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Cabral-Piccin MP, Briceño O, Papagno L, Liouville B, White E, Perdomo-Celis F, Autaa G, Volant S, Llewellyn-Lacey S, Fromentin R, Chomont N, Price DA, Sáez-Cirión A, Lambotte O, Katlama C, Appay V. CD8 + T-cell priming is quantitatively but not qualitatively impaired in people with HIV-1 on antiretroviral therapy. AIDS 2024; 38:161-166. [PMID: 37800637 DOI: 10.1097/qad.0000000000003746] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/07/2023]
Abstract
BACKGROUND The induction of de novo CD8 + T-cell responses is essential for protective antiviral immunity, but this process is often impaired in people with HIV-1 (PWH). We investigated the extent to which the immune competence of naive CD8 + T cells, a key determinant of priming efficacy, could be preserved or restored in PWH via long-term antiretroviral therapy (ART). METHODS We used flow cytometry, molecular analyses of gene transcription and telomere length, and a fully validated priming assay to characterize naive CD8 + T cells ex vivo and evaluate the induction of antigen-specific effector/memory CD8 + T cells in vitro , comparing age-matched healthy uninfected donors (HUDs), PWH on ART, and natural HIV-1 controllers (HICs). RESULTS We found that naive CD8 + T cells were numerically reduced and exhibited a trend toward shorter telomere lengths in PWH on ART compared with HUDs and HICs. These features associated with impaired priming efficacy. However, we also found that naive CD8 + T cells were fully equipped proliferatively and transcriptionally in PWH on ART, enabling the generation of antigen-specific effector/memory CD8 + T cells with functional and phenotypic attributes comparable to those primed from HUDs. CONCLUSION Our data suggest that naive CD8 + T cells in PWH on ART are intrinsically capable of generating functionally and phenotypically intact effector/memory CD8 + T cells in response to antigen, despite evidence of senescence and an overall numerical reduction that compromises priming efficacy relative to HUDs and HICs.
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Affiliation(s)
- Mariela P Cabral-Piccin
- Université de Bordeaux, CNRS UMR 5164, INSERM ERL 1303, ImmunoConcEpT, Bordeaux
- Sorbonne Université, INSERM U1135, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Paris, France
| | - Olivia Briceño
- Sorbonne Université, INSERM U1135, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Paris, France
- Departamento de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Calzada de Tlalpan 4502, Colonia Sección XVI, Tlalpan, Mexico City, Mexico
| | - Laura Papagno
- Université de Bordeaux, CNRS UMR 5164, INSERM ERL 1303, ImmunoConcEpT, Bordeaux
- Sorbonne Université, INSERM U1135, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Paris, France
| | - Benjamin Liouville
- Sorbonne Université, INSERM U1135, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Paris, France
| | - Eoghann White
- Université de Bordeaux, CNRS UMR 5164, INSERM ERL 1303, ImmunoConcEpT, Bordeaux
- Sorbonne Université, INSERM U1135, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Paris, France
| | | | - Gaëlle Autaa
- Université de Bordeaux, CNRS UMR 5164, INSERM ERL 1303, ImmunoConcEpT, Bordeaux
| | - Stevenn Volant
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
| | - Sian Llewellyn-Lacey
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Rémi Fromentin
- Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, Quebec, Canada
| | - Nicolas Chomont
- Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, Quebec, Canada
| | - David A Price
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
- Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, UK
| | - Asier Sáez-Cirión
- Institut Pasteur, Université Paris Cité, Unité HIV Inflammation et Persistance
- Institut Pasteur, Université Paris Cité, Viral Reservoirs and Immune Control Unit, Paris
| | - Olivier Lambotte
- Université Paris-Saclay, AP-HP Hôpitaux Universitaires Paris Saclay, Service de Médecine Interne, Bicêtre (UMR 1184), CEA (IDMIT Department, IBFJ), INSERM, Center for Immunology of Viral, Auto-Immune, Hematological and Bacterial Diseases (IMVA-HB), Le Kremlin Bicêtre
| | - Christine Katlama
- Infectious Diseases Department, Pitié-Salpêtrière Hospital, AP-HP, Pierre Louis Epidemiology and Public Health Institute (iPLESP), INSERM 1136, Sorbonne Université, Paris, France
| | - Victor Appay
- Université de Bordeaux, CNRS UMR 5164, INSERM ERL 1303, ImmunoConcEpT, Bordeaux
- Sorbonne Université, INSERM U1135, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Paris, France
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Bergsten E, Mestivier D, Donnadieu F, Pedron T, Barau C, Meda LT, Mettouchi A, Lemichez E, Gorgette O, Chamaillard M, Vaysse A, Volant S, Doukani A, Sansonetti PJ, Sobhani I, Nigro G. Parvimonas micra, an oral pathobiont associated with colorectal cancer, epigenetically reprograms human colonocytes. Gut Microbes 2023; 15:2265138. [PMID: 37842920 PMCID: PMC10580862 DOI: 10.1080/19490976.2023.2265138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 09/20/2023] [Indexed: 10/17/2023] Open
Abstract
Recently, an intestinal dysbiotic microbiota with enrichment in oral cavity bacteria has been described in colorectal cancer (CRC) patients. Here, we characterize and investigate one of these oral pathobionts, the Gram-positive anaerobic coccus Parvimonas micra. We identified two phylotypes (A and B) exhibiting different phenotypes and adhesion capabilities. We observed a strong association of phylotype A with CRC, with its higher abundance in feces and in tumoral tissue compared with the normal homologous colonic mucosa, which was associated with a distinct methylation status of patients. By developing an in vitro hypoxic co-culture system of human primary colonic cells with anaerobic bacteria, we show that P. micra phylotype A alters the DNA methylation profile promoters of key tumor-suppressor genes, oncogenes, and genes involved in epithelial-mesenchymal transition. In colonic mucosa of CRC patients carrying P. micra phylotype A, we found similar DNA methylation alterations, together with significant enrichment of differentially expressed genes in pathways involved in inflammation, cell adhesion, and regulation of actin cytoskeleton, providing evidence of P. micra's possible role in the carcinogenic process.
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Affiliation(s)
- Emma Bergsten
- Unité de Pathogénie Microbienne Moléculaire, INSERM U1202, Institut Pasteur, Paris, France
- Équipe universitaire EC2M3-EA7375, Université Paris- Est (UPEC), Créteil, France
| | - Denis Mestivier
- Équipe universitaire EC2M3-EA7375, Université Paris- Est (UPEC), Créteil, France
- Plateforme de Bio-informatique, Institut Mondor de Recherche Biomédicale (IMRB/INSERM U955), Université Paris-Est, Créteil, France
| | - Francoise Donnadieu
- Unité de Pathogénie Microbienne Moléculaire, INSERM U1202, Institut Pasteur, Paris, France
| | - Thierry Pedron
- Unité de Pathogénie Microbienne Moléculaire, INSERM U1202, Institut Pasteur, Paris, France
- Unité Bactériophage, Bactérie, Hôte, Institut Pasteur, Paris, France
| | - Caroline Barau
- Plateforme de Ressources Biologiques, CHU Henri Mondor Assistance Publique Hôpitaux de Paris (APHP), Créteil, France
| | - Landry Tsoumtsa Meda
- Unité des Toxines Bactériennes, Université Paris Cité, CNRS UMR6047, INSERM U1306, Institut Pasteur, Paris, France
| | - Amel Mettouchi
- Unité des Toxines Bactériennes, Université Paris Cité, CNRS UMR6047, INSERM U1306, Institut Pasteur, Paris, France
| | - Emmanuel Lemichez
- Unité des Toxines Bactériennes, Université Paris Cité, CNRS UMR6047, INSERM U1306, Institut Pasteur, Paris, France
| | - Olivier Gorgette
- Plateforme de Bio-Imagerie Ultrastructurale, Institut Pasteur, Université Paris Cité, Paris, France
| | - Mathias Chamaillard
- Laboratory of Cell Physiology, INSERM U1003, University of Lille, Lille, France
| | - Amaury Vaysse
- Bioinformatics and Biostatistics Hub, Institut Pasteur, Université Paris Cité, Paris, France
| | - Stevenn Volant
- Bioinformatics and Biostatistics Hub, Institut Pasteur, Université Paris Cité, Paris, France
| | - Abiba Doukani
- Sorbonne Université, Inserm, Unité Mixte de Service Production et Analyse de données en Sciences de la Vie et en Santé, Paris, France
| | - Philippe J. Sansonetti
- Unité de Pathogénie Microbienne Moléculaire, INSERM U1202, Institut Pasteur, Paris, France
- Chaire de Microbiologie et Maladies Infectieuses, Collège de France, Paris, France
| | - Iradj Sobhani
- Équipe universitaire EC2M3-EA7375, Université Paris- Est (UPEC), Créteil, France
- Service de Gastroentérologie, CHU Henri Mondor Assistance Publique Hôpitaux de Paris (APHP), Créteil, France
| | - Giulia Nigro
- Unité de Pathogénie Microbienne Moléculaire, INSERM U1202, Institut Pasteur, Paris, France
- Microenvironment and Immunity Unit, INSERM U1224, Institut Pasteur, Paris, France
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3
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Bennouna A, Tantely ML, Raharinosy V, Andriamandimby SF, Bigot T, Chrétien D, Jacquemet E, Volant S, Temmam S, Dussart P, Lacoste V, Girod R, Eloit M. Comprehensive Characterization of Viral Diversity of Female Mosquitoes in Madagascar. Viruses 2023; 15:1852. [PMID: 37766259 PMCID: PMC10537517 DOI: 10.3390/v15091852] [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] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/28/2023] [Accepted: 08/28/2023] [Indexed: 09/29/2023] Open
Abstract
The diversity and circulation of arboviruses are not much studied in Madagascar. The fact is that arboviral emergences are rarely detected. The existing surveillance system primarily relies on serological detection and records only a few human infections annually. The city of Mahajanga, however, experienced a confirmed dengue fever epidemic in 2020 and 2021. This study aimed to characterize and analyze the virome of mosquitoes collected in Mahajanga, near patients with dengue-like syndromes to detect known and unknown viruses as well as investigate the factors contributing to the relative low circulation of arboviruses in the area. A total of 4280 mosquitoes representing at least 12 species from the Aedes, Anopheles, and Culex genera were collected during the dry and the rainy seasons from three sites, following an urbanization gradient. The virome analysis of 2192 female mosquitoes identified a diverse range of viral families and genera and revealed different patterns that are signatures of the influence of the mosquito genus or the season of collection on the composition and abundance of the virome. Despite the absence of known human or veterinary arboviruses, the identification and characterization of viral families, genera, and species in the mosquito virome contribute to our understanding of viral ecology and diversity within mosquito populations in Madagascar. This study serves as a foundation for ongoing surveillance efforts and provides a basis for the development of preventive strategies against various mosquito-borne viral diseases, including known arboviruses.
