1
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Hamdi Y, Boujemaa M, Ben Aissa-Haj J, Radouani F, Khyatti M, Mighri N, Hannachi M, Ghedira K, Souiai O, Hkimi C, Kammoun MS, Mejri N, Bouaziz H, Beloufa MA, Charoute H, Barakat A, Najjar I, Taniguchi H, Pietrosemoli N, Dellagi K, Abdelhak S, Boubaker MS, Chica C, Rouleau E. A regionally based precision medicine implementation initiative in North Africa:The PerMediNA consortium. Transl Oncol 2024; 44:101940. [PMID: 38537326 DOI: 10.1016/j.tranon.2024.101940] [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: 12/06/2023] [Revised: 02/23/2024] [Accepted: 03/11/2024] [Indexed: 04/21/2024] Open
Abstract
Precision Medicine is being increasingly used in the developed world to improve health care. While several Precision Medicine (PM) initiatives have been launched worldwide, their implementations have proven to be more challenging particularly in low- and middle-income countries. To address this issue, the "Personalized Medicine in North Africa" initiative (PerMediNA) was launched in three North African countries namely Tunisia, Algeria and Morocco. PerMediNA is coordinated by Institut Pasteur de Tunis together with the French Ministry for Europe and Foreign Affairs, with the support of Institut Pasteur in France. The project is carried out along with Institut Pasteur d'Algérie and Institut Pasteur du Maroc in collaboration with national and international leading institutions in the field of PM including Institut Gustave Roussy in Paris. PerMediNA aims to assess the readiness level of PM implementation in North Africa, to strengthen PM infrastructure, to provide workforce training, to generate genomic data on North African populations, to implement cost effective, affordable and sustainable genetic testing for cancer patients and to inform policy makers on how to translate research knowledge into health products and services. Gender equity and involvement of young scientists in this implementation process are other key goals of the PerMediNA project. In this paper, we are describing PerMediNA as the first PM implementation initiative in North Africa. Such initiatives contribute significantly in shortening existing health disparities and inequities between developed and developing countries and accelerate access to innovative treatments for global health.
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Affiliation(s)
- Yosr Hamdi
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis 1002, Tunisia.
| | - Maroua Boujemaa
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis 1002, Tunisia
| | - Jihenne Ben Aissa-Haj
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis 1002, Tunisia; Department of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis 1002, Tunisia
| | - Fouzia Radouani
- Chlamydiae and Mycoplasmas Laboratory, Research Department, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Meriem Khyatti
- Laboratory of Viral Oncology, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Najah Mighri
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis 1002, Tunisia
| | - Mariem Hannachi
- Laboratory of Bioinformatics, Biomathematics and Biostatistics LR20IPT09, Pasteur Institute of Tunis, University of Tunis El Manar, Tunis 1002, Tunisia
| | - Kais Ghedira
- Laboratory of Bioinformatics, Biomathematics and Biostatistics LR20IPT09, Pasteur Institute of Tunis, University of Tunis El Manar, Tunis 1002, Tunisia
| | - Oussema Souiai
- Laboratory of Bioinformatics, Biomathematics and Biostatistics LR20IPT09, Pasteur Institute of Tunis, University of Tunis El Manar, Tunis 1002, Tunisia
| | - Chaima Hkimi
- Laboratory of Bioinformatics, Biomathematics and Biostatistics LR20IPT09, Pasteur Institute of Tunis, University of Tunis El Manar, Tunis 1002, Tunisia
| | - Mohamed Selim Kammoun
- Laboratory of Bioinformatics, Biomathematics and Biostatistics LR20IPT09, Pasteur Institute of Tunis, University of Tunis El Manar, Tunis 1002, Tunisia
| | - Nesrine Mejri
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis 1002, Tunisia; Medical Oncology Department, Abderrahmane Mami Hospital, Faculty of Medicine, University Tunis El Manar, Tunis, Tunisia
| | - Hanen Bouaziz
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis 1002, Tunisia; Department of Carcinological Surgery, Salah Azaiez Institute, Tunis, Tunisia
| | | | - Hicham Charoute
- Research unit of Epidemiology, Biostatistics and Bioinformatics, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Abdelhamid Barakat
- Laboratory of Genomics and Human Genetics, Institut Pasteur du Maroc 20360, Casablanca, Morocco
| | - Imène Najjar
- Biomics, Center for Technological Resources and Research (C2RT), Institut Pasteur, Paris 75015, France
| | - Hiroaki Taniguchi
- The Polish Academy of Sciences, Poland; University Mohamed VI, Morocco
| | - Natalia Pietrosemoli
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub F-75015, Paris, France
| | - Koussay Dellagi
- Pasteur Network Association, Institut Pasteur, Paris, France
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis 1002, Tunisia
| | - Mohamed Samir Boubaker
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis 1002, Tunisia; Department of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis 1002, Tunisia
| | - Claudia Chica
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub F-75015, Paris, France
| | - Etienne Rouleau
- Department of Biology and Pathology-Cancer Genetics Laboratory-Gustave Roussy 94805, Villejuif, France
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2
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Lafoux B, Baillet N, Picard C, Fourcaud G, Borges-Cardoso V, Reynard S, Journeaux A, Germain C, Perthame E, Mateo M, Hortion J, Carnec X, Pietrosemoli N, Moroso M, Lacroix O, Jourjon O, Barron S, Vallve A, Duthey A, Jacquot F, Barrot L, Dirheimer M, Raoul H, Nougier C, Baize S. Hemostasis defects underlying the hemorrhagic syndrome caused by mammarenaviruses in a cynomolgus macaque model. Blood 2023; 142:2092-2104. [PMID: 37699247 DOI: 10.1182/blood.2023020351] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 07/18/2023] [Accepted: 08/15/2023] [Indexed: 09/14/2023] Open
Abstract
Viral hemorrhagic fevers (HF) are a group of acute febrile diseases with high mortality rates. Although hemostatic dysfunction appears to be a major determinant of the severity of the disease, it is still unclear what pathogenic mechanisms lead to it. In clinical studies it is found that arenaviruses, such as Lassa, Machupo, and Guanarito viruses cause HF that vary in symptoms and biological alterations. In this study we aimed to characterize the hemostatic dysfunction induced by arenaviral HF to determine its implication in the severity of the disease and to elucidate the origin of this syndrome. We found that lethal infection with Machupo, Guanarito, and Lassa viruses is associated with cutaneomucosal, cerebral, digestive, and pulmonary hemorrhages. The affected animals developed a severe alteration of the coagulation system, which was concomitant with acute hepatitis, minor deficit of hepatic factor synthesis, presence of a plasmatic inhibitor of coagulation, and dysfunction of the fibrinolytic system. Despite signs of increased vascular permeability, endothelial cell infection was not a determinant factor of the hemorrhagic syndrome. There were also alterations of the primary hemostasis during lethal infection, with moderate to severe thrombocytopenia and platelet dysfunction. Finally, we show that lethal infection is accompanied by a reduced hematopoietic potential of the bone marrow. This study provides an unprecedented characterization of the hemostasis defects induced by several highly pathogenic arenaviruses.
