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Simphor E, Rognon A, Vignal E, Henry S, Allienne JF, Turtoi A, Chaparro C, Galinier R, Duval D, Gourbal B. Combining a transcriptomic approach and a targeted metabolomics approach for deciphering the molecular bases of compatibility phenotype in the snail Biomphalaria glabrata toward Schistosoma mansoni. Acta Trop 2024:107212. [PMID: 38641222 DOI: 10.1016/j.actatropica.2024.107212] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 04/21/2024]
Abstract
Biomphalaria glabrata is a freshwater snail and the obligatory intermediate host of Schistosoma mansoni parasite, the etiologic agent of intestinal Schistosomiasis, in South America and Caribbean. Interestingly in such host-parasite interactions, compatibility varies between populations, strains or individuals. This observed compatibility polymorphism is based on a complex molecular-matching-phenotype, the molecular bases of which have been investigated in numerous studies, notably by comparing between different strains or geographical isolates or clonal selected snail lines. Herein we propose to decipher the constitutive molecular support of this interaction in selected non-clonal resistant and susceptible snail strain originating from the same natural population from Brazil and thus having the same genetic background. Thanks to a global RNAseq transcriptomic approach on whole snail, we identified a total of 328 differentially expressed genes between resistant and susceptible phenotypes among which 129 were up-regulated and 199 down-regulated. Metabolomic studies were used to corroborate the RNAseq results. The activation of immune genes and specific metabolic pathways in resistant snails might provide them with the capacity to better respond to parasite infection.
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Affiliation(s)
- Elodie Simphor
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan via Domitia, Perpignan, France
| | - Anne Rognon
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan via Domitia, Perpignan, France
| | - Emmanuel Vignal
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan via Domitia, Perpignan, France
| | - Sylvain Henry
- Platform for Translational Oncometabolomics, Biocampus, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | | | - Andrei Turtoi
- Platform for Translational Oncometabolomics, Biocampus, CNRS, INSERM, Université de Montpellier, Montpellier, France; Tumor Microenvironment and Resistance to Therapy Laboratory, Institut de Recherche en Cancérologie de Montpellier, Université de Montpellier, INSERM, U1194, Montpellier, France
| | - Cristian Chaparro
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan via Domitia, Perpignan, France
| | - Richard Galinier
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan via Domitia, Perpignan, France
| | - David Duval
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan via Domitia, Perpignan, France
| | - Benjamin Gourbal
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan via Domitia, Perpignan, France.
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Brann T, Beltramini A, Chaparro C, Berriman M, Doyle SR, Protasio AV. Subtelomeric plasticity contributes to gene family expansion in the human parasitic flatworm Schistosoma mansoni. BMC Genomics 2024; 25:217. [PMID: 38413905 PMCID: PMC10900676 DOI: 10.1186/s12864-024-10032-8] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 01/19/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND The genomic region that lies between the telomere and chromosome body, termed the subtelomere, is heterochromatic, repeat-rich, and frequently undergoes rearrangement. Within this region, large-scale structural changes enable gene diversification, and, as such, large multicopy gene families are often found at the subtelomere. In some parasites, genes associated with proliferation, invasion, and survival are often found in these regions, where they benefit from the subtelomere's highly plastic, rapidly changing nature. The increasing availability of complete (or near complete) parasite genomes provides an opportunity to investigate these typically poorly defined and overlooked genomic regions and potentially reveal relevant gene families necessary for the parasite's lifestyle. RESULTS Using the latest chromosome-scale genome assembly and hallmark repeat richness observed at chromosome termini, we have identified and characterised the subtelomeres of Schistosoma mansoni, a metazoan parasitic flatworm that infects over 250 million people worldwide. Approximately 12% of the S. mansoni genome is classified as subtelomeric, and, in line with other organisms, we find these regions to be gene-poor but rich in transposable elements. We find that S. mansoni subtelomeres have undergone extensive interchromosomal recombination and that these sites disproportionately contribute to the 2.3% of the genome derived from segmental duplications. This recombination has led to the expansion of subtelomeric gene clusters containing 103 genes, including the immunomodulatory annexins and other gene families with unknown roles. The largest of these is a 49-copy plexin domain-containing protein cluster, exclusively expressed in the tegument-the tissue located at the host-parasite physical interface-of intramolluscan life stages. CONCLUSIONS We propose that subtelomeric regions act as a genomic playground for trial-and-error of gene duplication and subsequent divergence. Owing to the importance of subtelomeric genes in other parasites, gene families implicated in this subtelomeric expansion within S. mansoni warrant further characterisation for a potential role in parasitism.
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Affiliation(s)
- T Brann
- Department of Pathology, University of Cambridge, Cambridge, CB1 2PQ, UK
| | - A Beltramini
- Department of Pathology, University of Cambridge, Cambridge, CB1 2PQ, UK
| | - C Chaparro
- IHPE, CNRS, IFREMER, UPVD, University Montpellier, Perpignan, F-66860, France
| | - M Berriman
- School of Infection and Immunity, University of Glasgow, Glasgow, G12 8TA, UK
| | - S R Doyle
- Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - A V Protasio
- Department of Pathology, University of Cambridge, Cambridge, CB1 2PQ, UK.
- Christ's College, Cambridge, CB2 3BU, UK.
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Lasica C, de Carvalho Augusto R, Moné H, Mouahid G, Chaparro C, Veillard AC, Zelisko-Schmidt A, Grunau C. Automated ChIPmentation procedure on limited biological material of the human blood fluke Schistosoma mansoni. Wellcome Open Res 2024; 7:133. [PMID: 37521535 PMCID: PMC10372461 DOI: 10.12688/wellcomeopenres.17779.1] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/09/2024] [Indexed: 08/01/2023] Open
Abstract
In living cells, the genetic information stored in the DNA sequence is always associated with chromosomal and extra-chromosomal epigenetic information. Chromatin is formed by the DNA and associated proteins, in particular histones. Covalent histone modifications are important bearers of epigenetic information and as such have been increasingly studied since about the year 2000. One of the principal techniques to gather information about the association between DNA and modified histones is chromatin immunoprecipitation (ChIP), also combined with massive sequencing (ChIP-Seq). Automated ChIPmentation procedure is a convenient alternative to native chromatin immunoprecipitation (N-ChIP). It is now routinely used for ChIP-Seq in many model species, using in general roughly 10 6 cells per experiment. Such high cell numbers are sometimes difficult to produce. Using the human parasite Schistosoma mansoni, whose production requires sacrificing animals and should therefore be kept to a minimum, we show here that automated ChIPmentation is suitable for limited biological material. We define the operational limit as ≥20,000 Schistosoma cells with 30,000-300,000 cells as optimum. We also present a streamlined protocol for the preparation of ChIP input libraries.
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Affiliation(s)
- Chrystelle Lasica
- IHPE, Univ Perpignan Via Domitia, CNRS, IFREMER, Univ Montpellier, Perpignan, 66860, France
| | - Ronaldo de Carvalho Augusto
- IHPE, Univ Perpignan Via Domitia, CNRS, IFREMER, Univ Montpellier, Perpignan, 66860, France
- LBMC, Laboratoire de Biologie et Modélisation de la Cellule Univ Lyon, ENS de Lyon, Université Claude Bernard Lyon 1, CNRS, UMR 5239, INSERM, U1210,, Lyon, 69000, France
| | - Hélène Moné
- IHPE, Univ Perpignan Via Domitia, CNRS, IFREMER, Univ Montpellier, Perpignan, 66860, France
| | - Gabriel Mouahid
- IHPE, Univ Perpignan Via Domitia, CNRS, IFREMER, Univ Montpellier, Perpignan, 66860, France
| | - Cristian Chaparro
- IHPE, Univ Perpignan Via Domitia, CNRS, IFREMER, Univ Montpellier, Perpignan, 66860, France
| | | | | | - Christoph Grunau
- IHPE, Univ Perpignan Via Domitia, CNRS, IFREMER, Univ Montpellier, Perpignan, 66860, France
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Oyanedel D, Lagorce A, Bruto M, Haffner P, Morot A, Labreuche Y, Dorant Y, de La Forest Divonne S, Delavat F, Inguimbert N, Montagnani C, Morga B, Toulza E, Chaparro C, Escoubas JM, Gueguen Y, Vidal-Dupiol J, de Lorgeril J, Petton B, Degremont L, Tourbiez D, Pimparé LL, Leroy M, Romatif O, Pouzadoux J, Mitta G, Le Roux F, Charrière GM, Travers MA, Destoumieux-Garzón D. Cooperation and cheating orchestrate Vibrio assemblages and polymicrobial synergy in oysters infected with OsHV-1 virus. Proc Natl Acad Sci U S A 2023; 120:e2305195120. [PMID: 37751557 PMCID: PMC10556616 DOI: 10.1073/pnas.2305195120] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 08/10/2023] [Indexed: 09/28/2023] Open
Abstract
Polymicrobial infections threaten the health of humans and animals but remain understudied in natural systems. We recently described the Pacific Oyster Mortality Syndrome (POMS), a polymicrobial disease affecting oyster production worldwide. In the French Atlantic coast, the disease involves coinfection with ostreid herpesvirus 1 (OsHV-1) and virulent Vibrio. However, it is unknown whether consistent Vibrio populations are associated with POMS in different regions, how Vibrio contribute to POMS, and how they interact with OsHV-1 during pathogenesis. By connecting field-based approaches in a Mediterranean ecosystem, laboratory infection assays and functional genomics, we uncovered a web of interdependencies that shape the structure and function of the POMS pathobiota. We show that Vibrio harveyi and Vibrio rotiferianus are predominant in OsHV-1-diseased oysters and that OsHV-1 drives the partition of the Vibrio community observed in the field. However only V. harveyi synergizes with OsHV-1 by promoting mutual growth and accelerating oyster death. V. harveyi shows high-virulence potential and dampens oyster cellular defenses through a type 3 secretion system, making oysters a more favorable niche for microbe colonization. In addition, V. harveyi produces a key siderophore called vibrioferrin. This important resource promotes the growth of V. rotiferianus, which cooccurs with V. harveyi in diseased oysters, and behaves as a cheater by benefiting from V. harveyi metabolite sharing. Our data show that cooperative behaviors contribute to synergy between bacterial and viral coinfecting partners. Additional cheating behaviors further shape the polymicrobial consortium. Controlling cooperative behaviors or countering their effects opens avenues for mitigating polymicrobial diseases.
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Affiliation(s)
- Daniel Oyanedel
- Interactions Hôtes Pathogènes Environnements (IHPE), Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, MontpellierF-34090, France
| | - Arnaud Lagorce
- Interactions Hôtes Pathogènes Environnements (IHPE), Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, MontpellierF-34090, France
| | - Maxime Bruto
- Ifremer, Unité Physiologie Fonctionnelle des Organismes Marins, ZI de la Pointe du Diable, PlouzanéF-29280, France
- Sorbonne Université, Université Pierre et Marie Curie Paris 06, CNRS, UMR8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, RoscoffF-29680, France
| | - Philippe Haffner
- Interactions Hôtes Pathogènes Environnements (IHPE), Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, MontpellierF-34090, France
| | - Amandine Morot
- Université de Bretagne Occidentale, CNRS, Institut de recherche pour le développement (IRD), Ifremer, Laboratoire des sciences de l'environnement marin (LEMAR), Plouzané,F-29280, France
- Laboratoire de Biotechnologie et Chimie Marines, Université Bretagne Sud, EMR CNRS 6076, Institut Universitaire Européen de la Mer, LorientF-56100, France
| | - Yannick Labreuche
- Ifremer, Unité Physiologie Fonctionnelle des Organismes Marins, ZI de la Pointe du Diable, PlouzanéF-29280, France
- Sorbonne Université, Université Pierre et Marie Curie Paris 06, CNRS, UMR8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, RoscoffF-29680, France
| | - Yann Dorant
- Interactions Hôtes Pathogènes Environnements (IHPE), Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, MontpellierF-34090, France
| | - Sébastien de La Forest Divonne
- Interactions Hôtes Pathogènes Environnements (IHPE), Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, MontpellierF-34090, France
| | - François Delavat
- Nantes Université, CNRS, Unité en Sciences Biologiques et Biotechnologies (US2B), UMR6286, Nantes,F-44000, France
| | - Nicolas Inguimbert
- Centre de Recherches Insulaires et OBservatoire de l’Environnement (CRIOBE), UAR3278, Ecole Pratique des Hautes Etudes (EPHE), Université de Perpignan Via Domitia, CNRS, PerpignanF-66860, France
| | - Caroline Montagnani
- Interactions Hôtes Pathogènes Environnements (IHPE), Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, MontpellierF-34090, France
| | - Benjamin Morga
- Ifremer, Adaptation Santé des invertébrés Marins (ASIM), La TrembladeF-17390, France
| | - Eve Toulza
- Interactions Hôtes Pathogènes Environnements (IHPE), Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, MontpellierF-34090, France
| | - Cristian Chaparro
- Interactions Hôtes Pathogènes Environnements (IHPE), Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, MontpellierF-34090, France
| | - Jean-Michel Escoubas
- Interactions Hôtes Pathogènes Environnements (IHPE), Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, MontpellierF-34090, France
| | - Yannick Gueguen
- Interactions Hôtes Pathogènes Environnements (IHPE), Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, MontpellierF-34090, France
- MARine Biodiversity, Exploitation and Conservation (MARBEC) Univ Montpellier, CNRS, Ifremer, IRD, SèteF-34200, France
| | - Jeremie Vidal-Dupiol
- Interactions Hôtes Pathogènes Environnements (IHPE), Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, MontpellierF-34090, France
| | - Julien de Lorgeril
- Interactions Hôtes Pathogènes Environnements (IHPE), Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, MontpellierF-34090, France
- Ifremer, IRD, Univ Nouvelle-Calédonie, Univ La Réunion, ENTROPIE, Nouméa, Nouvelle-Calédonie,F-98800, France
| | - Bruno Petton
- Ifremer, Unité Physiologie Fonctionnelle des Organismes Marins, ZI de la Pointe du Diable, PlouzanéF-29280, France
- Université de Bretagne Occidentale, CNRS, Institut de recherche pour le développement (IRD), Ifremer, Laboratoire des sciences de l'environnement marin (LEMAR), Plouzané,F-29280, France
| | - Lionel Degremont
- Ifremer, Adaptation Santé des invertébrés Marins (ASIM), La TrembladeF-17390, France
| | - Delphine Tourbiez
- Ifremer, Adaptation Santé des invertébrés Marins (ASIM), La TrembladeF-17390, France
| | - Léa-Lou Pimparé
- Interactions Hôtes Pathogènes Environnements (IHPE), Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, MontpellierF-34090, France
| | - Marc Leroy
- Interactions Hôtes Pathogènes Environnements (IHPE), Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, MontpellierF-34090, France
| | - Océane Romatif
- Interactions Hôtes Pathogènes Environnements (IHPE), Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, MontpellierF-34090, France
| | - Juliette Pouzadoux
- Interactions Hôtes Pathogènes Environnements (IHPE), Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, MontpellierF-34090, France
| | - Guillaume Mitta
- Interactions Hôtes Pathogènes Environnements (IHPE), Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, MontpellierF-34090, France
- Ifremer, Université de Polynésie Française, IRD, Institut Louis Malardé (ILM), Ecosystèmes Insulaires Océaniens (EIO), VairaoF-98719, Polynésie Française
| | - Frédérique Le Roux
- Ifremer, Unité Physiologie Fonctionnelle des Organismes Marins, ZI de la Pointe du Diable, PlouzanéF-29280, France
- Sorbonne Université, Université Pierre et Marie Curie Paris 06, CNRS, UMR8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, RoscoffF-29680, France
| | - Guillaume M. Charrière
- Interactions Hôtes Pathogènes Environnements (IHPE), Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, MontpellierF-34090, France
| | - Marie-Agnès Travers
- Interactions Hôtes Pathogènes Environnements (IHPE), Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, MontpellierF-34090, France
| | - Delphine Destoumieux-Garzón
- Interactions Hôtes Pathogènes Environnements (IHPE), Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, MontpellierF-34090, France
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Ittiprasert W, Moescheid MF, Chaparro C, Mann VH, Quack T, Rodpai R, Miller A, Wisitpongpun P, Buakaew W, Mentink-Kane M, Schmid S, Popratiloff A, Grevelding CG, Grunau C, Brindley PJ. Targeted insertion and reporter transgene activity at a gene safe harbor of the human blood fluke, Schistosoma mansoni. Cell Rep Methods 2023; 3:100535. [PMID: 37533651 PMCID: PMC10391569 DOI: 10.1016/j.crmeth.2023.100535] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 05/22/2023] [Accepted: 06/25/2023] [Indexed: 08/04/2023]
Abstract
The identification and characterization of genomic safe harbor sites (GSHs) can facilitate consistent transgene activity with minimal disruption to the host cell genome. We combined computational genome annotation and chromatin structure analysis to predict the location of four GSHs in the human blood fluke, Schistosoma mansoni, a major infectious pathogen of the tropics. A transgene was introduced via CRISPR-Cas-assisted homology-directed repair into one of the GSHs in the egg of the parasite. Gene editing efficiencies of 24% and transgene-encoded fluorescence of 75% of gene-edited schistosome eggs were observed. The approach advances functional genomics for schistosomes by providing a tractable path for generating transgenics using homology-directed, repair-catalyzed transgene insertion. We also suggest that this work will serve as a roadmap for the development of similar approaches in helminths more broadly.
