101
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Cedres S, Assaf J, Iranzo P, Callejo A, Pardo N, Navarro A, Martinez-Marti A, Rodriguez G, Monton V, Gonzalo J, Miquel J, Pedrola A, Dienstmann R, Felip E. Real-world use of systemic therapy in elderly patients with malignant pleural mesothelioma (MPM). Ann Oncol 2019. [DOI: 10.1093/annonc/mdz266.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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102
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Peroni S, Sorosina M, Malhotra S, Clarelli F, Osiceanu AM, Ferrè L, Roostaei T, Rio J, Midaglia L, Villar LM, Álvarez-Cermeño JC, Guaschino C, Radaelli M, Citterio L, Lechner-Scott J, Spataro N, Navarro A, Martinelli V, Montalban X, Weiner HL, de Jager P, Comi G, Esposito F, Comabella M, Martinelli-Boneschi F. A pharmacogenetic study implicates NINJ2 in the response to Interferon-β in multiple sclerosis. Mult Scler 2019; 26:1074-1082. [PMID: 31221001 DOI: 10.1177/1352458519851428] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
BACKGROUND Multiple sclerosis (MS) is a disease in which biomarker identification is fundamental to predict response to treatments and to deliver the optimal drug to patients. We previously found an association between rs7298096, a polymorphism upstream to the NINJ2 gene, and the 4-year response to interferon-β (IFNβ) treatment in MS patients. OBJECTIVES To analyse the association between rs7298096 and time to first relapse (TTFR) during IFNβ therapy in MS patients and to better investigate its functional role. METHODS Survival analysis was applied in three MS cohorts from different countries (n = 1004). We also studied the role of the polymorphism on gene expression using GTEx portal and a luciferase assay. We interrogated GEO datasets to explore the relationship between NINJ2 expression, IFNβ and TTFR. RESULTS Rs7298096AA patients show a shorter TTFR than rs7298096G-carriers (Pmeta-analysis = 3 × 10-4, hazard ratio = 1.41). Moreover, rs7298096AA is associated with a higher NINJ2 expression in blood (p = 7.0 × 10-6), which was confirmed in vitro (p = 0.009). Finally, NINJ2 expression is downregulated by IFNβ treatment and related to TTFR. CONCLUSIONS Rs7298096 could influence MS disease activity during IFNβ treatment by modulating NINJ2 expression in blood. The gene encodes for an adhesion molecule involved in inflammation and endothelial cells activation, supporting its role in MS.
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Affiliation(s)
- Silvia Peroni
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology (INSPE), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Melissa Sorosina
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology (INSPE), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Sunny Malhotra
- Servei de Neurologia-Neuroimmunologia, Centre d'Esclerosi Múltiple de Catalunya (Cemcat), Institut de Recerca Vall d'Hebron (VHIR), Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Ferdinando Clarelli
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology (INSPE), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Ana Maria Osiceanu
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology (INSPE), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Laura Ferrè
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology (INSPE), IRCCS San Raffaele Scientific Institute, Milan, Italy/Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Tina Roostaei
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Jordi Rio
- Servei de Neurologia-Neuroimmunologia, Centre d'Esclerosi Múltiple de Catalunya (Cemcat), Institut de Recerca Vall d'Hebron (VHIR), Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Luciana Midaglia
- Servei de Neurologia-Neuroimmunologia, Centre d'Esclerosi Múltiple de Catalunya (Cemcat), Institut de Recerca Vall d'Hebron (VHIR), Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Luisa María Villar
- Departments of Neurology and Immunology, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigacion Sanitaria, Madrid, Spain
| | - José Carlos Álvarez-Cermeño
- Departments of Neurology and Immunology, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigacion Sanitaria, Madrid, Spain
| | - Clara Guaschino
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology (INSPE), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Marta Radaelli
- Department of Neurology, Institute of Experimental Neurology (INSPE), Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Lorena Citterio
- Genomics of Renal Diseases and Hypertension Unit, Division of Genetics and Cellular Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Jeannette Lechner-Scott
- Department of Neurology, John Hunter Hospital, Newcastle, NSW, Australia/Hunter Medical Research Institute, University of Newcastle, NSW, Australia
| | - Nino Spataro
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain/Institute of Evolutionary Biology (UPF-CSIC), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Arcadi Navarro
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain/Institute of Evolutionary Biology (UPF-CSIC), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain/National Institute for Bioinformatics (INB), Barcelona, Spain/Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona Biomedical Research Park (PRBB), Barcelona, Spain
| | - Vittorio Martinelli
- Department of Neurology, Institute of Experimental Neurology (INSPE), Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Xavier Montalban
- Servei de Neurologia-Neuroimmunologia, Centre d'Esclerosi Múltiple de Catalunya (Cemcat), Institut de Recerca Vall d'Hebron (VHIR), Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain/St. Michael's Hospital, University of Toronto, Toronto, ON, Canada
| | - Howard L Weiner
- Partners Multiple Sclerosis Center, Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Philip de Jager
- Center for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Medical Center, New York, NY, USA/Cell Circuits Program, Broad Institute, Cambridge, MA, USA
| | - Giancarlo Comi
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology (INSPE), IRCCS San Raffaele Scientific Institute, Milan, Italy/Department of Neurology, Institute of Experimental Neurology (INSPE), Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Federica Esposito
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology (INSPE), IRCCS San Raffaele Scientific Institute, Milan, Italy/Department of Neurology, Institute of Experimental Neurology (INSPE), Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Manuel Comabella
- Servei de Neurologia-Neuroimmunologia, Centre d'Esclerosi Múltiple de Catalunya (Cemcat), Institut de Recerca Vall d'Hebron (VHIR), Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Filippo Martinelli-Boneschi
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology (INSPE), IRCCS San Raffaele Scientific Institute, Milan, Italy/Department of Biomedical Sciences for Health, University of Milan, Milan, Italy/Department of Neurology, IRCCS Policlinico San Donato, San Donato Milanese, Italy
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103
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Muntané G, Farré X, Rodríguez JA, Pegueroles C, Hughes DA, de Magalhães JP, Gabaldón T, Navarro A. Biological Processes Modulating Longevity across Primates: A Phylogenetic Genome-Phenome Analysis. Mol Biol Evol 2019; 35:1990-2004. [PMID: 29788292 PMCID: PMC6063263 DOI: 10.1093/molbev/msy105] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Aging is a complex process affecting different species and individuals in different ways. Comparing genetic variation across species with their aging phenotypes will help understanding the molecular basis of aging and longevity. Although most studies on aging have so far focused on short-lived model organisms, recent comparisons of genomic, transcriptomic, and metabolomic data across lineages with different lifespans are unveiling molecular signatures associated with longevity. Here, we examine the relationship between genomic variation and maximum lifespan across primate species. We used two different approaches. First, we searched for parallel amino-acid mutations that co-occur with increases in longevity across the primate linage. Twenty-five such amino-acid variants were identified, several of which have been previously reported by studies with different experimental setups and in different model organisms. The genes harboring these mutations are mainly enriched in functional categories such as wound healing, blood coagulation, and cardiovascular disorders. We demonstrate that these pathways are highly enriched for pleiotropic effects, as predicted by the antagonistic pleiotropy theory of aging. A second approach was focused on changes in rates of protein evolution across the primate phylogeny. Using the phylogenetic generalized least squares, we show that some genes exhibit strong correlations between their evolutionary rates and longevity-associated traits. These include genes in the Sphingosine 1-phosphate pathway, PI3K signaling, and the Thrombin/protease-activated receptor pathway, among other cardiovascular processes. Together, these results shed light into human senescence patterns and underscore the power of comparative genomics to identify pathways related to aging and longevity.
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Affiliation(s)
- Gerard Muntané
- Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Catalonia, Spain.,Hospital Universitari Institut Pere Mata, IISPV, Universitat Rovira i Virgili, Biomedical Network Research Centre on Mental Health (CIBERSAM), Reus, Spain
| | - Xavier Farré
- Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | - Juan Antonio Rodríguez
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Cinta Pegueroles
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | - David A Hughes
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom.,MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
| | - João Pedro de Magalhães
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, United Kingdom
| | - Toni Gabaldón
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Arcadi Navarro
- Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Catalonia, Spain.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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104
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Almagro P, Acosta E, Navarro A, Murillo M, Valdivielso S, de la Sierra A. Study of arterial stiffness in patients with an acute coronary event and chronic obstructive pulmonary disease confirmed by spirometry. Rev Clin Esp 2019. [DOI: 10.1016/j.rceng.2019.01.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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105
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Fernández JA, Frutos MD, Ruiz-Manzanera JJ, Navarro A, Torres G, Soria T. Gastrointestinal Stromal Tumors After Laparoscopic Gastric Bypass for Morbid Obesity: a Diagnostic and Therapeutic Challenge. Obes Surg 2019; 29:2618-2621. [DOI: 10.1007/s11695-019-03944-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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106
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Owonikoko T, Kim H, Govindan R, Ready N, Reck M, Peters S, Dakhil S, Navarro A, Rodriguez-Cid J, Schenker M, Lee J, Gutierrez V, Percent I, Morgensztern D, Fairchild J, Baudelet C, Park K. Nivolumab (nivo) plus ipilimumab (ipi), nivo, or placebo (pbo) as maintenance therapy in patients (pts) with extensive disease small cell lung cancer (ED-SCLC) after first-line (1L) platinum-based chemotherapy (chemo): Results from the double-blind, randomized phase III CheckMate 451 study. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz094] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
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107
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Herreros Pomares A, Amado H, Calabuig Fariñas S, Escorihuela E, Murga J, Torres S, Durendez-Saez E, Zhang F, Blasco A, Navarro A, Sampedro C, Jantus-Lewintre E, Camps C. Lung tumorspheres as a drug screening platform against cancer stem cells. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz073.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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108
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Bueso-Ródenas J, Romero G, Navarro A, Pérez E, Díaz JR. Effect of the pulsation type (alternate or simultaneous) on milk yield and health status of the mammary gland of Murciano-Granadina goats. J Dairy Sci 2019; 102:3339-3347. [PMID: 30772030 DOI: 10.3168/jds.2018-15286] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 12/17/2018] [Indexed: 11/19/2022]
Abstract
Recent research into how the pulsation type affects goat milking concluded that alternate pulsation (AP) and simultaneous pulsation (SP) similarly affect the milking efficiency (milking duration and milking fractioning) and teat end condition after milking when both pulsations are employed in short-term experiments. However, the use of SP in high pipeline milking machines led to higher vacuum fluctuations, which, in the long term, may entail a potential risk factor for the mammary gland health status. The aim of this work was to study how AP and SP affect the milk yield, mammary gland health status, and milk composition of goats in the long term, during a complete lactation period, in a high pipeline milking machine. With this objective, 100 Murciano-Granadina goats with similar parturition dates (4 ± 1 postpartum weeks) were divided into 2 similar groups (50 goats per group) according their parity, milk yield, mammary gland health status, and milking duration (after a 15-d pre-experimental period). Throughout the experimental period (7 mo), one group was milked using SP and the other group using AP. Every month, samplings were carried out of the variables related to sanitary status of the mammary gland, milk fractioning, milking duration, average and maximum milk flows, milk composition, teat end status, vacuum fluctuations at the short milk tube during milking, and pulsation tests. Results showed that the use of SP in a high pipeline milking machine showed higher vacuum fluctuations without involving any difference in the other variables studied. We concluded that the use of AP in the milking of Murciano-Granadina goats offers little improvement of the milking performance and increases the investment required for installation and maintenance of the milking machines.
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Affiliation(s)
- J Bueso-Ródenas
- Dpto. Producción Animal y Salud Pública, Universidad Católica de Valencia (UCV), C/Guillem de Castro 94, 46001 Valencia, Spain
| | - G Romero
- Dpto. Tecnología Agroalimentaria, Universidad Miguel Hernández (UMH), Ctra. de Beniel km 3.2., 03312 Orihuela (Alicante), Spain
| | - A Navarro
- Dpto. Tecnología Agroalimentaria, Universidad Miguel Hernández (UMH), Ctra. de Beniel km 3.2., 03312 Orihuela (Alicante), Spain
| | - E Pérez
- Dpto. Tecnología Agroalimentaria, Universidad Miguel Hernández (UMH), Ctra. de Beniel km 3.2., 03312 Orihuela (Alicante), Spain
| | - J R Díaz
- Dpto. Tecnología Agroalimentaria, Universidad Miguel Hernández (UMH), Ctra. de Beniel km 3.2., 03312 Orihuela (Alicante), Spain.