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Affiliation(s)
- Blaise Lafoux
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, Lyon, France
- Centre International de Recherche en Infectiologie, Université de Lyon, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, Centre National de la Recherche Scientifique UMR5308, Lyon, France
| | - Nicolas Baillet
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, Lyon, France
- Centre International de Recherche en Infectiologie, Université de Lyon, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, Centre National de la Recherche Scientifique UMR5308, Lyon, France
| | - Caroline Picard
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, Lyon, France
- Centre International de Recherche en Infectiologie, Université de Lyon, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, Centre National de la Recherche Scientifique UMR5308, Lyon, France
| | - Gustave Fourcaud
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, Lyon, France
- Centre International de Recherche en Infectiologie, Université de Lyon, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, Centre National de la Recherche Scientifique UMR5308, Lyon, France
| | - Virginie Borges-Cardoso
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, Lyon, France
- Centre International de Recherche en Infectiologie, Université de Lyon, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, Centre National de la Recherche Scientifique UMR5308, Lyon, France
| | - Stéphanie Reynard
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, Lyon, France
- Centre International de Recherche en Infectiologie, Université de Lyon, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, Centre National de la Recherche Scientifique UMR5308, Lyon, France
| | - Alexandra Journeaux
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, Lyon, France
- Centre International de Recherche en Infectiologie, Université de Lyon, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, Centre National de la Recherche Scientifique UMR5308, Lyon, France
| | - Clara Germain
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, Lyon, France
- Centre International de Recherche en Infectiologie, Université de Lyon, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, Centre National de la Recherche Scientifique UMR5308, Lyon, France
| | - Emeline Perthame
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
| | - Mathieu Mateo
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, Lyon, France
- Centre International de Recherche en Infectiologie, Université de Lyon, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, Centre National de la Recherche Scientifique UMR5308, Lyon, France
| | - Jimmy Hortion
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, Lyon, France
- Centre International de Recherche en Infectiologie, Université de Lyon, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, Centre National de la Recherche Scientifique UMR5308, Lyon, France
| | - Xavier Carnec
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, Lyon, France
- Centre International de Recherche en Infectiologie, Université de Lyon, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, Centre National de la Recherche Scientifique UMR5308, Lyon, France
| | - Natalia Pietrosemoli
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
| | - Marie Moroso
- Laboratoire P4 INSERM-Jean Mérieux, INSERM US003, Lyon, France
| | - Orianne Lacroix
- Laboratoire P4 INSERM-Jean Mérieux, INSERM US003, Lyon, France
| | - Ophélie Jourjon
- Laboratoire P4 INSERM-Jean Mérieux, INSERM US003, Lyon, France
| | - Stéphane Barron
- Laboratoire P4 INSERM-Jean Mérieux, INSERM US003, Lyon, France
| | - Audrey Vallve
- Laboratoire P4 INSERM-Jean Mérieux, INSERM US003, Lyon, France
| | - Aurélie Duthey
- Laboratoire P4 INSERM-Jean Mérieux, INSERM US003, Lyon, France
| | | | - Laura Barrot
- Laboratoire P4 INSERM-Jean Mérieux, INSERM US003, Lyon, France
| | - Manon Dirheimer
- Laboratoire P4 INSERM-Jean Mérieux, INSERM US003, Lyon, France
| | - Hervé Raoul
- Laboratoire P4 INSERM-Jean Mérieux, INSERM US003, Lyon, France
| | - Christophe Nougier
- Service d'hématologie Biologique, Centre de Pathologie et Biologie Est, Groupement Hospitalier Est, Hospices Civils de Lyon, Bron, France
| | - Sylvain Baize
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, Lyon, France
- Centre International de Recherche en Infectiologie, Université de Lyon, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, Centre National de la Recherche Scientifique UMR5308, Lyon, France
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3
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Pasquereau-Kotula E, du Merle L, Sismeiro O, Pietrosemoli N, Varet H, Legendre R, Trieu-Cuot P, Dramsi S. Transcriptome profiling of human col\onic cells exposed to the gut pathobiont Streptococcus gallolyticus subsp. gallolyticus. PLoS One 2023; 18:e0294868. [PMID: 38033043 PMCID: PMC10688619 DOI: 10.1371/journal.pone.0294868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 11/09/2023] [Indexed: 12/02/2023] Open
Abstract
Streptococcus gallolyticus sp. gallolyticus (SGG) is a gut pathobiont involved in the development of colorectal cancer (CRC). To decipher SGG contribution in tumor initiation and/or acceleration respectively, a global transcriptome was performed in human normal colonic cells (FHC) and in human tumoral colonic cells (HT29). To identify SGG-specific alterations, we chose the phylogenetically closest relative, Streptococcus gallolyticus subsp. macedonicus (SGM) as control bacterium. We show that SGM, a bacterium generally considered as safe, did not induce any transcriptional changes on the two human colonic cells. The transcriptional reprogramming induced by SGG in normal FHC and tumoral HT29 cells was significantly different, although most of the genes up- and down-regulated were associated with cancer disease. Top up-regulated genes related to cancer were: (i) IL-20, CLK1, SORBS2, ERG1, PIM1, SNORD3A for normal FHC cells and (ii) TSLP, BHLHA15, LAMP3, ZNF27B, KRT17, ATF3 for cancerous HT29 cells. The total number of altered genes were much higher in cancerous than in normal colonic cells (2,090 vs 128 genes being affected, respectively). Gene set enrichment analysis reveals that SGG-induced strong ER- (endoplasmic reticulum) stress and UPR- (unfolded protein response) activation in colonic epithelial cells. Our results suggest that SGG induces a pro-tumoral shift in human colonic cells particularly in transformed cells potentially accelerating tumor development in the colon.
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Affiliation(s)
- Ewa Pasquereau-Kotula
- Institut Pasteur, Université Paris Cité, Biology of Gram-positive Pathogens Unit, Paris, France
| | - Laurence du Merle
- Institut Pasteur, Université Paris Cité, Biology of Gram-positive Pathogens Unit, Paris, France
| | - Odile Sismeiro
- Institut Pasteur, Université Paris Cité, Biology of Gram-positive Pathogens Unit, Paris, France
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
| | - Natalia Pietrosemoli
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
| | - Hugo Varet
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
| | - Rachel Legendre
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
| | - Patrick Trieu-Cuot
- Institut Pasteur, Université Paris Cité, Biology of Gram-positive Pathogens Unit, Paris, France
| | - Shaynoor Dramsi
- Institut Pasteur, Université Paris Cité, Biology of Gram-positive Pathogens Unit, Paris, France
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4
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Altamirano-Silva P, Meza-Torres J, Zúñiga-Pereira AM, Zamora-Jaen S, Pietrosemoli N, Cantos G, Peltier J, Pizarro-Cerdá J, Moreno E, Chacón-Díaz C, Guzmán-Verri C, Chaves-Olarte E. Phenotypes controlled by the Brucella abortus two component system BvrR/BvrS are differentially impacted by BvrR phosphorylation. Front Microbiol 2023; 14:1148233. [PMID: 37234533 PMCID: PMC10206243 DOI: 10.3389/fmicb.2023.1148233] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 04/14/2023] [Indexed: 05/28/2023] Open
Abstract
Brucella abortus is a zoonotic pathogen whose virulence depends on its ability to survive intracellularly at the endoplasmic reticulum derived compartment. The two-component system BvrR/BvrS (BvrRS) is essential for intracellular survival due to the transcriptional control of the type IV secretion system VirB and its transcriptional regulator VjbR. It is a master regulator of several traits including membrane homeostasis by controlling gene expression of membrane components, such as Omp25. BvrR phosphorylation is related to DNA binding at target regions, thereby repressing or activating gene transcription. To understand the role of BvrR phosphorylation we generated dominant positive and negative versions of this response regulator, mimicking phosphorylated and non-phosphorylated BvrR states and, in addition to the wild-type version, these variants were introduced in a BvrR negative background. We then characterized BvrRS-controlled phenotypes and assessed the expression of proteins regulated by the system. We found two regulatory patterns exerted by BvrR. The first pattern was represented by resistance to polymyxin and expression of Omp25 (membrane conformation) which were restored to normal levels by the dominant positive and the wild-type version, but not the dominant negative BvrR. The second pattern was represented by intracellular survival and expression of VjbR and VirB (virulence) which were, again, complemented by the wild-type and the dominant positive variants of BvrR but were also significantly restored by complementation with the dominant negative BvrR. These results indicate a differential transcriptional response of the genes controlled to the phosphorylation status of BvrR and suggest that unphosphorylated BvrR binds and impacts the expression of a subset of genes. We confirmed this hypothesis by showing that the dominant negative BvrR did not interact with the omp25 promoter whereas it could interact with vjbR promoter. Furthermore, a global transcriptional analysis revealed that a subset of genes responds to the presence of the dominant negative BvrR. Thus, BvrR possesses diverse strategies to exert transcriptional control on the genes it regulates and, consequently, impacting on the phenotypes controlled by this response regulator.
