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Song AT, Sindeaux RHM, Li Y, Affia H, Agnihotri T, Leclerc S, van Vliet PP, Colas M, Guimond JV, Patey N, Feulner L, Joyal JS, Haddad E, Barreiro L, Andelfinger G. Developmental role of macrophages modeled in human pluripotent stem cell-derived intestinal tissue. Cell Rep 2024; 43:113616. [PMID: 38150367 DOI: 10.1016/j.celrep.2023.113616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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] [Received: 10/25/2023] [Revised: 11/22/2023] [Accepted: 12/07/2023] [Indexed: 12/29/2023] Open
Abstract
Macrophages populate the embryo early in gestation, but their role in development is not well defined. In particular, specification and function of macrophages in intestinal development remain little explored. To study this event in the human developmental context, we derived and combined human intestinal organoid and macrophages from pluripotent stem cells. Macrophages migrate into the organoid, proliferate, and occupy the emerging microanatomical niches of epithelial crypts and ganglia. They also acquire a transcriptomic profile similar to that of fetal intestinal macrophages and display tissue macrophage behaviors, such as recruitment to tissue injury. Using this model, we show that macrophages reduce glycolysis in mesenchymal cells and limit tissue growth without affecting tissue architecture, in contrast to the pro-growth effect of enteric neurons. In short, we engineered an intestinal tissue model populated with macrophages, and we suggest that resident macrophages contribute to the regulation of metabolism and growth of the developing intestine.
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Affiliation(s)
- Andrew T Song
- Centre de Recherche, CHU Sainte-Justine, Montréal, QC, Canada; Department of Anatomy and Cell Biology, McGill University, Montréal, QC, Canada.
| | - Renata H M Sindeaux
- Centre de Recherche, CHU Sainte-Justine, Montréal, QC, Canada; Meakins Christie Laboratories, Department of Medicine, Department of Microbiology and Immunology, Department of Pathology Research Institute of McGill University Health Centre, Montréal, QC, Canada
| | - Yuanyi Li
- Centre de Recherche, CHU Sainte-Justine, Montréal, QC, Canada
| | - Hicham Affia
- Centre de Recherche, CHU Sainte-Justine, Montréal, QC, Canada
| | - Tapan Agnihotri
- Centre de Recherche, CHU Sainte-Justine, Montréal, QC, Canada; Department of Pharmacology and Therapeutics, McGill University, Montréal, QC, Canada
| | | | | | - Mathieu Colas
- Centre de Recherche, CHU Sainte-Justine, Montréal, QC, Canada
| | - Jean-Victor Guimond
- CLSC des Faubourgs, CIUSSS du Centre-Sud-de-l'Ile-de-Montréal, Montréal, QC, Canada
| | - Natalie Patey
- Department of Pathology, CHU Sainte-Justine, Université de Montréal, Montréal, QC, Canada
| | - Lara Feulner
- Centre de Recherche, CHU Sainte-Justine, Montréal, QC, Canada
| | - Jean-Sebastien Joyal
- Centre de Recherche, CHU Sainte-Justine, Montréal, QC, Canada; Département de Pédiatrie, Université de Montréal, Montréal, QC, Canada; Department of Pharmacology and Therapeutics, McGill University, Montréal, QC, Canada
| | - Elie Haddad
- Centre de Recherche, CHU Sainte-Justine, Montréal, QC, Canada; Département de Pédiatrie, Université de Montréal, Montréal, QC, Canada
| | - Luis Barreiro
- Centre de Recherche, CHU Sainte-Justine, Montréal, QC, Canada; Genetics Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Gregor Andelfinger
- Centre de Recherche, CHU Sainte-Justine, Montréal, QC, Canada; Department of Anatomy and Cell Biology, McGill University, Montréal, QC, Canada; Département de Pédiatrie, Université de Montréal, Montréal, QC, Canada.
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Taboada M, Almeida X, Cariñena A, Costa J, Carmona-Monge J, Agilda A, Barreiro L, Castillo J, Williams K, Segurola J, Álvarez J, Seoane-Pillado T. Complications and degree of difficulty of orotracheal intubation in the Intensive Care Unit before and after the establishment of an intubation protocol for critically ill patients: a prospective, observational study. Rev Esp Anestesiol Reanim (Engl Ed) 2024; 71:17-27. [PMID: 38104962 DOI: 10.1016/j.redare.2023.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 07/17/2023] [Indexed: 12/19/2023]
Abstract
OBJECTIVE The objective of our study was to compare the degree of difficulty and complications related to tracheal intubation in an Intensive Care Unit (ICU) before and after the introduction of an intubation protocol based on the Difficult Airway Society guidelines for the management of tracheal intubation in critically ill adults, published in 2018. METHODS Prospective, observational study comparing all intubations performed in our ICU over 2 periods: pre-protocol (January 2015-January 2019) and post-protocol (February 2019-July 2022). The material used for intubation, the degree of difficulty, and intubation-related complications were recorded. RESULTS During the study period, 661 patients were intubated - 437 in the pre-protocol period (96% by direct laryngoscopy) and 224 in the post-protocol period (53% with direct laryngoscopy, 46% with video laryngoscopy). We observed an improvement in laryngeal view in the post-protocol period compared to the pre-protocol period (Cormack-Lehane ≥ 2b in 7.6% vs. 29.8%, p < 0.001), and a decrease in the number of moderate-to-severely difficult intubations (6.7% vs. 17.4%, p < 0.001). The first-pass success rate was 92.8% in the post-protocol period compared to 90.2% pre-protocol (p = 0.508). We did not find significant differences in complications between the periods studied. CONCLUSIONS Intubations performed in the post-protocol period were associated with improved laryngeal view and fewer cases of difficult intubation compared with the pre-protocol period.