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Affiliation(s)
- Wannaporn Ittiprasert
- Department of Microbiology, Immunology & Tropical Medicine, School of Medicine & Health Sciences, George Washington University, Washington, DC 20037, USA
| | - Max F. Moescheid
- Department of Microbiology, Immunology & Tropical Medicine, School of Medicine & Health Sciences, George Washington University, Washington, DC 20037, USA
- Institute of Parasitology, Biomedical Research Center Seltersberg, Justus Liebig University Giessen, Giessen, Germany
| | - Cristian Chaparro
- IHPE, University of Perpignan Via Domitia, CNRS, IFREMER, University Montpellier, Perpignan, France
| | - Victoria H. Mann
- Department of Microbiology, Immunology & Tropical Medicine, School of Medicine & Health Sciences, George Washington University, Washington, DC 20037, USA
| | - Thomas Quack
- Institute of Parasitology, Biomedical Research Center Seltersberg, Justus Liebig University Giessen, Giessen, Germany
| | - Rutchanee Rodpai
- Department of Microbiology, Immunology & Tropical Medicine, School of Medicine & Health Sciences, George Washington University, Washington, DC 20037, USA
- Department of Parasitology and Excellence in Medical Innovation, and Technology Research Group, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - André Miller
- Schistosomiasis Resource Center, Biomedical Research Institute, Rockville, MD 20850, USA
| | - Prapakorn Wisitpongpun
- Department of Microbiology, Immunology & Tropical Medicine, School of Medicine & Health Sciences, George Washington University, Washington, DC 20037, USA
- Faculty of Medical Technology, Rangsit University, Pathum Thani 12000, Thailand
| | - Watunyoo Buakaew
- Department of Microbiology, Immunology & Tropical Medicine, School of Medicine & Health Sciences, George Washington University, Washington, DC 20037, USA
- Department of Microbiology, Faculty of Medicine, Srinakharinwirot University, Bangkok 10110, Thailand
| | - Margaret Mentink-Kane
- Schistosomiasis Resource Center, Biomedical Research Institute, Rockville, MD 20850, USA
| | - Sarah Schmid
- Schistosomiasis Resource Center, Biomedical Research Institute, Rockville, MD 20850, USA
| | - Anastas Popratiloff
- Nanofabrication and Imaging Center, Science & Engineering Hall, George Washington University, Washington, DC 20052, USA
| | - Christoph G. Grevelding
- Institute of Parasitology, Biomedical Research Center Seltersberg, Justus Liebig University Giessen, Giessen, Germany
| | - Christoph Grunau
- IHPE, University of Perpignan Via Domitia, CNRS, IFREMER, University Montpellier, Perpignan, France
| | - Paul J. Brindley
- Department of Microbiology, Immunology & Tropical Medicine, School of Medicine & Health Sciences, George Washington University, Washington, DC 20037, USA
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Walti L, Arora S, Donahoe L, Almansour S, Sorbo LD, Mazzulli T, Sidhu A, Martinu T, Keshavjee S, Chaparro C, Husain S. Donor Urease Producing Bacteria (DU) Detection and Serum Ammonium Screening for Hyperammonemia Syndrome (HS) Post-Lung Transplant: A Prospective Observational Study. J Heart Lung Transplant 2023. [DOI: 10.1016/j.healun.2023.02.1650] [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: 04/05/2023] Open
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7
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Bitterman R, Soualhine H, Poirier C, Ferraro P, Kabbani D, Hirji A, Tyrrell G, Bergeron C, Levy R, Wright A, Leung V, Singer L, Chaparro C, Keshavjee S, Richard-Greenblatt M, Husain S, Luong M. Mycobacterium Abscessus Complex Infections Among Lung Transplant Recipients: A National Retrospective Cohort Study. J Heart Lung Transplant 2023. [DOI: 10.1016/j.healun.2023.02.1646] [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: 04/05/2023] Open
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Pichon R, Pinaud S, Vignal E, Chaparro C, Pratlong M, Portet A, Duval D, Galinier R, Gourbal B. Single cell RNA sequencing reveals hemocyte heterogeneity in Biomphalaria glabrata: Plasticity over diversity. Front Immunol 2022; 13:956871. [PMID: 36131936 PMCID: PMC9484523 DOI: 10.3389/fimmu.2022.956871] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 05/30/2022] [Accepted: 08/08/2022] [Indexed: 11/30/2022] Open
Abstract
The freshwater snail Biomphalaria glabrata is an intermediate host of Schistosoma mansoni, the agent of human intestinal schistosomiasis. However, much is to be discovered about its innate immune system that appears as a complex black box, in which the immune cells (called hemocytes) play a major role in both cellular and humoral response towards pathogens. Until now, hemocyte classification has been based exclusively on cell morphology and ultrastructural description and depending on the authors considered from 2 to 5 hemocyte populations have been described. In this study, we proposed to evaluate the hemocyte heterogeneity at the transcriptomic level. To accomplish this objective, we used single cell RNA sequencing (scRNAseq) technology coupled to a droplet-based system to separate hemocytes and analyze their transcriptome at a unique cell level in naive Biomphalaria glabrata snails. We were able to demonstrate the presence of 7 hemocyte transcriptomic populations defined by the expression of specific marker genes. As a result, scRNAseq approach showed a high heterogeneity within hemocytes, but provides a detailed description of the different hemocyte transcriptomic populations in B. glabrata supported by distinct cellular functions and lineage trajectory. As a main result, scRNAseq revealed the 3 main population as a super-group of hemocyte diversity but, on the contrary, a great hemocytes plasticity with a probable capacity of hemocytes to engage to different activation pathways. This work opens a new field of research to understand the role of hemocytes particularly in response to pathogens, and towards S. mansoni parasites.
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Affiliation(s)
- Rémi Pichon
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Perpignan, France
| | - Silvain Pinaud
- Cambridge Institute, Li Ka Shing Center, Cancer Research UK, Cambridge, United Kingdom
| | - Emmanuel Vignal
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Montpellier, France
| | - Cristian Chaparro
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Perpignan, France
| | - Marine Pratlong
- Plateforme MGX - Montpellier GenomiX, Institut de Génomique Fonctionnelle, Montpellier, France
| | - Anaïs Portet
- Molecular Immunity Unit, Department of Medicine, Medical Research Council (MRC) Laboratory of Molecular Biology, University of Cambridge, Cambridge, United Kingdom
| | - David Duval
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Perpignan, France
| | - Richard Galinier
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Perpignan, France
| | - Benjamin Gourbal
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Perpignan, France
- *Correspondence: Benjamin Gourbal,
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9
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Fallet M, Montagnani C, Petton B, Dantan L, de Lorgeril J, Comarmond S, Chaparro C, Toulza E, Boitard S, Escoubas JM, Vergnes A, Le Grand J, Bulla I, Gueguen Y, Vidal-Dupiol J, Grunau C, Mitta G, Cosseau C. Early life microbial exposures shape the Crassostrea gigas immune system for lifelong and intergenerational disease protection. Microbiome 2022; 10:85. [PMID: 35659369 PMCID: PMC9167547 DOI: 10.1186/s40168-022-01280-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 04/14/2022] [Indexed: 05/21/2023]
Abstract
BACKGROUND The interaction of organisms with their surrounding microbial communities influences many biological processes, a notable example of which is the shaping of the immune system in early life. In the Pacific oyster, Crassostrea gigas, the role of the environmental microbial community on immune system maturation - and, importantly, protection from infectious disease - is still an open question. RESULTS Here, we demonstrate that early life microbial exposure durably improves oyster survival when challenged with the pathogen causing Pacific oyster mortality syndrome (POMS), both in the exposed generation and in the subsequent one. Combining microbiota, transcriptomic, genetic, and epigenetic analyses, we show that the microbial exposure induced changes in epigenetic marks and a reprogramming of immune gene expression leading to long-term and intergenerational immune protection against POMS. CONCLUSIONS We anticipate that this protection likely extends to additional pathogens and may prove to be an important new strategy for safeguarding oyster aquaculture efforts from infectious disease. tag the videobyte/videoabstract in this section Video Abstract.
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Affiliation(s)
- Manon Fallet
- IHPE, CNRS, Ifremer, Univ. Montpellier, Univ. Perpignan via Domitia, Perpignan, France
| | - Caroline Montagnani
- IHPE, CNRS, Ifremer, Univ. Montpellier, Univ. Perpignan via Domitia, Perpignan, France
| | - Bruno Petton
- Ifremer, UBO CNRS IRD, LEMAR UMR 6539, Argenton, France
| | - Luc Dantan
- IHPE, CNRS, Ifremer, Univ. Montpellier, Univ. Perpignan via Domitia, Perpignan, France
| | - Julien de Lorgeril
- IHPE, CNRS, Ifremer, Univ. Montpellier, Univ. Perpignan via Domitia, Perpignan, France
- Ifremer, IRD, Univ Nouvelle-Calédonie, Univ La Réunion, ENTROPIE, F-98800, Nouméa, Nouvelle-Calédonie, France
| | - Sébastien Comarmond
- IHPE, CNRS, Ifremer, Univ. Montpellier, Univ. Perpignan via Domitia, Perpignan, France
| | - Cristian Chaparro
- IHPE, CNRS, Ifremer, Univ. Montpellier, Univ. Perpignan via Domitia, Perpignan, France
| | - Eve Toulza
- IHPE, CNRS, Ifremer, Univ. Montpellier, Univ. Perpignan via Domitia, Perpignan, France
| | - Simon Boitard
- CBGP, CIRAD, INRAE, Institut Agro, IRD, Université de Montpellier, Montpellier, France
| | - Jean-Michel Escoubas
- IHPE, CNRS, Ifremer, Univ. Montpellier, Univ. Perpignan via Domitia, Perpignan, France
| | - Agnès Vergnes
- IHPE, CNRS, Ifremer, Univ. Montpellier, Univ. Perpignan via Domitia, Perpignan, France
| | | | - Ingo Bulla
- IHPE, CNRS, Ifremer, Univ. Montpellier, Univ. Perpignan via Domitia, Perpignan, France
| | - Yannick Gueguen
- IHPE, CNRS, Ifremer, Univ. Montpellier, Univ. Perpignan via Domitia, Perpignan, France
- MARBEC, CNRS, Ifremer, IRD, Univ Montpellier, Sète, France
| | - Jérémie Vidal-Dupiol
- IHPE, CNRS, Ifremer, Univ. Montpellier, Univ. Perpignan via Domitia, Perpignan, France
| | - Christoph Grunau
- IHPE, CNRS, Ifremer, Univ. Montpellier, Univ. Perpignan via Domitia, Perpignan, France
| | - Guillaume Mitta
- IHPE, CNRS, Ifremer, Univ. Montpellier, Univ. Perpignan via Domitia, Perpignan, France.
- Ifremer, UMR 241 Écosystèmes Insulaires Océaniens, Labex Corail, Centre Ifremer du Pacifique, BP 49, 98725, Tahiti, French Polynesia.
| | - Céline Cosseau
- IHPE, CNRS, Ifremer, Univ. Montpellier, Univ. Perpignan via Domitia, Perpignan, France.
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10
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Luong M, Silveira F, Morrissey O, Danziger-Isakov L, Verschuuren E, Wolfe C, Hadjiliadis D, Chambers D, Patel J, Dellgren G, So M, Verleden G, Blumberg E, Vos R, Perch M, Holm A, Müller N, Chaparro C, Husain S. Delphipanel on Antimicrobial Stewardship and Management of Clinical Syndromes in Thoracic Organ Transplants and Mechanical Circulatory Device Recipients. J Heart Lung Transplant 2022. [DOI: 10.1016/j.healun.2022.01.1560] [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: 10/18/2022] Open
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11
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Luviano N, Duval D, Ittiprasert W, Allienne JF, Tavernier G, Chaparro C, Cosseau C, Grunau C. Hit-and-Run Epigenetic Editing for Vectors of Snail-Borne Parasitic Diseases. Front Cell Dev Biol 2022; 10:794650. [PMID: 35295851 PMCID: PMC8920497 DOI: 10.3389/fcell.2022.794650] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 01/03/2022] [Indexed: 11/25/2022] Open
Abstract
Snail-borne parasitic diseases represent an important challenge to human and animal health. Control strategies that target the intermediate snail host has proved very effective. Epigenetic mechanisms are involved in developmental processes and therefore play a fundamental role in developmental variation. DNA methylation is an important epigenetic information carrier in eukaryotes that plays a major role in the control of chromatin structure. Epigenome editing tools have been instrumental to demonstrate functional importance of this mark for gene expression in vertebrates. In invertebrates, such tools are missing, and the role of DNA methylation remains unknown. Here we demonstrate that methylome engineering can be used to modify in vivo the CpG methylation level of a target gene in the freshwater snail Biomphalaria glabrata, intermediate host of the human parasite Schistosoma mansoni. We used a dCas9-SunTag-DNMT3A complex and synthetic sgRNA to transfect B. glabrata embryos and observed an increase of CpG methylation at the target site in 50% of the hatching snails.