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Affiliation(s)
- Pamela Altamirano-Silva
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Jazmín Meza-Torres
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Ana Mariel Zúñiga-Pereira
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Sigrid Zamora-Jaen
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Natalia Pietrosemoli
- Bioinformatics and Biostatistics Hub, CNRS USR3756, Institut Pasteur, Université Paris Cité, Paris, France
| | - Gabriela Cantos
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Johann Peltier
- Laboratoire Pathogenèse des Bactéries Anaérobies, CNRS UMR6047, Institut Pasteur, Université Paris Cité, Paris, France
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Gif-sur-Yvette, France
| | - Javier Pizarro-Cerdá
- Yersinia Research Unit, CNRS UMR6047, Institut Pasteur, Université Paris Cité, Paris, France
| | - Edgardo Moreno
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica
| | - Carlos Chacón-Díaz
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Caterina Guzmán-Verri
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica
| | - Esteban Chaves-Olarte
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
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5
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Mateo M, Reynard S, Pietrosemoli N, Perthame E, Journeaux A, Noy K, Germain C, Carnec X, Picard C, Borges-Cardoso V, Hortion J, Lopez-Maestre H, Regnard P, Fellmann L, Vallve A, Barron S, Jourjon O, Lacroix O, Duthey A, Dirheimer M, Daniau M, Legras-Lachuer C, Carbonnelle C, Raoul H, Tangy F, Baize S. Rapid protection induced by a single-shot Lassa vaccine in male cynomolgus monkeys. Nat Commun 2023; 14:1352. [PMID: 36906645 PMCID: PMC10008018 DOI: 10.1038/s41467-023-37050-6] [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: 10/17/2022] [Accepted: 02/22/2023] [Indexed: 03/13/2023] Open
Abstract
Lassa fever hits West African countries annually in the absence of licensed vaccine to limit the burden of this viral hemorrhagic fever. We previously developed MeV-NP, a single-shot vaccine protecting cynomolgus monkeys against divergent strains one month or more than a year before Lassa virus infection. Given the limited dissemination area during outbreaks and the risk of nosocomial transmission, a vaccine inducing rapid protection could be useful to protect exposed people during outbreaks in the absence of preventive vaccination. Here, we test whether the time to protection can be reduced after immunization by challenging measles virus pre-immune male cynomolgus monkeys sixteen or eight days after a single shot of MeV-NP. None of the immunized monkeys develop disease and they rapidly control viral replication. Animals immunized eight days before the challenge are the best controllers, producing a strong CD8 T-cell response against the viral glycoprotein. A group of animals was also vaccinated one hour after the challenge, but was not protected and succumbed to the disease as the control animals. This study demonstrates that MeV-NP can induce a rapid protective immune response against Lassa fever in the presence of MeV pre-existing immunity but can likely not be used as therapeutic vaccine.
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Affiliation(s)
- Mathieu Mateo
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, 69007, Lyon, France.,Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS UMR5308, 69007, Lyon, France
| | - Stéphanie Reynard
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, 69007, Lyon, France.,Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS UMR5308, 69007, Lyon, France
| | - Natalia Pietrosemoli
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
| | - Emeline Perthame
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
| | - Alexandra Journeaux
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, 69007, Lyon, France.,Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS UMR5308, 69007, Lyon, France
| | - Kodie Noy
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, 69007, Lyon, France.,Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS UMR5308, 69007, Lyon, France
| | - Clara Germain
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, 69007, Lyon, France.,Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS UMR5308, 69007, Lyon, France
| | - Xavier Carnec
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, 69007, Lyon, France.,Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS UMR5308, 69007, Lyon, France
| | - Caroline Picard
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, 69007, Lyon, France.,Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS UMR5308, 69007, Lyon, France
| | - Virginie Borges-Cardoso
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, 69007, Lyon, France.,Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS UMR5308, 69007, Lyon, France
| | - Jimmy Hortion
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, 69007, Lyon, France.,Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS UMR5308, 69007, Lyon, France
| | - Hélène Lopez-Maestre
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
| | - Pierrick Regnard
- SILABE, Université de Strasbourg, fort Foch, Niederhausbergen, France
| | - Lyne Fellmann
- SILABE, Université de Strasbourg, fort Foch, Niederhausbergen, France
| | - Audrey Vallve
- Laboratoire P4 INSERM - Jean Mérieux, INSERM US003, 69007, Lyon, France
| | - Stéphane Barron
- Laboratoire P4 INSERM - Jean Mérieux, INSERM US003, 69007, Lyon, France
| | - Ophélie Jourjon
- Laboratoire P4 INSERM - Jean Mérieux, INSERM US003, 69007, Lyon, France
| | - Orianne Lacroix
- Laboratoire P4 INSERM - Jean Mérieux, INSERM US003, 69007, Lyon, France
| | - Aurélie Duthey
- Laboratoire P4 INSERM - Jean Mérieux, INSERM US003, 69007, Lyon, France
| | - Manon Dirheimer
- INSERM, Délégation Régionale Auvergne Rhône-Alpes, 69500, Bron, France
| | | | | | | | - Hervé Raoul
- Laboratoire P4 INSERM - Jean Mérieux, INSERM US003, 69007, Lyon, France
| | - Frédéric Tangy
- Vaccine Innovation Laboratory, Institut Pasteur, 75015, Paris, France
| | - Sylvain Baize
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, 69007, Lyon, France. .,Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS UMR5308, 69007, Lyon, France.
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6
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Mateo M, Hortion J, Perthame E, Picard C, Reynard S, Journeaux A, Germain C, Carnec X, Baillet N, Borges-Cardoso V, Pietrosemoli N, Vallve A, Barron S, Jourjon O, Lacroix O, Duthey A, Dirheimer M, Daniau M, Legras-Lachuer C, Jouvion G, Carbonnelle C, Raoul H, Baize S. Pathogenesis of recent Lassa virus isolates from lineages II and VII in cynomolgus monkeys. Virulence 2022; 13:654-669. [PMID: 35437094 PMCID: PMC9037461 DOI: 10.1080/21505594.2022.2060170] [Citation(s) in RCA: 4] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The area of Lassa virus (LASV) circulation is expanding, with the emergence of highly pathogenic new LASV lineages. Benin recently became an endemic country for LASV and has seen the emergence of a new LASV lineage (VII). The first two outbreaks in 2014 and 2016 showed a relatively high mortality rate compared to other outbreaks. We infected cynomolgus monkeys with two strains belonging to lineage II and lineage VII that were isolated from deceased patients during the 2016 outbreak in Benin. The lineage VII strain (L7) caused uniform mortality. Death was associated with uncontrolled viral replication, unbalanced inflammatory responses characterized by increased concentrations of pro- and anti-inflammatory mediators, and the absence of efficient immune responses, resembling the pathogenesis associated with the prototypic Josiah strain in monkeys. The lineage II strain (L2) showed apparently lower virulence than its counterpart, with a prolonged time to death and a lower mortality rate. Prolonged survival was associated with better control of viral replication, a moderate inflammatory response, and efficient T-cell responses. Transcriptomic analyses also highlighted important differences in the immune responses associated with the outcome. Both strains caused strong inflammation in several organs. Notably, meningitis and encephalitis were observed in the cerebral cortex and cerebellum in all monkeys, independently of the outcome. Due to their apparently high pathogenicity, emerging strains from lineage VII should be considered in preclinical vaccine testing. Lineage II would also be beneficial in pathogenesis studies to study the entire spectrum of Lassa fever severity.