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Affiliation(s)
- M Taboada
- Unidad de Cuidados Intensivos, Servicio de Anestesia y Reanimación, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, A Coruña, Spain; Fundación Instituto de Investigaciones Sanitarias (FIDIS), Santiago de Compostela, La Coruña, Spain.
| | - X Almeida
- Unidad de Cuidados Intensivos, Servicio de Anestesia y Reanimación, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, A Coruña, Spain; Fundación Instituto de Investigaciones Sanitarias (FIDIS), Santiago de Compostela, La Coruña, Spain
| | - A Cariñena
- Unidad de Cuidados Intensivos, Servicio de Anestesia y Reanimación, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, A Coruña, Spain; Fundación Instituto de Investigaciones Sanitarias (FIDIS), Santiago de Compostela, La Coruña, Spain
| | - J Costa
- Unidad de Cuidados Intensivos, Servicio de Anestesia y Reanimación, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, A Coruña, Spain; Fundación Instituto de Investigaciones Sanitarias (FIDIS), Santiago de Compostela, La Coruña, Spain
| | - J Carmona-Monge
- Unidad de Cuidados Intensivos, Servicio de Anestesia y Reanimación, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, A Coruña, Spain; Fundación Instituto de Investigaciones Sanitarias (FIDIS), Santiago de Compostela, La Coruña, Spain
| | - A Agilda
- Unidad de Cuidados Intensivos, Servicio de Anestesia y Reanimación, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, A Coruña, Spain; Fundación Instituto de Investigaciones Sanitarias (FIDIS), Santiago de Compostela, La Coruña, Spain
| | - L Barreiro
- Unidad de Cuidados Intensivos, Servicio de Anestesia y Reanimación, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, A Coruña, Spain; Fundación Instituto de Investigaciones Sanitarias (FIDIS), Santiago de Compostela, La Coruña, Spain
| | - J Castillo
- Unidad de Cuidados Intensivos, Servicio de Anestesia y Reanimación, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, A Coruña, Spain; Fundación Instituto de Investigaciones Sanitarias (FIDIS), Santiago de Compostela, La Coruña, Spain
| | - K Williams
- Unidad de Cuidados Intensivos, Servicio de Anestesia y Reanimación, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, A Coruña, Spain; Fundación Instituto de Investigaciones Sanitarias (FIDIS), Santiago de Compostela, La Coruña, Spain
| | - J Segurola
- Unidad de Cuidados Intensivos, Servicio de Anestesia y Reanimación, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, A Coruña, Spain; Fundación Instituto de Investigaciones Sanitarias (FIDIS), Santiago de Compostela, La Coruña, Spain
| | - J Álvarez
- Unidad de Cuidados Intensivos, Servicio de Anestesia y Reanimación, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, A Coruña, Spain; Fundación Instituto de Investigaciones Sanitarias (FIDIS), Santiago de Compostela, La Coruña, Spain
| | - T Seoane-Pillado
- Preventive Medicine and Public Health Unit, Department of Health Sciences, University of A Coruña-INIBIC, La Coruña, Spain
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Demeure CE, Poinar H, Barreiro L, Pizarro-Cerdá J. [The Black Death, natural selection and susceptibility to auto-immune disorders]. Med Sci (Paris) 2023; 39:331-333. [PMID: 37094265 DOI: 10.1051/medsci/2023050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Affiliation(s)
- Christian E Demeure
- Unité de recherche Yersinia, Institut Pasteur, université Paris Cité, CNRS UMR6047, Paris, France
| | - Hendrik Poinar
- McMaster Ancient DNA Centre, Departments of anthropology, biology and biochemistry, université McMaster, Hamilton, Ontario, Canada - Michael G. DeGroote Institute of infectious disease research, université McMaster, Hamilton, Ontario, Canada
| | - Luis Barreiro
- Section of genetic medicine, Department of medicine, université de Chicago, Chicago, États-Unis - Department of human genetics, université de Chicago, Chicago, États-Unis
| | - Javier Pizarro-Cerdá
- Unité de recherche Yersinia, Institut Pasteur, université Paris Cité, CNRS UMR6047, Paris, France
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Trigodet F, Lolans K, Fogarty E, Shaiber A, Morrison HG, Barreiro L, Jabri B, Eren AM. High molecular weight DNA extraction strategies for long-read sequencing of complex metagenomes. Mol Ecol Resour 2022; 22:1786-1802. [PMID: 35068060 PMCID: PMC9177515 DOI: 10.1111/1755-0998.13588] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [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: 05/10/2021] [Revised: 12/10/2021] [Accepted: 01/14/2022] [Indexed: 11/28/2022]
Abstract