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Affiliation(s)
- Nelia Luviano
- IHPE, Univ Perpignan Via Domitia, CNRS, Ifremer, Univ Montpellier, Perpignan, France
| | - David Duval
- IHPE, Univ Perpignan Via Domitia, CNRS, Ifremer, Univ Montpellier, Perpignan, France
| | - Wannaporn Ittiprasert
- Department of Microbiology, Immunology and Tropical Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC, United States
- Research Center for Neglected Diseases of Poverty, School of Medicine and Health Sciences, George Washington University, Washington, DC, United States
| | | | - Geneviève Tavernier
- Transgenesis Core Facility of UMS006/Inserm/Paul Sabatier University/National Medical Veterinary School, Toulouse, France
- Inserm UMR 1048, Paul Sabatier University, Toulouse, France
| | - Cristian Chaparro
- IHPE, Univ Perpignan Via Domitia, CNRS, Ifremer, Univ Montpellier, Perpignan, France
| | - Celine Cosseau
- IHPE, Univ Perpignan Via Domitia, CNRS, Ifremer, Univ Montpellier, Perpignan, France
| | - Christoph Grunau
- IHPE, Univ Perpignan Via Domitia, CNRS, Ifremer, Univ Montpellier, Perpignan, France
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12
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Abstract
DNA methylation is the most studied epigenetic mark in both plants and animals. The gold standard for assaying genome-wide DNA methylation at single-base resolution is whole-genome bisulfite sequencing (WGBS). Here, we describe an improved procedure for WGBS and original bioinformatic workflows applied to unravel tissue-specific variations of the methylome in relation to gene expression and accumulation of secondary metabolites in the medicinal plant Catharanthus roseus.
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Affiliation(s)
- Thomas Dugé de Bernonville
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, France
- Limagrain, Centre de Recherches de Chappes, Route d'Ennezat, Chappes, France
| | - Christian Daviaud
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Université Paris Saclay, Evry, France
| | - Cristian Chaparro
- UMR5244 IHPE, Université Montpellier, CNRS, IFREMER, Université Perpignan, Perpignan, France
| | - Jörg Tost
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Université Paris Saclay, Evry, France
| | - Stéphane Maury
- EA1207 USC1328 Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRAe, Université d'Orléans, Orléans, France.
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13
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Luviano N, Lopez M, Gawehns F, Chaparro C, Arimondo PB, Ivanovic S, David P, Verhoeven K, Cosseau C, Grunau C. The methylome of Biomphalaria glabrata and other mollusks: enduring modification of epigenetic landscape and phenotypic traits by a new DNA methylation inhibitor. Epigenetics Chromatin 2021; 14:48. [PMID: 34702322 PMCID: PMC8549274 DOI: 10.1186/s13072-021-00422-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 07/16/2021] [Accepted: 10/01/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND 5-Methylcytosine (5mC) is an important epigenetic mark in eukaryotes. Little information about its role exists for invertebrates. To investigate the contribution of 5mC to phenotypic variation in invertebrates, alteration of methylation patterns needs to be produced. Here, we apply new non-nucleoside DNA methyltransferase inhibitors (DNMTi) to introduce aleatory changes into the methylome of mollusk species. RESULTS Flavanone inhibitor Flv1 was efficient in reducing 5mC in the freshwater snails Biomphalaria glabrata and Physa acuta, and to a lesser degree, probably due to lower stability in sea water, in the oyster Crassostrea gigas. Flv1 has no toxic effects and significantly decreased the 5mC level in the treated B. glabrata and in its offspring. Drug treatment triggers significant variation in the shell height in both generations. A reduced representation bisulfite-sequencing method called epiGBS corroborates hypomethylation effect of Flv1 in both B. glabrata generations and identifies seven Differential Methylated Regions (DMR) out of 32 found both in Flv1-exposed snails and its progeny, from which 5 were hypomethylated, demonstrating a multigenerational effect. By targeted bisulfite sequencing, we confirmed hypomethylation in a locus and show that it is associated with reduced gene expression. CONCLUSIONS Flv1 is a new and efficient DNMTi that can be used to induce transient and heritable modifications of the epigenetic landscape and phenotypic traits in mollusks, a phylum of the invertebrates in which epigenetics is understudied.
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Affiliation(s)
- Nelia Luviano
- IHPE, Univ Perpignan Via Domitia, CNRC, Ifremer, Univ Montpellier, Perpignan, France
| | - Marie Lopez
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, CNRS, Univ Montpellier, ENSCM, Montpellier, France
- Epigenetic Targeting of Cancer (ETaC), CNRS FRE3600, Centre de Recherche et Développement Pierre Fabre, Toulouse, France
| | - Fleur Gawehns
- Bioinformatics Unit, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Cristian Chaparro
- IHPE, Univ Perpignan Via Domitia, CNRC, Ifremer, Univ Montpellier, Perpignan, France
| | - Paola B Arimondo
- Epigenetic Targeting of Cancer (ETaC), CNRS FRE3600, Centre de Recherche et Développement Pierre Fabre, Toulouse, France
- Epigenetic Chemical Biology (EpiChBio), Department Structural Biology and Chemistry, UMR 3523, CNRS, Institute Pasteur, 75015, Paris, France
| | - Slavica Ivanovic
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Patrice David
- Centre d'Ecologie Fonctionnelle et Evolutive (CEFE), Univ. Montpellier, CNRS - Université Paul Valéry Montpellier - EPHE, 1919 Route de Mende, 34293, Montpellier Cedex 5, France
| | - Koen Verhoeven
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Céline Cosseau
- IHPE, Univ Perpignan Via Domitia, CNRC, Ifremer, Univ Montpellier, Perpignan, France
| | - Christoph Grunau
- IHPE, Univ Perpignan Via Domitia, CNRC, Ifremer, Univ Montpellier, Perpignan, France.
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14
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Sow MD, Le Gac AL, Fichot R, Lanciano S, Delaunay A, Le Jan I, Lesage-Descauses MC, Citerne S, Caius J, Brunaud V, Soubigou-Taconnat L, Cochard H, Segura V, Chaparro C, Grunau C, Daviaud C, Tost J, Brignolas F, Strauss SH, Mirouze M, Maury S. RNAi suppression of DNA methylation affects the drought stress response and genome integrity in transgenic poplar. New Phytol 2021; 232:80-97. [PMID: 34128549 DOI: 10.1111/nph.17555] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [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: 02/23/2021] [Accepted: 06/08/2021] [Indexed: 05/27/2023]
Abstract
Trees are long-lived organisms that continuously adapt to their environments, a process in which epigenetic mechanisms are likely to play a key role. Via downregulation of the chromatin remodeler DECREASED IN DNA METHYLATION 1 (DDM1) in poplar (Populus tremula × Populus alba) RNAi lines, we examined how DNA methylation coordinates genomic and physiological responses to moderate water deficit. We compared the growth and drought response of two RNAi-ddm1 lines to wild-type (WT) trees under well-watered and water deficit/rewatering conditions, and analyzed their methylomes, transcriptomes, mobilomes and phytohormone contents in the shoot apical meristem. The RNAi-ddm1 lines were more tolerant to drought-induced cavitation but did not differ in height or stem diameter growth. About 5000 differentially methylated regions were consistently detected in both RNAi-ddm1 lines, colocalizing with 910 genes and 89 active transposable elements. Under water deficit conditions, 136 differentially expressed genes were found, including many involved in phytohormone pathways; changes in phytohormone concentrations were also detected. Finally, the combination of hypomethylation and drought led to the mobility of two transposable elements. Our findings suggest major roles for DNA methylation in regulation of genes involved in hormone-related stress responses, and the maintenance of genome integrity through repression of transposable elements.
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Affiliation(s)
- Mamadou D Sow
- LBLGC, INRAE, Université d'Orléans, EA 1207 USC 1328, Orléans, 45067, France
| | - Anne-Laure Le Gac
- LBLGC, INRAE, Université d'Orléans, EA 1207 USC 1328, Orléans, 45067, France
| | - Régis Fichot
- LBLGC, INRAE, Université d'Orléans, EA 1207 USC 1328, Orléans, 45067, France
| | - Sophie Lanciano
- IRD, UMR 232 DIADE, Université de Montpellier, Montpellier, 34090, France
- Laboratory of Plant Genome and Development, Université de Perpignan, Perpignan, 66860, France
| | - Alain Delaunay
- LBLGC, INRAE, Université d'Orléans, EA 1207 USC 1328, Orléans, 45067, France
| | - Isabelle Le Jan
- LBLGC, INRAE, Université d'Orléans, EA 1207 USC 1328, Orléans, 45067, France
| | | | - Sylvie Citerne
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, 78000, France
| | - Jose Caius
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, Orsay, 91405, France
| | - Véronique Brunaud
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, Orsay, 91405, France
| | - Ludivine Soubigou-Taconnat
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, Orsay, 91405, France
| | - Hervé Cochard
- Université Clermont Auvergne, INRAE, PIAF, Clermont-Ferrand, 63000, France
| | - Vincent Segura
- BioForA, INRAE, ONF, UMR 0588, Orléans, 45075, France
- UMR AGAP Institut, Université Montpellier, CIRAD, INRAE, Institut Montpellier SupAgro, UMR 1334, Montpellier, F-34398, France
| | | | - Christoph Grunau
- UMR 5244, IHPE, Université de Perpignan, Perpignan, 66100, France
| | - Christian Daviaud
- Laboratory for Epigenetics and Environment Centre National de Recherche en Génomique Humaine, CEA- Institut de Biologie Francois Jacob, Université Paris-Saclay, Evry, 91057, France
| | - Jörg Tost
- Laboratory for Epigenetics and Environment Centre National de Recherche en Génomique Humaine, CEA- Institut de Biologie Francois Jacob, Université Paris-Saclay, Evry, 91057, France
| | - Franck Brignolas
- LBLGC, INRAE, Université d'Orléans, EA 1207 USC 1328, Orléans, 45067, France
| | - Steven H Strauss
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, 97331-5752, USA
| | - Marie Mirouze
- IRD, UMR 232 DIADE, Université de Montpellier, Montpellier, 34090, France
- Laboratory of Plant Genome and Development, Université de Perpignan, Perpignan, 66860, France
| | - Stéphane Maury
- LBLGC, INRAE, Université d'Orléans, EA 1207 USC 1328, Orléans, 45067, France
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15
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Stitz M, Chaparro C, Lu Z, Olzog VJ, Weinberg CE, Blom J, Goesmann A, Grunau C, Grevelding CG. Satellite-Like W-Elements: Repetitive, Transcribed, and Putative Mobile Genetic Factors with Potential Roles for Biology and Evolution of Schistosoma mansoni. Genome Biol Evol 2021; 13:6361599. [PMID: 34469545 PMCID: PMC8490949 DOI: 10.1093/gbe/evab204] [Citation(s) in RCA: 4] [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] [Subscribe] [Scholar Register] [Accepted: 08/28/2021] [Indexed: 12/17/2022] Open
Abstract
A large portion of animal and plant genomes consists of noncoding DNA. This part includes tandemly repeated sequences and gained attention because it offers exciting insights into genome biology. We investigated satellite-DNA elements of the platyhelminth Schistosoma mansoni, a parasite with remarkable biological features. Schistosoma mansoni lives in the vasculature of humans causing schistosomiasis, a disease of worldwide importance. Schistosomes are the only trematodes that have evolved separate sexes, and the sexual maturation of the female depends on constant pairing with the male. The schistosome karyotype comprises eight chromosome pairs, males are homogametic (ZZ) and females are heterogametic (ZW). Part of the repetitive DNA of S. mansoni are W-elements (WEs), originally discovered as female-specific satellite DNAs in the heterochromatic block of the W-chromosome. Based on new genome and transcriptome data, we performed a reanalysis of the W-element families (WEFs). Besides a new classification of 19 WEFs, we provide first evidence for stage-, sex-, pairing-, gonad-, and strain-specific/preferential transcription of WEs as well as their mobile nature, deduced from autosomal copies of full-length and partial WEs. Structural analyses suggested roles as sources of noncoding RNA-like hammerhead ribozymes, for which we obtained functional evidence. Finally, the variable WEF occurrence in different schistosome species revealed remarkable divergence. From these results, we propose that WEs potentially exert enduring influence on the biology of S. mansoni. Their variable occurrence in different strains, isolates, and species suggests that schistosome WEs may represent genetic factors taking effect on variability and evolution of the family Schistosomatidae.
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Affiliation(s)
- Maria Stitz
- Institute of Parasitology, BFS, Justus Liebig University Giessen, Giessen, Germany
| | - Cristian Chaparro
- IHPE, CNRS, IFREMER, UPVD, University Montpellier, Perpignan, France
| | - Zhigang Lu
- Institute of Parasitology, BFS, Justus Liebig University Giessen, Giessen, Germany
| | | | | | - Jochen Blom
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Germany
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Germany
| | - Christoph Grunau
- IHPE, CNRS, IFREMER, UPVD, University Montpellier, Perpignan, France
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16
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Kincaid-Smith J, Mathieu-Bégné E, Chaparro C, Reguera-Gomez M, Mulero S, Allienne JF, Toulza E, Boissier J. No pre-zygotic isolation mechanisms between Schistosoma haematobium and Schistosoma bovis parasites: From mating interactions to differential gene expression. PLoS Negl Trop Dis 2021; 15:e0009363. [PMID: 33945524 PMCID: PMC8127863 DOI: 10.1371/journal.pntd.0009363] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 09/04/2020] [Revised: 05/14/2021] [Accepted: 04/06/2021] [Indexed: 01/21/2023] Open
Abstract
Species usually develop reproductive isolation mechanisms allowing them to avoid interbreeding. These preventive barriers can act before reproduction, "pre-zygotic barriers", or after reproduction, "post-zygotic barriers". Pre-zygotic barriers prevent unfavourable mating, while post-zygotic barriers determine the viability and selective success of the hybrid offspring. Hybridization in parasites and the underlying reproductive isolation mechanisms maintaining their genetic integrity have been overlooked. Using an integrated approach this work aims to quantify the relative importance of pre-zygotic barriers in Schistosoma haematobium x S. bovis crosses. These two co-endemic species cause schistosomiasis, one of the major debilitating parasitic diseases worldwide, and can hybridize naturally. Using mate choice experiments we first tested if a specific mate recognition system exists between both species. Second, using RNA-sequencing we analysed differential gene expression between homo- and hetero-specific pairing in male and female adult parasites. We show that homo- and hetero-specific pairing occurs randomly between these two species, and few genes in both sexes are affected by hetero-specific pairing. This suggests that i) mate choice is not a reproductive isolating factor, and that ii) no pre-zygotic barrier except spatial isolation "by the final vertebrate host" seems to limit interbreeding between these two species. Interestingly, among the few genes affected by the pairing status of the worms, some can be related to pathways affected during male and female interactions and may also present interesting candidates for species isolation mechanisms and hybridization in schistosome parasites.