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Affiliation(s)
- Amal Bennouna
- Pathogen Discovery Laboratory, Institut Pasteur, Université de Paris, 75015 Paris, France; (A.B.); (S.T.)
- The WOAH (OIE) Collaborating Center for the Detection and Identification in Humans of Emerging Animal Pathogens, Institut Pasteur, Université Paris Cité, 75015 Paris, France
| | - Michael Luciano Tantely
- Medical Entomology Unit, Institut Pasteur de Madagascar, Antananarivo 101 1274, Madagascar; (M.L.T.)
| | | | | | - Thomas Bigot
- Pathogen Discovery Laboratory, Institut Pasteur, Université de Paris, 75015 Paris, France; (A.B.); (S.T.)
- Bioinformatics and Biostatistics Hub, Institut Pasteur, Université Paris Cité, 75015 Paris, France
| | - Delphine Chrétien
- Pathogen Discovery Laboratory, Institut Pasteur, Université de Paris, 75015 Paris, France; (A.B.); (S.T.)
- The WOAH (OIE) Collaborating Center for the Detection and Identification in Humans of Emerging Animal Pathogens, Institut Pasteur, Université Paris Cité, 75015 Paris, France
| | - Elise Jacquemet
- Bioinformatics and Biostatistics Hub, Institut Pasteur, Université Paris Cité, 75015 Paris, France
| | - Stevenn Volant
- Bioinformatics and Biostatistics Hub, Institut Pasteur, Université Paris Cité, 75015 Paris, France
| | - Sarah Temmam
- Pathogen Discovery Laboratory, Institut Pasteur, Université de Paris, 75015 Paris, France; (A.B.); (S.T.)
- The WOAH (OIE) Collaborating Center for the Detection and Identification in Humans of Emerging Animal Pathogens, Institut Pasteur, Université Paris Cité, 75015 Paris, France
| | - Philippe Dussart
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo 101 1274, Madagascar
| | - Vincent Lacoste
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo 101 1274, Madagascar
| | - Romain Girod
- Medical Entomology Unit, Institut Pasteur de Madagascar, Antananarivo 101 1274, Madagascar; (M.L.T.)
| | - Marc Eloit
- Pathogen Discovery Laboratory, Institut Pasteur, Université de Paris, 75015 Paris, France; (A.B.); (S.T.)
- The WOAH (OIE) Collaborating Center for the Detection and Identification in Humans of Emerging Animal Pathogens, Institut Pasteur, Université Paris Cité, 75015 Paris, France
- Ecole Nationale Vétérinaire d’Alfort, University of Paris-Est, 94700 Maisons-Alfort, France
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Mohamed Ali S, Rakotonirina A, Heng K, Jacquemet E, Volant S, Temmam S, Boyer S, Eloit M. Longitudinal Study of Viral Diversity Associated with Mosquito Species Circulating in Cambodia. Viruses 2023; 15:1831. [PMID: 37766237 PMCID: PMC10535147 DOI: 10.3390/v15091831] [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: 08/03/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
Arthropod-borne viruses (arboviruses) pose a significant global health threat and are primarily transmitted by mosquitoes. In Cambodia, there are currently 290 recorded mosquito species, with at least 17 of them considered potential vectors of arboviruses to humans. Effective surveillance of virome profiles in mosquitoes from Cambodia is vital, as it could help prevent and control arbovirus diseases in a country where epidemics occur frequently. The objective of this study was to identify and characterize the viral diversity in mosquitoes collected during a one-year longitudinal study conducted in various habitats across Cambodia. For this purpose, we used a metatranscriptomics approach and detected the presence of chikungunya virus in the collected mosquitoes. Additionally, we identified viruses categorized into 26 taxa, including those known to harbor arboviruses such as Flaviviridae and Orthomyxoviridae, along with a group of viruses not yet taxonomically identified and provisionally named "unclassified viruses". Interestingly, the taxa detected varied in abundance and composition depending on the mosquito genus, with no significant influence of the collection season. Furthermore, most of the identified viruses were either closely related to viruses found exclusively in insects or represented new viruses belonging to the Rhabdoviridae and Birnaviridae families. The transmission capabilities of these novel viruses to vertebrates remain unknown.
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Affiliation(s)
- Souand Mohamed Ali
- Pathogen Discovery Laboratory, Institut Pasteur, Université de Paris, 75015 Paris, France; (S.M.A.); (S.T.)
| | - Antsa Rakotonirina
- Medical and Veterinary Entomology Unit, Institut Pasteur du Cambodge, Phnom Penh 12201, Cambodia; (A.R.); (S.B.)
| | - Kimly Heng
- Medical and Veterinary Entomology Unit, Institut Pasteur du Cambodge, Phnom Penh 12201, Cambodia; (A.R.); (S.B.)
| | - Elise Jacquemet
- Bioinformatics and Biostatistics Hub, Institut Pasteur, Université Paris Cité, 75015 Paris, France (S.V.)
| | - Stevenn Volant
- Bioinformatics and Biostatistics Hub, Institut Pasteur, Université Paris Cité, 75015 Paris, France (S.V.)
| | - Sarah Temmam
- Pathogen Discovery Laboratory, Institut Pasteur, Université de Paris, 75015 Paris, France; (S.M.A.); (S.T.)
| | - Sebastien Boyer
- Medical and Veterinary Entomology Unit, Institut Pasteur du Cambodge, Phnom Penh 12201, Cambodia; (A.R.); (S.B.)
- Ecology and Emergence of Arthropod-Borne Diseases, Institut Pasteur, 75015 Paris, France
| | - Marc Eloit
- Pathogen Discovery Laboratory, Institut Pasteur, Université de Paris, 75015 Paris, France; (S.M.A.); (S.T.)