By offering extremely long contiguous characterization of individual DNA molecules, rapidly emerging long‐read sequencing strategies offer comprehensive insights into the organization of genetic information in genomes and metagenomes. However, successful long‐read sequencing experiments demand high concentrations of highly purified DNA of high molecular weight (HMW), which limits the utility of established DNA extraction kits designed for short‐read sequencing. The challenges associated with input DNA quality intensify further when working with complex environmental samples of low microbial biomass, which requires new protocols that are tailored to study metagenomes with long‐read sequencing. Here, we use human tongue scrapings to benchmark six HMW DNA extraction strategies that are based on commercially available kits, phenol–chloroform (PC) extraction and agarose encasement followed by agarase digestion. A typical end goal of HMW DNA extractions is to obtain the longest possible reads during sequencing, which is often achieved by PC extractions, as demonstrated in sequencing of cultured cells. Yet our analyses that consider overall read‐size distribution, assembly performance and the number of circularized elements found in sequencing results suggest that column‐based kits with enzyme supplementation, rather than PC methods, may be more appropriate for long‐read sequencing of metagenomes.
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Affiliation(s)
- Florian Trigodet
- Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Karen Lolans
- Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Emily Fogarty
- Committee on Microbiology, University of Chicago, Chicago, IL, 60637, USA
| | - Alon Shaiber
- BioPhysical Sciences Program, The University of Chicago, Chicago, IL, 60637, USA
| | - Hilary G Morrison
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
| | - Luis Barreiro
- Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Bana Jabri
- Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - A Murat Eren
- Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA.,Committee on Microbiology, University of Chicago, Chicago, IL, 60637, USA.,BioPhysical Sciences Program, The University of Chicago, Chicago, IL, 60637, USA.,Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
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Findley AS, Zhang X, Boye C, Lin YL, Kalita CA, Barreiro L, Lohmueller KE, Pique-Regi R, Luca F. A signature of Neanderthal introgression on molecular mechanisms of environmental responses. PLoS Genet 2021; 17:e1009493. [PMID: 34570765 PMCID: PMC8509894 DOI: 10.1371/journal.pgen.1009493] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 03/18/2021] [Revised: 10/12/2021] [Accepted: 08/18/2021] [Indexed: 12/17/2022] Open
Abstract
Ancient human migrations led to the settlement of population groups in varied environmental contexts worldwide. The extent to which adaptation to local environments has shaped human genetic diversity is a longstanding question in human evolution. Recent studies have suggested that introgression of archaic alleles in the genome of modern humans may have contributed to adaptation to environmental pressures such as pathogen exposure. Functional genomic studies have demonstrated that variation in gene expression across individuals and in response to environmental perturbations is a main mechanism underlying complex trait variation. We considered gene expression response to in vitro treatments as a molecular phenotype to identify genes and regulatory variants that may have played an important role in adaptations to local environments. We investigated if Neanderthal introgression in the human genome may contribute to the transcriptional response to environmental perturbations. To this end we used eQTLs for genes differentially expressed in a panel of 52 cellular environments, resulting from 5 cell types and 26 treatments, including hormones, vitamins, drugs, and environmental contaminants. We found that SNPs with introgressed Neanderthal alleles (N-SNPs) disrupt binding of transcription factors important for environmental responses, including ionizing radiation and hypoxia, and for glucose metabolism. We identified an enrichment for N-SNPs among eQTLs for genes differentially expressed in response to 8 treatments, including glucocorticoids, caffeine, and vitamin D. Using Massively Parallel Reporter Assays (MPRA) data, we validated the regulatory function of 21 introgressed Neanderthal variants in the human genome, corresponding to 8 eQTLs regulating 15 genes that respond to environmental perturbations. These findings expand the set of environments where archaic introgression may have contributed to adaptations to local environments in modern humans and provide experimental validation for the regulatory function of introgressed variants.