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Affiliation(s)
- Julien Kincaid-Smith
- Univ. Montpellier, CNRS, IFREMER, UPVD, IHPE, Perpignan, France
- Centre for Emerging, Endemic and Exotic Diseases (CEEED), Department of Pathobiology and Population Sciences (PPS), Royal Veterinary College, University of London, Hawkshead Campus, Herts, United Kingdom
| | | | | | - Marta Reguera-Gomez
- Departamento de Parasitología, Facultad de Farmacia, Universidad de Valencia, Burjassot, Valencia, Spain
| | - Stephen Mulero
- Univ. Montpellier, CNRS, IFREMER, UPVD, IHPE, Perpignan, France
| | | | - Eve Toulza
- Univ. Montpellier, CNRS, IFREMER, UPVD, IHPE, Perpignan, France
| | - Jérôme Boissier
- Univ. Montpellier, CNRS, IFREMER, UPVD, IHPE, Perpignan, France
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17
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Villalobos APC, Rotstein C, Martinu T, Chaparro C, Singer L, Keshavjee S, Husain S. Histoplasma in Explanted Tissue of Lung Transplant Recipients (LTRs) from a Moderate Endemic Region. J Heart Lung Transplant 2021. [DOI: 10.1016/j.healun.2021.01.959] [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: 10/21/2022] Open
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18
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Rawal K, Martinu T, Juvet S, Stephenson A, Keshavjee S, Chaparro C. Multi-Organ Transplant in Cystic Fibrosis and its Impact on Long-Term Survival. J Heart Lung Transplant 2021. [DOI: 10.1016/j.healun.2021.01.1013] [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: 11/28/2022] Open
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19
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Marks N, Singer L, Wickerson L, Chaparro C, Zilinskas G, Masino C, Won L, Dalton P, Keshavjee S, Sidhu A. Interdisciplinary Approach to Comprehensive Virtual Patient Care in Lung Transplant. J Heart Lung Transplant 2021. [DOI: 10.1016/j.healun.2021.01.447] [Citation(s) in RCA: 1] [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: 11/28/2022] Open
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20
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Villalobos APC, Martinu T, Chaparro C, Singer L, Keshavjee S, Husain S. Invasive Aspergillosis (IA) in Lung Transplant Recipients (LTRs) with Isolated Positive Bronchoalveolar Lavage Galactomannan (BAL GM) in the First Month Post-Transplant. J Heart Lung Transplant 2021. [DOI: 10.1016/j.healun.2021.01.954] [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: 11/17/2022] Open
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21
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Fernandez-Castillo J, Huszti E, Levy L, Ghany R, Riddell P, Chaparro C, Keshavjee S, Singer L, Yeung J, Martinu T. Association between Esophageal Dysmotility and Long-Term Outcomes in Lung Transplant Recipients. J Heart Lung Transplant 2021. [DOI: 10.1016/j.healun.2021.01.1917] [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: 10/21/2022] Open
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22
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Pinaud S, Tetreau G, Poteaux P, Galinier R, Chaparro C, Lassalle D, Portet A, Simphor E, Gourbal B, Duval D. New Insights Into Biomphalysin Gene Family Diversification in the Vector Snail Biomphalaria glabrata. Front Immunol 2021; 12:635131. [PMID: 33868258 PMCID: PMC8047071 DOI: 10.3389/fimmu.2021.635131] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 03/08/2021] [Indexed: 11/30/2022] Open
Abstract
Aerolysins initially characterized as virulence factors in bacteria are increasingly found in massive genome and transcriptome sequencing data from metazoans. Horizontal gene transfer has been demonstrated as the main way of aerolysin-related toxins acquisition in metazoans. However, only few studies have focused on their potential biological functions in such organisms. Herein, we present an extensive characterization of a multigene family encoding aerolysins - named biomphalysin - in Biomphalaria glabrata snail, the intermediate host of the trematode Schistosoma mansoni. Our results highlight that duplication and domestication of an acquired bacterial toxin gene in the snail genome result in the acquisition of a novel and diversified toxin family. Twenty-three biomphalysin genes were identified. All are expressed and exhibited a tissue-specific expression pattern. An in silico structural analysis was performed to highlight the central role played by two distinct domains i) a large lobe involved in the lytic function of these snail toxins which constrained their evolution and ii) a small lobe which is structurally variable between biomphalysin toxins and that matched to various functional domains involved in moiety recognition of targets cells. A functional approach suggests that the repertoire of biomphalysins that bind to pathogens, depends on the type of pathogen encountered. These results underline a neo-and sub-functionalization of the biomphalysin toxins, which have the potential to increase the range of effectors in the snail’s immune arsenal.
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Affiliation(s)
- Silvain Pinaud
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Perpignan, France.,CNRS, IFREMER, University of Montpellier, Perpignan, France
| | - Guillaume Tetreau
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Perpignan, France.,CNRS, IFREMER, University of Montpellier, Perpignan, France
| | - Pierre Poteaux
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Perpignan, France.,CNRS, IFREMER, University of Montpellier, Perpignan, France
| | - Richard Galinier
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Perpignan, France.,CNRS, IFREMER, University of Montpellier, Perpignan, France
| | - Cristian Chaparro
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Perpignan, France.,CNRS, IFREMER, University of Montpellier, Perpignan, France
| | - Damien Lassalle
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Perpignan, France.,CNRS, IFREMER, University of Montpellier, Perpignan, France
| | - Anaïs Portet
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Perpignan, France.,CNRS, IFREMER, University of Montpellier, Perpignan, France
| | - Elodie Simphor
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Perpignan, France.,CNRS, IFREMER, University of Montpellier, Perpignan, France
| | - Benjamin Gourbal
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Perpignan, France.,CNRS, IFREMER, University of Montpellier, Perpignan, France
| | - David Duval
- IHPE, Univ Montpellier, CNRS, IFREMER, Univ Perpignan Via Domitia, Perpignan, France.,CNRS, IFREMER, University of Montpellier, Perpignan, France
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23
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Rey O, Toulza E, Chaparro C, Allienne JF, Kincaid-Smith J, Mathieu-Begné E, Allan F, Rollinson D, Webster BL, Boissier J. Diverging patterns of introgression from Schistosoma bovis across S. haematobium African lineages. PLoS Pathog 2021; 17:e1009313. [PMID: 33544762 PMCID: PMC7891765 DOI: 10.1371/journal.ppat.1009313] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [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: 06/18/2020] [Revised: 02/18/2021] [Accepted: 01/13/2021] [Indexed: 12/29/2022] Open
Abstract
Hybridization is a fascinating evolutionary phenomenon that raises the question of how species maintain their integrity. Inter-species hybridization occurs between certain Schistosoma species that can cause important public health and veterinary issues. In particular hybrids between Schistosoma haematobium and S. bovis associated with humans and animals respectively are frequently identified in Africa. Recent genomic evidence indicates that some S. haematobium populations show signatures of genomic introgression from S. bovis. Here, we conducted a genomic comparative study and investigated the genomic relationships between S. haematobium, S. bovis and their hybrids using 19 isolates originating from a wide geographical range over Africa, including samples initially classified as S. haematobium (n = 11), S. bovis (n = 6) and S. haematobium x S. bovis hybrids (n = 2). Based on a whole genomic sequencing approach, we developed 56,181 SNPs that allowed a clear differentiation of S. bovis isolates from a genomic cluster including all S. haematobium isolates and a natural S. haematobium-bovis hybrid. All the isolates from the S. haematobium cluster except the isolate from Madagascar harbored signatures of genomic introgression from S. bovis. Isolates from Corsica, Mali and Egypt harbored the S. bovis-like Invadolysin gene, an introgressed tract that has been previously detected in some introgressed S. haematobium populations from Niger. Together our results highlight the fact that introgression from S. bovis is widespread across S. haematobium and that the observed introgression is unidirectional. Hybridization is a fascinating evolutionary phenomenon that raises the question of how species maintain their integrity. Inter-species hybridization occurs between certain Schistosoma species that can cause important public health and veterinary issues. In particular hybrids between Schistosoma haematobium and S. bovis associated with humans and animals respectively are frequently identified in Africa. Recent genomic evidence indicates that some S. haematobium populations show signatures of genomic introgression from S. bovis. Here we conducted a comparative genomic study to assess the genomic diversity within S. haematobium and S. bovis species and genetic differentation at the genome scale between these two sister species over the African continent. We also investigated traces of possible ancient introgression from one species to another. We found that S. haematobium display low genetic diversity compared to S. bovis. We also found that most S. haematobium samples harbor signature of past introgression with S. bovis at some genomic positions. Our results strongly suggest that introgression occurred long time ago and that such introgression is unidirectional from S. bovis within S. haematobium. Such introgresssion event(s) result in diverging patterns of genomic introgression across S. haematobium lineages.
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Affiliation(s)
- Olivier Rey
- Univ. Montpellier, CNRS, IFREMER, UPVD, IHPE, Perpignan, France
- * E-mail:
| | - Eve Toulza
- Univ. Montpellier, CNRS, IFREMER, UPVD, IHPE, Perpignan, France
| | | | | | - Julien Kincaid-Smith
- Univ. Montpellier, CNRS, IFREMER, UPVD, IHPE, Perpignan, France
- Centre for Emerging, Endemic and Exotic Diseases (CEEED), Department of Pathobiology and Population Sciences (PPS), Royal Veterinary College, University of London, Hawkshead Campus, Herts, United Kingdom
| | | | - Fiona Allan
- Wolfson Wellcome Biomedical Laboratories, Department of Life Sciences, Natural History Museum, London, United Kingdom
- London Centre for Neglected Tropical Disease Research, Imperial College London School of Public Health, London, United Kingdom
| | - David Rollinson
- Wolfson Wellcome Biomedical Laboratories, Department of Life Sciences, Natural History Museum, London, United Kingdom
- London Centre for Neglected Tropical Disease Research, Imperial College London School of Public Health, London, United Kingdom
| | - Bonnie L. Webster
- Wolfson Wellcome Biomedical Laboratories, Department of Life Sciences, Natural History Museum, London, United Kingdom
- London Centre for Neglected Tropical Disease Research, Imperial College London School of Public Health, London, United Kingdom
| | - Jérôme Boissier
- Univ. Montpellier, CNRS, IFREMER, UPVD, IHPE, Perpignan, France
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24
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Augusto RDC, Rey O, Cosseau C, Chaparro C, Vidal-Dupiol J, Allienne JF, Duval D, Pinaud S, Tönges S, Andriantsoa R, Luquet E, Aubret F, Dia Sow M, David P, Thomson V, Joly D, Gomes Lima M, Federico D, Danchin E, Minoda A, Grunau C. A simple ATAC-seq protocol for population epigenetics. Wellcome Open Res 2021; 5:121. [PMID: 33521328 PMCID: PMC7814285 DOI: 10.12688/wellcomeopenres.15552.2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/11/2020] [Indexed: 11/20/2022] Open
Abstract
We describe here a protocol for the generation of sequence-ready libraries for population epigenomics studies, and the analysis of alignment results. We show that the protocol can be used to monitor chromatin structure changes in populations when exposed to environmental cues. The protocol is a streamlined version of the Assay for transposase accessible chromatin with high-throughput sequencing (ATAC-seq) that provides a positive display of accessible, presumably euchromatic regions. The protocol is straightforward and can be used with small individuals such as daphnia and schistosome worms, and probably many other biological samples of comparable size (~10,000 cells), and it requires little molecular biology handling expertise.