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Affiliation(s)
- Mathieu Mateo
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, Lyon, France.,Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS UMR5308, Lyon France
| | - Jimmy Hortion
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, Lyon, France.,Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS UMR5308, Lyon France
| | - Emeline Perthame
- Bioinformatics and Biostatistics Hub, Institut Pasteur, Université de Paris, Paris, France
| | - Caroline Picard
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, Lyon, France.,Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS UMR5308, Lyon France
| | - Stéphanie Reynard
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, Lyon, France.,Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS UMR5308, Lyon France
| | - Alexandra Journeaux
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, Lyon, France.,Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS UMR5308, Lyon France
| | - Clara Germain
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, Lyon, France.,Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS UMR5308, Lyon France
| | - Xavier Carnec
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, Lyon, France.,Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS UMR5308, Lyon France
| | - Nicolas Baillet
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, Lyon, France.,Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS UMR5308, Lyon France
| | - Virginie Borges-Cardoso
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, Lyon, France.,Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS UMR5308, Lyon France
| | - Natalia Pietrosemoli
- Bioinformatics and Biostatistics Hub, Institut Pasteur, Université de Paris, Paris, France
| | - Audrey Vallve
- Laboratoire P4 INSERM-Jean Mérieux, INSERM US003, 69007 Lyon, France
| | - Stéphane Barron
- Laboratoire P4 INSERM-Jean Mérieux, INSERM US003, 69007 Lyon, France
| | - Ophélie Jourjon
- Laboratoire P4 INSERM-Jean Mérieux, INSERM US003, 69007 Lyon, France
| | - Orianne Lacroix
- Laboratoire P4 INSERM-Jean Mérieux, INSERM US003, 69007 Lyon, France
| | - Aurélie Duthey
- Laboratoire P4 INSERM-Jean Mérieux, INSERM US003, 69007 Lyon, France
| | - Manon Dirheimer
- INSERM, Délégation Régionale Auvergne Rhône-Alpes, Bron, France
| | | | | | - Gregory Jouvion
- Ecole Nationale Vétérinaire d'Alfort, Unité d'Histologie et d'Anatomie Pathologique, Maisons-Alfort, France.,Dynamic Research Group, Ecole Nationale Vétérinaired'Alfort, USC ANSES, Université Paris Est Créteil, Maisons-Alfort, France
| | | | - Hervé Raoul
- Laboratoire P4 INSERM-Jean Mérieux, INSERM US003, 69007 Lyon, France
| | - Sylvain Baize
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, Lyon, France.,Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS UMR5308, Lyon France
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7
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Merabet O, Pietrosemoli N, Perthame E, Armengaud J, Gaillard JC, Borges-Cardoso V, Daniau M, Legras-Lachuer C, Carnec X, Baize S. Infection of Human Endothelial Cells with Lassa Virus Induces Early but Transient Activation and Low Type I IFN Response Compared to the Closely-Related Nonpathogenic Mopeia Virus. Viruses 2022; 14:v14030652. [PMID: 35337059 PMCID: PMC8953476 DOI: 10.3390/v14030652] [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] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/10/2022] [Accepted: 03/16/2022] [Indexed: 02/01/2023] Open
Abstract
Lassa virus (LASV), an Old World arenavirus, is responsible for hemorrhagic fevers in western Africa. The privileged tropism of LASV for endothelial cells combined with a dysregulated inflammatory response are the main cause of the increase in vascular permeability observed during the disease. Mopeia virus (MOPV) is another arenavirus closely related to LASV but nonpathogenic for non-human primates (NHPs) and has never been described in humans. MOPV is more immunogenic than LASV in NHPs and in vitro in human immune cell models, with more intense type I IFN and adaptive cellular responses. Here, we compared the transcriptomic and proteomic responses of human umbilical vein endothelial cells (HUVECs) to infection with the two viruses to further decipher the mechanisms involved in their differences in immunogenicity and pathogenicity. Both viruses replicated durably and efficiently in HUVECs, but the responses they induced were strikingly different. Modest activation was observed at an early stage of LASV infection and then rapidly shut down. By contrast, MOPV induced a late but more intense response, characterized by the expression of genes and proteins mainly associated with the type I IFN response and antigen processing/presentation. Such a response is consistent with the higher immunogenicity of MOPV relative to LASV, whereas the lack of an innate response induced in HUVECs by LASV is consistent with its uncontrolled systemic dissemination through the vascular endothelium.
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Affiliation(s)
- Othmann Merabet
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, 69007 Lyon, France; (O.M.); (V.B.-C.); (X.C.)
- Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS, UMR5308, 69007 Lyon, France
| | - Natalia Pietrosemoli
- Bioinformatics and Biostatistics Hub, Institut Pasteur, Université de Paris, 75015 Paris, France; (N.P.); (E.P.)
| | - Emeline Perthame
- Bioinformatics and Biostatistics Hub, Institut Pasteur, Université de Paris, 75015 Paris, France; (N.P.); (E.P.)
| | - Jean Armengaud
- Laboratoire Innovations Technologiques pour la Détection et le Diagnostic (LI2D), Service de Pharmacologie et Immunoanalyse (SPI), Commissariat à l’Energie Atomique, 30200 Bagnols-sur-Cèze, France; (J.A.); (J.-C.G.)
| | - Jean-Charles Gaillard
- Laboratoire Innovations Technologiques pour la Détection et le Diagnostic (LI2D), Service de Pharmacologie et Immunoanalyse (SPI), Commissariat à l’Energie Atomique, 30200 Bagnols-sur-Cèze, France; (J.A.); (J.-C.G.)
| | - Virginie Borges-Cardoso
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, 69007 Lyon, France; (O.M.); (V.B.-C.); (X.C.)
- Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS, UMR5308, 69007 Lyon, France
| | - Maïlys Daniau
- ViroScan3D SAS, 01600 Trévoux, France; (M.D.); (C.L.-L.)
| | | | - Xavier Carnec
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, 69007 Lyon, France; (O.M.); (V.B.-C.); (X.C.)
- Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS, UMR5308, 69007 Lyon, France
| | - Sylvain Baize
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, 69007 Lyon, France; (O.M.); (V.B.-C.); (X.C.)
- Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, INSERM U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS, UMR5308, 69007 Lyon, France
- Correspondence: ; Tel.: +33-4-3728-2440
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8
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Declercq M, Biquand E, Karim M, Pietrosemoli N, Jacob Y, Demeret C, Barbezange C, van der Werf S. Influenza A virus co-opts ERI1 exonuclease bound to histone mRNA to promote viral transcription. Nucleic Acids Res 2020; 48:10428-10440. [PMID: 32960265 PMCID: PMC7544206 DOI: 10.1093/nar/gkaa771] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 07/31/2019] [Revised: 08/18/2020] [Accepted: 09/10/2020] [Indexed: 12/25/2022] Open
Abstract
Cellular exonucleases involved in the processes that regulate RNA stability and quality control have been shown to restrict or to promote the multiplication cycle of numerous RNA viruses. Influenza A viruses are major human pathogens that are responsible for seasonal epidemics, but the interplay between viral proteins and cellular exonucleases has never been specifically studied. Here, using a stringent interactomics screening strategy and an siRNA-silencing approach, we identified eight cellular factors among a set of 75 cellular proteins carrying exo(ribo)nuclease activities or involved in RNA decay processes that support influenza A virus multiplication. We show that the exoribonuclease ERI1 interacts with the PB2, PB1 and NP components of the viral ribonucleoproteins and is required for viral mRNA transcription. More specifically, we demonstrate that the protein-protein interaction is RNA dependent and that both the RNA binding and exonuclease activities of ERI1 are required to promote influenza A virus transcription. Finally, we provide evidence that during infection, the SLBP protein and histone mRNAs co-purify with vRNPs alongside ERI1, indicating that ERI1 is most probably recruited when it is present in the histone pre-mRNA processing complex in the nucleus.
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Affiliation(s)
- Marion Declercq
- Unité Génétique Moléculaire des Virus à ARN, UMR3569 CNRS, Université de Paris, Département de Virologie, Institut Pasteur, Paris, France
| | - Elise Biquand
- Unité Génétique Moléculaire des Virus à ARN, UMR3569 CNRS, Université de Paris, Département de Virologie, Institut Pasteur, Paris, France
| | - Marwah Karim
- Unité Génétique Moléculaire des Virus à ARN, UMR3569 CNRS, Université de Paris, Département de Virologie, Institut Pasteur, Paris, France
| | - Natalia Pietrosemoli
- Bioinformatics and Biostatistics Hub, Department of Computational Biology, Institut Pasteur, USR 3756 CNRS, Paris, France
| | - Yves Jacob
- Unité Génétique Moléculaire des Virus à ARN, UMR3569 CNRS, Université de Paris, Département de Virologie, Institut Pasteur, Paris, France
| | - Caroline Demeret
- Unité Génétique Moléculaire des Virus à ARN, UMR3569 CNRS, Université de Paris, Département de Virologie, Institut Pasteur, Paris, France
| | - Cyril Barbezange
- Unité Génétique Moléculaire des Virus à ARN, UMR3569 CNRS, Université de Paris, Département de Virologie, Institut Pasteur, Paris, France
| | - Sylvie van der Werf
- Unité Génétique Moléculaire des Virus à ARN, UMR3569 CNRS, Université de Paris, Département de Virologie, Institut Pasteur, Paris, France
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9
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Mateo M, Reynard S, Carnec X, Journeaux A, Baillet N, Schaeffer J, Picard C, Legras-Lachuer C, Allan R, Perthame E, Hillion KH, Pietrosemoli N, Dillies MA, Barrot L, Vallve A, Barron S, Fellmann L, Gaillard JC, Armengaud J, Carbonnelle C, Raoul H, Tangy F, Baize S. Vaccines inducing immunity to Lassa virus glycoprotein and nucleoprotein protect macaques after a single shot. Sci Transl Med 2019; 11:11/512/eaaw3163. [DOI: 10.1126/scitranslmed.aaw3163] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 04/16/2019] [Accepted: 08/02/2019] [Indexed: 01/01/2023]
Abstract
Lassa fever is a major threat in Western Africa. The large number of people living at risk for this disease calls for the development of a vaccine against Lassa virus (LASV). We generated live-attenuated LASV vaccines based on measles virus and Mopeia virus platforms and expressing different LASV antigens, with the aim to develop a vaccine able to protect after a single shot. We compared the efficacy of these vaccines against LASV in cynomolgus monkeys. The vaccines were well tolerated and protected the animals from LASV infection and disease after a single immunization but with varying efficacy. Analysis of the immune responses showed that complete protection was associated with robust secondary T cell and antibody responses against LASV. Transcriptomic and proteomic analyses showed an early activation of innate immunity and T cell priming after immunization with the most effective vaccines, with changes detectable as early as 2 days after immunization. The most efficacious vaccine candidate, a measles vector simultaneously expressing LASV glycoprotein and nucleoprotein, has been selected for further clinical evaluation.