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Affiliation(s)
- Anthony S. Findley
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, United States of America
| | - Xinjun Zhang
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, California, United States of America
| | - Carly Boye
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, United States of America
| | - Yen Lung Lin
- Genetics Section, Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - Cynthia A. Kalita
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, United States of America
| | - Luis Barreiro
- Genetics Section, Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - Kirk E. Lohmueller
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, California, United States of America
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, California, United States of America
| | - Roger Pique-Regi
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, United States of America
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan, United States of America
| | - Francesca Luca
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, United States of America
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan, United States of America
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Bogdan L, Barreiro L, Bourque G. Transposable elements have contributed human regulatory regions that are activated upon bacterial infection. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190332. [PMID: 32075553 DOI: 10.1098/rstb.2019.0332] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Transposable elements (TEs) are increasingly recognized as important contributors to mammalian regulatory systems. For instance, they have been shown to play a role in the human interferon response, but their involvement in other mechanisms of immune cell activation remains poorly understood. Here, we investigated the profile of accessible chromatin enhanced in stimulated human macrophages using ATAC-seq to assess the role of different TE subfamilies in regulating gene expression following an immune response. We found that both previously identified and new repeats belonging to the MER44, THE1, Tigger3 and MLT1 families provide 14 subfamilies that are enriched in differentially accessible chromatin and found near differentially expressed genes. These TEs also harbour binding motifs for several candidate transcription factors, including important immune regulators AP-1 and NF-κB, present in 96% of accessible MER44B and 83% of THE1C instances, respectively. To more directly assess their regulatory potential, we evaluated the presence of these TEs in regions putatively affecting gene expression, as defined by quantitative trait locus (QTL) analysis, and found that repeats are also contributing to accessible elements near QTLs. Together, these results suggest that a number of TE families have contributed to the regulation of gene expression in the context of the immune response to infection in humans. This article is part of a discussion meeting issue 'Crossroads between transposons and gene regulation'.
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Affiliation(s)
- Lucia Bogdan
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Luis Barreiro
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Canadian Center for Computational Genomics, McGill University, Montreal, Quebec, Canada
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Colamartino ABL, Lemieux W, Bifsha P, Nicoletti S, Chakravarti N, Sanz J, Roméro H, Selleri S, Béland K, Guiot M, Tremblay-Laganière C, Dicaire R, Barreiro L, Lee DA, Verhoeyen E, Haddad E. Efficient and Robust NK-Cell Transduction With Baboon Envelope Pseudotyped Lentivector. Front Immunol 2019; 10:2873. [PMID: 31921138 PMCID: PMC6927467 DOI: 10.3389/fimmu.2019.02873] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 11/22/2019] [Indexed: 12/11/2022] Open
Abstract
NK-cell resistance to transduction is a major technical hurdle for developing NK-cell immunotherapy. By using Baboon envelope pseudotyped lentiviral vectors (BaEV-LVs) encoding eGFP, we obtained a transduction rate of 23.0 ± 6.6% (mean ± SD) in freshly-isolated human NK-cells (FI-NK) and 83.4 ± 10.1% (mean ± SD) in NK-cells obtained from the NK-cell Activation and Expansion System (NKAES), with a sustained transgene expression for at least 21 days. BaEV-LVs outperformed Vesicular Stomatitis Virus type-G (VSV-G)-, RD114- and Measles Virus (MV)- pseudotyped LVs (p < 0.0001). mRNA expression of both BaEV receptors, ASCT1 and ASCT2, was detected in FI-NK and NKAES, with higher expression in NKAES. Transduction with BaEV-LVs encoding for CAR-CD22 resulted in robust CAR-expression on 38.3 ± 23.8% (mean ± SD) of NKAES cells, leading to specific killing of NK-resistant pre-B-ALL-RS4;11 cell line. Using a larger vector encoding a dual CD19/CD22-CAR, we were able to transduce and re-expand dual-CAR-expressing NKAES, even with lower viral titer. These dual-CAR-NK efficiently killed both CD19KO- and CD22KO-RS4;11 cells. Our results suggest that BaEV-LVs may efficiently enable NK-cell biological studies and translation of NK-cell-based immunotherapy to the clinic.