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109
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Karlsson Linnér R, Biroli P, Kong E, Meddens SFW, Wedow R, Fontana MA, Lebreton M, Tino SP, Abdellaoui A, Hammerschlag AR, Nivard MG, Okbay A, Rietveld CA, Timshel PN, Trzaskowski M, Vlaming RD, Zünd CL, Bao Y, Buzdugan L, Caplin AH, Chen CY, Eibich P, Fontanillas P, Gonzalez JR, Joshi PK, Karhunen V, Kleinman A, Levin RZ, Lill CM, Meddens GA, Muntané G, Sanchez-Roige S, Rooij FJV, Taskesen E, Wu Y, Zhang F, Auton A, Boardman JD, Clark DW, Conlin A, Dolan CC, Fischbacher U, Groenen PJF, Harris KM, Hasler G, Hofman A, Ikram MA, Jain S, Karlsson R, Kessler RC, Kooyman M, MacKillop J, Männikkö M, Morcillo-Suarez C, McQueen MB, Schmidt KM, Smart MC, Sutter M, Thurik AR, Uitterlinden AG, White J, Wit HD, Yang J, Bertram L, Boomsma DI, Esko T, Fehr E, Hinds DA, Johannesson M, Kumari M, Laibson D, Magnusson PKE, Meyer MN, Navarro A, Palmer AA, Pers TH, Posthuma D, Schunk D, Stein MB, Svento R, Tiemeier H, Timmers PRHJ, Turley P, Ursano RJ, Wagner GG, Wilson JF, Gratten J, Lee JJ, Cesarini D, Benjamin DJ, Koellinger PD, Beauchamp JP. Genome-wide association analyses of risk tolerance and risky behaviors in over 1 million individuals identify hundreds of loci and shared genetic influences. Nat Genet 2019; 51:245-257. [PMID: 30643258 PMCID: PMC6713272 DOI: 10.1038/s41588-018-0309-3] [Citation(s) in RCA: 337] [Impact Index Per Article: 67.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 11/07/2018] [Indexed: 02/02/2023]
Abstract
Humans vary substantially in their willingness to take risks. In a combined sample of over 1 million individuals, we conducted genome-wide association studies (GWAS) of general risk tolerance, adventurousness, and risky behaviors in the driving, drinking, smoking, and sexual domains. Across all GWAS, we identified hundreds of associated loci, including 99 loci associated with general risk tolerance. We report evidence of substantial shared genetic influences across risk tolerance and the risky behaviors: 46 of the 99 general risk tolerance loci contain a lead SNP for at least one of our other GWAS, and general risk tolerance is genetically correlated ([Formula: see text] ~ 0.25 to 0.50) with a range of risky behaviors. Bioinformatics analyses imply that genes near SNPs associated with general risk tolerance are highly expressed in brain tissues and point to a role for glutamatergic and GABAergic neurotransmission. We found no evidence of enrichment for genes previously hypothesized to relate to risk tolerance.
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Affiliation(s)
- Richard Karlsson Linnér
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, Amsterdam, the Netherlands.
- Erasmus University Rotterdam Institute for Behavior and Biology, Erasmus School of Economics, Erasmus University Rotterdam, Rotterdam, the Netherlands.
- Department of Economics, VU University Amsterdam, Amsterdam, the Netherlands.
| | - Pietro Biroli
- Department of Economics, University of Zurich, Zurich, Switzerland
| | - Edward Kong
- Department of Economics, Harvard University, Cambridge, MA, USA
| | - S Fleur W Meddens
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, Amsterdam, the Netherlands
- Erasmus University Rotterdam Institute for Behavior and Biology, Erasmus School of Economics, Erasmus University Rotterdam, Rotterdam, the Netherlands
- Department of Economics, VU University Amsterdam, Amsterdam, the Netherlands
| | - Robbee Wedow
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Analytic Translational Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Sociology, Harvard University, Cambridge, MA, USA
| | - Mark Alan Fontana
- Center for the Advancement of Value in Musculoskeletal Care, Hospital for Special Surgery, New York, NY, USA
- Department of Healthcare Policy and Research, Weill Cornell Medical College, Cornell University, New York, NY, USA
| | - Maël Lebreton
- Amsterdam School of Economics, University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Brain and Cognition, University of Amsterdam, Amsterdam, the Netherlands
| | - Stephen P Tino
- Department of Economics, University of Toronto, Toronto, Ontario, Canada
| | - Abdel Abdellaoui
- Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Anke R Hammerschlag
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, Amsterdam, the Netherlands
| | - Michel G Nivard
- Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Aysu Okbay
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, Amsterdam, the Netherlands
- Department of Economics, VU University Amsterdam, Amsterdam, the Netherlands
| | - Cornelius A Rietveld
- Erasmus University Rotterdam Institute for Behavior and Biology, Erasmus School of Economics, Erasmus University Rotterdam, Rotterdam, the Netherlands
- Department of Applied Economics, Erasmus School of Economics, Erasmus University Rotterdam, Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Pascal N Timshel
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Maciej Trzaskowski
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Ronald de Vlaming
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, Amsterdam, the Netherlands
- Erasmus University Rotterdam Institute for Behavior and Biology, Erasmus School of Economics, Erasmus University Rotterdam, Rotterdam, the Netherlands
- Department of Economics, VU University Amsterdam, Amsterdam, the Netherlands
| | - Christian L Zünd
- Department of Economics, University of Zurich, Zurich, Switzerland
| | - Yanchun Bao
- Institute for Social and Economic Research, University of Essex, Colchester, UK
| | - Laura Buzdugan
- Seminar for Statistics, Department of Mathematics, ETH Zurich, Zurich, Switzerland
- Department of Economics, University of Zurich, Zurich, Switzerland
| | | | - Chia-Yen Chen
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic Translational Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Psychiatric & Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Peter Eibich
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Socio-Economic Panel Study, DIW Berlin, Berlin, Germany
- Max Planck Institute for Demographic Research, Rostock, Germany
| | | | - Juan R Gonzalez
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Peter K Joshi
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, Scotland
| | - Ville Karhunen
- Center for Life Course Health Research, University of Oulu, Oulu, Finland
| | | | - Remy Z Levin
- Department of Economics, University of California San Diego, La Jolla, CA, USA
| | - Christina M Lill
- Genetic and Molecular Epidemiology Group, Lübeck Interdisciplinary Platform for Genome Analytics, Institutes of Neurogenetics & Cardiogenetics, University of Lübeck, Lübeck, Germany
| | | | - Gerard Muntané
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
- Research Department, Hospital Universitari Institut Pere Mata, Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain
- Centro de Investigación Biomédica en Red en Salud Mental (CIBERSAM), Reus, Spain
| | | | - Frank J van Rooij
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Erdogan Taskesen
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, Amsterdam, the Netherlands
| | - Yang Wu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Futao Zhang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Adam Auton
- Research, 23andMe, Inc., Mountain View, CA, USA
| | - Jason D Boardman
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA
- Institute of Behavioral Science, University of Colorado Boulder, Boulder, CO, USA
- Department of Sociology, University of Colorado Boulder, Boulder, CO, USA
| | - David W Clark
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, Scotland
| | - Andrew Conlin
- Department of Economics and Finance, Oulu Business School, University of Oulu, Oulu, Finland
| | - Conor C Dolan
- Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Urs Fischbacher
- Department of Economics, University of Konstanz, Konstanz, Germany
- Thurgau Institute of Economics, Kreuzlingen, Switzerland
| | - Patrick J F Groenen
- Erasmus University Rotterdam Institute for Behavior and Biology, Erasmus School of Economics, Erasmus University Rotterdam, Rotterdam, the Netherlands
- Department of Econometrics, Erasmus University Rotterdam, Rotterdam, Rotterdam, the Netherlands
| | - Kathleen Mullan Harris
- Department of Sociology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Gregor Hasler
- Unit of Psychiatry Research, University of Fribourg, Fribourg, Switzerland
| | - Albert Hofman
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Mohammad A Ikram
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Sonia Jain
- Family Medicine and Public Health, University of California San Diego, La Jolla, CA, USA
| | - Robert Karlsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Ronald C Kessler
- Department of Health Care Policy, Harvard Medical School, Boston, MA, USA
| | | | - James MacKillop
- Peter Boris Centre for Addictions Research, McMaster University/St. Joseph's Healthcare Hamilton, Hamilton, Ontario, Canada
- Homewood Research Institute, Guelph, Ontario, Canada
| | - Minna Männikkö
- Center for Life Course Health Research, University of Oulu, Oulu, Finland
| | - Carlos Morcillo-Suarez
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Matthew B McQueen
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
| | - Klaus M Schmidt
- Department of Economics, University of Munich, Munich, Germany
| | - Melissa C Smart
- Institute for Social and Economic Research, University of Essex, Colchester, UK
| | - Matthias Sutter
- Department of Economics, University of Cologne, Cologne, Germany
- Experimental Economics Group, Max Planck Institute for Research into Collective Goods, Bonn, Germany
- Department of Public Finance, University of Innsbruck, Innsbruck, Austria
| | - A Roy Thurik
- Erasmus University Rotterdam Institute for Behavior and Biology, Erasmus School of Economics, Erasmus University Rotterdam, Rotterdam, the Netherlands
- Montpellier Business School, Montpellier, France
| | - André G Uitterlinden
- Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Jon White
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Harriet de Wit
- Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, IL, USA
| | - Jian Yang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Lars Bertram
- Genetic and Molecular Epidemiology Group, Lübeck Interdisciplinary Platform for Genome Analytics, Institutes of Neurogenetics & Cardiogenetics, University of Lübeck, Lübeck, Germany
- Dept of Psychology, University of Olso, Oslo, Norway
- School of Public Health, Imperial College London, London, UK
| | - Dorret I Boomsma
- Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Tõnu Esko
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Ernst Fehr
- Department of Economics, University of Zurich, Zurich, Switzerland
| | | | - Magnus Johannesson
- Department of Economics, Stockholm School of Economics, Stockholm, Sweden
| | - Meena Kumari
- Institute for Social and Economic Research, University of Essex, Colchester, UK
| | - David Laibson
- Department of Economics, Harvard University, Cambridge, MA, USA
| | - Patrik K E Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Michelle N Meyer
- Center for Translational Bioethics and Health Care Policy, Geisinger Health System, Danville, PA, USA
| | - Arcadi Navarro
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
| | - Abraham A Palmer
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Tune H Pers
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Danielle Posthuma
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, Amsterdam, the Netherlands
- Department of Clinical Genetics, VU Medical Centre, Amsterdam, the Netherlands
| | - Daniel Schunk
- Department of Economics, Johannes Gutenberg University, Mainz, Germany
| | - Murray B Stein
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Family Medicine and Public Health, University of California San Diego, La Jolla, CA, USA
| | - Rauli Svento
- Department of Economics and Finance, Oulu Business School, University of Oulu, Oulu, Finland
| | - Henning Tiemeier
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Paul R H J Timmers
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, Scotland
| | - Patrick Turley
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic Translational Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Behavioral and Health Genomics Center, Center for Economic and Social Research, University of Southern California, Los Angeles, CA, USA
| | - Robert J Ursano
- Department of Psychiatry, Center for the Study of Traumatic Stress, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Gert G Wagner
- Socio-Economic Panel Study, DIW Berlin, Berlin, Germany
- Max Planck Institute for Human Development, Berlin, Germany
| | - James F Wilson
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, Scotland
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, Scotland
| | - Jacob Gratten
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
- Mater Medical Research Institute, Translational Research Institute, Brisbane, Australia
| | - James J Lee
- Department of Psychology, University of Minnesota Twin Cities, Minneapolis, MN, USA
| | - David Cesarini
- Department of Economics, New York University, New York, NY, USA
| | - Daniel J Benjamin
- Behavioral and Health Genomics Center, Center for Economic and Social Research, University of Southern California, Los Angeles, CA, USA
- Department of Economics, University of Southern California, Los Angeles, CA, USA
- National Bureau of Economic Research, Cambridge, MA, USA
| | - Philipp D Koellinger
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, Amsterdam, the Netherlands
- Department of Economics, VU University Amsterdam, Amsterdam, the Netherlands
- German Institute for Economic Research, DIW Berlin, Berlin, Germany
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Almagro P, Acosta E, Navarro A, Murillo MF, Valdivielso S, de la Sierra A. Study of arterial stiffness in patients with an acute coronary event and chronic obstructive pulmonary disease confirmed by spirometry. Rev Clin Esp 2019; 219:251-255. [PMID: 30660321 DOI: 10.1016/j.rce.2018.08.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Revised: 07/24/2018] [Accepted: 08/13/2018] [Indexed: 11/30/2022]
Abstract
BACKGROUND AND OBJECTIVES Chronic obstructive pulmonary disease (COPD) worsens the prognosis for patients with an acute coronary event (ACE) treated with percutaneous coronary intervention. Objective To assess the effect of COPD on arterial stiffness in patients with an ACE. METHODS The study included patients with an ACE treated with percutaneous coronary intervention. At 1 month, postbronchodilation spirometry was performed, and arterial stiffness and markers of myocardial damage (troponin T and ProBNP) were measured. RESULTS We included 68 patients, 33% of whom had COPD (59% undiagnosed). The patients with COPD presented higher arterial stiffness values after adjusting for age and blood pressure readings. The troponin T and ProBNP levels were higher in the patients with COPD. CONCLUSIONS Arterial stiffness is greater in patients with an ACE if they have concomitant COPD. These findings can help explain the poorer prognosis of patients with both conditions.