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10
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Schaeffer J, Reynard S, Carnec X, Pietrosemoli N, Dillies MA, Baize S. Non-Pathogenic Mopeia Virus Induces More Robust Activation of Plasmacytoid Dendritic Cells than Lassa Virus. Viruses 2019; 11:v11030287. [PMID: 30901952 PMCID: PMC6466290 DOI: 10.3390/v11030287] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 03/04/2019] [Accepted: 03/18/2019] [Indexed: 12/28/2022] Open
Abstract
Lassa virus (LASV) causes a viral haemorrhagic fever in humans and is a major public health concern in West Africa. An efficient immune response to LASV appears to rely on type I interferon (IFN-I) production and T-cell activation. We evaluated the response of plasmacytoid dendritic cells (pDC) to LASV, as they are an important and early source of IFN-I. We compared the response of primary human pDCs to LASV and Mopeia virus (MOPV), which is very closely related to LASV, but non-pathogenic. We showed that pDCs are not productively infected by either MOPV or LASV, but produce IFN-I. However, the activation of pDCs was more robust in response to MOPV than LASV. In vivo, pDC activation may support the control of viral replication through IFN-I production, but also improve the induction of a global immune response. Therefore, pDC activation could play a role in the control of LASV infection.
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Affiliation(s)
- Justine Schaeffer
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, 69007 Lyon, France.
- Centre International de Recherche en Infectiologie (INSERM, CNRS, ENS Lyon, Université Lyon I), 69007 Lyon, France.
| | - Stéphanie Reynard
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, 69007 Lyon, France.
- Centre International de Recherche en Infectiologie (INSERM, CNRS, ENS Lyon, Université Lyon I), 69007 Lyon, France.
| | - Xavier Carnec
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, 69007 Lyon, France.
- Centre International de Recherche en Infectiologie (INSERM, CNRS, ENS Lyon, Université Lyon I), 69007 Lyon, France.
| | - Natalia Pietrosemoli
- Hub de Bioinformatique et Biostatistique⁻C3BI, Institut Pasteur, USR 3756 CNRS, 75015 Paris, France.
| | - Marie-Agnès Dillies
- Hub de Bioinformatique et Biostatistique⁻C3BI, Institut Pasteur, USR 3756 CNRS, 75015 Paris, France.
| | - Sylvain Baize
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, 69007 Lyon, France.
- Centre International de Recherche en Infectiologie (INSERM, CNRS, ENS Lyon, Université Lyon I), 69007 Lyon, France.
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11
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Reynard S, Journeaux A, Gloaguen E, Schaeffer J, Varet H, Pietrosemoli N, Mateo M, Baillet N, Laouenan C, Raoul H, Mullaert J, Baize S. Immune parameters and outcomes during Ebola virus disease. JCI Insight 2019; 4:125106. [PMID: 30626757 DOI: 10.1172/jci.insight.125106] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [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: 09/24/2018] [Accepted: 11/29/2018] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND The West African Ebola virus epidemic from 2014-2016 highlighted the lack of knowledge about the pathogenicity of the virus and the factors responsible for outcome. A performant and rapid diagnosis is of crucial importance, as is overcoming the difficulty of providing high-quality patient management during such an extensive outbreak. Here, we propose to study the role of the immune mediators during Ebola virus disease and to define some molecules of importance in the outcome. METHODS Plasma from Guinean patients sampled during the outbreak were analyzed using RT-qPCR, magnetic bead assay, ELISA, and high-quality statistical analyses. We also performed a transcriptomic analysis in leukocytes samples. Therefore, we deeply characterized the immune responses involved in Ebola virus disease. RESULTS We evaluated the immune patterns depending on the outcome of the disease. Survivors presented an efficient and well-balanced immune response, whereas fatalities were characterized by an intense inflammatory response, overexpression of multiple cytokines, and a "chemokine storm." The plasma concentration of most of the parameters tested increased until death. Statistical analyses also allowed us to define a panel of markers highly predictive of outcome. CONCLUSION The immune response observed in fatalities was highly similar to that characterizing septic shock syndrome. Our results suggest that immune responses can play a major pathogenic role during severe Ebola virus infection and argue in favor of therapeutic approaches that act on both viral replication and the induction of shock syndrome. FUNDING French Ministry of Foreign Affairs, the Agence Française de Développement, and the Institut Pasteur.
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Affiliation(s)
- Stéphanie Reynard
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, Centre International de Recherche en Infectiologie, Université Lyon I, INSERM, CNRS, ENS Lyon, Lyon, France
| | - Alexandra Journeaux
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, Centre International de Recherche en Infectiologie, Université Lyon I, INSERM, CNRS, ENS Lyon, Lyon, France
| | - Emilie Gloaguen
- Infection Antimicrobials Modelling Evolution, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Justine Schaeffer
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, Centre International de Recherche en Infectiologie, Université Lyon I, INSERM, CNRS, ENS Lyon, Lyon, France
| | - Hugo Varet
- Institut Pasteur, Hub Bioinformatique et Biostatistique, Centre de Bioinformatique, Biostatistique et Biologie Intégrative, C3BI, USR 3756 IP CNRS, Paris, France
| | - Natalia Pietrosemoli
- Institut Pasteur, Hub Bioinformatique et Biostatistique, Centre de Bioinformatique, Biostatistique et Biologie Intégrative, C3BI, USR 3756 IP CNRS, Paris, France
| | - Mathieu Mateo
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, Centre International de Recherche en Infectiologie, Université Lyon I, INSERM, CNRS, ENS Lyon, Lyon, France
| | - Nicolas Baillet
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, Centre International de Recherche en Infectiologie, Université Lyon I, INSERM, CNRS, ENS Lyon, Lyon, France
| | - Cédric Laouenan
- Infection Antimicrobials Modelling Evolution, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, Paris, France.,Assistance Publique - Hôpitaux de Paris, Hôpital Bichat Claude Bernard, Paris, France
| | - Hervé Raoul
- Laboratoire P4 Jean Mérieux-INSERM, INSERM, Lyon, France
| | - Jimmy Mullaert
- Infection Antimicrobials Modelling Evolution, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Sylvain Baize
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur, Centre International de Recherche en Infectiologie, Université Lyon I, INSERM, CNRS, ENS Lyon, Lyon, France
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12
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Schaeffer J, Carnec X, Reynard S, Mateo M, Picard C, Pietrosemoli N, Dillies MA, Baize S. Lassa virus activates myeloid dendritic cells but suppresses their ability to stimulate T cells. PLoS Pathog 2018; 14:e1007430. [PMID: 30419076 PMCID: PMC6258464 DOI: 10.1371/journal.ppat.1007430] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [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: 06/05/2018] [Revised: 11/26/2018] [Accepted: 10/23/2018] [Indexed: 01/09/2023] Open
Abstract
Lassa virus (LASV) is responsible for a viral hemorrhagic fever in humans and the death of 3,000 to 5,000 people every year. The immune response to LASV is poorly understood, but type I interferon (IFN-I) and T-cell responses appear to be critical for the host. We studied the response of myeloid dendritic cells (mDC) to LASV, as mDCs are involved in both IFN-I production and T-cell activation. We compared the response of primary human mDCs to LASV and Mopeia virus (MOPV), which is similar to LASV, but non-pathogenic. We showed that mDCs produced substantial amounts of IFN-I in response to both LASV and MOPV. However, only MOPV-infected mDCs were able to activate T cells. More surprisingly, coculture with T cells completely inhibited the activation of LASV-infected mDCs. These differences between LASV and MOPV were mostly due to the LASV nucleoprotein, which has major immunosuppressive properties, but the glycoprotein was also involved. Overall, these results suggest that mDCs may be important for the global response to LASV and play a role in the outcome of Lassa fever. Lassa fever is a viral hemorrhagic fever and a major public health issue in West Africa. Lassa virus, the causative agent of Lassa fever, is listed by the World Health Organization as one of the emerging pathogens likely to cause severe outbreaks in the near future. Indeed, there is currently no vaccine and no treatment against Lassa virus. Determinants of Lassa virus high pathogenicity are not completely understood. However, it has been shown that rapid type I interferon response and efficient T cell response were critical to survive Lassa fever. Dendritic cells are at the crossroads of innate and adaptive immunity. Their direct response to viral infection includes type I interferon production. They can also present viral antigens, initiating the T cell responses. We decided to investigate how dendritic cells respond to Lassa virus to evaluate their importance in the global immune response. We showed that primary human myeloid dendritic cells are activated by Lassa virus infection, and produce type I interferon. However, Lassa virus-infected dendritic cells were not able to activate T cells. We also elucidated the roles of viral proteins in the modulation of dendritic cell responses.