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Affiliation(s)
- Ronaldo de Carvalho Augusto
- Univ. Montpellier, CNRS, IFREMER, UPVD, IHPE, F-66000 Perpignan and F-34095, Montpellier, France
- LBMC, Laboratoire de Biologie et Modélisation de la Cellule Univ Lyon, ENS de Lyon, Université Claude Bernard Lyon 1, CNRS, UMR 5239, INSERM, U1210, Lyon, 69007, France
| | - Oliver Rey
- Univ. Montpellier, CNRS, IFREMER, UPVD, IHPE, F-66000 Perpignan and F-34095, Montpellier, France
| | - Céline Cosseau
- Univ. Montpellier, CNRS, IFREMER, UPVD, IHPE, F-66000 Perpignan and F-34095, Montpellier, France
| | - Cristian Chaparro
- Univ. Montpellier, CNRS, IFREMER, UPVD, IHPE, F-66000 Perpignan and F-34095, Montpellier, France
| | - Jérémie Vidal-Dupiol
- Univ. Montpellier, CNRS, IFREMER, UPVD, IHPE, F-66000 Perpignan and F-34095, Montpellier, France
| | - Jean-François Allienne
- Univ. Montpellier, CNRS, IFREMER, UPVD, IHPE, F-66000 Perpignan and F-34095, Montpellier, France
| | - David Duval
- Univ. Montpellier, CNRS, IFREMER, UPVD, IHPE, F-66000 Perpignan and F-34095, Montpellier, France
| | - Silvain Pinaud
- Univ. Montpellier, CNRS, IFREMER, UPVD, IHPE, F-66000 Perpignan and F-34095, Montpellier, France
- Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Sina Tönges
- Division of Epigenetics, DKFZ ZMBH Alliance, German Cancer Research Center, Heidelberg, 69120, Germany
| | - Ranja Andriantsoa
- Division of Epigenetics, DKFZ ZMBH Alliance, German Cancer Research Center, Heidelberg, 69120, Germany
| | - Emilien Luquet
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Villeurbanne, 69622, France
| | - Fabien Aubret
- CNRS,Station d'Ecologie Théorique et Expérimentale, Université Paul Sabatier, Moulis, 09200, France
- School of Molecular and Life Sciences, Curtin University, Bentley, Australia
| | | | - Patrice David
- Univ. Montpellier, CNRS, CEFE, F-34293, Montpellier, France
| | - Vicki Thomson
- School of Biological Sciences, University of Adelaide, Adelaide, 5005, Australia
| | - Dominique Joly
- Laboratoire Evolution, Génomes Comportement, Ecologie, CNRS Université Paris Sud UMR 9191, Gif sur Yvette, 91198, France
| | - Mariana Gomes Lima
- Laboratório de Malacologia, Instituto Oswaldo Cruz/Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Déborah Federico
- Laboratoire Évolution & Diversité Biologique (EDB UMR 5174), Université Fédérale de Toulouse; CNRS, Toulouse, 31062, France
| | - Etienne Danchin
- Laboratoire Évolution & Diversité Biologique (EDB UMR 5174), Université Fédérale de Toulouse; CNRS, Toulouse, 31062, France
| | - Aki Minoda
- RIKEN Center for Integrative Medical Sciences, Epigenome Technology Exploration Unit, Tsurumi, Kanagawa, 230-0045, Japan
| | - Christoph Grunau
- Univ. Montpellier, CNRS, IFREMER, UPVD, IHPE, F-66000 Perpignan and F-34095, Montpellier, France
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25
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Dugé de Bernonville T, Maury S, Delaunay A, Daviaud C, Chaparro C, Tost J, O’Connor SE, Courdavault V. Developmental Methylome of the Medicinal Plant Catharanthus roseus Unravels the Tissue-Specific Control of the Monoterpene Indole Alkaloid Pathway by DNA Methylation. Int J Mol Sci 2020; 21:E6028. [PMID: 32825765 PMCID: PMC7503379 DOI: 10.3390/ijms21176028] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 07/21/2020] [Revised: 08/06/2020] [Accepted: 08/18/2020] [Indexed: 02/07/2023] Open
Abstract
Catharanthus roseus produces a wide spectrum of monoterpene indole alkaloids (MIAs). MIA biosynthesis requires a tightly coordinated pathway involving more than 30 enzymatic steps that are spatio-temporally and environmentally regulated so that some MIAs specifically accumulate in restricted plant parts. The first regulatory layer involves a complex network of transcription factors from the basic Helix Loop Helix (bHLH) or AP2 families. In the present manuscript, we investigated whether an additional epigenetic layer could control the organ-, developmental- and environmental-specificity of MIA accumulation. We used Whole-Genome Bisulfite Sequencing (WGBS) together with RNA-seq to identify differentially methylated and expressed genes among nine samples reflecting different plant organs and experimental conditions. Tissue specific gene expression was associated with specific methylation signatures depending on cytosine contexts and gene parts. Some genes encoding key enzymatic steps from the MIA pathway were found to be simultaneously differentially expressed and methylated in agreement with the corresponding MIA accumulation. In addition, we found that transcription factors were strikingly concerned by DNA methylation variations. Altogether, our integrative analysis supports an epigenetic regulation of specialized metabolisms in plants and more likely targeting transcription factors which in turn may control the expression of enzyme-encoding genes.
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Affiliation(s)
- Thomas Dugé de Bernonville
- Faculté des Sciences et Techniques, Université de Tours, EA2106 Biomolécules et Biotechnologies Végétales, F-37200 Tours, France;
| | - Stéphane Maury
- INRA, EA1207 USC1328 Laboratoire de Biologie des Ligneux et des Grandes Cultures, Université d’Orléans, F-45067 Orléans, France;
| | - Alain Delaunay
- INRA, EA1207 USC1328 Laboratoire de Biologie des Ligneux et des Grandes Cultures, Université d’Orléans, F-45067 Orléans, France;
| | - Christian Daviaud
- Laboratoire Epigénétique et Environnement, LEE, Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, F-92265 Evry, France; (C.D.); (J.T.)
| | - Cristian Chaparro
- CNRS, IFREMER, UMR5244 Interactions Hôtes-Pathogènes-Environnments, Université de Montpellier, Université de Perpignan Via Domitia, F-66860 Perpignan, France;
| | - Jörg Tost
- Laboratoire Epigénétique et Environnement, LEE, Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, F-92265 Evry, France; (C.D.); (J.T.)
| | - Sarah Ellen O’Connor
- Max Planck Institute for Chemical Ecology, Department of Natural Product Biosynthesis, 07745 Jena, Germany;
| | - Vincent Courdavault
- Faculté des Sciences et Techniques, Université de Tours, EA2106 Biomolécules et Biotechnologies Végétales, F-37200 Tours, France;
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26
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Delmotte J, Chaparro C, Galinier R, de Lorgeril J, Petton B, Stenger PL, Vidal-Dupiol J, Destoumieux-Garzon D, Gueguen Y, Montagnani C, Escoubas JM, Mitta G. Contribution of Viral Genomic Diversity to Oyster Susceptibility in the Pacific Oyster Mortality Syndrome. Front Microbiol 2020; 11:1579. [PMID: 32754139 PMCID: PMC7381293 DOI: 10.3389/fmicb.2020.01579] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 06/17/2020] [Indexed: 12/13/2022] Open
Abstract
Juvenile Pacific oysters (Crassostrea gigas) are subjected to recurrent episodes of mass mortalities that constitute a threat for the oyster industry. This mortality syndrome named “Pacific Oyster Mortality Syndrome” (POMS) is a polymicrobial disease whose pathogenesis is initiated by a primary infection by a variant of an Ostreid herpes virus named OsHV-1 μVar. The characterization of the OsHV-1 genome during different disease outbreaks occurring in different geographic areas has revealed the existence of a genomic diversity for OsHV-1 μVar. However, the biological significance of this diversity is still poorly understood. To go further in understanding the consequences of OsHV-1 diversity on POMS, we challenged five biparental families of oysters to two different infectious environments on the French coasts (Atlantic and Mediterranean). We observed that the susceptibility to POMS can be different among families within the same environment but also for the same family between the two environments. Viral diversity analysis revealed that Atlantic and Mediterranean POMS are caused by two distinct viral populations. Moreover, we observed that different oyster families are infected by distinct viral populations within a same infectious environment. Altogether these results suggest that the co-evolutionary processes at play between OsHV-1 μVar and oyster populations have selected a viral diversity that could facilitate the infection process and the transmission in oyster populations. These new data must be taken into account in the development of novel selective breeding programs better adapted to the oyster culture environment.
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Affiliation(s)
- Jean Delmotte
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Montpellier, France
| | - Cristian Chaparro
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Montpellier, France
| | - Richard Galinier
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Montpellier, France
| | - Julien de Lorgeril
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Montpellier, France
| | - Bruno Petton
- LEMAR UMR 6539, Université de Bretagne Occidentale, CNRS, IRD, Ifremer, Argenton-en-Landunvez, France
| | - Pierre-Louis Stenger
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Montpellier, France
| | - Jeremie Vidal-Dupiol
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Montpellier, France
| | | | - Yannick Gueguen
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Montpellier, France
| | - Caroline Montagnani
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Montpellier, France
| | - Jean-Michel Escoubas
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Montpellier, France
| | - Guillaume Mitta
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Montpellier, France
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27
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Augusto RDC, Rey O, Cosseau C, Chaparro C, Vidal-Dupiol J, Allienne JF, Duval D, Pinaud S, Tönges S, Andriantsoa R, Luquet E, Aubret F, Dia Sow M, David P, Thomson V, Joly D, Gomes Lima M, Federico D, Danchin E, Minoda A, Grunau C. A simple ATAC-seq protocol for population epigenetics. Wellcome Open Res 2020; 5:121. [PMID: 33521328 PMCID: PMC7814285 DOI: 10.12688/wellcomeopenres.15552.1] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/29/2020] [Indexed: 08/04/2023] Open
Abstract
We describe here a protocol for the generation of sequence-ready libraries for population epigenomics studies. The protocol is a streamlined version of the Assay for transposase accessible chromatin with high-throughput sequencing (ATAC-seq) that provides a positive display of accessible, presumably euchromatic regions. The protocol is straightforward and can be used with small individuals such as daphnia and schistosome worms, and probably many other biological samples of comparable size, and it requires little molecular biology handling expertise.
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Affiliation(s)
- Ronaldo de Carvalho Augusto
- Univ. Montpellier, CNRS, IFREMER, UPVD, IHPE, F-66000 Perpignan and F-34095, Montpellier, France
- LBMC, Laboratoire de Biologie et Modélisation de la Cellule Univ Lyon, ENS de Lyon, Université Claude Bernard Lyon 1, CNRS, UMR 5239, INSERM, U1210, Lyon, 69007, France
| | - Oliver Rey
- Univ. Montpellier, CNRS, IFREMER, UPVD, IHPE, F-66000 Perpignan and F-34095, Montpellier, France
| | - Céline Cosseau
- Univ. Montpellier, CNRS, IFREMER, UPVD, IHPE, F-66000 Perpignan and F-34095, Montpellier, France
| | - Cristian Chaparro
- Univ. Montpellier, CNRS, IFREMER, UPVD, IHPE, F-66000 Perpignan and F-34095, Montpellier, France
| | - Jérémie Vidal-Dupiol
- Univ. Montpellier, CNRS, IFREMER, UPVD, IHPE, F-66000 Perpignan and F-34095, Montpellier, France
| | - Jean-François Allienne
- Univ. Montpellier, CNRS, IFREMER, UPVD, IHPE, F-66000 Perpignan and F-34095, Montpellier, France
| | - David Duval
- Univ. Montpellier, CNRS, IFREMER, UPVD, IHPE, F-66000 Perpignan and F-34095, Montpellier, France
| | - Silvain Pinaud
- Univ. Montpellier, CNRS, IFREMER, UPVD, IHPE, F-66000 Perpignan and F-34095, Montpellier, France
- Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Sina Tönges
- Division of Epigenetics, DKFZ ZMBH Alliance, German Cancer Research Center, Heidelberg, 69120, Germany
| | - Ranja Andriantsoa
- Division of Epigenetics, DKFZ ZMBH Alliance, German Cancer Research Center, Heidelberg, 69120, Germany
| | - Emilien Luquet
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Villeurbanne, 69622, France
| | - Fabien Aubret
- CNRS,Station d'Ecologie Théorique et Expérimentale, Université Paul Sabatier, Moulis, 09200, France
- School of Molecular and Life Sciences, Curtin University, Bentley, Australia
| | | | - Patrice David
- Univ. Montpellier, CNRS, CEFE, F-34293, Montpellier, France
| | - Vicki Thomson
- School of Biological Sciences, University of Adelaide, Adelaide, 5005, Australia
| | - Dominique Joly
- Laboratoire Evolution, Génomes Comportement, Ecologie, CNRS Université Paris Sud UMR 9191, Gif sur Yvette, 91198, France
| | - Mariana Gomes Lima
- Laboratório de Malacologia, Instituto Oswaldo Cruz/Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Déborah Federico
- Laboratoire Évolution & Diversité Biologique (EDB UMR 5174), Université Fédérale de Toulouse; CNRS, Toulouse, 31062, France
| | - Etienne Danchin
- Laboratoire Évolution & Diversité Biologique (EDB UMR 5174), Université Fédérale de Toulouse; CNRS, Toulouse, 31062, France
| | - Aki Minoda
- RIKEN Center for Integrative Medical Sciences, Epigenome Technology Exploration Unit, Tsurumi, Kanagawa, 230-0045, Japan
| | - Christoph Grunau
- Univ. Montpellier, CNRS, IFREMER, UPVD, IHPE, F-66000 Perpignan and F-34095, Montpellier, France
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28
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de Carvalho Augusto R, Roquis D, Al Picard M, Chaparro C, Cosseau C, Grunau C. Correction to: Measuring Histone Modifications in the Human Parasite Schistosoma mansoni. Methods Mol Biol 2020; 2151:C1. [PMID: 32970301 DOI: 10.1007/978-1-0716-0635-3_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Correction to: Chapter 9 in: David J. Timson (ed.), Schistosoma mansoni: Methods and Protocols, Methods in Molecular Biology, vol. 2151.
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Affiliation(s)
- Ronaldo de Carvalho Augusto
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan Via Domitia, Perpignan, France.
- LBMC, Laboratoire de Biologie et Modélisation de la Cellule Univ Lyon, ENS de Lyon, Université Claude Bernard Lyon 1, CNRS, UMR 5239, INSERM, U1210, Lyon, France.
| | - David Roquis
- Amélioration des Grandes Cultures et Ressources Génétiques, Agroscope, Changins, Switzerland
| | - Marion Al Picard
- Centre National de la Recherche Scientifique (CNRS), Laboratory MIVEGEC (CNRS IRD Uni Montpellier), Montpellier, France
| | - Cristian Chaparro
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan Via Domitia, Perpignan, France
| | - Celine Cosseau
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan Via Domitia, Perpignan, France
| | - Christoph Grunau
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan Via Domitia, Perpignan, France
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29
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Alba A, Tetreau G, Chaparro C, Sánchez J, Vázquez AA, Gourbal B. Natural resistance to Fasciola hepatica (Trematoda) in Pseudosuccinea columella snails: A review from literature and insights from comparative "omic" analyses. Dev Comp Immunol 2019; 101:103463. [PMID: 31381929 DOI: 10.1016/j.dci.2019.103463] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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: 01/15/2019] [Revised: 07/25/2019] [Accepted: 08/01/2019] [Indexed: 06/10/2023]
Abstract
The snail Pseudosuccinea columella is one of the main vectors of the medically-important trematode Fasciola hepatica. In Cuba, the existence of natural P. columella populations that are either susceptible or resistant to F. hepatica infection offers a unique snail-parasite for study of parasite-host compatibility and immune function in gastropods. Here, we review all previous literature on this system and present new "omic" data that provide a molecular baseline of both P. columella phenotypes from naïve snails. Comparison of whole snail transcriptomes (RNAseq) and the proteomes of the albumen gland (2D-electrophoresis, MS) revealed that resistant and susceptible strains differed mainly in an enrichment of particular biological processes/functions and a greater abundance of proteins/transcripts associated with immune defense/stress response in resistant snails. These results indicate a differential allocation of molecular resources to self-maintenance and survival in resistant P. columella that may cause enhanced responsiveness to stressors (i.e. F. hepatica infection or tolerance to variations in environmental pH/total water hardness), possibly as trade-off against reproduction and the ecological cost of resistance previously suggested in resistant populations of P. columella.