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Affiliation(s)
- Aurelien B. L. Colamartino
- Department of Microbiology, Infectiology and Immunology, University of Montréal, Montréal, QC, Canada
- CHU Sainte-Justine Research Center, Montréal, QC, Canada
| | - William Lemieux
- Department of Microbiology, Infectiology and Immunology, University of Montréal, Montréal, QC, Canada
- CHU Sainte-Justine Research Center, Montréal, QC, Canada
| | - Panojot Bifsha
- CHU Sainte-Justine Research Center, Montréal, QC, Canada
| | - Simon Nicoletti
- CHU Sainte-Justine Research Center, Montréal, QC, Canada
- INSERM U1163 and CNRS ERL 8254, Medicine Faculty, Paris Descartes University, Necker Hospital, Paris, France
| | - Nitin Chakravarti
- Department of Medical Oncology, Thomas Jefferson University, Philadelphia, PA, United States
| | - Joaquín Sanz
- Institute for Bio-computation and Physics of Complex Systems (BIFI), University of Zaragoza, Zaragoza, Spain
- Department of Theoretical Physics, Faculty of Sciences, University of Zaragoza, Zaragoza, Spain
| | - Hugo Roméro
- CHU Sainte-Justine Research Center, Montréal, QC, Canada
| | - Silvia Selleri
- Department of Microbiology, Infectiology and Immunology, University of Montréal, Montréal, QC, Canada
- CHU Sainte-Justine Research Center, Montréal, QC, Canada
| | - Kathie Béland
- CHU Sainte-Justine Research Center, Montréal, QC, Canada
| | - Mélanie Guiot
- Pierre and Marie Curie University (PMCU) Paris 6, Paris, France
- Assistance Publique Hopitaux De Paris (AP-HP), Paris, France
| | - Camille Tremblay-Laganière
- Department of Microbiology, Infectiology and Immunology, University of Montréal, Montréal, QC, Canada
- CHU Sainte-Justine Research Center, Montréal, QC, Canada
| | - Renée Dicaire
- CHU Sainte-Justine Research Center, Montréal, QC, Canada
| | - Luis Barreiro
- CHU Sainte-Justine Research Center, Montréal, QC, Canada
- Genetics Section, Department of Medicine, University of Chicago, Chicago, IL, United States
| | - Dean A. Lee
- Center for Childhood Cancer and Blood Disorders, Research Institute of Nationwide Children's Hospital, Columbus, OH, United States
| | - Els Verhoeyen
- CIRI, Université de Lyon, INSERM U1111, ENS de Lyon, Université Lyon 1, CNRS UMR 5308, Lyon, France
- Université Côte d'Azur, INSERM, C3M, Nice, France
| | - Elie Haddad
- Department of Microbiology, Infectiology and Immunology, University of Montréal, Montréal, QC, Canada
- CHU Sainte-Justine Research Center, Montréal, QC, Canada
- Department of Pediatrics, University of Montréal, Montréal, QC, Canada
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Piché J, Gosset N, Legault LM, Pacis A, Oneglia A, Caron M, Chetaille P, Barreiro L, Liu D, Qi X, Nattel S, Leclerc S, Breton-Larrivée M, McGraw S, Andelfinger G. Molecular Signature of CAID Syndrome: Noncanonical Roles of SGO1 in Regulation of TGF-β Signaling and Epigenomics. Cell Mol Gastroenterol Hepatol 2018; 7:411-431. [PMID: 30739867 PMCID: PMC6369230 DOI: 10.1016/j.jcmgh.2018.10.011] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 10/17/2018] [Accepted: 10/17/2018] [Indexed: 01/14/2023]
Abstract
BACKGROUND & AIMS A generalized human pacemaking syndrome, chronic atrial and intestinal dysrhythmia (CAID) (OMIM 616201), is caused by a homozygous SGO1 mutation (K23E), leading to chronic intestinal pseudo-obstruction and arrhythmias. Because CAID patients do not show phenotypes consistent with perturbation of known roles of SGO1, we hypothesized that noncanonical roles of SGO1 drive the clinical manifestations observed. METHODS To identify a molecular signature for CAID syndrome, we achieved unbiased screens in cell lines and gut tissues from CAID patients vs wild-type controls. We performed RNA sequencing along with stable isotope labeling with amino acids in cell culture. In addition, we determined the genome-wide DNA methylation and chromatin accessibility signatures using reduced representative bisulfite sequencing and assay for transposase-accessible chromatin with high-throughput sequencing. Functional studies included patch-clamp, quantitation of transforming growth factor-β (TGF-β) signaling, and immunohistochemistry in CAID patient gut biopsy specimens. RESULTS Proteome and transcriptome studies converge on cell-cycle regulation, cardiac conduction, and smooth muscle regulation as drivers of CAID syndrome. Specifically, the inward rectifier current, an important regulator of cellular function, was disrupted. Immunohistochemistry confirmed overexpression of Budding Uninhibited By Benzimidazoles 1 (BUB1) in patients, implicating the TGF-β pathway in CAID pathogenesis. Canonical TGF-β signaling was up-regulated and uncoupled from noncanonical signaling in CAID patients. Reduced representative bisulfite sequencing and assay for transposase-accessible chromatin with high-throughput sequencing experiments showed significant changes of chromatin states in CAID, pointing to epigenetic regulation as a possible pathologic mechanism. CONCLUSIONS Our findings point to impaired inward rectifier potassium current, dysregulation of canonical TGF-β signaling, and epigenetic regulation as potential drivers of intestinal and cardiac manifestations of CAID syndrome. Transcript profiling and genomics data are as follows: repository URL: https://www.ncbi.nlm.nih.gov/geo; SuperSeries GSE110612 was composed of the following subseries: GSE110309, GSE110576, and GSE110601.