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Affiliation(s)
- Justine Schaeffer
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur; Centre International de Recherche en Infectiologie (INSERM, CNRS, ENS Lyon, Université Lyon I), Lyon, France
| | - Xavier Carnec
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur; Centre International de Recherche en Infectiologie (INSERM, CNRS, ENS Lyon, Université Lyon I), Lyon, France
| | - Stéphanie Reynard
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur; Centre International de Recherche en Infectiologie (INSERM, CNRS, ENS Lyon, Université Lyon I), Lyon, France
| | - Mathieu Mateo
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur; Centre International de Recherche en Infectiologie (INSERM, CNRS, ENS Lyon, Université Lyon I), Lyon, France
| | - Caroline Picard
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur; Centre International de Recherche en Infectiologie (INSERM, CNRS, ENS Lyon, Université Lyon I), Lyon, France
| | - Natalia Pietrosemoli
- Bioinformatics and Biostatistics Hub, Centre de Bioinformatique Biostatistique et Biologie Intégrative (C3BI, USR 3756, IP CNRS), Institut Pasteur, Paris, France
| | - Marie-Agnès Dillies
- Bioinformatics and Biostatistics Hub, Centre de Bioinformatique Biostatistique et Biologie Intégrative (C3BI, USR 3756, IP CNRS), Institut Pasteur, Paris, France
| | - Sylvain Baize
- Unité de Biologie des Infections Virales Emergentes, Institut Pasteur; Centre International de Recherche en Infectiologie (INSERM, CNRS, ENS Lyon, Université Lyon I), Lyon, France
- * E-mail:
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Morel JD, Paatero AO, Wei J, Yewdell JW, Guenin-Macé L, Van Haver D, Impens F, Pietrosemoli N, Paavilainen VO, Demangel C. Proteomics Reveals Scope of Mycolactone-mediated Sec61 Blockade and Distinctive Stress Signature. Mol Cell Proteomics 2018; 17:1750-1765. [PMID: 29915147 DOI: 10.1074/mcp.ra118.000824] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 06/17/2018] [Indexed: 11/06/2022] Open
Abstract
Mycolactone is a bacteria-derived macrolide that blocks the biogenesis of a large array of secretory and integral transmembrane proteins (TMP) through potent inhibition of the Sec61 translocon. Here, we used quantitative proteomics to delineate the direct and indirect effects of mycolactone-mediated Sec61 blockade in living cells. In T lymphocytes, dendritic cells and sensory neurons, Sec61 substrates downregulated by mycolactone were in order of incidence: secretory proteins (with a signal peptide but no transmembrane domain), TMPs with a signal peptide (Type I) and TMPs without signal peptide and a cytosolic N terminus (Type II). TMPs without a signal peptide and the opposite N terminus topology (Type III) were refractory to mycolactone inhibition. This rule applied comparably to single- and multi-pass TMPs, and extended to exogenous viral proteins. Parallel to its broad-spectrum inhibition of Sec61-mediated protein translocation, mycolactone rapidly induced cytosolic chaperones Hsp70/Hsp90. Moreover, it activated an atypical endoplasmic reticulum stress response, differing from conventional unfolded protein response by the down-regulation of Bip. In addition to refining our mechanistic understanding of Sec61 inhibition by mycolactone, our findings thus reveal that Sec61 blockade induces proteostatic stress in the cytosol and the endoplasmic reticulum.
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Affiliation(s)
- Jean-David Morel
- From the ‡Immunobiology of Infection Unit, Institut Pasteur, 75015 Paris, France.,§INSERM, U1221, 75005 Paris, France
| | - Anja O Paatero
- ¶Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Jiajie Wei
- ‖Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892
| | - Jonathan W Yewdell
- ‖Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892
| | - Laure Guenin-Macé
- From the ‡Immunobiology of Infection Unit, Institut Pasteur, 75015 Paris, France.,§INSERM, U1221, 75005 Paris, France
| | - Delphi Van Haver
- **VIB-UGent Center for Medical Biotechnology, 9000 Ghent, Belgium.,‡‡VIB Proteomics Core, 9000 Ghent, Belgium.,§§Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Francis Impens
- **VIB-UGent Center for Medical Biotechnology, 9000 Ghent, Belgium.,‡‡VIB Proteomics Core, 9000 Ghent, Belgium.,§§Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Natalia Pietrosemoli
- ¶¶Bioinformatics and Biostatistics Hub, Center of Bioinformatics, Biostatistics, and Integrative Biology, Institut Pasteur, Unité de Service et de Recherche 3756 Institut Pasteur CNRS, 75015 Paris, France
| | - Ville O Paavilainen
- ¶Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Caroline Demangel
- From the ‡Immunobiology of Infection Unit, Institut Pasteur, 75015 Paris, France; .,§INSERM, U1221, 75005 Paris, France
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14
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Pietrosemoli N, Mella S, Yennek S, Baghdadi MB, Sakai H, Sambasivan R, Pala F, Di Girolamo D, Tajbakhsh S. Correction to: Comparison of multiple transcriptomes exposes unified and divergent features of quiescent and activated skeletal muscle stem cells. Skelet Muscle 2018; 8:19. [PMID: 29875011 PMCID: PMC5991463 DOI: 10.1186/s13395-018-0165-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Natalia Pietrosemoli
- Bioinformatics and Biostatistics Hub, C3BI, USR 3756 IP CNRS, Institut Pasteur, 75015, Paris, France
| | - Sébastien Mella
- Stem Cells and Development, Department of Developmental and Stem Cell Biology, Institut Pasteur, 75015, Paris, France.,CNRS UMR 3738, Institut Pasteur, 75015, Paris, France
| | - Siham Yennek
- Stem Cells and Development, Department of Developmental and Stem Cell Biology, Institut Pasteur, 75015, Paris, France.,CNRS UMR 3738, Institut Pasteur, 75015, Paris, France.,Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, University of Copenhagen, 3B Blegdamsvej, DK-2200, Copenhagen N, Denmark
| | - Meryem B Baghdadi
- Stem Cells and Development, Department of Developmental and Stem Cell Biology, Institut Pasteur, 75015, Paris, France.,CNRS UMR 3738, Institut Pasteur, 75015, Paris, France
| | - Hiroshi Sakai
- Stem Cells and Development, Department of Developmental and Stem Cell Biology, Institut Pasteur, 75015, Paris, France.,CNRS UMR 3738, Institut Pasteur, 75015, Paris, France
| | - Ramkumar Sambasivan
- Institute for Stem Cell Biology and Regenerative Medicine, GKVK PO, Bellary Road, Bengaluru, 560065, India
| | - Francesca Pala
- Stem Cells and Development, Department of Developmental and Stem Cell Biology, Institut Pasteur, 75015, Paris, France.,CNRS UMR 3738, Institut Pasteur, 75015, Paris, France
| | - Daniela Di Girolamo
- Stem Cells and Development, Department of Developmental and Stem Cell Biology, Institut Pasteur, 75015, Paris, France.,Dipartimento di Medicina Clinica e Chirurgia, Università degli Studi di Napoli Federico II, Via S. Pansini 5, 80131, Naples, Italy
| | - Shahragim Tajbakhsh
- Stem Cells and Development, Department of Developmental and Stem Cell Biology, Institut Pasteur, 75015, Paris, France. .,CNRS UMR 3738, Institut Pasteur, 75015, Paris, France.