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Affiliation(s)
- P Almagro
- Unidad de Pacientes Crónicos Complejos, Departamento de Medicina Interna, Hospital Universitario Mútua Terrasa, Universidad de Barcelona, Terrasa, Barcelona, España; Departamento de Medicina Interna, Hospital Universitario Mútua Terrasa, Universidad de Barcelona, Terrasa, Barcelona, España.
| | - E Acosta
- Departamento de Medicina Interna, Hospital Universitario Mútua Terrasa, Universidad de Barcelona, Terrasa, Barcelona, España
| | - A Navarro
- Servicio de Neumología, Hospital Universitario Mútua Terrasa, Universidad de Barcelona, Terrasa, Barcelona, España
| | - M F Murillo
- Departamento de Medicina Interna, Hospital Universitario Mútua Terrasa, Universidad de Barcelona, Terrasa, Barcelona, España
| | - S Valdivielso
- Servicio de Cardiología, Hospital Universitario Mútua Terrassa, Universidad de Barcelona, Terrasa, Barcelona, España
| | - A de la Sierra
- Departamento de Medicina Interna, Hospital Universitario Mútua Terrasa, Universidad de Barcelona, Terrasa, Barcelona, España
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Navarrete F, Mellisho E, Wang Y, Cabezas J, Rodriguez-Alvarez LL, Navarro A, Saravia F, Castro FO. 128 Next-generation RNA sequencing of horse adipose and endometrial mesenchymal stem cells from the same donors unveils striking differences in their transcriptomic pattern. Reprod Fertil Dev 2019. [DOI: 10.1071/rdv31n1ab128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Earlier we successfully isolated and characterised endometrial (eMSC) and adipose (aMSC) mesenchymal stem cells from the same donors. Mesenchymal stem cells share biological traits but display different surface marker phenotype and migration ability. Here we extended our research to their mRNA signature using next-generation sequencing. The RNA from cells (3 biological replicates from each cell type and 3 technical replicates) at 90% confluence was extracted using a total RNA extraction kit and sent for mRNA-Seq (Norgen, Ontario, Canada; Illumina Sequencing Platform NextSEqn 500). Raw 76-bp single-end reads were aligned against the EquCab3 genome using RNA-STAR aligner. Counts were filtrated at a minimum of 5. Pairwise comparisons between the cell types were the input for gene ontology enrichment analysis. Only genes differentially expressed (DE) with 5 folds change (FC; P<0.05) were analysed. For DE analysis, eMSC were set as control and compared with aMSC. Unsupervised hierarchical clustering of the global gene expression signatures was done to compare the samples from each line using principal component analysis (PCA) and EdgeR: v3.20.9. Gene expression was normalized using FPKM. The heat map was built using R studio with G-plot package. A total of 14,896 transcripts with at least 5 reads were found; of these, 1598 were DE: 627 up-regulated (FC range: 2 to 236×) and 971 down-regulated (FC range: 2 to 464×) in eMSC. There was a marked dispersion in the FC of up- and down-regulated genes (>50×: 8 and 13; >20×, <50×: 9 and 17; >10×, <20×: 29 and 63; >5×, <10×: 91 and 130 and >2×, <5×: 490 and 748, respectively). Only genes DE with FC at least 5× were used for gene ontology and PCA analysis. Though 14,058 genes were common to both cell types, specific set of genes were found only in eMSC (n=162) or aMSC (n=676). Among the top 50 genes overexpressed in eMSC, several genes key for stem cell growth, immune response, migration and angiogenesis were found: TRIL, CXCL8, PDGF-D, SEMA5A, PTGS2, FGD, LAMA2, IL36G. In the top 50 down-regulated genes, some pivotal for osteoblast, adipogenic and neural differentiation were dramatically down-regulated (GPM6B, SCARA5 and NOTCH3 or NEFM, respectively), but no genes involved in immune rejection or stem cell proliferation were found. In gene ontology, the categories represented the most were cellular, developmental, metabolic, and immune system processes, as well as biological regulation, response to stimuli, organellar biogenesis, locomotion, localization and biological adhesion. Heat map and PCA analysis showed that one individual cell line from each type diverged markedly from the shared pattern. Individual variability of the donors may impinge upon the results; nevertheless, striking differences in the mRNA portfolio of eMSC and aMSC were detected. The importance and potential biological role of several of the genes and processes named above will be discussed in detail elsewhere.
This work was supported by grant FONDECYT REGULAR 1150757 and the Government of Chile.
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112
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Tiongco RE, Arceo E, Dizon D, Navarro A, Rivera N, Salita C, Singian E. Phenotypic evaluation of ESBL- and carbapenemaseproducing Escherichia coli and Klebsiella pneumoniae from a teaching hospital in the Philippines. Trop Biomed 2018; 35:1064-1074. [PMID: 33601853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Antimicrobial resistance is a worldwide public health concern. Rise in the number of antimicrobial resistant organisms, such as extended spectrum β-lactamase- (ESBL) and carbapenemase-producing Escherichia coli and Klebsiella pneumoniae, continue to burden millions of people worldwide. E. coli and K. pneumoniae were isolated and collected for four months from a teaching hospital in the Philippines. All isolates were subjected to ESBL and carbapenemase testing using the double disk synergy test and modified Hodge test, respectively. Their pattern of resistance among different classes of antimicrobial agents was also investigated using the Kirby-Bauer disk diffusion test. Among the 32 clinical isolates tested, 28.1% were positive for ESBL production and 6.3% were positive for carbapenemase production. Species-specific classification showed that E. coli (44.4%) has the highest rate of ESBL production whereas both E. coli (5.6%) and K. pneumoniae (7.1%) showed almost similar rates of carbapenemase production. Antimicrobial resistance pattern of drug resistant isolates showed that all organisms were resistant to ampicillin, and majority showed resistance towards ciprofloxacin, cefotaxime, ceftriaxone, and sulfamethoxazole/trimethoprim. ESBL production is seen highest among E. coli isolates while similar rates of carbapenemase production was observed to both E. coli and K. pneumoniae isolates. Overall, antimicrobial resistance continues to rise and poses a huge threat in public health worldwide. Efforts should be made in developing rapid tests for antimicrobial resistance and to search for effective treatment from infections caused by multidrug resistant organisms.
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Affiliation(s)
- R E Tiongco
- Department of Medical Technology, College of Allied Medical Professions, Angeles University Foundation, Angeles City, Philippines
| | - E Arceo
- Department of Medical Technology, College of Allied Medical Professions, Angeles University Foundation, Angeles City, Philippines
| | - D Dizon
- Department of Medical Technology, College of Allied Medical Professions, Angeles University Foundation, Angeles City, Philippines
| | - A Navarro
- Department of Medical Technology, College of Allied Medical Professions, Angeles University Foundation, Angeles City, Philippines
| | - N Rivera
- Department of Medical Technology, College of Allied Medical Professions, Angeles University Foundation, Angeles City, Philippines
| | - C Salita
- Department of Medical Technology, College of Allied Medical Professions, Angeles University Foundation, Angeles City, Philippines
| | - E Singian
- Department of Medical Technology, College of Allied Medical Professions, Angeles University Foundation, Angeles City, Philippines
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Hartasánchez DA, Brasó-Vives M, Heredia-Genestar JM, Pybus M, Navarro A. Effect of Collapsed Duplications on Diversity Estimates: What to Expect. Genome Biol Evol 2018; 10:2899-2905. [PMID: 30364947 PMCID: PMC6239678 DOI: 10.1093/gbe/evy223] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/08/2018] [Indexed: 12/19/2022] Open
Abstract
The study of segmental duplications (SDs) and copy-number variants (CNVs) is of great importance in the fields of genomics and evolution. However, SDs and CNVs are usually excluded from genome-wide scans for natural selection. Because of high identity between copies, SDs and CNVs that are not included in reference genomes are prone to be collapsed-that is, mistakenly aligned to the same region-when aligning sequence data from single individuals to the reference. Such collapsed duplications are additionally challenging because concerted evolution between duplications alters their site frequency spectrum and linkage disequilibrium patterns. To investigate the potential effect of collapsed duplications upon natural selection scans we obtained expectations for four summary statistics from simulations of duplications evolving under a range of interlocus gene conversion and crossover rates. We confirm that summary statistics traditionally used to detect the action of natural selection on DNA sequences cannot be applied to SDs and CNVs since in some cases values for known duplications mimic selective signatures. As a proof of concept of the pervasiveness of collapsed duplications, we analyzed data from the 1,000 Genomes Project. We find that, within regions identified as variable in copy number, diversity between individuals with the duplication is consistently higher than between individuals without the duplication. Furthermore, the frequency of single nucleotide variants (SNVs) deviating from Hardy-Weinberg Equilibrium is higher in individuals with the duplication, which strongly suggests that higher diversity is a consequence of collapsed duplications and incorrect evaluation of SNVs within these CNV regions.
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Affiliation(s)
- Diego A Hartasánchez
- Institute of Evolutionary Biology (Universitat Pompeu Fabra - CSIC), PRBB, Barcelona, Catalonia, Spain.,Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain.,Laboratoire de Biométrie et Biologie Évolutive UMR 5558, Université de Lyon, Université Lyon 1, CNRS, Villeurbanne, France
| | - Marina Brasó-Vives
- Institute of Evolutionary Biology (Universitat Pompeu Fabra - CSIC), PRBB, Barcelona, Catalonia, Spain.,Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | - Jose Maria Heredia-Genestar
- Institute of Evolutionary Biology (Universitat Pompeu Fabra - CSIC), PRBB, Barcelona, Catalonia, Spain.,Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | - Marc Pybus
- Institute of Evolutionary Biology (Universitat Pompeu Fabra - CSIC), PRBB, Barcelona, Catalonia, Spain.,Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | - Arcadi Navarro
- Institute of Evolutionary Biology (Universitat Pompeu Fabra - CSIC), PRBB, Barcelona, Catalonia, Spain.,Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain.,National Institute for Bioinformatics (INB), Barcelona, Catalonia, Spain.,Centre for Genomic Regulation (CRG), Barcelona, Catalonia, Spain
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Aguilar I, Navarro A, Wilber K. A STRATEGIC PLAN FOR CRITICAL MISSING PERSONS WITH DEMENTIA IN LOS ANGELES COUNTY. Innov Aging 2018. [DOI: 10.1093/geroni/igy023.1964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- I Aguilar
- USC Edward R. Roybal Institute on Aging
| | | | - K Wilber
- University of Southern California
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115
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Santoro A, Su WC, Navarro A, Simonelli M, Yang JH, Ardizzoni A, Barlesi F, Kang J, Didominick S, Abdelhady A, Goswami B, Crystal A, Felip E. Dose-determination results from a phase Ib/II study of ceritinib (CER) + ribociclib (RIB) in ALK-positive (ALK+) non-small cell lung cancer (NSCLC). Ann Oncol 2018. [DOI: 10.1093/annonc/mdy292.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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116
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Malhotra S, Sorosina M, Río J, Peroni S, Midaglia L, Villar LM, Álvarez-Cermeño JC, Schroeder I, Esposito F, Clarelli F, Zettl UK, Lechner-Scott J, Spataro N, Navarro A, Comi G, Montalban X, Martinelli-Boneschi F, Comabella M. NLRP3 polymorphisms and response to interferon-beta in multiple sclerosis patients. Mult Scler 2018; 24:1507-1510. [PMID: 29117789 DOI: 10.1177/1352458517739137] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
We aimed to investigate whether NLR family, pyrin domain containing 3 (NLRP3) polymorphisms are associated with the response to interferon-beta (IFNβ) in multiple sclerosis (MS) patients. A total of 14 NLRP3 polymorphisms were genotyped in a cohort of 665 relapsing-remitting MS patients recruited across 5 centers and classified into responders and non-responders according to clinical-radiological criteria after 1 year of IFNβ treatment. A meta-analysis failed to demonstrate significant associations between the response to IFNβ and NLRP3 polymorphisms. These findings do not support a role of polymorphisms located in the NLRP3 gene and the response to IFNβ in MS patients.