- Ecole Nationale Vétérinaire d’Alfort, University of Paris-Est, 94704 Maisons-Alfort, France
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Cabral-Piccin MP, Papagno L, Lahaye X, Perdomo-Celis F, Volant S, White E, Monceaux V, Llewellyn-Lacey S, Fromentin R, Price DA, Chomont N, Manel N, Saez-Cirion A, Appay V. Primary role of type I interferons for the induction of functionally optimal antigen-specific CD8 + T cells in HIV infection. EBioMedicine 2023; 91:104557. [PMID: 37058769 PMCID: PMC10130611 DOI: 10.1016/j.ebiom.2023.104557] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 03/20/2023] [Accepted: 03/23/2023] [Indexed: 04/16/2023] Open
Abstract
BACKGROUND CD8+ T cells equipped with a full arsenal of antiviral effector functions are critical for effective immune control of HIV-1. It has nonetheless remained unclear how best to elicit such potent cellular immune responses in the context of immunotherapy or vaccination. HIV-2 has been associated with milder disease manifestations and more commonly elicits functionally replete virus-specific CD8+ T cell responses compared with HIV-1. We aimed to learn from this immunological dichotomy and to develop informed strategies that could enhance the induction of robust CD8+ T cell responses against HIV-1. METHODS We developed an unbiased in vitro system to compare the de novo induction of antigen-specific CD8+ T cell responses after exposure to HIV-1 or HIV-2. The functional properties of primed CD8+ T cells were assessed using flow cytometry and molecular analyses of gene transcription. FINDINGS HIV-2 primed functionally optimal antigen-specific CD8+ T cells with enhanced survival properties more effectively than HIV-1. This superior induction process was dependent on type I interferons (IFNs) and could be mimicked via the adjuvant delivery of cyclic GMP-AMP (cGAMP), a known agonist of the stimulator of interferon genes (STING). CD8+ T cells elicited in the presence of cGAMP were polyfunctional and highly sensitive to antigen stimulation, even after priming from people living with HIV-1. INTERPRETATION HIV-2 primes CD8+ T cells with potent antiviral functionality by activating the cyclic GMP-AMP synthase (cGAS)/STING pathway, which results in the production of type I IFNs. This process may be amenable to therapeutic development via the use of cGAMP or other STING agonists to bolster CD8+ T cell-mediated immunity against HIV-1. FUNDING This work was funded by INSERM, the Institut Curie, and the University of Bordeaux (Senior IdEx Chair) and by grants from Sidaction (17-1-AAE-11097, 17-1-FJC-11199, VIH2016126002, 20-2-AEQ-12822-2, and 22-2-AEQ-13411), the Agence Nationale de la Recherche sur le SIDA (ECTZ36691, ECTZ25472, ECTZ71745, and ECTZ118797), and the Fondation pour la Recherche Médicale (EQ U202103012774). D.A.P. was supported by a Wellcome Trust Senior Investigator Award (100326/Z/12/Z).
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Affiliation(s)
- Mariela P Cabral-Piccin
- Université de Bordeaux, CNRS UMR 5164, INSERM ERL 1303, ImmunoConcEpT, 33000, Bordeaux, France; Sorbonne Université, INSERM U1135, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), 75013, Paris, France
| | - Laura Papagno
- Université de Bordeaux, CNRS UMR 5164, INSERM ERL 1303, ImmunoConcEpT, 33000, Bordeaux, France; Sorbonne Université, INSERM U1135, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), 75013, Paris, France
| | - Xavier Lahaye
- Institut Curie, INSERM U932, Immunity and Cancer Department, PSL Research University, 75005, Paris, France
| | | | - Stevenn Volant
- Institut Pasteur, Hub Bioinformatique et Biostatistique, 75015, Paris, France
| | - Eoghann White
- Université de Bordeaux, CNRS UMR 5164, INSERM ERL 1303, ImmunoConcEpT, 33000, Bordeaux, France; Sorbonne Université, INSERM U1135, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), 75013, Paris, France
| | - Valérie Monceaux
- Institut Pasteur, Unité HIV Inflammation et Persistance, 75015, Paris, France
| | - Sian Llewellyn-Lacey
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, CF14 4XN, UK
| | - Rémi Fromentin
- Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - David A Price
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, CF14 4XN, UK; Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, CF14 4XN, UK
| | - Nicolas Chomont
- Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Nicolas Manel
- Institut Curie, INSERM U932, Immunity and Cancer Department, PSL Research University, 75005, Paris, France.
| | - Asier Saez-Cirion
- Institut Pasteur, Unité HIV Inflammation et Persistance, 75015, Paris, France; Institut Pasteur, Université Paris Cité, Viral Reservoirs and Immune Control Unit, 75015, Paris, France.
| | - Victor Appay
- Université de Bordeaux, CNRS UMR 5164, INSERM ERL 1303, ImmunoConcEpT, 33000, Bordeaux, France; Sorbonne Université, INSERM U1135, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), 75013, Paris, France; International Research Center of Medical Sciences, Kumamoto University, Kumamoto, 860-0811, Japan.
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Khalfi P, Suspène R, Raymond KA, Caval V, Caignard G, Berry N, Thiers V, Combredet C, Rufie C, Rigaud S, Ghozlane A, Volant S, Komarova AV, Tangy F, Vartanian JP. Antagonism of ALAS1 by the Measles Virus V protein contributes to degradation of the mitochondrial network and promotes interferon response. PLoS Pathog 2023; 19:e1011170. [PMID: 36802406 PMCID: PMC9983871 DOI: 10.1371/journal.ppat.1011170] [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] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 03/03/2023] [Accepted: 02/01/2023] [Indexed: 02/23/2023] Open
Abstract
Viruses have evolved countless mechanisms to subvert and impair the host innate immune response. Measles virus (MeV), an enveloped, non-segmented, negative-strand RNA virus, alters the interferon response through different mechanisms, yet no viral protein has been described as directly targeting mitochondria. Among the crucial mitochondrial enzymes, 5'-aminolevulinate synthase (ALAS) is an enzyme that catalyzes the first step in heme biosynthesis, generating 5'-aminolevulinate from glycine and succinyl-CoA. In this work, we demonstrate that MeV impairs the mitochondrial network through the V protein, which antagonizes the mitochondrial enzyme ALAS1 and sequesters it to the cytosol. This re-localization of ALAS1 leads to a decrease in mitochondrial volume and impairment of its metabolic potential, a phenomenon not observed in MeV deficient for the V gene. This perturbation of the mitochondrial dynamics demonstrated both in culture and in infected IFNAR-/- hCD46 transgenic mice, causes the release of mitochondrial double-stranded DNA (mtDNA) in the cytosol. By performing subcellular fractionation post infection, we demonstrate that the most significant source of DNA in the cytosol is of mitochondrial origin. Released mtDNA is then recognized and transcribed by the DNA-dependent RNA polymerase III. The resulting double-stranded RNA intermediates will be captured by RIG-I, ultimately initiating type I interferon production. Deep sequencing analysis of cytosolic mtDNA editing divulged an APOBEC3A signature, primarily analyzed in the 5'TpCpG context. Finally, in a negative feedback loop, APOBEC3A an interferon inducible enzyme will orchestrate the catabolism of mitochondrial DNA, decrease cellular inflammation, and dampen the innate immune response.
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Affiliation(s)
- Pierre Khalfi
- Virus and Cellular Stress Unit, Department of Virology, Institut Pasteur, Université de Paris Cité, Paris, France
- Sorbonne Université, Complexité du Vivant, ED515, Paris, France
| | - Rodolphe Suspène
- Virus and Cellular Stress Unit, Department of Virology, Institut Pasteur, Université de Paris Cité, Paris, France
| | - Kyle A. Raymond
- Virus and Cellular Stress Unit, Department of Virology, Institut Pasteur, Université de Paris Cité, Paris, France
- Sorbonne Université, Complexité du Vivant, ED515, Paris, France
| | - Vincent Caval
- Virus and Cellular Stress Unit, Department of Virology, Institut Pasteur, Université de Paris Cité, Paris, France
| | | | - Noémie Berry
- Virus and Cellular Stress Unit, Department of Virology, Institut Pasteur, Université de Paris Cité, Paris, France
- Sorbonne Université, Complexité du Vivant, ED515, Paris, France
- UMR1161 Virologie, ANSES-INRAE-ENVA, Maisons-Alfort, France
| | - Valérie Thiers
- Virus and Cellular Stress Unit, Department of Virology, Institut Pasteur, Université de Paris Cité, Paris, France
| | - Chantal Combredet
- Vaccines Innovation Laboratory, Institut Pasteur, Université de Paris Cité, Paris, France
| | - Claude Rufie
- Vaccines Innovation Laboratory, Institut Pasteur, Université de Paris Cité, Paris, France
| | - Stéphane Rigaud
- Image Analysis Hub, Institut Pasteur, Université de Paris Cité, Paris, France
| | - Amine Ghozlane
- Bioinformatics and Biostatistics HUB, Institut Pasteur, Université de Paris Cité, Paris, France
| | - Stevenn Volant
- Bioinformatics and Biostatistics HUB, Institut Pasteur, Université de Paris Cité, Paris, France
| | - Anastassia V. Komarova
- Interactomics, RNA and Immunity Laboratory, Institut Pasteur, Université de Paris Cité, Paris, France
| | - Frédéric Tangy
- Vaccines Innovation Laboratory, Institut Pasteur, Université de Paris Cité, Paris, France
| | - Jean-Pierre Vartanian
- Virus and Cellular Stress Unit, Department of Virology, Institut Pasteur, Université de Paris Cité, Paris, France
- * E-mail:
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7
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Perdomo-Celis F, Passaes C, Monceaux V, Volant S, Boufassa F, de Truchis P, Marcou M, Bourdic K, Weiss L, Jung C, Bourgeois C, Goujard C, Meyer L, Müller-Trutwin M, Lambotte O, Sáez-Cirión A. Reprogramming dysfunctional CD8+ T cells to promote properties associated with natural HIV control. J Clin Invest 2023; 133:167843. [PMID: 36647831 PMCID: PMC9843039 DOI: 10.1172/jci167843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
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8
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Delavy M, Burdet C, Sertour N, Chatelier EL, Doquier JD, Volant S, Ghozlane A, Grall N, Duval X, Mentré F, Duffy D, D'Enfert C, Bougnoux ME. S10.3c Clinical studies provide new insights on the association between the microbiota and host resistance to Candida albicans intestinal colonization. Med Mycol 2022. [PMCID: PMC9511560 DOI: 10.1093/mmy/myac072.s10.3c] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
S10.3 The mycobiome characterization: future perspectives or just a trend?, September 24, 2022, 10:30 AM - 12:00 PM
Objectives
Candida albicans is both a harmless commensal intestinal yeast in healthy individuals and a harmful opportunistic pathogen in immunocompromised patients, causing life-threatening invasive candidiasis. C. albicans intestinal overgrowth is a prerequisite for intestinal translocation, which is at the root of invasive candidiasis. Therefore, to prevent invasive candidiasis in immunocompromised patients, it is necessary to curb intestinal C. albicans overgrowth. However, little is known of the role of bacterial species of the microbiota in dampening C. albicans intestinal colonization.