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15
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Pietrosemoli N, Mella S, Yennek S, Baghdadi MB, Sakai H, Sambasivan R, Pala F, Di Girolamo D, Tajbakhsh S. Comparison of multiple transcriptomes exposes unified and divergent features of quiescent and activated skeletal muscle stem cells. Skelet Muscle 2017; 7:28. [PMID: 29273087 PMCID: PMC5741941 DOI: 10.1186/s13395-017-0144-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [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: 08/03/2017] [Accepted: 11/29/2017] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Skeletal muscle satellite (stem) cells are quiescent in adult mice and can undergo multiple rounds of proliferation and self-renewal following muscle injury. Several labs have profiled transcripts of myogenic cells during the developmental and adult myogenesis with the aim of identifying quiescent markers. Here, we focused on the quiescent cell state and generated new transcriptome profiles that include subfractionations of adult satellite cell populations, and an artificially induced prenatal quiescent state, to identify core signatures for quiescent and proliferating. METHODS Comparison of available data offered challenges related to the inherent diversity of datasets and biological conditions. We developed a standardized workflow to homogenize the normalization, filtering, and quality control steps for the analysis of gene expression profiles allowing the identification up- and down-regulated genes and the subsequent gene set enrichment analysis. To share the analytical pipeline of this work, we developed Sherpa, an interactive Shiny server that allows multi-scale comparisons for extraction of desired gene sets from the analyzed datasets. This tool is adaptable to cell populations in other contexts and tissues. RESULTS A multi-scale analysis comprising eight datasets of quiescent satellite cells had 207 and 542 genes commonly up- and down-regulated, respectively. Shared up-regulated gene sets include an over-representation of the TNFα pathway via NFKβ signaling, Il6-Jak-Stat3 signaling, and the apical surface processes, while shared down-regulated gene sets exhibited an over-representation of Myc and E2F targets and genes associated to the G2M checkpoint and oxidative phosphorylation. However, virtually all datasets contained genes that are associated with activation or cell cycle entry, such as the immediate early stress response genes Fos and Jun. An empirical examination of fixed and isolated satellite cells showed that these and other genes were absent in vivo, but activated during procedural isolation of cells. CONCLUSIONS Through the systematic comparison and individual analysis of diverse transcriptomic profiles, we identified genes that were consistently differentially expressed among the different datasets and shared underlying biological processes key to the quiescent cell state. Our findings provide impetus to define and distinguish transcripts associated with true in vivo quiescence from those that are first responding genes due to disruption of the stem cell niche.
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Affiliation(s)
- Natalia Pietrosemoli
- Bioinformatics and Biostatistics Hub, C3BI, USR 3756 IP CNRS, Institut Pasteur, 75015 Paris, France
| | - Sébastien Mella
- Stem Cells and Development, Department of Developmental and Stem Cell Biology, Institut Pasteur, 75015 Paris, France
- CNRS UMR 3738, Institut Pasteur, 75015 Paris, France
| | - Siham Yennek
- Stem Cells and Development, Department of Developmental and Stem Cell Biology, Institut Pasteur, 75015 Paris, France
- CNRS UMR 3738, Institut Pasteur, 75015 Paris, France
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, University of Copenhagen, 3B Blegdamsvej, DK-2200 Copenhagen N, Denmark
| | - Meryem B. Baghdadi
- Stem Cells and Development, Department of Developmental and Stem Cell Biology, Institut Pasteur, 75015 Paris, France
- CNRS UMR 3738, Institut Pasteur, 75015 Paris, France
| | - Hiroshi Sakai
- Stem Cells and Development, Department of Developmental and Stem Cell Biology, Institut Pasteur, 75015 Paris, France
- CNRS UMR 3738, Institut Pasteur, 75015 Paris, France
| | - Ramkumar Sambasivan
- Institute for Stem Cell Biology and Regenerative Medicine, GKVK PO, Bellary Road, Bengaluru, 560065 India
| | - Francesca Pala
- Stem Cells and Development, Department of Developmental and Stem Cell Biology, Institut Pasteur, 75015 Paris, France
- CNRS UMR 3738, Institut Pasteur, 75015 Paris, France
| | - Daniela Di Girolamo
- Stem Cells and Development, Department of Developmental and Stem Cell Biology, Institut Pasteur, 75015 Paris, France
- Dipartimento di Medicina Clinica e Chirurgia, Università degli Studi di Napoli Federico II, Via S. Pansini 5, 80131 Naples, Italy
| | - Shahragim Tajbakhsh
- Stem Cells and Development, Department of Developmental and Stem Cell Biology, Institut Pasteur, 75015 Paris, France
- CNRS UMR 3738, Institut Pasteur, 75015 Paris, France
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16
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Paquet ER, Cui J, Davidson D, Pietrosemoli N, Hassan HH, Tsofack SP, Maltais A, Hallett MT, Delorenzi M, Batist G, Aloyz R, Lebel M. A 12-gene signature to distinguish colon cancer patients with better clinical outcome following treatment with 5-fluorouracil or FOLFIRI. J Pathol Clin Res 2015; 1:160-72. [PMID: 27499901 PMCID: PMC4939880 DOI: 10.1002/cjp2.17] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [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: 11/07/2014] [Accepted: 02/03/2015] [Indexed: 12/12/2022]
Abstract
Currently, there is no marker in use in the clinical management of colon cancer to predict which patients will respond efficiently to 5‐fluorouracil (5‐FU), a common component of all cytotoxic therapies. Our aim was to develop and validate a multigene signature associated with clinical outcome from 5‐FU therapy and to determine if it could be used to identify patients who might respond better to alternate treatments. Using a panel of 5‐FU resistant and sensitive colon cancer cell lines, we identified 103 differentially expressed genes providing us with a 5‐FU response signature. We refined this signature using a clinically relevant DNA microarray‐based dataset of 359 formalin‐fixed and paraffin‐embedded (FFPE) colon cancer samples. We then validated the final signature in an external independent DNA microarray‐based dataset of 316 stage III FFPE samples from the PETACC‐3 (Pan‐European Trails in Alimentary Tract Cancers) clinical trial. Finally, using a drug sensitivity database of 658 cell lines, we generated a list of drugs that could sensitize 5‐FU resistant patients using our signature. We confirmed using the PETACC‐3 dataset that the overall survival of subjects responding well to 5‐FU did not improve with the addition of irinotecan (FOLFIRI; two‐sided log‐rank test p = 0.795). Conversely, patients who responded poorly to 5‐FU based on our 12‐gene signature were associated with better survival on FOLFIRI therapy (one‐sided log‐rank test p = 0.039). This new multigene signature is readily applicable to FFPE samples and provides a new tool to help manage treatment in stage III colon cancer. It also provides the first evidence that a subgroup of colon cancer patients can respond better to FOLFIRI than 5‐FU treatment alone.
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Affiliation(s)
- Eric R Paquet
- Molecular and Cellular Biology division, Centre de Recherche sur le Cancer de l'Université LavalQuebec City, QuébecCanada; Department of BiochemistryCentre for BioinformaticsMcGill UniversityThe Rosalind and Morris Goodman Cancer Research CentreMontrealQuebec, Canada
| | - Jing Cui
- Swiss Institute of Bioinformatics, Bioinformatics Core Facility Lausanne Switzerland
| | - David Davidson
- Division of Experimental Medicine & Department of Oncology McGill University Segal Cancer Centre Jewish General Hospital Montreal, Quebec Canada
| | - Natalia Pietrosemoli
- Swiss Institute of Bioinformatics, Bioinformatics Core Facility Lausanne Switzerland
| | - Houssein Hajj Hassan
- Biological Sciences Department School of Arts and Sciences Lebanese International University Beirut Lebanon
| | - Serges P Tsofack
- Molecular and Cellular Biology division, Centre de Recherche sur le Cancer de l'Université Laval Quebec City, Québec Canada
| | - Annie Maltais
- Molecular and Cellular Biology division, Centre de Recherche sur le Cancer de l'Université Laval Quebec City, Québec Canada
| | - Michael T Hallett
- Department of Biochemistry Centre for Bioinformatics McGill University The Rosalind and Morris Goodman Cancer Research Centre Montreal Quebec, Canada
| | - Mauro Delorenzi
- Swiss Institute of Bioinformatics, Bioinformatics Core FacilityLausanneSwitzerland; Department of OncologyUniversity of LausanneLudwig Center for Cancer ResearchLausanneSwitzerland
| | - Gerald Batist
- Division of Experimental Medicine & Department of Oncology McGill University Segal Cancer Centre Jewish General Hospital Montreal, Quebec Canada
| | - Raquel Aloyz
- Division of Experimental Medicine & Department of Oncology McGill University Segal Cancer Centre Jewish General Hospital Montreal, Quebec Canada
| | - Michel Lebel
- Department of molecular biology medical biochemistry and pathology Laval University Centre de Recherche du CHU de Québec, Centre Hospitalier de l'Université Laval Québec Canada
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Espaillat A, Carrasco-López C, Bernardo-García N, Pietrosemoli N, Otero LH, Álvarez L, de Pedro MA, Pazos F, Davis BM, Waldor MK, Hermoso JA, Cava F. Structural basis for the broad specificity of a new family of amino-acid racemases. ACTA ACUST UNITED AC 2013; 70:79-90. [PMID: 24419381 DOI: 10.1107/s1399004713024838] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 09/05/2013] [Indexed: 02/02/2023]
Abstract
Broad-spectrum amino-acid racemases (Bsrs) enable bacteria to generate noncanonical D-amino acids, the roles of which in microbial physiology, including the modulation of cell-wall structure and the dissolution of biofilms, are just beginning to be appreciated. Here, extensive crystallographic, mutational, biochemical and bioinformatic studies were used to define the molecular features of the racemase BsrV that enable this enzyme to accommodate more diverse substrates than the related PLP-dependent alanine racemases. Conserved residues were identified that distinguish BsrV and a newly defined family of broad-spectrum racemases from alanine racemases, and these residues were found to be key mediators of the multispecificity of BrsV. Finally, the structural analysis of an additional Bsr that was identified in the bioinformatic analysis confirmed that the distinguishing features of BrsV are conserved among Bsr family members.