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Affiliation(s)
- Annia Alba
- Centro de Investigaciones, Diagnóstico y Referencia, Instituto de Medicina Tropical "Pedro Kourí", La Habana, Cuba; University of Perpignan Via Domitia, Interactions Hosts Pathogens Environments UMR 5244, CNRS, IFREMER, Univ. Montpellier, F-66860, Perpignan, France.
| | - Guillaume Tetreau
- University of Perpignan Via Domitia, Interactions Hosts Pathogens Environments UMR 5244, CNRS, IFREMER, Univ. Montpellier, F-66860, Perpignan, France
| | - Cristian Chaparro
- University of Perpignan Via Domitia, Interactions Hosts Pathogens Environments UMR 5244, CNRS, IFREMER, Univ. Montpellier, F-66860, Perpignan, France
| | - Jorge Sánchez
- Centro de Investigaciones, Diagnóstico y Referencia, Instituto de Medicina Tropical "Pedro Kourí", La Habana, Cuba
| | - Antonio A Vázquez
- Centro de Investigaciones, Diagnóstico y Referencia, Instituto de Medicina Tropical "Pedro Kourí", La Habana, Cuba; MIVEGEC, IRD, CNRS, Université de Montpellier, Montpellier, France
| | - Benjamin Gourbal
- University of Perpignan Via Domitia, Interactions Hosts Pathogens Environments UMR 5244, CNRS, IFREMER, Univ. Montpellier, F-66860, Perpignan, France.
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30
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Fernandez-Castillo J, Huszti E, Zhang K, Ghany R, Levy L, Darley D, Chaparro C, Tikkanen J, Keshavjee S, Singer L, Yeung J, Martinu T. A Combination of Delayed Gastric Emptying and Gastroesophageal Reflux Disease is Associated with Worse Outcomes in Lung Transplantation. J Heart Lung Transplant 2019. [DOI: 10.1016/j.healun.2019.01.285] [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: 10/27/2022] Open
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31
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Lerat E, Casacuberta J, Chaparro C, Vieira C. On the Importance to Acknowledge Transposable Elements in Epigenomic Analyses. Genes (Basel) 2019; 10:genes10040258. [PMID: 30935103 PMCID: PMC6523952 DOI: 10.3390/genes10040258] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 03/27/2019] [Accepted: 03/27/2019] [Indexed: 12/21/2022] Open
Abstract
Eukaryotic genomes comprise a large proportion of repeated sequences, an important fraction of which are transposable elements (TEs). TEs are mobile elements that have a significant impact on genome evolution and on gene functioning. Although some TE insertions could provide adaptive advantages to species, transposition is a highly mutagenic event that has to be tightly controlled to ensure its viability. Genomes have evolved sophisticated mechanisms to control TE activity, the most important being epigenetic silencing. However, the epigenetic control of TEs can also affect genes located nearby that can become epigenetically regulated. It has been proposed that the combination of TE mobilization and the induced changes in the epigenetic landscape could allow a rapid phenotypic adaptation to global environmental changes. In this review, we argue the crucial need to take into account the repeated part of genomes when studying the global impact of epigenetic modifications on an organism. We emphasize more particularly why it is important to carefully consider TEs and what bioinformatic tools can be used to do so.
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Affiliation(s)
- Emmanuelle Lerat
- CNRS, Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, Université Lyon 1, UMR 5558, F-69622 Villeurbanne, France.
| | - Josep Casacuberta
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Cerdanyola del Vallès, 08193 Barcelona, Spain.
| | - Cristian Chaparro
- CNRS, IHPE UMR 5244, University of Perpignan Via Domitia, IFREMER, University Montpellier, F-66860 Perpignan, France.
| | - Cristina Vieira
- CNRS, Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, Université Lyon 1, UMR 5558, F-69622 Villeurbanne, France.
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32
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Portet A, Pinaud S, Chaparro C, Galinier R, Dheilly NM, Portela J, Charriere GM, Allienne JF, Duval D, Gourbal B. Sympatric versus allopatric evolutionary contexts shape differential immune response in Biomphalaria / Schistosoma interaction. PLoS Pathog 2019; 15:e1007647. [PMID: 30893368 PMCID: PMC6443186 DOI: 10.1371/journal.ppat.1007647] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [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: 09/07/2018] [Revised: 04/01/2019] [Accepted: 02/19/2019] [Indexed: 12/22/2022] Open
Abstract
Selective pressures between hosts and their parasites can result in reciprocal evolution or adaptation of specific life history traits. Local adaptation of resident hosts and parasites should lead to increase parasite infectivity/virulence (higher compatibility) when infecting hosts from the same location (in sympatry) than from a foreign location (in allopatry). Analysis of geographic variations in compatibility phenotypes is the most common proxy used to infer local adaptation. However, in some cases, allopatric host-parasite systems demonstrate similar or greater compatibility than in sympatry. In such cases, the potential for local adaptation remains unclear. Here, we study the interaction between Schistosoma and its vector snail Biomphalaria in which such discrepancy in local versus foreign compatibility phenotype has been reported. Herein, we aim at bridging this gap of knowledge by comparing life history traits (immune cellular response, host mortality, and parasite growth) and molecular responses in highly compatible sympatric and allopatric Schistosoma/Biomphalaria interactions originating from different geographic localities (Brazil, Venezuela and Burundi). We found that despite displaying similar prevalence phenotypes, sympatric schistosomes triggered a rapid immune suppression (dual-RNAseq analyses) in the snails within 24h post infection, whereas infection by allopatric schistosomes (regardless of the species) was associated with immune cell proliferation and triggered a non-specific generalized immune response after 96h. We observed that, sympatric schistosomes grow more rapidly. Finally, we identify miRNAs differentially expressed by Schistosoma mansoni that target host immune genes and could be responsible for hijacking the host immune response during the sympatric interaction. We show that despite having similar prevalence phenotypes, sympatric and allopatric snail-Schistosoma interactions displayed strong differences in their immunobiological molecular dialogue. Understanding the mechanisms allowing parasites to adapt rapidly and efficiently to new hosts is critical to control disease emergence and risks of Schistosomiasis outbreaks. Schistosomiasis, the second most widespread human parasitic disease after malaria, is caused by helminth parasites of the genus Schistosoma. More than 200 million people in 74 countries suffer from the pathological, and societal consequences of this disease. To complete its life cycle, the parasite requires an intermediate host, a freshwater snail of the genus Biomphalaria for its transmission. Given the limited options for treating Schistosoma mansoni infections in humans, much research has focused on developing methods to control transmission by its intermediate snail host. Biomphalaria glabrata. Comparative studies have shown that infection of the snail triggers complex cellular and humoral immune responses resulting in significant variations in parasite infectivity and snail susceptibility, known as the so-called polymorphism of compatibility. However, studies have mostly focused on characterizing the immunobiological mechanisms in sympatric interactions. Herein we used a combination of molecular and phenotypic approaches to compare the effect of infection in various sympatric and allopatric evolutionary contexts, allowing us to better understand the mechanisms of host-parasite local adaptation. Learning more about the immunobiological interactions between B. glabrata and S. mansoni could have important socioeconomic and public health impacts by changing the way we attempt to eradicate parasitic diseases and prevent or control schistosomiasis in the field.
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Affiliation(s)
- Anaïs Portet
- Univ. Perpignan Via Domitia, Interactions Hôtes Pathogènes Environnements UMR 5244, CNRS, IFREMER, Univ. Montpellier, Perpignan, France
| | - Silvain Pinaud
- Univ. Perpignan Via Domitia, Interactions Hôtes Pathogènes Environnements UMR 5244, CNRS, IFREMER, Univ. Montpellier, Perpignan, France
| | - Cristian Chaparro
- Univ. Perpignan Via Domitia, Interactions Hôtes Pathogènes Environnements UMR 5244, CNRS, IFREMER, Univ. Montpellier, Perpignan, France
| | - Richard Galinier
- Univ. Perpignan Via Domitia, Interactions Hôtes Pathogènes Environnements UMR 5244, CNRS, IFREMER, Univ. Montpellier, Perpignan, France
| | - Nolwenn M. Dheilly
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York, United States of America
| | - Julien Portela
- Univ. Perpignan Via Domitia, Interactions Hôtes Pathogènes Environnements UMR 5244, CNRS, IFREMER, Univ. Montpellier, Perpignan, France
| | - Guillaume M. Charriere
- Interactions Hôtes-Pathogènes-Environnements (IHPE), UMR 5244, CNRS, Ifremer, Université de Perpignan Via Domitia, Université de Montpellier, Montpellier, France
| | - Jean-François Allienne
- Univ. Perpignan Via Domitia, Interactions Hôtes Pathogènes Environnements UMR 5244, CNRS, IFREMER, Univ. Montpellier, Perpignan, France
| | - David Duval
- Univ. Perpignan Via Domitia, Interactions Hôtes Pathogènes Environnements UMR 5244, CNRS, IFREMER, Univ. Montpellier, Perpignan, France
| | - Benjamin Gourbal
- Univ. Perpignan Via Domitia, Interactions Hôtes Pathogènes Environnements UMR 5244, CNRS, IFREMER, Univ. Montpellier, Perpignan, France
- * E-mail:
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33
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de Lorgeril J, Lucasson A, Petton B, Toulza E, Montagnani C, Clerissi C, Vidal-Dupiol J, Chaparro C, Galinier R, Escoubas JM, Haffner P, Dégremont L, Charrière GM, Lafont M, Delort A, Vergnes A, Chiarello M, Faury N, Rubio T, Leroy MA, Pérignon A, Régler D, Morga B, Alunno-Bruscia M, Boudry P, Le Roux F, Destoumieux-Garzόn D, Gueguen Y, Mitta G. Immune-suppression by OsHV-1 viral infection causes fatal bacteraemia in Pacific oysters. Nat Commun 2018; 9:4215. [PMID: 30310074 PMCID: PMC6182001 DOI: 10.1038/s41467-018-06659-3] [Citation(s) in RCA: 128] [Impact Index Per Article: 21.3] [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: 02/12/2018] [Accepted: 09/18/2018] [Indexed: 11/09/2022] Open
Abstract
Infectious diseases are mostly explored using reductionist approaches despite repeated evidence showing them to be strongly influenced by numerous interacting host and environmental factors. Many diseases with a complex aetiology therefore remain misunderstood. By developing a holistic approach to tackle the complexity of interactions, we decipher the complex intra-host interactions underlying Pacific oyster mortality syndrome affecting juveniles of Crassostrea gigas, the main oyster species exploited worldwide. Using experimental infections reproducing the natural route of infection and combining thorough molecular analyses of oyster families with contrasted susceptibilities, we demonstrate that the disease is caused by multiple infection with an initial and necessary step of infection of oyster haemocytes by the Ostreid herpesvirus OsHV-1 µVar. Viral replication leads to the host entering an immune-compromised state, evolving towards subsequent bacteraemia by opportunistic bacteria. We propose the application of our integrative approach to decipher other multifactorial diseases that affect non-model species worldwide. Pacific oyster mortality syndrome is a poorly understood cause of mortality in commercially important oyster species. Here, the authors use multiple infection experiments to show that the syndrome is caused by sequential infection by herpesvirus and opportunistic bacteria.
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Affiliation(s)
- Julien de Lorgeril
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Place E. Bataillon, 34095, Montpellier, France
| | - Aude Lucasson
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Place E. Bataillon, 34095, Montpellier, France
| | - Bruno Petton
- LEMAR UMR 6539, UBO/CNRS/IRD/Ifremer, 11 presqu'île du vivier, 29840, Argenton-en-Landunvez, France
| | - Eve Toulza
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Place E. Bataillon, 34095, Montpellier, France
| | - Caroline Montagnani
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Place E. Bataillon, 34095, Montpellier, France
| | - Camille Clerissi
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Place E. Bataillon, 34095, Montpellier, France
| | - Jeremie Vidal-Dupiol
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Place E. Bataillon, 34095, Montpellier, France
| | - Cristian Chaparro
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Place E. Bataillon, 34095, Montpellier, France
| | - Richard Galinier
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Place E. Bataillon, 34095, Montpellier, France
| | - Jean-Michel Escoubas
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Place E. Bataillon, 34095, Montpellier, France
| | - Philippe Haffner
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Place E. Bataillon, 34095, Montpellier, France
| | - Lionel Dégremont
- Laboratoire de Génétique et Pathologie des Mollusques Marins, Ifremer, Avenue du Mus de Loup, 17930, La Tremblade, France
| | - Guillaume M Charrière
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Place E. Bataillon, 34095, Montpellier, France
| | - Maxime Lafont
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Place E. Bataillon, 34095, Montpellier, France
| | - Abigaïl Delort
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Place E. Bataillon, 34095, Montpellier, France
| | - Agnès Vergnes
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Place E. Bataillon, 34095, Montpellier, France
| | - Marlène Chiarello
- Marine Biodiversity, Exploitation and Conservation (MARBEC), Université de Montpellier, CNRS, IRD, Ifremer, Place E. Bataillon, 34095, Montpellier, France
| | - Nicole Faury
- Laboratoire de Génétique et Pathologie des Mollusques Marins, Ifremer, Avenue du Mus de Loup, 17930, La Tremblade, France
| | - Tristan Rubio
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Place E. Bataillon, 34095, Montpellier, France
| | - Marc A Leroy
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Place E. Bataillon, 34095, Montpellier, France
| | - Adeline Pérignon
- CRCM, Comité de la Conchyliculture de Méditerranée, Quai Baptiste Guitard, 34140, Mèze, France
| | - Denis Régler
- CRCM, Comité de la Conchyliculture de Méditerranée, Quai Baptiste Guitard, 34140, Mèze, France
| | - Benjamin Morga
- Laboratoire de Génétique et Pathologie des Mollusques Marins, Ifremer, Avenue du Mus de Loup, 17930, La Tremblade, France
| | - Marianne Alunno-Bruscia
- LEMAR UMR 6539, UBO/CNRS/IRD/Ifremer, 11 presqu'île du vivier, 29840, Argenton-en-Landunvez, France
| | - Pierre Boudry
- LEMAR UMR6539, CNRS/UBO/IRD/Ifremer, ZI pointe du diable, CS 10070, F-29280, Plouzané, France
| | - Frédérique Le Roux
- Sorbonne Universités, UPMC Paris 06, CNRS, UMR 8227, LBI2M, Ifremer, Station Biologique de Roscoff, CS 90074, F-29680, Roscoff, France
| | - Delphine Destoumieux-Garzόn
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Place E. Bataillon, 34095, Montpellier, France
| | - Yannick Gueguen
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Place E. Bataillon, 34095, Montpellier, France.
| | - Guillaume Mitta
- IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, Place E. Bataillon, 34095, Montpellier, France.