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Affiliation(s)
- Sunny Malhotra
- Servei de Neurologia-Neuroimmunologia, Centre d'Esclerosi Múltiple de Catalunya (Cemcat) and Institut de Recerca Vall d'Hebron (VHIR), Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Melissa Sorosina
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology (INSPE), Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Jordi Río
- Servei de Neurologia-Neuroimmunologia, Centre d'Esclerosi Múltiple de Catalunya (Cemcat) and Institut de Recerca Vall d'Hebron (VHIR), Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Silvia Peroni
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology (INSPE), Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Luciana Midaglia
- Servei de Neurologia-Neuroimmunologia, Centre d'Esclerosi Múltiple de Catalunya (Cemcat) and Institut de Recerca Vall d'Hebron (VHIR), Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Luisa M Villar
- Departments of Neurology and Immunology, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigacion Sanitaria, Madrid, Spain
| | - José C Álvarez-Cermeño
- Departments of Neurology and Immunology, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigacion Sanitaria, Madrid, Spain
| | - Ina Schroeder
- Department of Neurology, Neuroimmunological Section, University of Rostock, Rostock, Germany
| | - Federica Esposito
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology (INSPE), Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy/Department of Neurology, Institute of Experimental Neurology (INSPE), Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Ferdinando Clarelli
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology (INSPE), Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Uwe K Zettl
- Department of Neurology, Neuroimmunological Section, University of Rostock, Rostock, Germany
| | - Jeannette Lechner-Scott
- Department of Neurology, John Hunter Hospital, Newcastle, NSW, Australia/Hunter Medical Research Institute, The University of Newcastle, Newcastle, NSW, Australia
| | - Nino Spataro
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain/Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Arcadi Navarro
- National Institute for Bioinformatics, Universitat Pompeu Fabra, Barcelona, Spain/Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Giancarlo Comi
- Department of Neurology, Institute of Experimental Neurology (INSPE), Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Xavier Montalban
- Servei de Neurologia-Neuroimmunologia, Centre d'Esclerosi Múltiple de Catalunya (Cemcat) and Institut de Recerca Vall d'Hebron (VHIR), Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Filippo Martinelli-Boneschi
- Laboratory of Genetics of Complex Disorders and Department of Neurology, IRCCS Policlinico San Donato, Milan, Italy/Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Manuel Comabella
- Servei de Neurologia-Neuroimmunologia, Centre d'Esclerosi Múltiple de Catalunya (Cemcat) and Institut de Recerca Vall d'Hebron (VHIR), Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
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Herreros-Pomares A, Calabuig Fariñas S, de Maya J, Escorihuela E, Durendez-Saez E, Blasco Cordellat A, Navarro A, García-Del-Olmo E, Lucas R, Farràs R, Jantus-Lewintre E, Camps C. An expression signature characterizes cancer stem cells from lung adenocarcinoma patients. Ann Oncol 2018. [DOI: 10.1093/annonc/mdy303.051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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118
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Alemany M, Domènech M, Vilariño N, Jové M, Brao I, Arellano M, Lucas A, Navarro A, Palmero R, Simó M, Velasco R, Nadal E, Bruna J. P05.21 T1-flair to T1-gadolinium MRI ratio as a predictive value of treatment response in non-small-cell lung cancer (NSCLC) patients affected by multiple brain metastases. Neuro Oncol 2018. [DOI: 10.1093/neuonc/noy139.347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- M Alemany
- Neuro-Oncology Unit. Bellvitge University Hospital-ICO, L’Hospitalet, Spain
| | - M Domènech
- Thoracic Oncology Unit. Department of Medical Oncology, Catalan Institute of Oncology, L’Hospitalet, Spain
| | - N Vilariño
- Thoracic Oncology Unit. Department of Medical Oncology, Catalan Institute of Oncology, L’Hospitalet, Spain
| | - M Jové
- Thoracic Oncology Unit. Department of Medical Oncology, Catalan Institute of Oncology, L’Hospitalet, Spain
| | - I Brao
- Thoracic Oncology Unit. Department of Medical Oncology, Catalan Institute of Oncology, L’Hospitalet, Spain
| | - M Arellano
- Thoracic Oncology Unit. Department of Medical Oncology, Catalan Institute of Oncology, L’Hospitalet, Spain
| | - A Lucas
- Department of Radiation. Catalan Institute of Oncology, L’Hospitalet, Spain
| | - A Navarro
- Department of Radiation. Catalan Institute of Oncology, L’Hospitalet, Spain
| | - R Palmero
- Thoracic Oncology Unit. Department of Medical Oncology, Catalan Institute of Oncology, L’Hospitalet, Spain
| | - M Simó
- Neuro-Oncology Unit. Bellvitge University Hospital-ICO, L’Hospitalet, Spain
| | - R Velasco
- Neuro-Oncology Unit. Bellvitge University Hospital-ICO, L’Hospitalet, Spain
| | - E Nadal
- Thoracic Oncology Unit. Department of Medical Oncology, Catalan Institute of Oncology, L’Hospitalet, Spain
| | - J Bruna
- Neuro-Oncology Unit. Bellvitge University Hospital-ICO, L’Hospitalet, Spain
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119
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Gamiz P, Rendon M, de los Santos J, Remohi J, Navarro A, Serra V, De Los Santos M. The use of atmospheric oxygen (O2) concentration during embryo culture until day 3 of development, does not affect obstetric and perinatal outcomes. Fertil Steril 2018. [DOI: 10.1016/j.fertnstert.2018.07.160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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120
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Martínez H, Barrachina S, Castillo M, Quintana-OrtÍ ES, Rambla de Argila J, Farré X, Navarro A. FaST-LMM for Two-Way Epistasis Tests on High-Performance Clusters. J Comput Biol 2018; 25:862-870. [PMID: 30020811 DOI: 10.1089/cmb.2018.0087] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
We introduce a version of the epistasis test in FaST-LMM for clusters of multithreaded processors. This new software maintains the sensitivity of the original FaST-LMM while delivering acceleration that is close to linear on 12-16 nodes of two recent platforms, with respect to improved implementation of FaST-LMM presented in an earlier work. This efficiency is attained through several enhancements on the original single-node version of FaST-LMM, together with the development of a message passing interface (MPI)-based version that ensures a balanced distribution of the workload as well as a multigraphics processing unit (GPU) module that can exploit the presence of multiple GPUs per node.
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Affiliation(s)
- Héctor Martínez
- 1 Department of Computer Science and Engineering, Jaume I University , Castellón, Spain
| | - Sergio Barrachina
- 1 Department of Computer Science and Engineering, Jaume I University , Castellón, Spain
| | - Maribel Castillo
- 1 Department of Computer Science and Engineering, Jaume I University , Castellón, Spain
| | | | - Jordi Rambla de Argila
- 2 Department of Experimental and Health Sciences, Pompeu Fabra University , Barcelona, Spain
| | - Xavier Farré
- 2 Department of Experimental and Health Sciences, Pompeu Fabra University , Barcelona, Spain
| | - Arcadi Navarro
- 2 Department of Experimental and Health Sciences, Pompeu Fabra University , Barcelona, Spain
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Kuderna LFK, Tomlinson C, Hillier LW, Tran A, Fiddes IT, Armstrong J, Laayouni H, Gordon D, Huddleston J, Garcia Perez R, Povolotskaya I, Serres Armero A, Gómez Garrido J, Ho D, Ribeca P, Alioto T, Green RE, Paten B, Navarro A, Betranpetit J, Herrero J, Eichler EE, Sharp AJ, Feuk L, Warren WC, Marques-Bonet T. A 3-way hybrid approach to generate a new high-quality chimpanzee reference genome (Pan_tro_3.0). Gigascience 2018; 6:1-6. [PMID: 29092041 PMCID: PMC5714192 DOI: 10.1093/gigascience/gix098] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 09/08/2017] [Indexed: 11/14/2022] Open
Abstract
The chimpanzee is arguably the most important species for the study of human origins. A key resource for these studies is a high-quality reference genome assembly; however, as with most mammalian genomes, the current iteration of the chimpanzee reference genome assembly is highly fragmented. In the current iteration of the chimpanzee reference genome assembly (Pan_tro_2.1.4), the sequence is scattered across more then 183 000 contigs, incorporating more than 159 000 gaps, with a genome-wide contig N50 of 51 Kbp. In this work, we produce an extensive and diverse array of sequencing datasets to rapidly assemble a new chimpanzee reference that surpasses previous iterations in bases represented and organized in large scaffolds. To this end, we show substantial improvements over the current release of the chimpanzee genome (Pan_tro_2.1.4) by several metrics, such as increased contiguity by >750% and 300% on contigs and scaffolds, respectively, and closure of 77% of gaps in the Pan_tro_2.1.4 assembly gaps spanning >850 Kbp of the novel coding sequence based on RNASeq data. We further report more than 2700 genes that had putatively erroneous frame-shift predictions to human in Pan_tro_2.1.4 and show a substantial increase in the annotation of repetitive elements. We apply a simple 3-way hybrid approach to considerably improve the reference genome assembly for the chimpanzee, providing a valuable resource for the study of human origins. Furthermore, we produce extensive sequencing datasets that are all derived from the same cell line, generating a broad non-human benchmark dataset.
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Affiliation(s)
- Lukas F K Kuderna
- Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain
| | - Chad Tomlinson
- McDonnell Genome Institute, Department of Medicine, Department of Genetics, Washington University School of Medicine, 4444 Forest Park Ave., St. Louis, MO 63108, USA
| | - LaDeana W Hillier
- McDonnell Genome Institute, Department of Medicine, Department of Genetics, Washington University School of Medicine, 4444 Forest Park Ave., St. Louis, MO 63108, USA
| | - Annabel Tran
- Bill Lyons Informatics Centre, UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6DD, UK
| | - Ian T Fiddes
- Genomics Institute, University of California Santa Cruz and Howard Hughes Medical Institute, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Joel Armstrong
- Genomics Institute, University of California Santa Cruz and Howard Hughes Medical Institute, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Hafid Laayouni
- Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain.,Bioinformatics Studies, ESCI-UPF, Pg. Pujades 1, 08003, Barcelona, Spain
| | - David Gordon
- Department of Genome Sciences, University of Washington School of Medicine, Box 355065, Seattle, WA 98195, USA.,Howard Hughes Medical Institute, University of Washington, Box 355065, Seattle, WA 98195, USA
| | - John Huddleston
- Department of Genome Sciences, University of Washington School of Medicine, Box 355065, Seattle, WA 98195, USA.,Howard Hughes Medical Institute, University of Washington, Box 355065, Seattle, WA 98195, USA
| | - Raquel Garcia Perez
- Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain
| | - Inna Povolotskaya
- Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain
| | - Aitor Serres Armero
- Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain
| | - Jèssica Gómez Garrido
- Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain
| | - Daniel Ho
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Paolo Ribeca
- The Pirbright Institute, Ash Road, Pirbright, Woking, GU24 0NF, UK
| | - Tyler Alioto
- Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain
| | - Richard E Green
- Department of Biomolecular Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95060, USA.,Dovetail Genomics, Santa Cruz, 2161 Delaware Ave., Santa Cruz, CA 95060, USA
| | - Benedict Paten
- Genomics Institute, University of California Santa Cruz and Howard Hughes Medical Institute, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Arcadi Navarro
- Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain.,Institucio Catalana de Recerca i Estudis Avancats (ICREA), Passeig Lluís Companys 23, Barcelona, Catalonia 08010, Spain
| | - Jaume Betranpetit
- Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain
| | - Javier Herrero
- Bill Lyons Informatics Centre, UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6DD, UK
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Box 355065, Seattle, WA 98195, USA.,Howard Hughes Medical Institute, University of Washington, Box 355065, Seattle, WA 98195, USA
| | - Andrew J Sharp
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lars Feuk
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Box 815, Uppsala University 751 08 Uppsala, Sweden
| | - Wesley C Warren
- McDonnell Genome Institute, Department of Medicine, Department of Genetics, Washington University School of Medicine, 4444 Forest Park Ave., St. Louis, MO 63108, USA
| | - Tomas Marques-Bonet
- Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain.,Institucio Catalana de Recerca i Estudis Avancats (ICREA), Passeig Lluís Companys 23, Barcelona, Catalonia 08010, Spain
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122
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Marigorta UM, Rodríguez JA, Gibson G, Navarro A. Replicability and Prediction: Lessons and Challenges from GWAS. Trends Genet 2018; 34:504-517. [PMID: 29716745 PMCID: PMC6003860 DOI: 10.1016/j.tig.2018.03.005] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 03/12/2018] [Accepted: 03/26/2018] [Indexed: 12/29/2022]
Abstract
Since the publication of the Wellcome Trust Case Control Consortium (WTCCC) landmark study a decade ago, genome-wide association studies (GWAS) have led to the discovery of thousands of risk variants involved in disease etiology. This success story has two angles that are often overlooked. First, GWAS findings are highly replicable. This is an unprecedented phenomenon in complex trait genetics, and indeed in many areas of science, which in past decades have been plagued by false positives. At a time of increasing concerns about the lack of reproducibility, we examine the biological and methodological reasons that account for the replicability of GWAS and identify the challenges ahead. In contrast to the exemplary success of disease gene discovery, at present GWAS findings are not useful for predicting phenotypes. We close with an overview of the prospects for individualized prediction of disease risk and its foreseeable impact in clinical practice.