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Affiliation(s)
- Akbar Espaillat
- Centro de Biología Molecular `Severo Ochoa', Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain
| | - César Carrasco-López
- Department of Crystallography and Structural Biology, Instituto de Química-Física `Rocasolano'-CSIC, 28006 Madrid, Spain
| | - Noelia Bernardo-García
- Department of Crystallography and Structural Biology, Instituto de Química-Física `Rocasolano'-CSIC, 28006 Madrid, Spain
| | | | - Lisandro H Otero
- Department of Crystallography and Structural Biology, Instituto de Química-Física `Rocasolano'-CSIC, 28006 Madrid, Spain
| | - Laura Álvarez
- Centro de Biología Molecular `Severo Ochoa', Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain
| | - Miguel A de Pedro
- Centro de Biología Molecular `Severo Ochoa', Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain
| | | | - Brigid M Davis
- Division of Infectious Diseases, Brigham and Women's Hospital and Department of Microbiology and Immunobiology, Harvard Medical School and HHMI, Boston, MA 02115, USA
| | - Matthew K Waldor
- Division of Infectious Diseases, Brigham and Women's Hospital and Department of Microbiology and Immunobiology, Harvard Medical School and HHMI, Boston, MA 02115, USA
| | - Juan A Hermoso
- Department of Crystallography and Structural Biology, Instituto de Química-Física `Rocasolano'-CSIC, 28006 Madrid, Spain
| | - Felipe Cava
- Centro de Biología Molecular `Severo Ochoa', Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain
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Pazos F, Pietrosemoli N, García-Martín JA, Solano R. Protein intrinsic disorder in plants. Front Plant Sci 2013; 4:363. [PMID: 24062761 PMCID: PMC3770944 DOI: 10.3389/fpls.2013.00363] [Citation(s) in RCA: 36] [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] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 08/27/2013] [Indexed: 05/21/2023]
Abstract
To some extent contradicting the classical paradigm of the relationship between protein 3D structure and function, now it is clear that large portions of the proteomes, especially in higher organisms, lack a fixed structure and still perform very important functions. Proteins completely or partially unstructured in their native (functional) form are involved in key cellular processes underlain by complex networks of protein interactions. The intrinsic conformational flexibility of these disordered proteins allows them to bind multiple partners in transient interactions of high specificity and low affinity. In concordance, in plants this type of proteins has been found in processes requiring these complex and versatile interaction networks. These include transcription factor networks, where disordered proteins act as integrators of different signals or link different transcription factor subnetworks due to their ability to interact (in many cases simultaneously) with different partners. Similarly, they also serve as signal integrators in signaling cascades, such as those related to response to external stimuli. Disordered proteins have also been found in plants in many stress-response processes, acting as protein chaperones or protecting other cellular components and structures. In plants, it is especially important to have complex and versatile networks able to quickly and efficiently respond to changing environmental conditions since these organisms cannot escape and have no other choice than adapting to them. Consequently, protein disorder can play an especially important role in plants, providing them with a fast mechanism to obtain complex, interconnected and versatile molecular networks.
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Affiliation(s)
- Florencio Pazos
- Computational Systems Biology Group, National Centre for Biotechnology, Spanish National Research CouncilMadrid, Spain
- *Correspondence: Florencio Pazos, Computational Systems Biology Group, National Centre for Biotechnology, Spanish National Research Council, c/Darwin 3, Madrid 28049, Spain e-mail:
| | - Natalia Pietrosemoli
- Computational Systems Biology Group, National Centre for Biotechnology, Spanish National Research CouncilMadrid, Spain
| | - Juan A. García-Martín
- Plant Molecular Genetics Department, National Centre for Biotechnology, Spanish National Research CouncilMadrid, Spain
- Present address:Juan A. García-Martín, Biology Department, Boston College, Boston, MA, USA
| | - Roberto Solano
- Plant Molecular Genetics Department, National Centre for Biotechnology, Spanish National Research CouncilMadrid, Spain
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Pietrosemoli N, García-Martín JA, Solano R, Pazos F. Genome-wide analysis of protein disorder in Arabidopsis thaliana: implications for plant environmental adaptation. PLoS One 2013; 8:e55524. [PMID: 23408995 PMCID: PMC3567104 DOI: 10.1371/journal.pone.0055524] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [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: 08/29/2012] [Accepted: 12/27/2012] [Indexed: 01/31/2023] Open
Abstract
Intrinsically Disordered Proteins/Regions (IDPs/IDRs) are currently recognized as a widespread phenomenon having key cellular functions. Still, many aspects of the function of these proteins need to be unveiled. IDPs conformational flexibility allows them to recognize and interact with multiple partners, and confers them larger interaction surfaces that may increase interaction speed. For this reason, molecular interactions mediated by IDPs/IDRs are particularly abundant in certain types of protein interactions, such as those of signaling and cell cycle control. We present the first large-scale study of IDPs in Arabidopsis thaliana, the most widely used model organism in plant biology, in order to get insight into the biological roles of these proteins in plants. The work includes a comparative analysis with the human proteome to highlight the differential use of disorder in both species. Results show that while human proteins are in general more disordered, certain functional classes, mainly related to environmental response, are significantly more enriched in disorder in Arabidopsis. We propose that because plants cannot escape from environmental conditions as animals do, they use disorder as a simple and fast mechanism, independent of transcriptional control, for introducing versatility in the interaction networks underlying these biological processes so that they can quickly adapt and respond to challenging environmental conditions.
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Affiliation(s)
- Natalia Pietrosemoli
- Computational System Biology Group, National Centre for Biotechnology, Madrid, Spain
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Bert A, Dmitriev I, Agliozzo S, Pietrosemoli N, Mandelkern M, Gallo T, Regge D. An automatic method for colon segmentation in CT colonography. Comput Med Imaging Graph 2009; 33:325-31. [PMID: 19304454 DOI: 10.1016/j.compmedimag.2009.02.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2006] [Revised: 01/15/2009] [Accepted: 02/23/2009] [Indexed: 11/25/2022]
Abstract
An automatic method for the segmentation of the colonic wall is proposed for abdominal computed tomography (CT) of the cleansed and air-inflated colon. This multistage approach uses an adaptive 3D region-growing algorithm, with a self-adjusting growing condition depending on local variations of the intensity at the air-tissue boundary. The method was evaluated using retrospectively collected CT scans based on visual segmentation of the colon by expert radiologists. This evaluation showed that the procedure identifies 97% of the colon segments, representing 99.8% of the colon surface, and accurately replicates the anatomical profile of the colonic wall. The parameter settings and performance of the method are relatively independent of the scanner and acquisition conditions. The method is intended for application to the computer-aided detection of polyps in CT colonography.
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Affiliation(s)
- Alberto Bert
- im3D S.p.A. Medical Imaging Lab, Via Lessolo 3, 10153 Torino, Italy.
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Abstract
Soluble folded proteins maintain their structural integrity by properly shielding most backbone amides and carbonyls from full hydration. This structure "wrapping" entails a proper packing of the intramolecular hydrogen bonds. Thus, a poorly wrapped hydrogen bond constitutes an identifiable packing defect. Such defects are promoters of protein associations since they favor the removal of hydrating molecules. In this work we show that large clusters of packing defects generate the most significant dehydration hot spots on the protein surface, inducing a strong dielectric modulation that is reflected by a local quenching of the dielectric permittivity. The PDB-reported proteins with the largest clusters of packing defects are found to be three cancer-related transcription factors, four highly interactive proteins related to cell signaling and cytoskeleton, and a cellular prion protein. A large concentration of packing defects in a soluble protein constitutes a structural singularity that is intermediate between order and disorder. The functional implications of this singularity are investigated to delineate diverse interrelated roles. The presence of these large clusters signals a structural vulnerability, a pronounced dehydration propensity, and a strong electrostatic enhancement.
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