We aimed to decipher the influence of the bacterial and fungal intestinal microbiota on C. albicans gut colonization in healthy individuals in whom their microbiota was modified or not by antibiotic treatment.
Methods
We studied two cohorts of healthy individuals: the first cohort included 22 volunteers for which fecal samples were collected before, during and after a 3-day regimen of third-generation cephalosporin antibiotics. The second cohort gathered 1000 healthy individuals for which a single fecal sample was collected. We quantified C. albicans carriage using a specific quantitative PCR approach. We monitored the antibiotic effect on the composition of the fungal microbiota—the so called mycobiota—in the gut of the individuals up to 180 days post-antibiotic exposure, using both the qPCR data and ITS1 targeted metagenomic. We also monitored the level of fecal β-lactamase activity, which is known to modulate the intensity of post-cephalosporin intestinal dysbiosis. Finally, to identify potential C. albicans inhibiting bacteria, we used MaAsLin2 to search for associations between C. albicans levels and bacterial species abundance, deduced from shotgun metagenomics data obtained from all individuals and annotated at the species level.
Results
A very high level of C. albicans carriage was observed in both cohorts, with a prevalence of 95.2% and 83.1% in the first and second cohort, respectively. Yet, the quantity of C. albicans DNA detected varied greatly between subjects. The mycobiota composition was significantly altered by antibiotics and the fungal load was increased both at short and long term. Particularly, C. albicans abundance was increased but with wide inter-subject variations. A part of these variations was explained by changes in the levels of endogenous fecal β-lactamase activity, with subjects characterized by a low increase of β-lactamase activity displaying a higher increase of C. albicans levels. Finally, using shotgun metagenomics data, we identified a first set of 50 bacterial and archaeal species whose abundance inversely correlated with C. albicans abundance.
Conclusion
These results (1) bring a new understanding of C. albicans overgrowth in healthy individuals, (2) lead to the identification of microbial signatures with a potential key role in controlling C. albicans gut colonization, and finally (3) show for the first time that changes in endogenous fecal β-lactamase activity is a key factor for C. albicans overgrowth in the gut after antibiotic exposure. Taken together, these results open the way for new intervention strategies to curb C. albicans intestinal overgrowth.
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Affiliation(s)
- Margot Delavy
- Institut Pasteur , Université Paris Cité, Fungal Biology and Pathogenicity Unit, Paris , France
| | - Charles Burdet
- Université Paris Cité , IAME, INSERM, Paris , France
- Assistance Publique des Hôpitaux de Paris (APHP) , Hôpital Bichat, Departement of Epidemiology, Biostatistic and Clinical Research, Paris , France
| | - Natacha Sertour
- Institut Pasteur , Université Paris Cité, Fungal Biology and Pathogenicity Unit, Paris , France
| | | | | | - Stevenn Volant
- Institut Pasteur , Université de Paris, Bioinformatics and Biostatistics Hub, Paris , France
| | - Amine Ghozlane
- Institut Pasteur , Université de Paris, Bioinformatics and Biostatistics Hub, Paris , France
| | | | - Xavier Duval
- Université Paris Cité , IAME, INSERM, Paris , France
- INSERM Clinical Investigation Center 1425 , Paris , France
| | - France Mentré
- Université Paris Cité , IAME, INSERM, Paris , France
- Assistance Publique des Hôpitaux de Paris (APHP) , Hôpital Bichat, Departement of Epidemiology, Biostatistic and Clinical Research, Paris , France
| | - Darragh Duffy
- Institut Pasteur , Université Paris Cité, Immunobiology of Dendritic Cells laboratory, Paris , France
| | - Christophe D'Enfert
- Institut Pasteur , Université Paris Cité, Fungal Biology and Pathogenicity Unit, Paris , France
| | - Marie-Elisabeth Bougnoux
- Institut Pasteur , Université Paris Cité, Fungal Biology and Pathogenicity Unit, Paris , France
- Assistance Publique des Hôpitaux de Paris (APHP) , Hôpital Necker-Enfants-Malades, Service de Microbiologie Clinique, Unité de Parasitologie-Mycologie, Paris , France
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9
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Dargél AA, Mosconi E, Volant S, Taieb D, Brenot P. Sexual dysfunction among males and females with bipolar disorder and healthy subjects: The burden of illness severity. Bipolar Disord 2022; 24:637-646. [PMID: 36000440 DOI: 10.1111/bdi.13249] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVES Sexual dysfunction has wide-ranging impacts on the person's functioning and quality of life, being associated with higher severity of psychiatric illnesses and poor therapeutic response. Given the paucity of data on this topic in bipolar disorder (BD), we investigated sexual functioning among males and females with BD and healthy controls (HCs) as well as whether illness severity markers and subthreshold mood symptoms were associated with sexual dysfunctions in BD patients. METHODS The study included 80 BD outpatients and 70 HCs. Sexual functioning was evaluated using the validated, gender-specific Changes in Sexual Functioning Questionnaire (CSFQ-14). RESULTS BD patients had a significantly poorer sexual functioning than HCs (p < 0.00001). The odds of sexual dysfunction doubled given a one-unit increase in the number of suicide attempts (adjusted OR = 2.01, 95% CI:1.23-3.55; p < 0.01) and increased by 60% for every additional hospitalization (p < 0.05). Greater illness duration was associated with arousal/orgasmic (p < 0.05) and overall sexual dysfunctions (p < 0.01). BD patients with more mixed or (hypo)manic episodes had a lower likelihood of libido loss and arousal/orgasmic disturbances (p < 0.01), respectively. Higher levels of subthreshold depressive symptoms increased by 20% the odds of sexual interest/frequency dysfunctions (p < 0.05), and up to 60% regarding orgasmic disturbances (p < 0.01). CONCLUSIONS Sexual functioning may be a useful proxy of illness severity as well as a relevant dimension to more deeply characterize BD patients. Further studies are warranted to replicate our findings, to evaluate temporal associations between sexual dysfunctions and illness severity across the BD mood and treatment spectrums and to explore neurobiological underpinnings of these associations.
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Affiliation(s)
- Aroldo A Dargél
- Institut Pasteur, Unité Perception et Mémoire, Paris, France.,Centre National de la Recherche Scientifique, Unité Mixte de Recherche, Paris, France
| | - Elise Mosconi
- Centre d'étude de la Sexologie et de la Sexualité Humaine, Université Paris 5-René Descartes, Paris, France
| | - Stevenn Volant
- Hub de Bioinformatique, Biostatistique et Biologie Intégrative, Institut Pasteur, Paris, France
| | - David Taieb
- Centre d'étude de la Sexologie et de la Sexualité Humaine, Université Paris 5-René Descartes, Paris, France
| | - Philippe Brenot
- Centre d'étude de la Sexologie et de la Sexualité Humaine, Université Paris 5-René Descartes, Paris, France
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10
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Perdomo-Celis F, Passaes C, Monceaux V, Volant S, Boufassa F, de Truchis P, Marcou M, Bourdic K, Weiss L, Jung C, Bourgeois C, Goujard C, Meyer L, Müller-Trutwin M, Lambotte O, Sáez-Cirión A. Reprogramming dysfunctional CD8+ T cells to promote properties associated with natural HIV control. J Clin Invest 2022; 132:e157549. [PMID: 35380989 PMCID: PMC9151687 DOI: 10.1172/jci157549] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [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: 12/13/2021] [Accepted: 03/29/2022] [Indexed: 01/21/2023] Open
Abstract
Virus-specific CD8+ T cells play a central role in HIV-1 natural controllers to maintain suppressed viremia in the absence of antiretroviral therapy. These cells display a memory program that confers them stemness properties, high survival, polyfunctionality, proliferative capacity, metabolic plasticity, and antiviral potential. The development and maintenance of such qualities by memory CD8+ T cells appear crucial to achieving natural HIV-1 control. Here, we show that targeting the signaling pathways Wnt/transcription factor T cell factor 1 (Wnt/TCF-1) and mTORC through GSK3 inhibition to reprogram HIV-specific CD8+ T cells from noncontrollers promoted functional capacities associated with natural control of infection. Features of such reprogrammed cells included enrichment in TCF-1+ less-differentiated subsets, a superior response to antigen, enhanced survival, polyfunctionality, metabolic plasticity, less mTORC1 dependency, an improved response to γ-chain cytokines, and a stronger HIV-suppressive capacity. Thus, such CD8+ T cell reprogramming, combined with other available immunomodulators, might represent a promising strategy for adoptive cell therapy in the search for an HIV-1 cure.