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Geyer KK, Munshi SE, Vickers M, Squance M, Wilkinson TJ, Berrar D, Chaparro C, Swain MT, Hoffmann KF. Corrigendum to 'the anti-fecundity effect of 5-azacytidine (5-AzaC) on Schistosoma mansoni is linked to dis-regulated transcription, translation and stem cell activities' [Int. J. Parasitol. Drugs and Drug Resist. 8 (2018) 213-222]. Int J Parasitol Drugs Drug Resist 2018; 8:493. [PMID: 30029996 PMCID: PMC6288006 DOI: 10.1016/j.ijpddr.2018.07.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kathrin K Geyer
- Institute of Biological, Environmental and Rural Sciences (IBERS), Edward Llwyd Building, Aberystwyth University, Aberystwyth, SY23 3DA, United Kingdom.
| | - Sabrina E Munshi
- Institute of Biological, Environmental and Rural Sciences (IBERS), Edward Llwyd Building, Aberystwyth University, Aberystwyth, SY23 3DA, United Kingdom.
| | - Martin Vickers
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.
| | - Michael Squance
- Institute of Biological, Environmental and Rural Sciences (IBERS), Edward Llwyd Building, Aberystwyth University, Aberystwyth, SY23 3DA, United Kingdom.
| | - Toby J Wilkinson
- The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, United Kingdom.
| | - Daniel Berrar
- Data Science Laboratory, Tokyo Institute of Technology, Tokyo, 152-8550, Japan.
| | - Cristian Chaparro
- University of Perpignan Via Domitia, 58 Avenue Paul Alduy, Bat R, F-66860, Perpignan Cedex, France.
| | - Martin T Swain
- Institute of Biological, Environmental and Rural Sciences (IBERS), Edward Llwyd Building, Aberystwyth University, Aberystwyth, SY23 3DA, United Kingdom.
| | - Karl F Hoffmann
- Institute of Biological, Environmental and Rural Sciences (IBERS), Edward Llwyd Building, Aberystwyth University, Aberystwyth, SY23 3DA, United Kingdom.
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35
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Mouahid G, Clerissi C, Allienne JF, Chaparro C, Al Yafae S, Mintsa Nguema R, Ibikounlé M, Moné H. The phylogeny of the genus Indoplanorbis
(Gastropoda, Planorbidae) from Africa and the French West Indies. ZOOL SCR 2018. [DOI: 10.1111/zsc.12297] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gabriel Mouahid
- IHPE; CNRS; IFREMER; University of Perpignan Via Domitia; University of Montpellier; Perpignan France
| | - Camille Clerissi
- IHPE; CNRS; IFREMER; University of Perpignan Via Domitia; University of Montpellier; Perpignan France
| | - Jean-François Allienne
- IHPE; CNRS; IFREMER; University of Perpignan Via Domitia; University of Montpellier; Perpignan France
| | - Cristian Chaparro
- IHPE; CNRS; IFREMER; University of Perpignan Via Domitia; University of Montpellier; Perpignan France
| | | | | | | | - Hélène Moné
- IHPE; CNRS; IFREMER; University of Perpignan Via Domitia; University of Montpellier; Perpignan France
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Mariscal A, Caldarone L, Tikkanen J, Klement W, Donahoe L, Yeung J, Yasufuku K, de Perrot M, Pierre A, Binnie M, Chow C, Chaparro C, Singer L, Waddell T, Juvet S, Martinu T, Keshavjee S, Cypel M. Bronchial Complications in Contemporary Lung Transplantation: A Rare Event in a 5-Year Single Center Study. J Heart Lung Transplant 2018. [DOI: 10.1016/j.healun.2018.01.627] [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: 10/17/2022] Open
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37
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Sidhu A, Colman R, Tikkanen J, Binnie M, Chaparro C, Keshavjee S, Singer L. Outcomes of Telehealth Assessment of Lung Transplant Candidates. J Heart Lung Transplant 2018. [DOI: 10.1016/j.healun.2018.01.075] [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: 10/17/2022] Open
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38
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Aguilar C, Gohir W, Tikkanen J, Del Sorbo L, Chaparro C, Mazzulli T, Humar A, Kumar D, Cypel M, Singer L, Keshavjee S, Husain S. Ureaplasma spp. and Mycoplasma hominis PCR in Respiratory Samples from Lung Transplant Recipients with Hyperammonemia Syndrome and Cerebral Edema. J Heart Lung Transplant 2018. [DOI: 10.1016/j.healun.2018.01.924] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
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39
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Geyer KK, Munshi SE, Vickers M, Squance M, Wilkinson TJ, Berrar D, Chaparro C, Swain MT, Hoffmann KF. The anti-fecundity effect of 5-azacytidine (5-AzaC) on Schistosoma mansoni is linked to dis-regulated transcription, translation and stem cell activities. Int J Parasitol Drugs Drug Resist 2018; 8:213-222. [PMID: 29649665 PMCID: PMC6039303 DOI: 10.1016/j.ijpddr.2018.03.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 03/27/2018] [Accepted: 03/29/2018] [Indexed: 12/15/2022]
Abstract
Uncontrolled host immunological reactions directed against tissue-trapped eggs precipitate a potentially lethal, pathological cascade responsible for schistosomiasis. Blocking schistosome egg production, therefore, presents a strategy for simultaneously reducing immunopathology as well as limiting disease transmission in endemic or emerging areas. We recently demonstrated that the ribonucleoside analogue 5-azacytidine (5-AzaC) inhibited Schistosoma mansoni oviposition, egg maturation and ovarian development. While these anti-fecundity effects were associated with a loss of DNA methylation, other molecular processes affected by 5-AzaC were not examined at the time. By comparing the transcriptomes of 5-AzaC-treated females to controls, we provide evidence that this ribonucleoside analogue also modulates other crucial aspects of schistosome egg-laying biology. For example, S. mansoni gene products associated with amino acid-, carbohydrate-, fatty acid-, nucleotide- and tricarboxylic acid (TCA)- homeostasis are all dysregulated in 5-AzaC treated females. To validate the metabolic pathway most significantly affected by 5-AzaC, amino acid metabolism, nascent protein synthesis was subsequently quantified in adult schistosomes. Here, 5-AzaC inhibited this process by 68% ±16.7% (SEM) in male- and 81% ±4.8% (SEM) in female-schistosomes. Furthermore, the transcriptome data indicated that adult female stem cells were also affected by 5-AzaC. For instance, 40% of transcripts associated with proliferating schistosome cells were significantly down-regulated by 5-AzaC. This finding correlated with a considerable reduction (95%) in the number of 5-ethynyl-2'-deoxyuridine (EdU) positive cells found in 5-AzaC-treated females. In addition to protein coding genes, the effect that 5-AzaC had on repetitive element expression was also assessed. Here, 46 repeats were found differentially transcribed between 5-AzaC-treated and control females with long terminal repeat (LTR) and DNA transposon classes being amongst the most significant. This study demonstrates that the anti-fecundity activity of 5-AzaC affects more than just DNA methylation in schistosome parasites. Further characterisation of these processes may reveal novel targets for schistosomiasis control.
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Affiliation(s)
- Kathrin K Geyer
- Institute of Biological, Environmental and Rural Sciences (IBERS), Edward Llwyd Building, Aberystwyth University, Aberystwyth SY23 3DA, United Kingdom.
| | - Sabrina E Munshi
- Institute of Biological, Environmental and Rural Sciences (IBERS), Edward Llwyd Building, Aberystwyth University, Aberystwyth SY23 3DA, United Kingdom.
| | - Martin Vickers
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom.
| | - Michael Squance
- Institute of Biological, Environmental and Rural Sciences (IBERS), Edward Llwyd Building, Aberystwyth University, Aberystwyth SY23 3DA, United Kingdom.
| | - Toby J Wilkinson
- The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, United Kingdom.
| | - Daniel Berrar
- Data Science Laboratory, Tokyo Institute of Technology, Tokyo 152-8550, Japan.
| | - Cristian Chaparro
- University of Perpignan Via Domitia, 58 Avenue Paul Alduy, Bat R, F-66860 Perpignan Cedex, France.
| | - Martin T Swain
- Institute of Biological, Environmental and Rural Sciences (IBERS), Edward Llwyd Building, Aberystwyth University, Aberystwyth SY23 3DA, United Kingdom.
| | - Karl F Hoffmann
- Institute of Biological, Environmental and Rural Sciences (IBERS), Edward Llwyd Building, Aberystwyth University, Aberystwyth SY23 3DA, United Kingdom.
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Bulla I, Aliaga B, Lacal V, Bulla J, Grunau C, Chaparro C. Notos - a galaxy tool to analyze CpN observed expected ratios for inferring DNA methylation types. BMC Bioinformatics 2018; 19:105. [PMID: 29587630 PMCID: PMC5870242 DOI: 10.1186/s12859-018-2115-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [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: 07/01/2017] [Accepted: 03/13/2018] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND DNA methylation patterns store epigenetic information in the vast majority of eukaryotic species. The relatively high costs and technical challenges associated with the detection of DNA methylation however have created a bias in the number of methylation studies towards model organisms. Consequently, it remains challenging to infer kingdom-wide general rules about the functions and evolutionary conservation of DNA methylation. Methylated cytosine is often found in specific CpN dinucleotides, and the frequency distributions of, for instance, CpG observed/expected (CpG o/e) ratios have been used to infer DNA methylation types based on higher mutability of methylated CpG. RESULTS Predominantly model-based approaches essentially founded on mixtures of Gaussian distributions are currently used to investigate questions related to the number and position of modes of CpG o/e ratios. These approaches require the selection of an appropriate criterion for determining the best model and will fail if empirical distributions are complex or even merely moderately skewed. We use a kernel density estimation (KDE) based technique for robust and precise characterization of complex CpN o/e distributions without a priori assumptions about the underlying distributions. CONCLUSIONS We show that KDE delivers robust descriptions of CpN o/e distributions. For straightforward processing, we have developed a Galaxy tool, called Notos and available at the ToolShed, that calculates these ratios of input FASTA files and fits a density to their empirical distribution. Based on the estimated density the number and shape of modes of the distribution is determined, providing a rational for the prediction of the number and the types of different methylation classes. Notos is written in R and Perl.
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Affiliation(s)
- Ingo Bulla
- Institut für Mathematik und Informatik, Universität Greifswald, Walther-Rathenau-Str. 47, Greifswald, 17487 Germany
- Theoretical Biology and Biophysics, Group T-6, Los Alamos National Laboratory, New Mexico, Los Alamos USA
| | - Benoît Aliaga
- Univ. Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Univ. Montpellier, 58 Avenue Paul Alduy, Perpignan, 66860 France
| | - Virginia Lacal
- Department of Mathematics, University of Bergen, P.O. Box 7803, Bergen, 5020 Norway
| | - Jan Bulla
- Department of Mathematics, University of Bergen, P.O. Box 7803, Bergen, 5020 Norway
| | - Christoph Grunau
- Univ. Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Univ. Montpellier, 58 Avenue Paul Alduy, Perpignan, 66860 France
| | - Cristian Chaparro
- Univ. Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Univ. Montpellier, 58 Avenue Paul Alduy, Perpignan, 66860 France
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Barbas A, Dib M, Al-Adra D, Goldaracena N, Sapisochin G, Waddell T, Keshavjee S, Selzner N, Chaparro C, Cattral M. Combined lung-liver-pancreas transplantation in a recipient with cystic fibrosis. J Cyst Fibros 2018; 17:e1-e4. [DOI: 10.1016/j.jcf.2017.05.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 05/09/2017] [Accepted: 05/09/2017] [Indexed: 11/15/2022]
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Khan B, Singer LG, Lilly LB, Chaparro C, Martinu T, Juvet S, Pipkin M, Waddell TK, Keshavjee S, Humar A, Cypel M. Successful Lung Transplantation From Hepatitis C Positive Donor to Seronegative Recipient. Am J Transplant 2017; 17:1129-1131. [PMID: 27873483 DOI: 10.1111/ajt.14137] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [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: 08/18/2016] [Revised: 11/16/2016] [Accepted: 11/16/2016] [Indexed: 01/25/2023]
Abstract
Lung transplantation using RNA+ hepatitis C (HCV+) donors to seronegative recipients is not currently performed due to the very high risk of transmission. Previous reports have shown poor survival when this practice was applied. The emergence of new direct-acting antiviral drugs (DAA) suggests a high chance of sustained virologic response in immunocompetent patients. We report here successful transplantation of lungs from HCV+ donor to HCV- recipient. The recipient was an HCV- patient with chronic lung allograft dysfunction. Viral transmission occurred early posttransplant but excellent clinical outcomes were observed including elimination of HCV after 12 weeks of treatment using DAAs.
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Affiliation(s)
- B Khan
- Toronto Lung Transplant Program, University Health Network, University of Toronto, Toronto, Canada
| | - L G Singer
- Toronto Lung Transplant Program, University Health Network, University of Toronto, Toronto, Canada
| | - L B Lilly
- Toronto Multi-Organ Transplant Program, University of Toronto, Toronto, Canada
| | - C Chaparro
- Toronto Lung Transplant Program, University Health Network, University of Toronto, Toronto, Canada
| | - T Martinu
- Toronto Lung Transplant Program, University Health Network, University of Toronto, Toronto, Canada
| | - S Juvet
- Toronto Lung Transplant Program, University Health Network, University of Toronto, Toronto, Canada
| | - M Pipkin
- Toronto Lung Transplant Program, University Health Network, University of Toronto, Toronto, Canada
| | - T K Waddell
- Toronto Lung Transplant Program, University Health Network, University of Toronto, Toronto, Canada
| | - S Keshavjee
- Toronto Lung Transplant Program, University Health Network, University of Toronto, Toronto, Canada
| | - A Humar
- Toronto Multi-Organ Transplant Program, University of Toronto, Toronto, Canada
| | - M Cypel
- Toronto Lung Transplant Program, University Health Network, University of Toronto, Toronto, Canada
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Khan B, Husain S, Binnie M, Chow C, Martinu T, Chaparro C, Keshavjee S, Singer L, Tikkanen J. Impact of Prolonging CMV Prophylaxis in High Risk (CMV D+/R-) Lung Transplant Recipients. J Heart Lung Transplant 2017. [DOI: 10.1016/j.healun.2017.01.1529] [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: 10/19/2022] Open
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Galinier R, Roger E, Moné Y, Duval D, Portet A, Pinaud S, Chaparro C, Grunau C, Genthon C, Dubois E, Rognon A, Arancibia N, Dejean B, Théron A, Gourbal B, Mitta G. A multistrain approach to studying the mechanisms underlying compatibility in the interaction between Biomphalaria glabrata and Schistosoma mansoni. PLoS Negl Trop Dis 2017; 11:e0005398. [PMID: 28253264 PMCID: PMC5349689 DOI: 10.1371/journal.pntd.0005398] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [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: 10/21/2016] [Revised: 03/14/2017] [Accepted: 02/07/2017] [Indexed: 12/03/2022] Open
Abstract
In recent decades, numerous studies have sought to better understand the mechanisms underlying the compatibility between Biomphalaria glabrata and Schistosoma mansoni. The developments of comparative transcriptomics, comparative genomics, interactomics and more targeted approaches have enabled researchers to identify a series of candidate genes. However, no molecular comparative work has yet been performed on multiple populations displaying different levels of compatibility. Here, we seek to fill this gap in the literature. We focused on B. glabrata FREPs and S. mansoni SmPoMucs, which were previously demonstrated to be involved in snail/schistosome compatibility. We studied the expression and polymorphisms of these factors in combinations of snail and schistosome isolates that display different levels of compatibility. We found that the polymorphism and expression levels of FREPs and SmPoMucs could be linked to the compatibility level of S. mansoni. These data and our complementary results obtained by RNA-seq of samples from various snail strains indicate that the mechanism of compatibility is much more complex than previously thought, and that it is likely to be highly variable within and between populations. This complexity must be taken into account if we hope to identify the molecular pathways that are most likely to be good targets for strategies aimed at blocking transmission of the parasite through the snail intermediate host. Schistosomiasis is the second most widespread human tropical parasitic disease after malaria. It is caused by flatworms of the genus Schistosoma, and poses a considerable threat for human health in numerous Asian, African and South American countries. The World Health Organization has set the goal of eradicating schistosomiasis by 2025. However, no vaccine is available, and we currently have only one drug (praziquantel) that can effectively and efficiently treat the disease. As treatment by mass drug administration would enhance the risk of drug resistance in schistosome parasites, complementary strategies to fight this parasitic disease are urgently needed. Freshwater snails of the Biomphalaria genus act as intermediate hosts in the transmission of the schistosome species. Thus, learning more about the mechanisms of the interaction between these snails and the schistosomes could critically facilitate the identification of potential new candidate molecules that may be targeted to prevent schistosome transmission in the field.