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Affiliation(s)
- Urko M Marigorta
- Center for Integrative Genomics, Georgia Institute of Technology, Atlanta, GA, USA; These authors contributed equally
| | - Juan Antonio Rodríguez
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Catalonia, Spain; Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona, Catalonia, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain; These authors contributed equally. https://twitter.com/jrotwitguez
| | - Greg Gibson
- Center for Integrative Genomics, Georgia Institute of Technology, Atlanta, GA, USA
| | - Arcadi Navarro
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Catalonia, Spain; Institute of Evolutionary Biology (UPF-CSIC), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain; National Institute for Bioinformatics (INB), Barcelona, Catalonia, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), PRBB, Barcelona, Catalonia, Spain.
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123
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Navarro A, Martínez-Murcia A. Phylogenetic analyses of the genusAeromonasbased on housekeeping gene sequencing and its influence on systematics. J Appl Microbiol 2018; 125:622-631. [DOI: 10.1111/jam.13887] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 03/14/2018] [Accepted: 04/11/2018] [Indexed: 11/27/2022]
Affiliation(s)
- A. Navarro
- Genetic Analysis Strategies S.L.; CEEI; Elche, Alicante Spain
| | - A. Martínez-Murcia
- Genetic Analysis Strategies S.L.; CEEI; Elche, Alicante Spain
- Area de Microbiología; EPSO; Universidad Miguel Hernández; Orihuela, Alicante Spain
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124
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Martinez-Marti A, Felip E, Matito J, Mereu E, Navarro A, Cedrés S, Pardo N, Martinez de Castro A, Remon J, Miquel JM, Guillaumet-Adkins A, Nadal E, Rodriguez-Esteban G, Arqués O, Fasani R, Nuciforo P, Heyn H, Villanueva A, Palmer HG, Vivancos A. Dual MET and ERBB inhibition overcomes intratumor plasticity in osimertinib-resistant-advanced non-small-cell lung cancer (NSCLC). Ann Oncol 2018; 28:2451-2457. [PMID: 28961841 PMCID: PMC5834054 DOI: 10.1093/annonc/mdx396] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background Third-generation epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) such as osimertinib are the last line of targeted treatment of metastatic non-small-cell lung cancer (NSCLC) EGFR-mutant harboring T790M. Different mechanisms of acquired resistance to third-generation EGFR-TKIs have been proposed. It is therefore crucial to identify new and effective strategies to overcome successive acquired mechanisms of resistance. Methods For Amplicon-seq analysis, samples from the index patient (primary and metastasis lesions at different timepoints) as well as the patient-derived orthotopic xenograft tumors corresponding to the different treatment arms were used. All samples were formalin-fixed paraffin-embedded, selected and evaluated by a pathologist. For droplet digital PCR, 20 patients diagnosed with NSCLC at baseline or progression to different lines of TKI therapies were selected. Formalin-fixed paraffin-embedded blocks corresponding to either primary tumor or metastasis specimens were used for analysis. For single-cell analysis, orthotopically grown metastases were dissected from the brain of an athymic nu/nu mouse and cryopreserved at -80°C. Results In a brain metastasis lesion from a NSCLC patient presenting an EGFR T790M mutation, we detected MET gene amplification after prolonged treatment with osimertinib. Importantly, the combination of capmatinib (c-MET inhibitor) and afatinib (ErbB-1/2/4 inhibitor) completely suppressed tumor growth in mice orthotopically injected with cells derived from this brain metastasis. In those mice treated with capmatinib or afatinib as monotherapy, we observed the emergence of KRAS G12C clones. Single-cell gene expression analyses also revealed intratumor heterogeneity, indicating the presence of a KRAS-driven subclone. We also detected low-frequent KRAS G12C alleles in patients treated with various EGFR-TKIs. Conclusion Acquired resistance to subsequent EGFR-TKI treatment lines in EGFR-mutant lung cancer patients may induce genetic plasticity. We assess the biological insights of tumor heterogeneity in an osimertinib-resistant tumor with acquired MET-amplification and propose new treatment strategies in this situation.
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Affiliation(s)
- A Martinez-Marti
- Department of Medical Oncology, Vall d'Hebron University Hospital, Barcelona;; Department of Medical Oncology, Vall d'Hebron Institute of Oncology (VHIO), Barcelona;; Autonomous University of Barcelona (UAB), Barcelona
| | - E Felip
- Department of Medical Oncology, Vall d'Hebron University Hospital, Barcelona;; Department of Medical Oncology, Vall d'Hebron Institute of Oncology (VHIO), Barcelona;; Autonomous University of Barcelona (UAB), Barcelona;.
| | - J Matito
- Cancer Genomics Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona
| | - E Mereu
- Single Cell Genomics Group, Centro Nacional de Análisis Genómico (CNAG) - Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona;; Pompeu Fabra University (UPF), Barcelona
| | - A Navarro
- Department of Medical Oncology, Vall d'Hebron University Hospital, Barcelona;; Department of Medical Oncology, Vall d'Hebron Institute of Oncology (VHIO), Barcelona
| | - S Cedrés
- Department of Medical Oncology, Vall d'Hebron University Hospital, Barcelona;; Department of Medical Oncology, Vall d'Hebron Institute of Oncology (VHIO), Barcelona
| | - N Pardo
- Department of Medical Oncology, Vall d'Hebron University Hospital, Barcelona;; Department of Medical Oncology, Vall d'Hebron Institute of Oncology (VHIO), Barcelona;; Autonomous University of Barcelona (UAB), Barcelona
| | - A Martinez de Castro
- Department of Medical Oncology, Vall d'Hebron University Hospital, Barcelona;; Department of Medical Oncology, Vall d'Hebron Institute of Oncology (VHIO), Barcelona
| | - J Remon
- Department of Medical Oncology, Vall d'Hebron University Hospital, Barcelona;; Department of Medical Oncology, Vall d'Hebron Institute of Oncology (VHIO), Barcelona
| | - J M Miquel
- Department of Medical Oncology, Vall d'Hebron Institute of Oncology (VHIO), Barcelona
| | - A Guillaumet-Adkins
- Single Cell Genomics Group, Centro Nacional de Análisis Genómico (CNAG) - Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona;; Pompeu Fabra University (UPF), Barcelona
| | - E Nadal
- Chemoresistance and Predictive Factors Group, Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO) Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Barcelona;; Department of Medical Oncology, ICO, IDIBELL, L'Hospitalet, Barcelona
| | - G Rodriguez-Esteban
- Single Cell Genomics Group, Centro Nacional de Análisis Genómico (CNAG) - Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona;; Pompeu Fabra University (UPF), Barcelona
| | | | - R Fasani
- Molecular Oncology Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona
| | - P Nuciforo
- Molecular Oncology Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona
| | - H Heyn
- Single Cell Genomics Group, Centro Nacional de Análisis Genómico (CNAG) - Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona;; Pompeu Fabra University (UPF), Barcelona
| | - A Villanueva
- Chemoresistance and Predictive Factors Group, Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO) Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Barcelona;; Xenopat S.L., Business Bioincubator, Bellvitge Health Science Campus, Barcelona, Spain
| | | | - A Vivancos
- Cancer Genomics Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona;.
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125
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Mandage R, Telford M, Rodríguez JA, Farré X, Laayouni H, Marigorta UM, Cundiff C, Heredia-Genestar JM, Navarro A, Santpere G. Correction: Genetic factors affecting EBV copy number in lymphoblastoid cell lines derived from the 1000 Genome Project samples. PLoS One 2018; 13:e0196623. [PMID: 29709034 PMCID: PMC5927406 DOI: 10.1371/journal.pone.0196623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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126
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Edelman M, Juan O, Navarro A, Golden G, Saunders A. 88P Feasibility of outpatient dinutuximab (D) and irinotecan (I) for second-line treatment of relapsed or refractory small cell lung cancer (RR SCLC): Part 1 of an open-label, randomized, phase 2/3 study. J Thorac Oncol 2018. [DOI: 10.1016/s1556-0864(18)30363-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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127
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Van Seijen M, Brcic L, Navarro A, Sansano I, Béndek M, Witte B, Brcic I, Kammler R, Stahel R, Thunnissen E. 21P Influence of delayed and prolonged fixation on the evaluation of immunohistochemical staining on pulmonary resection specimen. J Thorac Oncol 2018. [DOI: 10.1016/s1556-0864(18)30301-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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128
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Soler A, López M, Martínez D, Benedicto A, Navarro A, Monroy J, Albert M, Domingo C, Soler M. EP-1620: Muscle-Invasive Bladder Cancer Bladder-Preservation by Combined-Modality Therapy: Long-Term Outcomes. Radiother Oncol 2018. [DOI: 10.1016/s0167-8140(18)31929-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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129
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Nadeu F, Clot G, Delgado J, Martín-García D, Baumann T, Salaverria I, Beà S, Pinyol M, Jares P, Navarro A, Suárez-Cisneros H, Aymerich M, Rozman M, Villamor N, Colomer D, González M, Alcoceba M, Terol MJ, Navarro B, Colado E, Payer ÁR, Puente XS, López-Otín C, López-Guillermo A, Enjuanes A, Campo E. Clinical impact of the subclonal architecture and mutational complexity in chronic lymphocytic leukemia. Leukemia 2018; 32:645-653. [PMID: 28924241 PMCID: PMC5843898 DOI: 10.1038/leu.2017.291] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 08/07/2017] [Accepted: 09/05/2017] [Indexed: 12/11/2022]
Abstract
Genome studies of chronic lymphocytic leukemia (CLL) have revealed the remarkable subclonal heterogeneity of the tumors, but the clinical implications of this phenomenon are not well known. We assessed the mutational status of 28 CLL driver genes by deep-targeted next-generation sequencing and copy number alterations (CNA) in 406 previously untreated patients and 48 sequential samples. We detected small subclonal mutations (0.6-25% of cells) in nearly all genes (26/28), and they were the sole alteration in 22% of the mutated cases. CNA tended to be acquired early in the evolution of the disease and remained stable, whereas the mutational heterogeneity increased in a subset of tumors. The prognostic impact of different genes was related to the size of the mutated clone. Combining mutations and CNA, we observed that the accumulation of driver alterations (mutational complexity) gradually shortened the time to first treatment independently of the clonal architecture, IGHV status and Binet stage. Conversely, the overall survival was associated with the increasing subclonal diversity of the tumors but it was related to the age of patients, IGHV and TP53 status of the tumors. In conclusion, our study reveals that both the mutational complexity and subclonal diversity influence the evolution of CLL.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Biomarkers, Tumor
- Clonal Evolution/genetics
- DNA Copy Number Variations
- Disease Progression
- Female
- Follow-Up Studies
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/diagnosis
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/mortality
- Male
- Middle Aged
- Mutation/genetics
- Neoplasm Staging
- Prognosis
- Proportional Hazards Models
- Signal Transduction
- Young Adult
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Affiliation(s)
- F Nadeu
- Lymphoid Neoplasms Program, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - G Clot
- Lymphoid Neoplasms Program, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - J Delgado
- Lymphoid Neoplasms Program, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hematology Department, Hospital Clínic, Barcelona, Spain
| | - D Martín-García
- Lymphoid Neoplasms Program, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - T Baumann
- Hematology Department, Hospital Clínic, Barcelona, Spain
| | - I Salaverria
- Lymphoid Neoplasms Program, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - S Beà
- Lymphoid Neoplasms Program, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - M Pinyol
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Unitat de Genòmica, IDIBAPS, Barcelona, Spain
| | - P Jares
- Lymphoid Neoplasms Program, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hematology Department, Hospital Clínic, Barcelona, Spain
| | - A Navarro
- Lymphoid Neoplasms Program, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | | | - M Aymerich
- Lymphoid Neoplasms Program, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hematology Department, Hospital Clínic, Barcelona, Spain
| | - M Rozman
- Lymphoid Neoplasms Program, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hematology Department, Hospital Clínic, Barcelona, Spain
| | - N Villamor
- Lymphoid Neoplasms Program, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hematology Department, Hospital Clínic, Barcelona, Spain
| | - D Colomer
- Lymphoid Neoplasms Program, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hematology Department, Hospital Clínic, Barcelona, Spain
| | - M González
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Biología Molecular e Histocompatibilidad, Hospital Universitario, Salamanca, Spain
| | - M Alcoceba
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Biología Molecular e Histocompatibilidad, Hospital Universitario, Salamanca, Spain
| | - M J Terol
- Unidad de Hematología, Hospital Clínico Universitario, Valencia, Spain
| | - B Navarro
- Unidad de Hematología, Hospital Clínico Universitario, Valencia, Spain
| | - E Colado
- Servicio de Hematología y Hemoterapia, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - ÁR Payer
- Servicio de Hematología y Hemoterapia, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - X S Puente
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología, Universidad de Oviedo, Oviedo, Spain
| | - C López-Otín
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología, Universidad de Oviedo, Oviedo, Spain
| | - A López-Guillermo
- Lymphoid Neoplasms Program, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hematology Department, Hospital Clínic, Barcelona, Spain
- Medical School, Universitat de Barcelona, Barcelona, Spain
| | - A Enjuanes
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Unitat de Genòmica, IDIBAPS, Barcelona, Spain
| | - E Campo
- Lymphoid Neoplasms Program, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hematology Department, Hospital Clínic, Barcelona, Spain
- Medical School, Universitat de Barcelona, Barcelona, Spain
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130
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Gramajo Feijoo M, Fernández-Liencres M, Gil D, Gómez M, Ben Altabef A, Navarro A, Tuttolomondo M. A detailed study of intermolecular interactions, electronic and vibrational properties of the metal complex bis(uracilato)diammine copper(ii) dihydrate. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2017.11.030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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131
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Telford M, Navarro A, Santpere G. Whole genome diversity of inherited chromosomally integrated HHV-6 derived from healthy individuals of diverse geographic origin. Sci Rep 2018; 8:3472. [PMID: 29472617 PMCID: PMC5823862 DOI: 10.1038/s41598-018-21645-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 01/31/2018] [Indexed: 12/13/2022] Open
Abstract
Human herpesviruses 6-A and -B (HHV-6A, HHV-6B) are ubiquitous in human populations worldwide. These viruses have been associated with several diseases such as multiple sclerosis, Hodgkin's lymphoma or encephalitis. Despite of the need to understand the genetic diversity and geographic stratification of these viruses, the availability of complete viral sequences from different populations is still limited. Here, we present nine new inherited chromosomally integrated HHV-6 sequences from diverse geographical origin which were generated through target DNA enrichment on lymphoblastoid cell lines derived from healthy individuals. Integration with available HHV-6 sequences allowed the assessment of HHV-6A and -6B phylogeny, patterns of recombination and signatures of natural selection. Analysis of the intra-species variability showed differences between A and B diversity levels and revealed that the HHV-6B reference (Z29) is an uncommon sequence, suggesting the need for an alternative reference sequence. Signs of geographical variation are present and more defined in HHV-6A, while they appear partly masked by recombination in HHV-6B. Finally, we conducted a scan for signatures of selection in protein coding genes that yielded at least 6 genes (4 and 2 respectively for the A and B species) showing significant evidence for accelerated evolution, and 1 gene showing evidence of positive selection in HHV-6A.