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Affiliation(s)
- Federico Perdomo-Celis
- Institut Pasteur, Université Paris Cité, Unité HIV Inflammation et Persistance, Paris, France
| | - Caroline Passaes
- Institut Pasteur, Université Paris Cité, Unité HIV Inflammation et Persistance, Paris, France
| | - Valérie Monceaux
- Institut Pasteur, Université Paris Cité, Unité HIV Inflammation et Persistance, Paris, France
| | - Stevenn Volant
- Institut Pasteur, Université Paris Cité, Hub Bioinformatique et Biostatistique, Paris, France
| | - Faroudy Boufassa
- Université Paris Saclay, INSERM Centre de Recherche en Épidémiologie et Santé des Populations (CESP) U1018, Assistance Publique–Hôpitaux de Paris (AP-HP), Department of Public Health, Bicêtre Hospital, Paris, France
| | - Pierre de Truchis
- Université Paris-Saclay, AP-HP Hôpital Raymond Poincaré, Garches, France
| | - Morgane Marcou
- Université Paris-Saclay, AP-HP Hôpital Raymond Poincaré, Garches, France
| | - Katia Bourdic
- Université Paris-Saclay, AP-HP, Bicêtre Hospital, UMR1184 INSERM Commissariat à l’énergie atomique et aux énergies alternatives (CEA), Le Kremlin Bicêtre, France
| | - Laurence Weiss
- Université de Paris Cité, AP-HP, Paris Centre, Hôtel Dieu, Paris, France
| | - Corinne Jung
- Université de Paris Cité, AP-HP, Paris Centre, Hôtel Dieu, Paris, France
| | - Christine Bourgeois
- Université Paris-Saclay, AP-HP, Bicêtre Hospital, UMR1184 INSERM Commissariat à l’énergie atomique et aux énergies alternatives (CEA), Le Kremlin Bicêtre, France
| | - Cécile Goujard
- Université Paris-Saclay, AP-HP, Hôpital Bicêtre, Départements Médico-Universitaires (DMU) 7, INSERM U1018, CESP, Le Kremlin Bicêtre, France
| | - Laurence Meyer
- Université Paris Saclay, INSERM Centre de Recherche en Épidémiologie et Santé des Populations (CESP) U1018, Assistance Publique–Hôpitaux de Paris (AP-HP), Department of Public Health, Bicêtre Hospital, Paris, France
| | - Michaela Müller-Trutwin
- Institut Pasteur, Université Paris Cité, Unité HIV Inflammation et Persistance, Paris, France
| | - Olivier Lambotte
- Université Paris-Saclay, AP-HP, Bicêtre Hospital, UMR1184 INSERM Commissariat à l’énergie atomique et aux énergies alternatives (CEA), Le Kremlin Bicêtre, France
| | - Asier Sáez-Cirión
- Institut Pasteur, Université Paris Cité, Unité HIV Inflammation et Persistance, Paris, France
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11
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Snelders E, Moyrand F, Sturny-Leclère A, Vernel-Pauillac F, Volant S, Janbon G, Alanio A. The role of glycosylphosphatidylinositol (gpi) anchored proteins in Cryptococcus neoformans. Microbes Infect 2022; 24:105016. [DOI: 10.1016/j.micinf.2022.105016] [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] [Received: 02/01/2022] [Revised: 04/25/2022] [Accepted: 05/20/2022] [Indexed: 10/31/2022]
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12
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Claireaux M, Robinot R, Kervevan J, Patgaonkar M, Staropoli I, Brelot A, Nouël A, Gellenoncourt S, Tang X, Héry M, Volant S, Perthame E, Avettand-Fenoël V, Buchrieser J, Cokelaer T, Bouchier C, Ma L, Boufassa F, Hendou S, Libri V, Hasan M, Zucman D, de Truchis P, Schwartz O, Lambotte O, Chakrabarti LA. Low CCR5 expression protects HIV-specific CD4+ T cells of elite controllers from viral entry. Nat Commun 2022; 13:521. [PMID: 35082297 PMCID: PMC8792008 DOI: 10.1038/s41467-022-28130-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 01/10/2022] [Indexed: 11/09/2022] Open
Abstract
HIV elite controllers maintain a population of CD4 + T cells endowed with high avidity for Gag antigens and potent effector functions. How these HIV-specific cells avoid infection and depletion upon encounter with the virus remains incompletely understood. Ex vivo characterization of single Gag-specific CD4 + T cells reveals an advanced Th1 differentiation pattern in controllers, except for the CCR5 marker, which is downregulated compared to specific cells of treated patients. Accordingly, controller specific CD4 + T cells show decreased susceptibility to CCR5-dependent HIV entry. Two controllers carried biallelic mutations impairing CCR5 surface expression, indicating that in rare cases CCR5 downregulation can have a direct genetic cause. Increased expression of β-chemokine ligands upon high-avidity antigen/TCR interactions contributes to autocrine CCR5 downregulation in controllers without CCR5 mutations. These findings suggest that genetic and functional regulation of the primary HIV coreceptor CCR5 play a key role in promoting natural HIV control.
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Affiliation(s)
- Mathieu Claireaux
- Virus and Immunity Unit, Institut Pasteur, Université de Paris, Paris, France.,CNRS UMR3569, Paris, France
| | - Rémy Robinot
- Virus and Immunity Unit, Institut Pasteur, Université de Paris, Paris, France.,CNRS UMR3569, Paris, France
| | - Jérôme Kervevan
- Virus and Immunity Unit, Institut Pasteur, Université de Paris, Paris, France.,CNRS UMR3569, Paris, France
| | - Mandar Patgaonkar
- Virus and Immunity Unit, Institut Pasteur, Université de Paris, Paris, France.,CNRS UMR3569, Paris, France
| | - Isabelle Staropoli
- Virus and Immunity Unit, Institut Pasteur, Université de Paris, Paris, France.,CNRS UMR3569, Paris, France
| | - Anne Brelot
- Virus and Immunity Unit, Institut Pasteur, Université de Paris, Paris, France.,CNRS UMR3569, Paris, France
| | - Alexandre Nouël
- Virus and Immunity Unit, Institut Pasteur, Université de Paris, Paris, France.,CNRS UMR3569, Paris, France
| | - Stacy Gellenoncourt
- Virus and Immunity Unit, Institut Pasteur, Université de Paris, Paris, France.,CNRS UMR3569, Paris, France
| | - Xian Tang
- Virus and Immunity Unit, Institut Pasteur, Université de Paris, Paris, France.,CNRS UMR3569, Paris, France
| | - Mélanie Héry
- Virus and Immunity Unit, Institut Pasteur, Université de Paris, Paris, France.,CNRS UMR3569, Paris, France
| | - Stevenn Volant
- Bioinformatics and Biostatistics Hub, Department of Computational Biology, Institut Pasteur, Université de Paris, Paris, France
| | - Emeline Perthame
- Bioinformatics and Biostatistics Hub, Department of Computational Biology, Institut Pasteur, Université de Paris, Paris, France
| | - Véronique Avettand-Fenoël
- AP-HP Hôpital Necker-Enfants Malades, Laboratoire de Microbiologie clinique, Paris, France.,CNRS 8104, INSERM U1016, Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine, Paris, France
| | - Julian Buchrieser
- Virus and Immunity Unit, Institut Pasteur, Université de Paris, Paris, France.,CNRS UMR3569, Paris, France
| | - Thomas Cokelaer
- Bioinformatics and Biostatistics Hub, Department of Computational Biology, Institut Pasteur, Université de Paris, Paris, France.,Biomics Platform, C2RT, Institut Pasteur, Université de Paris, Paris, France
| | - Christiane Bouchier
- Biomics Platform, C2RT, Institut Pasteur, Université de Paris, Paris, France
| | - Laurence Ma
- Biomics Platform, C2RT, Institut Pasteur, Université de Paris, Paris, France
| | - Faroudy Boufassa
- INSERM U1018, Center for Research in Epidemiology and Population Health (CESP), Le Kremlin-Bicêtre, France
| | - Samia Hendou
- INSERM U1018, Center for Research in Epidemiology and Population Health (CESP), Le Kremlin-Bicêtre, France
| | - Valentina Libri
- Cytometry and Biomarkers (CB UTechS), Translational Research Center, Institut Pasteur, Université de Paris, Paris, France
| | - Milena Hasan
- Cytometry and Biomarkers (CB UTechS), Translational Research Center, Institut Pasteur, Université de Paris, Paris, France
| | | | - Pierre de Truchis
- AP-HP, Infectious and Tropical Diseases Department, Raymond Poincaré Hospital, Garches, France
| | - Olivier Schwartz
- Virus and Immunity Unit, Institut Pasteur, Université de Paris, Paris, France.,CNRS UMR3569, Paris, France
| | - Olivier Lambotte
- INSERM U1184, Université Paris Sud, CEA, Center for Immunology of Viral Infections and Autoimmune Diseases, Le Kremlin-Bicêtre, France.,AP-HP, Department of Internal Medicine and Clinical Immunology, University Hospital Paris Sud, Le Kremlin-Bicêtre, France
| | - Lisa A Chakrabarti
- Virus and Immunity Unit, Institut Pasteur, Université de Paris, Paris, France. .,CNRS UMR3569, Paris, France.