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Affiliation(s)
- Richard Galinier
- Univ. Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Univ. Montpellier, Perpignan, France
| | - Emmanuel Roger
- Univ. Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Univ. Montpellier, Perpignan, France
| | - Yves Moné
- Univ. Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Univ. Montpellier, Perpignan, France
| | - David Duval
- Univ. Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Univ. Montpellier, Perpignan, France
| | - Anaïs Portet
- Univ. Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Univ. Montpellier, Perpignan, France
| | - Silvain Pinaud
- Univ. Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Univ. Montpellier, Perpignan, France
| | - Cristian Chaparro
- Univ. Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Univ. Montpellier, Perpignan, France
| | - Christoph Grunau
- Univ. Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Univ. Montpellier, Perpignan, France
| | - Clémence Genthon
- MGX-Montpellier GenomiX, Montpellier Genomics and Bioinformatics Facility, Montpellier, France
| | - Emeric Dubois
- MGX-Montpellier GenomiX, Montpellier Genomics and Bioinformatics Facility, Montpellier, France
| | - Anne Rognon
- Univ. Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Univ. Montpellier, Perpignan, France
| | - Nathalie Arancibia
- Univ. Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Univ. Montpellier, Perpignan, France
| | - Bernard Dejean
- Univ. Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Univ. Montpellier, Perpignan, France
| | - André Théron
- Univ. Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Univ. Montpellier, Perpignan, France
| | - Benjamin Gourbal
- Univ. Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Univ. Montpellier, Perpignan, France
- * E-mail: (BG); (GM)
| | - Guillaume Mitta
- Univ. Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Univ. Montpellier, Perpignan, France
- * E-mail: (BG); (GM)
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Rondon R, Grunau C, Fallet M, Charlemagne N, Sussarellu R, Chaparro C, Montagnani C, Mitta G, Bachère E, Akcha F, Cosseau C. Effects of a parental exposure to diuron on Pacific oyster spat methylome. Environ Epigenet 2017; 3:dvx004. [PMID: 29492306 PMCID: PMC5804544 DOI: 10.1093/eep/dvx004] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 02/14/2017] [Accepted: 03/07/2017] [Indexed: 05/18/2023]
Abstract
Environmental epigenetic is an emerging field that studies the cause-effect relationship between environmental factors and heritable trait via an alteration in epigenetic marks. This field has received much attentions since the impact of environmental factors on different epigenetic marks have been shown to be associated with a broad range of phenotypic disorders in natural ecosystems. Chemical pollutants have been shown to affect immediate epigenetic information carriers of several aquatic species but the heritability of the chromatin marks and the consequences for long term adaptation remain open questions. In this work, we investigated the impact of the diuron herbicide on the DNA methylation pattern of spat from exposed Crassotrea gigas genitors. This oyster is one of the most important mollusk species produced worldwide and a key coastal economic resource in France. The whole genome bisulfite sequencing (WGBS, BS-Seq) was applied to obtain a methylome at single nucleotide resolution on DNA extracted from spat issued from diuron exposed genitors comparatively to control spat. We showed that the parental diuron exposure has an impact on the DNA methylation pattern of its progeny. Most of the differentially methylated regions occurred within coding sequences and we showed that this change in methylation level correlates with RNA level only in a very small group of genes. Although the DNA methylation profile is variable between individuals, we showed conserved DNA methylation patterns in response to parental diuron exposure. This relevant result opens perspectives for the setting of new markers based on epimutations as early indicators of marine pollutions.
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Affiliation(s)
- Rodolfo Rondon
- Ifremer, IHPE UMR 5244, Univ. Perpignan Via Domitia, CNRS, Univ. Montpellier, F-34095 Montpellier, France
- Univ. Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Univ. Montpellier, F-66860 Perpignan, France
| | - Christoph Grunau
- Univ. Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Univ. Montpellier, F-66860 Perpignan, France
| | - Manon Fallet
- Univ. Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Univ. Montpellier, F-66860 Perpignan, France
| | - Nicolas Charlemagne
- Ifremer, Department of Biogeochemistry and Ecotoxicology, Laboratory of Ecotoxicology, Rue de l’ile d’Yeu, BP 21105, 44311 Nantes Cedex 03, France
| | - Rossana Sussarellu
- Ifremer, Department of Biogeochemistry and Ecotoxicology, Laboratory of Ecotoxicology, Rue de l’ile d’Yeu, BP 21105, 44311 Nantes Cedex 03, France
| | - Cristian Chaparro
- Univ. Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Univ. Montpellier, F-66860 Perpignan, France
| | - Caroline Montagnani
- Ifremer, IHPE UMR 5244, Univ. Perpignan Via Domitia, CNRS, Univ. Montpellier, F-34095 Montpellier, France
| | - Guillaume Mitta
- Univ. Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Univ. Montpellier, F-66860 Perpignan, France
| | - Evelyne Bachère
- Ifremer, IHPE UMR 5244, Univ. Perpignan Via Domitia, CNRS, Univ. Montpellier, F-34095 Montpellier, France
| | - Farida Akcha
- Ifremer, Department of Biogeochemistry and Ecotoxicology, Laboratory of Ecotoxicology, Rue de l’ile d’Yeu, BP 21105, 44311 Nantes Cedex 03, France
| | - Céline Cosseau
- Univ. Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Univ. Montpellier, F-66860 Perpignan, France
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Roquis D, Rognon A, Chaparro C, Boissier J, Arancibia N, Cosseau C, Parrinello H, Grunau C. Frequency and mitotic heritability of epimutations inSchistosoma mansoni. Mol Ecol 2016; 25:1741-58. [DOI: 10.1111/mec.13555] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 01/22/2016] [Accepted: 01/23/2016] [Indexed: 12/28/2022]
Affiliation(s)
- David Roquis
- Université de Perpignan Via Domitia; Perpignan F-66860 France
- CNRS; UMR 5244; Interactions Hôtes-Pathogènes-Environnements (IHPE); Perpignan F-66860 France
| | - Anne Rognon
- Université de Perpignan Via Domitia; Perpignan F-66860 France
- CNRS; UMR 5244; Interactions Hôtes-Pathogènes-Environnements (IHPE); Perpignan F-66860 France
| | - Cristian Chaparro
- Université de Perpignan Via Domitia; Perpignan F-66860 France
- CNRS; UMR 5244; Interactions Hôtes-Pathogènes-Environnements (IHPE); Perpignan F-66860 France
| | - Jerome Boissier
- Université de Perpignan Via Domitia; Perpignan F-66860 France
- CNRS; UMR 5244; Interactions Hôtes-Pathogènes-Environnements (IHPE); Perpignan F-66860 France
| | - Nathalie Arancibia
- Université de Perpignan Via Domitia; Perpignan F-66860 France
- CNRS; UMR 5244; Interactions Hôtes-Pathogènes-Environnements (IHPE); Perpignan F-66860 France
| | - Celine Cosseau
- Université de Perpignan Via Domitia; Perpignan F-66860 France
- CNRS; UMR 5244; Interactions Hôtes-Pathogènes-Environnements (IHPE); Perpignan F-66860 France
| | - Hugues Parrinello
- MGX - Montpellier GenomiX IBiSA, Institut de Génomique Fonctionnelle; 141, rue de la Cardonille F-34094 Montpellier Cedex 05 France
| | - Christoph Grunau
- Université de Perpignan Via Domitia; Perpignan F-66860 France
- CNRS; UMR 5244; Interactions Hôtes-Pathogènes-Environnements (IHPE); Perpignan F-66860 France
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Hirji A, Zhao H, Ospina M, Tikkanen J, Tinckam K, Singer L, Chaparro C. Outcomes of Suspected Antibody-Mediated Rejection Post-Lung Transplantation. J Heart Lung Transplant 2016. [DOI: 10.1016/j.healun.2016.01.861] [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: 11/25/2022] Open
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Kabbani D, Kozlowski H, Chaparro C, Singer L, Rotstein C, Keshavjee S, Husain S. Lung Transplant Recipients (LTRs) With Granulomas in the Explanted Lungs: Assessment of Outcomes Related to Non-Tuberculous Mycobacteria. J Heart Lung Transplant 2015. [DOI: 10.1016/j.healun.2015.01.863] [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: 10/23/2022] Open
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Tinckam KJ, Keshavjee S, Chaparro C, Barth D, Azad S, Binnie M, Chow CW, de Perrot M, Pierre AF, Waddell TK, Yasufuku K, Cypel M, Singer LG. Survival in sensitized lung transplant recipients with perioperative desensitization. Am J Transplant 2015; 15:417-26. [PMID: 25612494 DOI: 10.1111/ajt.13076] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 08/19/2014] [Accepted: 09/06/2014] [Indexed: 01/25/2023]
Abstract
Donor-specific HLA antibodies (DSA) have an adverse effect on short-term and long-term lung transplant outcomes. We implemented a perioperative strategy to treat DSA-positive recipients, leading to equivalent rejection and graft survival outcomes. Pretransplant DSA were identified to HLA-A, B, C, DR and DQ antigens. DSA-positive patients were transplanted if panel reactive antibody (PRA) ≥30% or medically urgent and desensitized with perioperative plasma exchange, intravenous immune globulin, antithymocyte globulin (ATG), and mycophenolic acid (MPA). PRA-positive/DSA-negative recipients received MPA. Unsensitized patients received routine cyclosporine, azathioprine and prednisone without ATG. From 2008-2011, 340 lung-only first transplants were performed: 53 DSA-positive, 93 PRA-positive/DSA-negative and 194 unsensitized. Thirty-day survival was 96 %/99%/96% in the three groups, respectively. One-year graft survival was 89%/88%/86% (p = 0.47). DSA-positive and PRA-positive/DSA-negative patients were less likely to experience any ≥ grade 2 acute rejection (9% and 9% vs. 18% unsensitized p = 0.04). Maximum predicted forced expiratory volume (1 s) (81%/74%/76%, p = NS) and predicted forced vital capacity (81%/77%/78%, respectively, p = NS) were equivalent between groups. With the application of this perioperative treatment protocol, lung transplantation can be safely performed in DSA/PRA-positive patients, with similar outcomes to unsensitized recipients.
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Affiliation(s)
- K J Tinckam
- Laboratory Medicine Program and Department of Medicine, University Health Network, University of Toronto, Toronto, ON, Canada
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Shalhoub S, Luong ML, Howard SJ, Richardson S, Singer LG, Chaparro C, Keshavjee S, Akinlolu Y, Rotstein C, Mazzulli T, Husain S. Rate of cyp51A mutation in Aspergillus fumigatus among lung transplant recipients with targeted prophylaxis. J Antimicrob Chemother 2015; 70:1064-7. [PMID: 25604745 DOI: 10.1093/jac/dku528] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
OBJECTIVES The most common mechanism of azole (itraconazole and voriconazole) resistance in Aspergillus fumigatus is a mutation at the cyp51A locus. The aim of our study was to determine the rate of cyp51A mutations in lung transplant recipients (LTR) undergoing targeted antifungal prophylaxis with 12 weeks of voriconazole. METHODS We conducted a prospective study that included 22 LTR with A. fumigatus between October 2008 and November 2011. Of those, 10 LTR were colonized with A. fumigatus and 12 had invasive pulmonary aspergillosis. RESULTS Four patients were found to have A. fumigatus isolates with a cyp51A mutation, two had colonization and two had invasive pulmonary aspergillosis. The remaining 18 LTR had WT cyp51A A. fumigatus isolates. All A. fumigatus isolates (except one due to mixed growth) were tested for antifungal susceptibility. A total of nine LTR were exposed to azoles prior to A. fumigatus isolation for a median duration of 249 (IQR 99-524) days. Azole exposure preceded the isolation of two mutant isolates and seven WT isolates. None of the cyp51A mutant isolates conferred phenotypic resistance to azoles. CONCLUSIONS Targeted antifungal prophylaxis in LTR did not lead to cyp51A resistance mutations in this cohort. Data on larger cohorts who receive universal antifungal prophylaxis are needed.
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Affiliation(s)
- S Shalhoub
- Multi-Organ Transplant Program, University of Toronto, Toronto, Canada
| | - M-L Luong
- Multi-Organ Transplant Program, University of Toronto, Toronto, Canada
| | - S J Howard
- Division of Microbiology, University of Manchester, Manchester, UK
| | - S Richardson
- Division of Microbiology, Hospital for Sick Children and Public Health Ontario Laboratories, Public Health Ontario, University of Toronto, Toronto, Canada
| | - L G Singer
- Multi-Organ Transplant Program, University of Toronto, Toronto, Canada
| | - C Chaparro
- Multi-Organ Transplant Program, University of Toronto, Toronto, Canada
| | - S Keshavjee
- Multi-Organ Transplant Program, University of Toronto, Toronto, Canada
| | - Y Akinlolu
- Multi-Organ Transplant Program, University of Toronto, Toronto, Canada
| | - C Rotstein
- Multi-Organ Transplant Program, University of Toronto, Toronto, Canada
| | - T Mazzulli
- Division of Microbiology, Hospital for Sick Children and Public Health Ontario Laboratories, Public Health Ontario, University of Toronto, Toronto, Canada
| | - S Husain
- Multi-Organ Transplant Program, University of Toronto, Toronto, Canada
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