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Affiliation(s)
- Jessica Piché
- Cardiovascular Genetics, Department of Pediatrics, Centre Hospitalier Universitaire Sainte Justine Research Center, Université de Montréal, Montréal, Québec, Canada
| | - Natacha Gosset
- Cardiovascular Genetics, Department of Pediatrics, Centre Hospitalier Universitaire Sainte Justine Research Center, Université de Montréal, Montréal, Québec, Canada
| | - Lisa-Marie Legault
- Department of Biochemistry and Molecular Medicine, Centre Hospitalier Universitaire Sainte Justine Research Center, Université de Montréal, Montréal, Québec, Canada
| | - Alain Pacis
- Department of Genetics, Centre Hospitalier Universitaire Sainte Justine Research Center, Université de Montréal, Montréal, Québec, Canada,Department of Biochemistry, Université de Montréal, Montréal, Québec, Canada
| | - Andrea Oneglia
- Cardiovascular Genetics, Department of Pediatrics, Centre Hospitalier Universitaire Sainte Justine Research Center, Université de Montréal, Montréal, Québec, Canada
| | - Maxime Caron
- Centre Hospitalier Universitaire Sainte Justine Research Center, Université de Montréal, Montréal, Québec, Canada
| | - Philippe Chetaille
- Service of Pediatric Cardiology, Department of Pediatrics, Centre Mère Enfants Soleil, Centre Hospitalier de l’Université de Québec, Québec City, Québec, Canada
| | - Luis Barreiro
- Department of Genetics, Centre Hospitalier Universitaire Sainte Justine Research Center, Université de Montréal, Montréal, Québec, Canada,Department of Biochemistry, Université de Montréal, Montréal, Québec, Canada,Department of Pediatrics, Université de Montréal, Québec, Canada
| | - Donghai Liu
- Research Center, Montreal Heart Institute, Université de Montréal, Montréal, Québec, Canada
| | - Xioyan Qi
- Research Center, Montreal Heart Institute, Université de Montréal, Montréal, Québec, Canada
| | - Stanley Nattel
- Research Center, Montreal Heart Institute, Université de Montréal, Montréal, Québec, Canada
| | - Séverine Leclerc
- Cardiovascular Genetics, Department of Pediatrics, Centre Hospitalier Universitaire Sainte Justine Research Center, Université de Montréal, Montréal, Québec, Canada
| | - Mélanie Breton-Larrivée
- Department of Biochemistry and Molecular Medicine, Centre Hospitalier Universitaire Sainte Justine Research Center, Université de Montréal, Montréal, Québec, Canada
| | | | - Serge McGraw
- Department of Biochemistry and Molecular Medicine, Centre Hospitalier Universitaire Sainte Justine Research Center, Université de Montréal, Montréal, Québec, Canada,Departement of Obstetrics and Gynecology, Centre Hospitalier Universitaire Sainte Justine Research Center, Université de Montréal, Montréal, Québec, Canada
| | - Gregor Andelfinger
- Cardiovascular Genetics, Department of Pediatrics, Centre Hospitalier Universitaire Sainte Justine Research Center, Université de Montréal, Montréal, Québec, Canada,Correspondence Address correspondence to: Gregor Andelfinger, MD, FRCPC, Service of Cardiology, Department of Pediatrics, Cardiovascular Genetics Research Laboratory, Centre Hospitalier Sainte Justine Research Center, Université de Montréal 3175, Chemin Côte Sainte Catherine, Montréal, Québec, H3T 1C5 Canada. fax: (514) 345-4896.
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9
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Orlova M, Cobat A, Huong NT, Ba NN, Van Thuc N, Spencer J, Nédélec Y, Barreiro L, Thai VH, Abel L, Alcaïs A, Schurr E. Gene set signature of reversal reaction type I in leprosy patients. PLoS Genet 2013; 9:e1003624. [PMID: 23874223 PMCID: PMC3708838 DOI: 10.1371/journal.pgen.1003624] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [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: 01/02/2013] [Accepted: 05/24/2013] [Indexed: 11/26/2022] Open
Abstract
Leprosy reversal reactions type 1 (T1R) are acute immune episodes that affect a subset of leprosy patients and remain a major cause of nerve damage. Little is known about the relative importance of innate versus environmental factors in the pathogenesis of T1R. In a retrospective design, we evaluated innate differences in response to Mycobacterium leprae between healthy individuals and former leprosy patients affected or free of T1R by analyzing the transcriptome response of whole blood to M. leprae sonicate. Validation of results was conducted in a subsequent prospective study. We observed the differential expression of 581 genes upon exposure of whole blood to M. leprae sonicate in the retrospective study. We defined a 44 T1R gene set signature of differentially regulated genes. The majority of the T1R set genes were represented by three functional groups: i) pro-inflammatory regulators; ii) arachidonic acid metabolism mediators; and iii) regulators of anti-inflammation. The validity of the T1R gene set signature was replicated in the prospective arm of the study. The T1R genetic signature encompasses genes encoding pro- and anti-inflammatory mediators of innate immunity. This suggests an innate defect in the regulation of the inflammatory response to M. leprae antigens. The identified T1R gene set represents a critical first step towards a genetic profile of leprosy patients who are at increased risk of T1R and concomitant nerve damage. Leprosy type 1 reversal reactions (T1R) are an important cause of nerve damage in leprosy patients and accurate prediction of patients at increased risk of T1R is a major challenge of current leprosy control. The incidence of T1R differs widely from 6% to 67% of leprosy patients in different leprosy endemic settings. Whether or not this reflects the impact of unknown environmental triggers or differences in the genetic background across ethnicities is not known. We performed a comparative transcriptome analysis between leprosy patients affected and free of T1R in response to M. leprae antigens. As the discovery sample we enrolled cured leprosy patients who had been diagnosed with T1R at the time of leprosy diagnosis and leprosy patients who had never undergone T1R (retrospective arm). Whole genome transcriptome analysis after stimulation of blood with M. leprae antigen resulted in the definition of a T1R signature gene set. We validated the T1R gene set in RNA samples obtained from T1R-free patients at the time of leprosy diagnosis and followed for 3 years for development of T1R (prospective arm). These results confirm the role of innate factors in T1R and are a first step towards a predictive genetic T1R signature.