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13
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Dargél AA, Volant S, Brietzke E, Etain B, Olié E, Azorin JM, Gard S, Bellivier F, Bougerol T, Kahn JP, Roux P, Aubin V, Courtet P, Leboyer M, Henry C. Allostatic load, emotional hyper-reactivity, and functioning in individuals with bipolar disorder. Bipolar Disord 2020; 22:711-721. [PMID: 32415900 DOI: 10.1111/bdi.12927] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
OBJECTIVES Diagnosis and management of bipolar disorder (BD) are limited by the absence of available biomarkers. Allostatic load (AL) represents the strain that stress, including the effects of acute phases and inter-episode chronic mood instability, exerts on interconnected biological systems. This study aimed to operationalize an AL index and explore whether it could be relevant to better characterize BD patients with and without emotional hyper-reactivity particularly those at higher risk of immune-cardiometabolic dysregulation and functional impairment. METHODS Levels of biomarkers of chronic inflammation (hsCRP and albumin), cardiovascular (systolic/diastolic blood pressure) and metabolic functions (fasting glucose, glycosylated hemoglobin, total cholesterol, LDL, HDL, and triglycerides) were measured in 1072 adult BD outpatients. Patients were classified in two groups (with/without emotional hyper-reactivity) assessed by the Multidimensional Assessment of Thymic States scale. An Allostatic Load Index for BD (BALLI), comprising six biomarkers, was constructed using data-driven biomarker selection. RESULTS BALLI showed 81.1% accuracy with good sensitivity (81%) and specificity (81.2%) for characterizing BD patients presenting emotional hyper-reactivity, elevated risk of inflammation (increased hsCRP, hypoalbuminemia) and cardiometabolic disturbances (hypertension, hyperglycemia, and hypertriglyceridemia). Patients classified by the BALLI as presenting emotional hyper-reactivity had significantly lower global and cognitive functioning than those without emotional hyper-reactivity (P < .0001). CONCLUSIONS A multidimensional approach based on a simple AL score (eg, BALLI) and dimensions of behavior (eg, emotional hyper-reactivity) alongside mood is clinically relevant. AL index could be a useful tool to detect multisystemic physiological dysregulations in BD patients with/without emotional hyper-reactivity particularly those at higher risk of immune-cardiometabolic disturbances and functional impairment.
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Affiliation(s)
- Aroldo A Dargél
- Institut Pasteur, Unité Perception et Mémoire, Paris, France.,Centre National de la Recherche Scientifique, Unité Mixte de Recherche 3571, Paris, France
| | - Stevenn Volant
- Institut Pasteur, Bioinformatics and Biostatistics Hub (C3BI), Paris, France
| | - Elisa Brietzke
- Department of Psychiatry, Providence Care Hospital, Queen's University, Kingston, Canada
| | - Bruno Etain
- Fondation FondaMental, Fondation de Coopération Scientifique, Créteil, France.,AP-HP, GH Saint-Louis - Lariboisière - Fernand Widal, Pôle Neurosciences Tête et Cou, Université de Paris, Paris, France
| | - Emilie Olié
- Fondation FondaMental, Fondation de Coopération Scientifique, Créteil, France.,Department of Emergency Psychiatry and Acute Care, CHU Montpellier, Montpellier University, Montpellier, France
| | - Jean-Michel Azorin
- Fondation FondaMental, Fondation de Coopération Scientifique, Créteil, France.,Département de Psychiatrie, Hôpital Sainte-Marguerite, Marseille, France
| | - Sebastian Gard
- Fondation FondaMental, Fondation de Coopération Scientifique, Créteil, France.,Hôpital Charles-Perrens, Centre Expert Troubles Bipolaires, Bordeaux, France
| | - Frank Bellivier
- Fondation FondaMental, Fondation de Coopération Scientifique, Créteil, France.,AP-HP, GH Saint-Louis - Lariboisière - Fernand Widal, Pôle Neurosciences Tête et Cou, Université de Paris, Paris, France
| | - Thierry Bougerol
- Fondation FondaMental, Fondation de Coopération Scientifique, Créteil, France.,Université Grenoble Alpes, CHU de Grenoble et des Alpes, Grenoble Institut des Neurosciences (GIN), Grenoble, France
| | - Jean-Pierre Kahn
- Fondation FondaMental, Fondation de Coopération Scientifique, Créteil, France.,Centre Hospitalier Universitaire de Nancy - Hôpitaux de Brabois, Université de Lorraine, Nancy, France
| | - Paul Roux
- Fondation FondaMental, Fondation de Coopération Scientifique, Créteil, France.,Department of Adult Psychiatry, Versailles Hospital, Le Chesnay, France.,EA4047, University of Versailles Saint-Quentin-En-Yvelines, Montigny-le-Bretonneux, France
| | - Valerie Aubin
- Fondation FondaMental, Fondation de Coopération Scientifique, Créteil, France.,Pôle de Psychiatrie, Centre Hospitalier Princesse Grace, Monaco, France
| | - Philippe Courtet
- Fondation FondaMental, Fondation de Coopération Scientifique, Créteil, France.,Department of Emergency Psychiatry and Acute Care, CHU Montpellier, Montpellier University, Montpellier, France
| | - Marion Leboyer
- Fondation FondaMental, Fondation de Coopération Scientifique, Créteil, France.,AP-HP, Hôpital H. Mondor - A. Chenevier, Créteil, France.,Université Paris-Est, Créteil, France
| | - Chantal Henry
- Institut Pasteur, Unité Perception et Mémoire, Paris, France.,Fondation FondaMental, Fondation de Coopération Scientifique, Créteil, France.,AP-HP, Hôpital H. Mondor - A. Chenevier, Créteil, France.,Université Paris-Est, Créteil, France
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14
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Stressmann FA, Bernal-Bayard J, Perez-Pascual D, Audrain B, Rendueles O, Briolat V, Bruchmann S, Volant S, Ghozlane A, Häussler S, Duchaud E, Levraud JP, Ghigo JM. Mining zebrafish microbiota reveals key community-level resistance against fish pathogen infection. ISME J 2020; 15:702-719. [PMID: 33077888 DOI: 10.1038/s41396-020-00807-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 09/30/2020] [Accepted: 10/05/2020] [Indexed: 02/08/2023]
Abstract
The long-known resistance to pathogens provided by host-associated microbiota fostered the notion that adding protective bacteria could prevent or attenuate infection. However, the identification of endogenous or exogenous bacteria conferring such protection is often hindered by the complexity of host microbial communities. Here, we used zebrafish and the fish pathogen Flavobacterium columnare as a model system to study the determinants of microbiota-associated colonization resistance. We compared infection susceptibility in germ-free, conventional and reconventionalized larvae and showed that a consortium of 10 culturable bacterial species are sufficient to protect zebrafish. Whereas survival to F. columnare infection does not rely on host innate immunity, we used antibiotic dysbiosis to alter zebrafish microbiota composition, leading to the identification of two different protection strategies. We first identified that the bacterium Chryseobacterium massiliae individually protects both larvae and adult zebrafish. We also showed that an assembly of 9 endogenous zebrafish species that do not otherwise protect individually confer a community-level resistance to infection. Our study therefore provides a rational approach to identify key endogenous protecting bacteria and promising candidates to engineer resilient microbial communities. It also shows how direct experimental analysis of colonization resistance in low-complexity in vivo models can reveal unsuspected ecological strategies at play in microbiota-based protection against pathogens.