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Affiliation(s)
- Marco Telford
- Institute of Evolutionary Biology (UPF-CSIC), Departament de Ciències Experimentals i la Salut, Universitat Pompeu Fabra, PRBB, Barcelona, Catalonia, Spain
| | - Arcadi Navarro
- Institute of Evolutionary Biology (UPF-CSIC), Departament de Ciències Experimentals i la Salut, Universitat Pompeu Fabra, PRBB, Barcelona, Catalonia, Spain.
- National Institute for Bioinformatics (INB), PRBB, Barcelona, Catalonia, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), PRBB, Barcelona, Catalonia, Spain.
- Center for Genomic Regulation (CRG), PRBB, Barcelona, Catalonia, Spain.
| | - Gabriel Santpere
- Institute of Evolutionary Biology (UPF-CSIC), Departament de Ciències Experimentals i la Salut, Universitat Pompeu Fabra, PRBB, Barcelona, Catalonia, Spain.
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, 06510, USA.
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132
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Remon J, Pardo N, Martinez-Martí A, Cedrés S, Navarro A, Martinez de Castro AM, Felip E. Corrigendum to "Immune-checkpoint inhibition in first-line treatment of advanced non-small cell lung cancer patients: Current status and future approaches" [Lung Cancer 106 (2017) 70-75]. Lung Cancer 2018; 117:80. [PMID: 29398170 DOI: 10.1016/j.lungcan.2017.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- J Remon
- Hospital Vall d'Hebron, Medical Oncology Department, Passeig de la Vall d'Hebron, 119-129, 08035, Barcelona, Spain.
| | - N Pardo
- Hospital Vall d'Hebron, Medical Oncology Department, Passeig de la Vall d'Hebron, 119-129, 08035, Barcelona, Spain.
| | - A Martinez-Martí
- Hospital Vall d'Hebron, Medical Oncology Department, Passeig de la Vall d'Hebron, 119-129, 08035, Barcelona, Spain.
| | - S Cedrés
- Hospital Vall d'Hebron, Medical Oncology Department, Passeig de la Vall d'Hebron, 119-129, 08035, Barcelona, Spain.
| | - A Navarro
- Hospital Vall d'Hebron, Medical Oncology Department, Passeig de la Vall d'Hebron, 119-129, 08035, Barcelona, Spain.
| | - A M Martinez de Castro
- Hospital Vall d'Hebron, Medical Oncology Department, Passeig de la Vall d'Hebron, 119-129, 08035, Barcelona, Spain.
| | - E Felip
- Hospital Vall d'Hebron, Medical Oncology Department, Passeig de la Vall d'Hebron, 119-129, 08035, Barcelona, Spain.
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133
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Murakami AA, Goldstein H, Navarro A, Seabrooks JR, Ryder DS. Investigation of Beer Flavor by Gas Chromatography-Olfactometry. Journal of the American Society of Brewing Chemists 2018. [DOI: 10.1094/asbcj-61-0023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- A. A. Murakami
- Miller Brewing Company, 3939 W. Highland Blvd., Milwaukee, WI 53201, U.S.A
| | - H. Goldstein
- Miller Brewing Company, 3939 W. Highland Blvd., Milwaukee, WI 53201, U.S.A
| | - A. Navarro
- Miller Brewing Company, 3939 W. Highland Blvd., Milwaukee, WI 53201, U.S.A
| | - J. R. Seabrooks
- Miller Brewing Company, 3939 W. Highland Blvd., Milwaukee, WI 53201, U.S.A
| | - D. S. Ryder
- Miller Brewing Company, 3939 W. Highland Blvd., Milwaukee, WI 53201, U.S.A
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134
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Santasusagna S, Moreno I, Navarro A, Muñoz C, Martinez F, Hernández R, Castellano JJ, Monzo M. miR-328 mediates a metabolic shift in colon cancer cells by targeting SLC2A1/GLUT1. Clin Transl Oncol 2018; 20:1161-1167. [PMID: 29374351 PMCID: PMC6105238 DOI: 10.1007/s12094-018-1836-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 01/09/2018] [Indexed: 12/22/2022]
Abstract
Purpose Increasing evidence shows that altered metabolism is a critical hallmark in colon cancer. There is a strong need to explore the molecular mechanisms underlying cancer metabolism. Whether the aberrant expression of microRNAs contributes to cancer metabolism is not fully understood. miR-328 is a putative potential target of SLC2A1, but the regulating mechanism between them remains unknown. We have examined whether miR-328 directly regulates SLC2A1/GLUT1 expression in colon cancer cells. Methods We performed in silico bioinformatic analyses to identify miR-328-mediated molecular pathways and targets. We also performed luciferase assays and western blot analyses in LOVO and SW480 colon cancer cell lines. In addition, we assessed miR-328 expression in 47 paired tumor and normal tissue specimens from resected colon cancer patients. Results Luciferase reporter assays showed that miR-328 directly targeted SLC2A1 3′-untranslated region (UTR), with a significant decrease in luciferase activity in both LOVO and SW480 cell lines. These results were validated by western blot. miR-328 expression was significantly downregulated in tumor tissue compared with paired normal tissue. Conclusions Our results show that miR-328 targets SLC2A1/GLUT1. We suggest that miR-328 may be involved in the orchestration of the Warburg effect in colon cancer cells. Furthermore, miR‐328 expression is reduced in colon cancer patients and thus inversely correlates with the classically reported upregulated SLC2A1/GLUT1 expression in tumors.
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Affiliation(s)
- S Santasusagna
- Molecular Oncology and Embryology Laboratory, Human Anatomy Unit, School of Medicine, University of Barcelona, IDIBAPS, Barcelona, Spain
| | - I Moreno
- Department of Medical Oncology and Surgery, Hospital Municipal de Badalona, Badalona, Spain
| | - A Navarro
- Molecular Oncology and Embryology Laboratory, Human Anatomy Unit, School of Medicine, University of Barcelona, IDIBAPS, Barcelona, Spain
| | - C Muñoz
- Molecular Oncology and Embryology Laboratory, Human Anatomy Unit, School of Medicine, University of Barcelona, IDIBAPS, Barcelona, Spain
| | - F Martinez
- Department of Medical Oncology and Surgery, Hospital Municipal de Badalona, Badalona, Spain
| | - R Hernández
- Department of Medical Oncology and Surgery, Hospital Municipal de Badalona, Badalona, Spain
| | - J J Castellano
- Molecular Oncology and Embryology Laboratory, Human Anatomy Unit, School of Medicine, University of Barcelona, IDIBAPS, Barcelona, Spain
| | - M Monzo
- Molecular Oncology and Embryology Laboratory, Human Anatomy Unit, School of Medicine, University of Barcelona, IDIBAPS, Barcelona, Spain. .,Unit of Human Anatomy and Embryology, School of Medicine, Hospital Clinic, University of Barcelona, Casanova 143, 08036, Barcelona, Spain.
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135
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Serres-Armero A, Povolotskaya IS, Quilez J, Ramirez O, Santpere G, Kuderna LFK, Hernandez-Rodriguez J, Fernandez-Callejo M, Gomez-Sanchez D, Freedman AH, Fan Z, Novembre J, Navarro A, Boyko A, Wayne R, Vilà C, Lorente-Galdos B, Marques-Bonet T. Similar genomic proportions of copy number variation within gray wolves and modern dog breeds inferred from whole genome sequencing. BMC Genomics 2017; 18:977. [PMID: 29258433 PMCID: PMC5735816 DOI: 10.1186/s12864-017-4318-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 11/17/2017] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Whole genome re-sequencing data from dogs and wolves are now commonly used to study how natural and artificial selection have shaped the patterns of genetic diversity. Single nucleotide polymorphisms, microsatellites and variants in mitochondrial DNA have been interrogated for links to specific phenotypes or signals of domestication. However, copy number variation (CNV), despite its increasingly recognized importance as a contributor to phenotypic diversity, has not been extensively explored in canids. RESULTS Here, we develop a new accurate probabilistic framework to create fine-scale genomic maps of segmental duplications (SDs), compare patterns of CNV across groups and investigate their role in the evolution of the domestic dog by using information from 34 canine genomes. Our analyses show that duplicated regions are enriched in genes and hence likely possess functional importance. We identify 86 loci with large CNV differences between dogs and wolves, enriched in genes responsible for sensory perception, immune response, metabolic processes, etc. In striking contrast to the observed loss of nucleotide diversity in domestic dogs following the population bottlenecks that occurred during domestication and breed creation, we find a similar proportion of CNV loci in dogs and wolves, suggesting that other dynamics are acting to particularly select for CNVs with potentially functional impacts. CONCLUSIONS This work is the first comparison of genome wide CNV patterns in domestic and wild canids using whole-genome sequencing data and our findings contribute to study the impact of novel kinds of genetic changes on the evolution of the domestic dog.
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Affiliation(s)
- Aitor Serres-Armero
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain
| | - Inna S Povolotskaya
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain
| | - Javier Quilez
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Oscar Ramirez
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain.,Vetgenomics, 08193, Barcelona, Spain
| | - Gabriel Santpere
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain.,Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Lukas F K Kuderna
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain
| | - Jessica Hernandez-Rodriguez
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain
| | - Marcos Fernandez-Callejo
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Daniel Gomez-Sanchez
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain
| | - Adam H Freedman
- UCLA, Department of Ecology and Evolutionary Biology, Los Angeles, CA, 90095, USA
| | - Zhenxin Fan
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - John Novembre
- UCLA, Department of Ecology and Evolutionary Biology, Los Angeles, CA, 90095, USA
| | - Arcadi Navarro
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010, Barcelona, Catalonia, Spain
| | - Adam Boyko
- Cornell University, Department of Biological Statistics and Computational Biology, New York, NY, 14853, USA
| | - Robert Wayne
- UCLA, Department of Ecology and Evolutionary Biology, Los Angeles, CA, 90095, USA
| | - Carles Vilà
- Estación Biológica de Doñana EBD-CSIC, Department of Integrative Ecology, 41092, Sevilla, Spain
| | - Belen Lorente-Galdos
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain. .,Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA.
| | - Tomas Marques-Bonet
- IBE, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Ciencies Experimentals i de la Salut, 08003, Barcelona, Spain. .,CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain. .,Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010, Barcelona, Catalonia, Spain.