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Affiliation(s)
- Marianna Orlova
- McGill International TB Centre, The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Aurélie Cobat
- McGill International TB Centre, The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- Departments of Human Genetics and Medicine, McGill University, Montreal, Quebec, Canada
| | | | - Nguyen Ngoc Ba
- Hospital for Dermato-Venereology, Ho Chi Minh City, Vietnam
| | | | - John Spencer
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine & Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Yohann Nédélec
- Department of Pediatrics, Sainte-Justine Hospital Research Centre, University of Montreal, Montreal, Quebec, Canada
| | - Luis Barreiro
- Department of Pediatrics, Sainte-Justine Hospital Research Centre, University of Montreal, Montreal, Quebec, Canada
| | - Vu Hong Thai
- Hospital for Dermato-Venereology, Ho Chi Minh City, Vietnam
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale, Paris, France
- University Paris Descartes, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, United States of America
| | - Alexandre Alcaïs
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale, Paris, France
- University Paris Descartes, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, United States of America
- URC-CIC, Hopital Tarnier, Paris, France
| | - Erwin Schurr
- McGill International TB Centre, The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- Departments of Human Genetics and Medicine, McGill University, Montreal, Quebec, Canada
- * E-mail:
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10
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Goyette G, Boulais J, Carruthers NJ, Landry CR, Jutras I, Duclos S, Dermine JF, Michnick SW, LaBoissière S, Lajoie G, Barreiro L, Thibault P, Desjardins M. Proteomic characterization of phagosomal membrane microdomains during phagolysosome biogenesis and evolution. Mol Cell Proteomics 2012; 11:1365-77. [PMID: 22915823 DOI: 10.1074/mcp.m112.021048] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
After their formation at the cell surface, phagosomes become fully functional through a complex maturation process involving sequential interactions with various intracellular organelles. In the last decade, series of data indicated that some of the phagosome functional properties occur in specialized membrane microdomains. The molecules associated with membrane microdomains, as well as the organization of these structures during phagolysosome biogenesis are largely unknown. In this study, we combined proteomics and bioinformatics analyses to characterize the dynamic association of proteins to maturing phagosomes. Our data indicate that groups of proteins shuffle from detergent-soluble to detergent-resistant membrane microdomains during maturation, supporting a model in which the modulation of the phagosome functional properties involves an important reorganization of the phagosome proteome by the coordinated spatial segregation of proteins.
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Affiliation(s)
- Guillaume Goyette
- Département de pathologie et biologie cellulaire, Université de Montréal, and Département de pédiatrie, Centre de recherche de l'hôpital Sainte-Justine, C.P. 6128, Succ centre ville, Montréal, Québec, H3C 3J7, Canada
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11
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González-Neves G, Gil G, Barreiro L, Favre G. Pigment profile of red wines cv. Tannat made with alternative winemaking techniques. J Food Compost Anal 2010. [DOI: 10.1016/j.jfca.2009.08.021] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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12
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Boga JA, de Oña M, Fernández-Verdugo A, González D, Morilla A, Arias M, Barreiro L, Hidalgo F, Melón S. Molecular identification of two genotypes of mumps virus causing two regional outbreaks in Asturias, Spain. J Clin Virol 2008; 42:425-8. [PMID: 18440271 DOI: 10.1016/j.jcv.2008.03.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2008] [Accepted: 03/18/2008] [Indexed: 10/22/2022]
Abstract
BACKGROUND In spite of universal vaccination, several sporadic cases of mumps infection, which could produce outbreaks, are detected every year in different countries. OBJECTIVE Mumps virus strains causing two regional outbreaks in Asturias (Spain) were phylogenetically characterized. STUDY DESIGN Mumps virus strains, which were detected in samples from patients belonging to two regional outbreaks in Asturias, were characterized by sequencing of the SH gene and further alignment to homologous sequences of representative strains of the different mumps genotypes. RESULTS Two different strains (Ast/SP02 and Ast/SP07) were isolated. Sequence analysis revealed that while Ast/SP02 belonged to genotype H, Ast/SP07 was phylogenetically close to UK02-19, a reference strain for a new genotype. Both strains belonged to different genotypes from those used in the vaccination (Jeryl-Lynn strain is genotype A). CONCLUSION Mumps virus strains different from those used in vaccination program can cause mumps outbreaks even in vaccinated patients.