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Affiliation(s)
- Franziska A Stressmann
- Genetics of Biofilms Laboratory, Institut Pasteur, UMR CNRS2001, 75015, Paris, France.,Department of Chemical Analytics and Biogeochemistry, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 310, 12587, Berlin, Germany
| | - Joaquín Bernal-Bayard
- Genetics of Biofilms Laboratory, Institut Pasteur, UMR CNRS2001, 75015, Paris, France.,Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Apartado 1095, 41080, Sevilla, Spain
| | - David Perez-Pascual
- Genetics of Biofilms Laboratory, Institut Pasteur, UMR CNRS2001, 75015, Paris, France
| | - Bianca Audrain
- Genetics of Biofilms Laboratory, Institut Pasteur, UMR CNRS2001, 75015, Paris, France
| | - Olaya Rendueles
- Genetics of Biofilms Laboratory, Institut Pasteur, UMR CNRS2001, 75015, Paris, France.,Microbial Evolutionary Genomics Laboratory, Institut Pasteur, UMR3525, 75015, Paris, France
| | - Valérie Briolat
- Macrophages and Development of Immunity Laboratory, Institut Pasteur, UMR3738 CNRS, 75015, Paris, France
| | - Sebastian Bruchmann
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK
| | - Stevenn Volant
- Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, Paris, France
| | - Amine Ghozlane
- Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, Paris, France
| | - Susanne Häussler
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Department of Clinical Microbiology, Rigshospitalet, 2100, Copenhagen, Denmark
| | - Eric Duchaud
- Unité VIM, INRAE, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Jean-Pierre Levraud
- Macrophages and Development of Immunity Laboratory, Institut Pasteur, UMR3738 CNRS, 75015, Paris, France
| | - Jean-Marc Ghigo
- Genetics of Biofilms Laboratory, Institut Pasteur, UMR CNRS2001, 75015, Paris, France.
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15
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Volant S, Lechat P, Woringer P, Motreff L, Campagne P, Malabat C, Kennedy S, Ghozlane A. SHAMAN: a user-friendly website for metataxonomic analysis from raw reads to statistical analysis. BMC Bioinformatics 2020; 21:345. [PMID: 32778056 PMCID: PMC7430814 DOI: 10.1186/s12859-020-03666-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [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: 02/13/2020] [Accepted: 07/16/2020] [Indexed: 01/04/2023] Open
Abstract
Background Comparing the composition of microbial communities among groups of interest (e.g., patients vs healthy individuals) is a central aspect in microbiome research. It typically involves sequencing, data processing, statistical analysis and graphical display. Such an analysis is normally obtained by using a set of different applications that require specific expertise for installation, data processing and in some cases, programming skills. Results Here, we present SHAMAN, an interactive web application we developed in order to facilitate the use of (i) a bioinformatic workflow for metataxonomic analysis, (ii) a reliable statistical modelling and (iii) to provide the largest panel of interactive visualizations among the applications that are currently available. SHAMAN is specifically designed for non-expert users. A strong benefit is to use an integrated version of the different analytic steps underlying a proper metagenomic analysis. The application is freely accessible at http://shaman.pasteur.fr/, and may also work as a standalone application with a Docker container (aghozlane/shaman), conda and R. The source code is written in R and is available at https://github.com/aghozlane/shaman. Using two different datasets (a mock community sequencing and a published 16S rRNA metagenomic data), we illustrate the strengths of SHAMAN in quickly performing a complete metataxonomic analysis. Conclusions With SHAMAN, we aim at providing the scientific community with a platform that simplifies reproducible quantitative analysis of metagenomic data.
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Affiliation(s)
- Stevenn Volant
- Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, 28 Rue Du Docteur Roux, Paris, 75015, France
| | - Pierre Lechat
- Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, 28 Rue Du Docteur Roux, Paris, 75015, France
| | - Perrine Woringer
- Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, 28 Rue Du Docteur Roux, Paris, 75015, France
| | - Laurence Motreff
- Biomics - Département Génomes et Génétique, Institut Pasteur, 28 Rue du Docteur Roux, Paris, 75015, France
| | - Pascal Campagne
- Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, 28 Rue Du Docteur Roux, Paris, 75015, France
| | - Christophe Malabat
- Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, 28 Rue Du Docteur Roux, Paris, 75015, France
| | - Sean Kennedy
- Biomics - Département Génomes et Génétique, Institut Pasteur, 28 Rue du Docteur Roux, Paris, 75015, France
| | - Amine Ghozlane
- Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, 28 Rue Du Docteur Roux, Paris, 75015, France. .,Biomics - Département Génomes et Génétique, Institut Pasteur, 28 Rue du Docteur Roux, Paris, 75015, France.
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16
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Mikhailova A, Valle-Casuso JC, David A, Monceaux V, Volant S, Passaes C, Elfidha A, Müller-Trutwin M, Poyet JL, Sáez-Cirión A. Antiapoptotic Clone 11-Derived Peptides Induce In Vitro Death of CD4 + T Cells Susceptible to HIV-1 Infection. J Virol 2020; 94:e00611-20. [PMID: 32350074 PMCID: PMC7343195 DOI: 10.1128/jvi.00611-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 04/06/2020] [Accepted: 04/23/2020] [Indexed: 02/08/2023] Open
Abstract
HIV-1 successfully establishes long-term infection in its target cells despite viral cytotoxic effects. We have recently shown that cell metabolism is an important factor driving CD4+ T cell susceptibility to HIV-1 and the survival of infected cells. We show here that expression of antiapoptotic clone 11 (AAC-11), an antiapoptotic factor upregulated in many cancers, increased with progressive CD4+ T cell memory differentiation in association with the expression of cell cycle, activation, and metabolism genes and was correlated with susceptibility to HIV-1 infection. Synthetic peptides based on the LZ domain sequence of AAC-11, responsible for its interaction with molecular partners, were previously shown to be cytotoxic to cancer cells. Here, we observed that these peptides also blocked HIV-1 infection by inducing the death of HIV-1-susceptible primary CD4+ T cells across all T cell subsets. The peptides targeted metabolically active cells and had the greatest effect on effector and transitional CD4+ T cell memory subsets. Our results suggest that the AAC-11 survival pathway is potentially involved in the survival of HIV-1-infectible cells and provide proof of principle that some cellular characteristics can be targeted to eliminate the cells offering the best conditions to sustain HIV-1 replication.IMPORTANCE Although antiretroviral treatment efficiently blocks HIV multiplication, it cannot eliminate cells already carrying integrated proviruses. In the search for an HIV cure, the identification of new potential targets to selectively eliminate infected cells is of the outmost importance. We show here that peptides derived from antiapoptotic clone 11 (AAC-11), whose expression levels correlated with susceptibility to HIV-1 infection of CD4+ T cells, induced cytotoxicity in CD4+ T cells showing the highest levels of activation and metabolic activity, conditions known to favor HIV-1 infection. Accordingly, CD4+ T cells that survived the cytotoxic action of the AAC-11 peptides were resistant to HIV-1 replication. Our results identify a new potential molecular pathway to target HIV-1 infection.
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Affiliation(s)
- Anastassia Mikhailova
- Institut Pasteur, Unité HIV Inflammation et Persistance, Paris, France
- Université Paris Diderot, Université de Paris, Paris, France
| | | | - Annie David
- Institut Pasteur, Unité HIV Inflammation et Persistance, Paris, France
| | - Valérie Monceaux
- Institut Pasteur, Unité HIV Inflammation et Persistance, Paris, France
| | - Stevenn Volant
- Institut Pasteur, Hub Bioinformatique et Biostatistique, C3BI, USR 3756 IP CNRS, Paris, France
| | - Caroline Passaes
- Institut Pasteur, Unité HIV Inflammation et Persistance, Paris, France
| | - Amal Elfidha
- Institut Pasteur, Unité HIV Inflammation et Persistance, Paris, France
- Université Paris Descartes, Université de Paris, Paris, France
| | | | - Jean-Luc Poyet
- INSERM UMRS976, Institut de Recherche Saint Louis, Hôpital Saint Louis, Paris, France
| | - Asier Sáez-Cirión
- Institut Pasteur, Unité HIV Inflammation et Persistance, Paris, France
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17
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Mitri C, Bischoff E, Belda Cuesta E, Volant S, Ghozlane A, Eiglmeier K, Holm I, Dieme C, Brito-Fravallo E, Guelbeogo WM, Sagnon N, Riehle MM, Vernick KD. Leucine-Rich Immune Factor APL1 Is Associated With Specific Modulation of Enteric Microbiome Taxa in the Asian Malaria Mosquito Anopheles stephensi. Front Microbiol 2020; 11:306. [PMID: 32174902 PMCID: PMC7054466 DOI: 10.3389/fmicb.2020.00306] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 10/29/2019] [Accepted: 02/11/2020] [Indexed: 01/14/2023] Open
Abstract
The commensal gut microbiome is contained by the enteric epithelial barrier, but little is known about the degree of specificity of host immune barrier interactions for particular bacterial taxa. Here, we show that depletion of leucine-rich repeat immune factor APL1 in the Asian malaria mosquito Anopheles stephensi is associated with higher midgut abundance of just the family Enterobacteraceae, and not generalized dysbiosis of the microbiome. The effect is explained by the response of a narrow clade containing two main taxa related to Klebsiella and Cedecea. Analysis of field samples indicate that these two taxa are recurrent members of the wild Anopheles microbiome. Triangulation using sequence and functional data incriminated relatives of C. neteri and Cedecea NFIX57 as candidates for the Cedecea component, and K. michiganensis, K. oxytoca, and K.sp. LTGPAF-6F as candidates for the Klebsiella component. APL1 presence is associated with host ability to specifically constrain the abundance of a narrow microbiome clade of the Enterobacteraceae, and the immune factor may promote homeostasis of this clade in the enteric microbiome for host benefit.