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136
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Hernandez-Rodriguez J, Arandjelovic M, Lester J, de Filippo C, Weihmann A, Meyer M, Angedakin S, Casals F, Navarro A, Vigilant L, Kühl HS, Langergraber K, Boesch C, Hughes D, Marques-Bonet T. The impact of endogenous content, replicates and pooling on genome capture from faecal samples. Mol Ecol Resour 2017; 18:319-333. [PMID: 29058768 PMCID: PMC5900898 DOI: 10.1111/1755-0998.12728] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 10/06/2017] [Accepted: 10/16/2017] [Indexed: 12/11/2022]
Abstract
Target-capture approach has improved over the past years, proving to be very efficient tool for selectively sequencing genetic regions of interest. These methods have also allowed the use of noninvasive samples such as faeces (characterized by their low quantity and quality of endogenous DNA) to be used in conservation genomic, evolution and population genetic studies. Here we aim to test different protocols and strategies for exome capture using the Roche SeqCap EZ Developer kit (57.5 Mb). First, we captured a complex pool of DNA libraries. Second, we assessed the influence of using more than one faecal sample, extract and/or library from the same individual, to evaluate its effect on the molecular complexity of the experiment. We validated our experiments with 18 chimpanzee faecal samples collected from two field sites as a part of the Pan African Programme: The Cultured Chimpanzee. Those two field sites are in Kibale National Park, Uganda (N = 9) and Loango National Park, Gabon (N = 9). We demonstrate that at least 16 libraries can be pooled, target enriched through hybridization, and sequenced allowing for the genotyping of 951,949 exome markers for population genetic analyses. Further, we observe that molecule richness, and thus, data acquisition, increase when using multiple libraries from the same extract or multiple extracts from the same sample. Finally, repeated captures significantly decrease the proportion of off-target reads from 34.15% after one capture round to 7.83% after two capture rounds, supporting our conclusion that two rounds of target enrichment are advisable when using complex faecal samples.
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Affiliation(s)
- Jessica Hernandez-Rodriguez
- Departament de Ciencies Experimentals i de la Salut, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Barcelona, Spain
| | - Mimi Arandjelovic
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Jack Lester
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Cesare de Filippo
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Antje Weihmann
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Samuel Angedakin
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Ferran Casals
- Genomics Core Facility, Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Arcadi Navarro
- Departament de Ciencies Experimentals i de la Salut, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Barcelona, Spain.,Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain.,Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Linda Vigilant
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Hjalmar S Kühl
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Leipzig-Jena, Leipzig, Germany
| | - Kevin Langergraber
- School of Human Evolution & Social Change, Arizona State University, Tempe, AZ, USA
| | - Christophe Boesch
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - David Hughes
- Departament de Ciencies Experimentals i de la Salut, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Barcelona, Spain.,MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Tomas Marques-Bonet
- Departament de Ciencies Experimentals i de la Salut, Institut de Biologia Evolutiva (Universitat Pompeu Fabra/CSIC), Barcelona, Spain.,Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain.,Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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137
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Solis-Moruno M, de Manuel M, Hernandez-Rodriguez J, Fontsere C, Gomara-Castaño A, Valsera-Naranjo C, Crailsheim D, Navarro A, Llorente M, Riera L, Feliu-Olleta O, Marques-Bonet T. Potential damaging mutation in LRP5 from genome sequencing of the first reported chimpanzee with the Chiari malformation. Sci Rep 2017; 7:15224. [PMID: 29123202 PMCID: PMC5680330 DOI: 10.1038/s41598-017-15544-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 10/30/2017] [Indexed: 12/29/2022] Open
Abstract
The genus Pan is the closest related to humans (Homo sapiens) and it includes two species: Pan troglodytes (chimpanzees) and Pan paniscus (bonobos). Different characteristics, some of biomedical aspect, separate them from us. For instance, some common human medical conditions are rare in chimpanzees (menopause, Alzheimer disease) although it is unclear to which extent longevity plays an active role in these differences. However, both humans and chimpanzees present similar pathologies, thus, understanding traits in chimpanzees can help unravel the molecular basis of human conditions. Here, we sequenced the genome of Nico, a central chimpanzee diagnosed with a particular biomedical condition, the Chiari malformation. We performed a variant calling analysis comparing his genome to 25 whole genomes from healthy individuals (bonobos and chimpanzees), and after predicting the effects of the genetic variants, we looked for genes within the OMIM database. We found a novel, private, predicted as damaging mutation in Nico in LRP5, a gene related to bone density alteration pathologies, and we suggest a link between this mutation and his Chiari malformation as previously shown in humans. Our results reinforce the idea that a comparison between humans and chimpanzees can be established in this genetic frame of common diseases.
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Affiliation(s)
- Manuel Solis-Moruno
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Doctor Aiguader 88, Barcelona, 08003, Spain.
| | - Marc de Manuel
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Doctor Aiguader 88, Barcelona, 08003, Spain
| | - Jessica Hernandez-Rodriguez
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Doctor Aiguader 88, Barcelona, 08003, Spain
| | - Claudia Fontsere
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Doctor Aiguader 88, Barcelona, 08003, Spain
| | - Alba Gomara-Castaño
- Fundació Mona, Carretera C-25, s/n, Riudellots de la Selva, 17457, Girona, Spain
| | | | - Dietmar Crailsheim
- Fundació Mona, Carretera C-25, s/n, Riudellots de la Selva, 17457, Girona, Spain
| | - Arcadi Navarro
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Doctor Aiguader 88, Barcelona, 08003, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, Barcelona, 08010, Spain
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, Barcelona, 08028, Spain
| | - Miquel Llorente
- Fundació Mona, Carretera C-25, s/n, Riudellots de la Selva, 17457, Girona, Spain
| | - Laura Riera
- Fundació Mona, Carretera C-25, s/n, Riudellots de la Selva, 17457, Girona, Spain
| | - Olga Feliu-Olleta
- Fundació Mona, Carretera C-25, s/n, Riudellots de la Selva, 17457, Girona, Spain
| | - Tomas Marques-Bonet
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Doctor Aiguader 88, Barcelona, 08003, Spain.
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, Barcelona, 08010, Spain.
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, Barcelona, 08028, Spain.
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138
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Schuler M, Nogova L, Heidenreich A, Tai D, Cassier P, Richly H, Cho B, Sayehli C, Navarro A, Bender S, Ocker M, Nogai H, Wagner A, Ince S, Ellinghaus P, Joerger M. Anti-tumor activity of the pan-FGFR inhibitor rogaratinib in patients with advanced urothelial carcinomas selected based on tumor FGFR mRNA expression levels. Ann Oncol 2017. [DOI: 10.1093/annonc/mdx371.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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139
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Santasusagna S, Navarro A, Moreno I, Ibeas R, Martinez F, Castellano J, Muñoz C, Canals J, Morales S, Hernandez R, Moreno J, Monzo M. Exosomal ECM1 protein expression in plasma from the tumor-draining vein (mesenteric vein) and time to relapse in colon cancer patients. Ann Oncol 2017. [DOI: 10.1093/annonc/mdx393.103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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140
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Remon J, Martinez-Marti A, Carcereny Costa E, Zeron-Medina Cuairan J, Sansano I, Mate J, Pardo N, Cedres S, Navarro A, Martinez de castro A, Moran T, Felip Font E. Major pathological response after preoperative chemotherapy as a surrogate marker of survival in early-stage non-small cell lung cancer: cohort of NATCH phase III trial. Ann Oncol 2017. [DOI: 10.1093/annonc/mdx381.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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141
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Kerr K, Thunnissen E, Dafni U, Soltermann A, Finn S, Bubendorf L, Verbeken E, Biernat W, Warth A, Marchetti A, Speel EJ, Pokharel S, Quinn A, Monkhorst K, Navarro A, Polydoropoulou V, Kammler R, Peters S, Stahel R, Lungscape Consortium O. Association of programmed cell death 1 ligand (PD-L1) expression with molecular alterations in non-small cell lung cancer (NSCLC) patients (pts): Results from the European Thoracic Oncology Platform (ETOP) Lungscape cohort. Ann Oncol 2017. [DOI: 10.1093/annonc/mdx390.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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142
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Herreros Pomares A, Calabuig Fariñas S, Escorihuela E, Amado H, Guijarro R, Gallach Garcia S, Navarro A, Jantus-Lewintre E, Camps Herrero C. Stemness characterization of tumorspheres from non-small cell lung cancer: Differential expression in CSC-related markers and signaling pathways. Ann Oncol 2017. [DOI: 10.1093/annonc/mdx381.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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143
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Cedres S, Martinez Marti A, Navarro A, Pardo N, Remon J, Matos I, Ochoa de Olza M, Hierro C, Martin Liberal J, Miquel J, Viaplana C, Villacampa Javierre G, Dienstmann R, Felip Font E. Outcomes of malignant pleural mesothelioma (MPM) patients (p) treated with immune-oncology drugs (IO) in clinical trials. Ann Oncol 2017. [DOI: 10.1093/annonc/mdx389.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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144
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Joerger M, Soo R, Cho B, Navarro A, Sayehli C, Richly H, Tai D, Kim DW, Wolf J, Cassier P, Bender S, Ellinghaus P, Ince S, Rajagopalan P, Ocker M, Schuler M. A novel mRNA-based patient selection strategy identifies fibroblast growth factor receptor (FGFR) inhibitor-sensitive tumors: Results from rogaratinib Phase-1 study. Ann Oncol 2017. [DOI: 10.1093/annonc/mdx367.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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145
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Navarro A, Santasusagna S, Vinolas Segarra N, Castellano J, Moises J, Morales S, Canals J, Muñoz C, Ramírez J, Marrades R, Molins L, Monzo M. HOXA-related long non-coding RNAs impact prognosis in early stage NSCLC patients. Ann Oncol 2017. [DOI: 10.1093/annonc/mdx381.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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146
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Navarro A, Martinez-Gonzalez M, Gea A, Bazal-Chacon P, De La Fuente-Arrillaga C, Toledo E. 1199Coffee consumption and all-cause mortality in a Mediterranean cohort: the SUN project. Eur Heart J 2017. [DOI: 10.1093/eurheartj/ehx502.1199] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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147
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Karube K, Enjuanes A, Dlouhy I, Jares P, Martin-Garcia D, Nadeu F, Ordóñez GR, Rovira J, Clot G, Royo C, Navarro A, Gonzalez-Farre B, Vaghefi A, Castellano G, Rubio-Perez C, Tamborero D, Briones J, Salar A, Sancho JM, Mercadal S, Gonzalez-Barca E, Escoda L, Miyoshi H, Ohshima K, Miyawaki K, Kato K, Akashi K, Mozos A, Colomo L, Alcoceba M, Valera A, Carrió A, Costa D, Lopez-Bigas N, Schmitz R, Staudt LM, Salaverria I, López-Guillermo A, Campo E. Integrating genomic alterations in diffuse large B-cell lymphoma identifies new relevant pathways and potential therapeutic targets. Leukemia 2017; 32:675-684. [PMID: 28804123 PMCID: PMC5843901 DOI: 10.1038/leu.2017.251] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 07/24/2017] [Accepted: 07/27/2017] [Indexed: 02/08/2023]
Abstract
Genome studies of diffuse large B-cell lymphoma (DLBCL) have revealed a large number of somatic mutations and structural alterations. However, the clinical significance of these alterations is still not well defined. In this study, we have integrated the analysis of targeted next-generation sequencing of 106 genes and genomic copy number alterations (CNA) in 150 DLBCL. The clinically significant findings were validated in an independent cohort of 111 patients. Germinal center B-cell and activated B-cell DLBCL had a differential profile of mutations, altered pathogenic pathways and CNA. Mutations in genes of the NOTCH pathway and tumor suppressor genes (TP53/CDKN2A), but not individual genes, conferred an unfavorable prognosis, confirmed in the independent validation cohort. A gene expression profiling analysis showed that tumors with NOTCH pathway mutations had a significant modulation of downstream target genes, emphasizing the relevance of this pathway in DLBCL. An in silico drug discovery analysis recognized 69 (46%) cases carrying at least one genomic alteration considered a potential target of drug response according to early clinical trials or preclinical assays in DLBCL or other lymphomas. In conclusion, this study identifies relevant pathways and mutated genes in DLBCL and recognizes potential targets for new intervention strategies.