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Affiliation(s)
- J A Boga
- Servicio de Microbiología, Hospital Universitario Central de Asturias, Oviedo, Spain.
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13
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Solloso A, Barreiro L, Seoane R, Nogueira E, Cañibano C, Alvarez CV, Zalvide J, Diéguez C, Pombo CM. GHRH proliferative action on somatotrophs is cell-type specific and dependent on Pit-1/GHF-1 expression. J Cell Physiol 2008; 215:140-50. [PMID: 17941086 DOI: 10.1002/jcp.21295] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
To investigate the mechanisms by which the hypothalamic peptide GHRH influences cell division, we analyzed its effects on the proliferation of two different cell lines: CHO-4, an ovary-derived cell line, and GH3, a pituitary-derived cell line. We found that GHRH induces the proliferation of pituitary-derived cells but inhibits the proliferation of ovary-derived cells. We further characterized this dual effect of GHRH to find that the cytoplasmic signals induced by this hormone are similar in both cell lines. Moreover, in CHO-4 cells GHRH stimulates two well-known positive cell cycle regulators, c-myc and cyclin D1, but is unable to induce the degradation of the negative cell cycle regulator p27(Kip1). Significantly, when the Pit-1/GHF-1 gene is exogenously expressed in CHO-4 cells, the negative effect of GHRH on the proliferation of these cells is attenuated. Furthermore, when the levels of Pit-1 are downregulated by siRNA in GH3-GHRHR cells, the positive effects of GHRH on the proliferation of these cells are diminished. These findings add to our understanding of the molecules involved in the regulation of cell proliferation by GHRH, as we demonstrate for the first time that Pit-1 is not only required to drive the expression of the GHRH receptor, as previously described, but is also needed for the downstream effects that occur after its activation to modulate cell proliferation. These data suggest that the regulation of cell proliferation in response to a specific growth factor depends in certain cell populations on the presence of a tissue-specific transcription factor.
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Affiliation(s)
- A Solloso
- Department of Physiology, School of Medicine, University of Santiago de Compostela, Santiago de Compostela, Spain
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14
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Zhang SY, Jouanguy E, Ugolini S, Smahi A, Elain G, Romero P, Segal D, Sancho-Shimizu V, Lorenzo L, Puel A, Picard C, Chapgier A, Plancoulaine S, Titeux M, Cognet C, von Bernuth H, Ku CL, Casrouge A, Zhang XX, Barreiro L, Leonard J, Hamilton C, Lebon P, Héron B, Vallée L, Quintana-Murci L, Hovnanian A, Rozenberg F, Vivier E, Geissmann F, Tardieu M, Abel L, Casanova JL. TLR3 deficiency in patients with herpes simplex encephalitis. Science 2007; 317:1522-7. [PMID: 17872438 DOI: 10.1126/science.1139522] [Citation(s) in RCA: 821] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Some Toll and Toll-like receptors (TLRs) provide immunity to experimental infections in animal models, but their contribution to host defense in natural ecosystems is unknown. We report a dominant-negative TLR3 allele in otherwise healthy children with herpes simplex virus 1 (HSV-1) encephalitis. TLR3 is expressed in the central nervous system (CNS), where it is required to control HSV-1, which spreads from the epithelium to the CNS via cranial nerves. TLR3 is also expressed in epithelial and dendritic cells, which apparently use TLR3-independent pathways to prevent further dissemination of HSV-1 and to provide resistance to other pathogens in TLR3-deficient patients. Human TLR3 appears to be redundant in host defense to most microbes but is vital for natural immunity to HSV-1 in the CNS, which suggests that neurotropic viruses have contributed to the evolutionary maintenance of TLR3.
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Affiliation(s)
- Shen-Ying Zhang
- Human Genetics of Infectious Diseases, Institut National de la Santé et de la Recherche Médicale (INSERM), U550, Faculty Necker, Paris 75015, France
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15
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Torres C, Barreiro L, Dallagiovanna B, Gamarro F, Castanys S. Characterization of a new ATP-binding cassette transporter in Trypanosoma cruzi associated to a L1Tc retrotransposon. Biochim Biophys Acta 1999; 1489:428-32. [PMID: 10673046 DOI: 10.1016/s0167-4781(99)00195-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We have characterized the tcpgp1-like gene of Trypanosoma cruzi, a new ATP-binding cassette (ABC) transporter. tcpgp1 codes for a 1035 amino acid protein with a considerable homology to LtpgpA of Leishmania. Tcpgp1 lacks the conserved sequences corresponding to the second nucleotide-binding domain of other ABC transporters due to the insertion of the L1Tc non-LTR retrotransposon.
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Affiliation(s)
- C Torres
- Departamento de Bioquímica y Farmacología Molecular, Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Cientficas, Granada, Spain
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