Campus) ;
Richardson, David (European Molecular Biology Laboratory. European Bioinformatics Institute) ;
Datta, Avik (European Molecular Biology Laboratory. European Bioinformatics Institute) ;
Flicek, Paul (European Molecular Biology Laboratory. European Bioinformatics Institute) ;
Clarke, Laura (European Molecular Biology Laboratory. European Bioinformatics Institute) ;
Downes, Kate (National Health Service Blood and Transplant) ;
Pastinen, Tomi (Center for Pediatric Genomic Medicine. Children's Mercy) ;
Fraser, Peter (Florida State University) ;
Frontini, Mattia (University of Exeter Medical School) ;
Javierre, B. M (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Spivakov, Mikhail (Imperial College Faculty of Medicine) ;
Soranzo, Nicole (University of Cambridge)
Neutrophils play fundamental roles in innate immune response, shape adaptive immunity, and are a potentially causal cell type underpinning genetic associations with immune system traits and diseases. [...]
2021 - 10.1038/s41467-021-22548-8
Nature communications, Vol. 12 Núm. 1 (january 2021) , p. 2298
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6.
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19 p, 7.2 MB |
The onset of PI3K-related vascular malformations occurs during angiogenesis and is prevented by the AKT inhibitor miransertib
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Kobialka, Piotr (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Sabata, Helena (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Vilalta, Odena (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Gouveia, Leonor (Uppsala University) ;
Angulo-Urarte, Ana (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Muixí, Laia (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Zanoncello, Jasmina (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Muñoz-Aznar, Oscar (Institut de Recerca Sant Joan de Déu) ;
Olaciregui, Nagore G. (Institut de Recerca Sant Joan de Déu) ;
Fanlo, Lucia (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Esteve-Codina, Anna (Universitat Pompeu Fabra) ;
Lavarino, Cinzia (Institut de Recerca Sant Joan de Déu) ;
Javierre, B. M (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Celis, Verónica Paola (Hospital Sant Joan de Déu (Barcelona, Catalunya)) ;
Rovira, Cinzia (Hospital Sant Joan de Déu (Barcelona, Catalunya)) ;
López-Fernández, Susana (Institut d'Investigació Biomèdica Sant Pau) ;
Baselga Torres, Eulàlia (Hospital Sant Joan de Déu (Barcelona, Catalunya)) ;
Mora, J. (Hospital Sant Joan de Déu (Barcelona, Catalunya)) ;
Castillo, Sandra D. (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Graupera, Mariona (Centro de Investigación Biomédica en Red de Cáncer) ;
Universitat Autònoma de Barcelona.
Departament de Cirurgia
Low-flow vascular malformations are congenital overgrowths composed of abnormal blood vessels potentially causing pain, bleeding and obstruction of different organs. These diseases are caused by oncogenic mutations in the endothelium, which result in overactivation of the PI3K/AKT pathway. [...]
2022 - 10.15252/emmm.202115619
EMBO Molecular Medicine, Vol. 14 Núm. 7 (july 2022) , p. e15619
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7.
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9 p, 742.8 KB |
The Genome in a Three-Dimensional Context : Deciphering the Contribution of Noncoding Mutations at Enhancers to Blood Cancer
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Rovirosa Mulet, Llorenç (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Ramos-Morales, Alberto (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Javierre, B. M. (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Universitat Autònoma de Barcelona
Associations between blood cancer and genetic predisposition, including both inherited variants and acquired mutations and epimutations, have been well characterized. However, the majority of these variants affect noncoding regions, making their mechanisms difficult to hypothesize and hindering the translation of these insights into patient benefits. [...]
2020 - 10.3389/fimmu.2020.592087
Frontiers in immunology, Vol. 11 (july 2020) , p. 592087
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8.
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17 p, 3.1 MB |
Epigenomics and transcriptomics of systemic sclerosis CD4+ T cells reveal long-range dysregulation of key inflammatory pathways mediated by disease-associated susceptibility loci
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Li, Tianlu (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Ortiz-Fernández, Lourdes (Instituto de Parasitología y Biomedicina "López-Neyra") ;
Andrés-León, Eduardo (Instituto de Parasitología y Biomedicina "López-Neyra") ;
Ciudad, Laura (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Javierre, B. M. (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
López-Isac, E. (Instituto de Parasitología y Biomedicina "López-Neyra") ;
Guillén-Del-Castillo, A. (Hospital Universitari Vall d'Hebron) ;
Simeón-Aznar, C. P. (Hospital Universitari Vall d'Hebron) ;
Ballestar, Esteban (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Martín, Javier (Instituto de Parasitología y Biomedicina "López-Neyra") ;
Universitat Autònoma de Barcelona
Background: Systemic sclerosis (SSc) is a genetically complex autoimmune disease mediated by the interplay between genetic and epigenetic factors in a multitude of immune cells, with CD4+ T lymphocytes as one of the principle drivers of pathogenesis. [...]
2020 - 10.1186/s13073-020-00779-6
Genome Medicine, Vol. 12 Núm. 1 (25 2020) , p. 81
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9.
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5 p, 786.3 KB |
B-cell leukemia transdifferentiation to macrophage involves reconfiguration of DNA methylation for long-range regulation
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Bueno-Costa, Alberto (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Piñeyro, David (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Soler, Marta (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Javierre, B. M. (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Raurell Vila, Helena (Institut Germans Trias i Pujol. Hospital Universitari Germans Trias i Pujol) ;
Subirana-Granés, Marc (Institut Germans Trias i Pujol. Hospital Universitari Germans Trias i Pujol) ;
Pasquali, Lorenzo (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Martinez-Climent, J. A. (Centro de Investigación Biomédica en Red de Cáncer) ;
Esteller, M. (Institut Germans Trias i Pujol. Institut de Recerca contra la Leucèmia Josep Carreras) ;
Universitat Autònoma de Barcelona
2020 - 10.1038/s41375-019-0643-1
Leukemia, Vol. 34 Núm. 4 (april 2020) , p. 1158-1162
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