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Affiliation(s)
- K Karube
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain.,Department of Pathology and Cell Biology, Graduate School of Medicine and Faculty of Medicine, University of the Ryukyus, Nishihara, Japan
| | - A Enjuanes
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain.,CIBERONC, Madrid, Spain
| | - I Dlouhy
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - P Jares
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain.,CIBERONC, Madrid, Spain
| | - D Martin-Garcia
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain.,CIBERONC, Madrid, Spain
| | - F Nadeu
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain.,CIBERONC, Madrid, Spain
| | | | - J Rovira
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - G Clot
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain.,CIBERONC, Madrid, Spain
| | - C Royo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - A Navarro
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain.,CIBERONC, Madrid, Spain
| | - B Gonzalez-Farre
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain.,CIBERONC, Madrid, Spain
| | - A Vaghefi
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - G Castellano
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - C Rubio-Perez
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Research Unit on Biomedical Informatics, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - D Tamborero
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Research Unit on Biomedical Informatics, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - J Briones
- Servei de Patologia, Hospital de Sant Pau, Barcelona, Spain
| | - A Salar
- Department of Pathology, Hospital del Mar, Universitat Pompeu Fabra, Barcelona, Spain
| | - J M Sancho
- ICO-Hospital Germans Trias i Pujol, Barcelona, Spain
| | - S Mercadal
- ICO-Hospital Duran i Reynals, L'Hospitalet, Barcelona, Spain
| | | | - L Escoda
- Department of Hematology, Hospital Universitari Joan XXIII, Tarragona, Spain
| | - H Miyoshi
- Department of Pathology, Kurume University School of Medicine, Kurume, Japan
| | - K Ohshima
- Department of Pathology, Kurume University School of Medicine, Kurume, Japan
| | - K Miyawaki
- Department of Medicine and Biosystemic Science, Graduate School of Medical Science, Kyushu University, Fukuoka, Japan
| | - K Kato
- Department of Medicine and Biosystemic Science, Graduate School of Medical Science, Kyushu University, Fukuoka, Japan
| | - K Akashi
- Department of Medicine and Biosystemic Science, Graduate School of Medical Science, Kyushu University, Fukuoka, Japan
| | - A Mozos
- Servei de Patologia, Hospital de Sant Pau, Barcelona, Spain
| | - L Colomo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain.,Department of Pathology, Hospital del Mar, Universitat Pompeu Fabra, Barcelona, Spain
| | - M Alcoceba
- CIBERONC, Madrid, Spain.,Unidad de Biología Molecular/Histocompatibilidad, Servicio de Hematología, Hospital Universitario de Salamanca, Salamanca, Spain
| | - A Valera
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - A Carrió
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain.,CIBERONC, Madrid, Spain
| | - D Costa
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain.,CIBERONC, Madrid, Spain
| | - N Lopez-Bigas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Research Unit on Biomedical Informatics, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - R Schmitz
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - L M Staudt
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - I Salaverria
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain.,CIBERONC, Madrid, Spain
| | - A López-Guillermo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain.,CIBERONC, Madrid, Spain
| | - E Campo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain.,CIBERONC, Madrid, Spain
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148
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Mandage R, Telford M, Rodríguez JA, Farré X, Layouni H, Marigorta UM, Cundiff C, Heredia-Genestar JM, Navarro A, Santpere G. Genetic factors affecting EBV copy number in lymphoblastoid cell lines derived from the 1000 Genome Project samples. PLoS One 2017; 12:e0179446. [PMID: 28654678 PMCID: PMC5487016 DOI: 10.1371/journal.pone.0179446] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 05/29/2017] [Indexed: 12/22/2022] Open
Abstract
Epstein-Barr virus (EBV), human herpes virus 4, has been classically associated with infectious mononucleosis, multiple sclerosis and several types of cancers. Many of these diseases show marked geographical differences in prevalence, which points to underlying genetic and/or environmental factors. Those factors may include a different susceptibility to EBV infection and viral copy number among human populations. Since EBV is commonly used to transform B-cells into lymphoblastoid cell lines (LCLs) we hypothesize that differences in EBV copy number among individual LCLs may reflect differential susceptibility to EBV infection. To test this hypothesis, we retrieved whole-genome sequenced EBV-mapping reads from 1,753 LCL samples derived from 19 populations worldwide that were sequenced within the context of the 1000 Genomes Project. An in silico methodology was developed to estimate the number of EBV copy number in LCLs and validated these estimations by real-time PCR. After experimentally confirming that EBV relative copy number remains stable over cell passages, we performed a genome wide association analysis (GWAS) to try detecting genetic variants of the host that may be associated with EBV copy number. Our GWAS has yielded several genomic regions suggestively associated with the number of EBV genomes per cell in LCLs, unraveling promising candidate genes such as CAND1, a known inhibitor of EBV replication. While this GWAS does not unequivocally establish the degree to which genetic makeup of individuals determine viral levels within their derived LCLs, for which a larger sample size will be needed, it potentially highlighted human genes affecting EBV-related processes, which constitute interesting candidates to follow up in the context of EBV related pathologies.
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Affiliation(s)
- Rajendra Mandage
- Institute of Evolutionary Biology (UPF-CSIC), Departament de Ciències Experimentals i la Salut, Universitat Pompeu Fabra, PRBB, Barcelona, Catalonia, Spain
| | - Marco Telford
- Institute of Evolutionary Biology (UPF-CSIC), Departament de Ciències Experimentals i la Salut, Universitat Pompeu Fabra, PRBB, Barcelona, Catalonia, Spain
| | - Juan Antonio Rodríguez
- Institute of Evolutionary Biology (UPF-CSIC), Departament de Ciències Experimentals i la Salut, Universitat Pompeu Fabra, PRBB, Barcelona, Catalonia, Spain
| | - Xavier Farré
- Institute of Evolutionary Biology (UPF-CSIC), Departament de Ciències Experimentals i la Salut, Universitat Pompeu Fabra, PRBB, Barcelona, Catalonia, Spain
| | - Hafid Layouni
- Institute of Evolutionary Biology (UPF-CSIC), Departament de Ciències Experimentals i la Salut, Universitat Pompeu Fabra, PRBB, Barcelona, Catalonia, Spain
- Bioinformatics Studies, ESCI-UPF, Pg. Pujades 1, Barcelona, Spain
| | - Urko M. Marigorta
- Institute of Evolutionary Biology (UPF-CSIC), Departament de Ciències Experimentals i la Salut, Universitat Pompeu Fabra, PRBB, Barcelona, Catalonia, Spain
- Georgia Institute of Technology, Department of Biology, Atlanta, Georgia, United States of America
| | - Caitlin Cundiff
- Georgia Institute of Technology, Department of Biology, Atlanta, Georgia, United States of America
| | - Jose Maria Heredia-Genestar
- Institute of Evolutionary Biology (UPF-CSIC), Departament de Ciències Experimentals i la Salut, Universitat Pompeu Fabra, PRBB, Barcelona, Catalonia, Spain
| | - Arcadi Navarro
- Institute of Evolutionary Biology (UPF-CSIC), Departament de Ciències Experimentals i la Salut, Universitat Pompeu Fabra, PRBB, Barcelona, Catalonia, Spain
- National Institute for Bioinformatics (INB), PRBB, Barcelona, Catalonia, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), PRBB, Barcelona, Catalonia, Spain
- Center for Genomic Regulation (CRG), PRBB, Barcelona, Catalonia, Spain
- * E-mail: (AN); (GS)
| | - Gabriel Santpere
- Institute of Evolutionary Biology (UPF-CSIC), Departament de Ciències Experimentals i la Salut, Universitat Pompeu Fabra, PRBB, Barcelona, Catalonia, Spain
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, United States of America
- * E-mail: (AN); (GS)
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149
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Colás C, Brosa M, Antón E, Montoro J, Navarro A, Dordal MT, Dávila I, Fernández-Parra B, Ibáñez MDP, Lluch-Bernal M, Matheu V, Rondón C, Sánchez MC, Valero A. Estimate of the total costs of allergic rhinitis in specialized care based on real-world data: the FERIN Study. Allergy 2017; 72:959-966. [PMID: 27886391 DOI: 10.1111/all.13099] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/21/2016] [Indexed: 01/22/2023]
Abstract
BACKGROUND Despite the socioeconomic importance of allergic rhinitis (AR), very few prospective studies have been performed under conditions of clinical practice and with a sufficiently long observation period outside the clinical trial scenario. We prospectively estimated the direct and indirect costs of AR in patients attending specialized clinics in Spain. METHODS Patients were recruited at random from allergy outpatient clinics in 101 health centers throughout Spain over 12 months. We performed a multicenter, observational, prospective study under conditions of clinical practice. We analyzed direct costs from a funder perspective (healthcare costs) and from a societal perspective (healthcare and non-healthcare costs). Indirect costs (absenteeism and presenteeism [productivity lost in the workplace]) were also calculated. The cost of treating conjunctivitis was evaluated alongside that of AR. RESULTS The total mean cost of AR per patient-year (n = 498) was €2326.70 (direct, €553.80; indirect, €1772.90). Direct costs were significantly higher in women (€600.34 vs €484.46, P = 0.02). Total costs for intermittent AR were significantly lower than for persistent AR (€1484.98 vs €2655.86, P < 0.001). Total indirect costs reached €1772.90 (presenteeism, €1682.71; absenteeism, €90.19). The direct costs of AR in patients with intermittent asthma (€507.35) were lower than in patients with mild-persistent asthma (€719.07) and moderate-persistent asthma (€798.71) (P = 0.006). CONCLUSIONS The total cost of AR for society is considerable. Greater frequency of symptoms and more severe AR are associated with higher costs. Indirect costs are almost threefold direct costs, especially in presenteeism. A reduction in presenteeism would generate considerable savings for society.
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Affiliation(s)
- C. Colás
- Department of Allergology; Hospital Clínico-Instituto de Investigación Sanitaria de Aragón; Zaragoza Spain
| | - M. Brosa
- Oblikue Consulting; Barcelona Spain
| | - E. Antón
- Department of Allergology; University Hospital Marqués de Valdecilla; Santander Spain
| | - J. Montoro
- Allergy Unit; Hospital Universitario Arnau de Vilanova; Facultad de Medicina; Universidad Católica de Valencia “San Vicente Mártir”; Valencia Spain
| | - A. Navarro
- UGC Intercentros Alergología de Sevilla; Hospital El Tomillar; Sevilla Spain
| | - M. T. Dordal
- Department of Allergology; Hospital Municipal; Badalona Serveis Assistencials; Badalona Spain
- Sant Pere Claver Fundació Sanitària; Barcelona Spain
| | - I. Dávila
- Department of Allergology; University Hospital of Salamanca; Instituto de Investigaciones Biosanitarias de Salamanca; IBSAL; Salamanca Spain
| | | | - M. D. P. Ibáñez
- Department of Allergology; Hospital Infantil Universitario Niño Jesús; IIS Princesa; Madrid Spain
| | | | - V. Matheu
- Department of Allergology; Hospital Universitario de Canarias; Tenerife Spain
| | - C. Rondón
- Allergy Unit; IBIMA-Regional University Hospital of Málaga; UMA; Malaga Spain
| | - M. C. Sánchez
- UGC Neumología-Alergia; Complejo Hospitalario Universitario de Huelva; Spain
| | - A. Valero
- Allergy Unit; Servei de Pneumologia i Al.lèrgia Respiratòria; Hospital Clínic; Barcelona Spain
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS) Barcelona; Spain
- Centro de Investigación Biomédica en red en Enfermedades Respiratorias (CIBERES); Barcelona Spain
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150
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Schmidt J, Ramis-Záldivar J, Nadeu F, Gonzalez-Farre B, Navarro A, Dojcinov S, Rosenwald A, Ott G, Campo E, Fend F, Egan C, Jaffe E, Salaverria I, Quintanilla-Martinez L. INTEGRATIVE MUTATIONAL ANALYSIS OF PEDIATRIC-TYPE FOLLICULAR LYMPHOMA REVEALS TNFRSF14
AND MAP2K1
AS THE MOST FREQUENTLY MUTATED GENES. Hematol Oncol 2017. [DOI: 10.1002/hon.2438_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- J. Schmidt
- Institute of Pathology; University Hospital Tübingen; Tübingen Germany
| | - J. Ramis-Záldivar
- Institut d'Investigacions Biomèdiques August Pi iSunyer; Hospital Clínic; Barcelona Spain
| | - F. Nadeu
- Institut d'Investigacions Biomèdiques August Pi iSunyer; Hospital Clínic; Barcelona Spain
| | - B. Gonzalez-Farre
- Institut d'Investigacions Biomèdiques August Pi iSunyer; Hospital Clínic; Barcelona Spain
| | - A. Navarro
- Institut d'Investigacions Biomèdiques August Pi iSunyer; Hospital Clínic; Barcelona Spain
| | - S. Dojcinov
- Department of Pathology, All Wales Lymphoma Panel; University Hospital Wales; Cardiff UK
| | - A. Rosenwald
- Institute of Pathology; University of Würzburg; Würzburg Germany
| | - G. Ott
- Department of Clinical Pathology; Robert-Bosch Hospital; Stuttgart Germany
| | - E. Campo
- Institut d'Investigacions Biomèdiques August Pi iSunyer; Hospital Clínic; Barcelona Spain
| | - F. Fend
- Institute of Pathology; University Hospital Tübingen; Tübingen Germany
| | - C. Egan
- Laboratory of Pathology; National Cancer Institute; Bethesda USA
| | - E. Jaffe
- Laboratory of Pathology; National Cancer Institute; Bethesda USA
| | - I. Salaverria
- Institut d'Investigacions Biomèdiques August Pi iSunyer; Hospital Clínic; Barcelona Spain
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