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Affiliation(s)
- Christian Mitri
- Unit of Insect Vector Genetics and Genomics, Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France
- CNRS Unit of Evolutionary Genomics, Modeling, and Health (UMR2000), Institut Pasteur, Paris, France
| | - Emmanuel Bischoff
- Unit of Insect Vector Genetics and Genomics, Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France
- CNRS Unit of Evolutionary Genomics, Modeling, and Health (UMR2000), Institut Pasteur, Paris, France
| | - Eugeni Belda Cuesta
- Integromics Unit, Institute of Cardiometabolism and Nutrition, Assistance Publique Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Paris, France
| | - Stevenn Volant
- Bioinformatics and Biostatistics Hub, Department of Computational Biology, Institut Pasteur, Paris, France
- CNRS USR 3756, Institut Pasteur, Paris, France
| | - Amine Ghozlane
- Bioinformatics and Biostatistics Hub, Department of Computational Biology, Institut Pasteur, Paris, France
- CNRS USR 3756, Institut Pasteur, Paris, France
| | - Karin Eiglmeier
- Unit of Insect Vector Genetics and Genomics, Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France
- CNRS Unit of Evolutionary Genomics, Modeling, and Health (UMR2000), Institut Pasteur, Paris, France
| | - Inge Holm
- Unit of Insect Vector Genetics and Genomics, Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France
- CNRS Unit of Evolutionary Genomics, Modeling, and Health (UMR2000), Institut Pasteur, Paris, France
| | - Constentin Dieme
- Unit of Insect Vector Genetics and Genomics, Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France
- CNRS Unit of Evolutionary Genomics, Modeling, and Health (UMR2000), Institut Pasteur, Paris, France
| | - Emma Brito-Fravallo
- Unit of Insect Vector Genetics and Genomics, Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France
- CNRS Unit of Evolutionary Genomics, Modeling, and Health (UMR2000), Institut Pasteur, Paris, France
| | - Wamdaogo M. Guelbeogo
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - N’Fale Sagnon
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Michelle M. Riehle
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Kenneth D. Vernick
- Unit of Insect Vector Genetics and Genomics, Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France
- CNRS Unit of Evolutionary Genomics, Modeling, and Health (UMR2000), Institut Pasteur, Paris, France
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18
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Hommel B, Sturny-Leclère A, Volant S, Veluppillai N, Duchateau M, Yu CH, Hourdel V, Varet H, Matondo M, Perfect JR, Casadevall A, Dromer F, Alanio A. Correction: Cryptococcus neoformans resists to drastic conditions by switching to viable but non-culturable cell phenotype. PLoS Pathog 2019; 15:e1008070. [PMID: 31527911 PMCID: PMC6748408 DOI: 10.1371/journal.ppat.1008070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
[This corrects the article DOI: 10.1371/journal.ppat.1007945.].
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19
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Hommel B, Sturny-Leclère A, Volant S, Veluppillai N, Duchateau M, Yu CH, Hourdel V, Varet H, Matondo M, Perfect JR, Casadevall A, Dromer F, Alanio A. Cryptococcus neoformans resists to drastic conditions by switching to viable but non-culturable cell phenotype. PLoS Pathog 2019; 15:e1007945. [PMID: 31356623 PMCID: PMC6687208 DOI: 10.1371/journal.ppat.1007945] [Citation(s) in RCA: 21] [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: 03/05/2019] [Revised: 08/08/2019] [Accepted: 06/27/2019] [Indexed: 01/22/2023] Open
Abstract
Metabolically quiescent pathogens can persist in a viable non-replicating state for months or even years. For certain infectious diseases, such as tuberculosis, cryptococcosis, histoplasmosis, latent infection is a corollary of this dormant state, which has the risk for reactivation and clinical disease. During murine cryptococcosis and macrophage uptake, stress and host immunity induce Cryptococcus neoformans heterogeneity with the generation of a sub-population of yeasts that manifests a phenotype compatible with dormancy (low stress response, latency of growth). In this subpopulation, mitochondrial transcriptional activity is regulated and this phenotype has been considered as a hallmark of quiescence in stem cells. Based on these findings, we worked to reproduce this phenotype in vitro and then standardize the experimental conditions to consistently generate this dormancy in C. neoformans. We found that incubation of stationary phase yeasts (STAT) in nutriment limited conditions and hypoxia for 8 days (8D-HYPOx) was able to produced cells that mimic the phenotype obtained in vivo. In these conditions, mortality and/or apoptosis occurred in less than 5% of the yeasts compared to 30-40% of apoptotic or dead yeasts upon incubation in normoxia (8D-NORMOx). Yeasts in 8D-HYPOx harbored a lower stress response, delayed growth and less that 1% of culturability on agar plates, suggesting that these yeasts are viable but non culturable cells (VBNC). These VBNC were able to reactivate in the presence of pantothenic acid, a vitamin that is known to be involved in quorum sensing and a precursor of acetyl-CoA. Global metabolism of 8D-HYPOx cells showed some specific requirements and was globally shut down compared to 8D-NORMOx and STAT conditions. Mitochondrial analyses showed that the mitochondrial mass increased with mitochondria mostly depolarized in 8D-HYPOx compared to 8D-NORMox, with increased expression of mitochondrial genes. Proteomic and transcriptomic analyses of 8D-HYPOx revealed that the number of secreted proteins and transcripts detected also decreased compared to 8D-NORMOx and STAT, and the proteome, secretome and transcriptome harbored specific profiles that are engaged as soon as four days of incubation. Importantly, acetyl-CoA and the fatty acid pathway involving mitochondria are required for the generation and viability maintenance of VBNC. Altogether, these data show that we were able to generate for the first time VBNC phenotype in C. neoformans. This VBNC state is associated with a specific metabolism that should be further studied to understand dormancy/quiescence in this yeast.
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Affiliation(s)
- Benjamin Hommel
- Institut Pasteur, CNRS, Molecular Mycology Unit, UMR2000, Paris, France
- Laboratoire de Parasitologie-Mycologie, Hôpital Saint-Louis, Groupe Hospitalier Lariboisière, Saint-Louis, Fernand Widal, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | | | - Stevenn Volant
- Institut Pasteur - Bioinformatics and Biostatistics Hub - C3BI, USR 3756 IP CNRS, Paris, France
| | | | - Magalie Duchateau
- Institut Pasteur, Unité de spectrométrie de masse et Protéomique, Paris, France
| | - Chen-Hsin Yu
- Division of Infectious Diseases, Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Véronique Hourdel
- Institut Pasteur, Unité de spectrométrie de masse et Protéomique, Paris, France
| | - Hugo Varet
- Institut Pasteur - Bioinformatics and Biostatistics Hub - C3BI, USR 3756 IP CNRS, Paris, France
- Institut Pasteur - Transcriptome and Epigenome Platform - Biomics Pole - C2RT, Paris, France
| | - Mariette Matondo
- Institut Pasteur, Unité de spectrométrie de masse et Protéomique, Paris, France
| | - John R. Perfect
- Division of Infectious Diseases, Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Arturo Casadevall
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Françoise Dromer
- Institut Pasteur, CNRS, Molecular Mycology Unit, UMR2000, Paris, France
| | - Alexandre Alanio
- Institut Pasteur, CNRS, Molecular Mycology Unit, UMR2000, Paris, France
- Laboratoire de Parasitologie-Mycologie, Hôpital Saint-Louis, Groupe Hospitalier Lariboisière, Saint-Louis, Fernand Widal, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
- * E-mail:
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20
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Angin M, Volant S, Passaes C, Lecuroux C, Monceaux V, Dillies MA, Valle-Casuso JC, Pancino G, Vaslin B, Le Grand R, Weiss L, Goujard C, Meyer L, Boufassa F, Müller-Trutwin M, Lambotte O, Sáez-Cirión A. Metabolic plasticity of HIV-specific CD8 + T cells is associated with enhanced antiviral potential and natural control of HIV-1 infection. Nat Metab 2019; 1:704-716. [PMID: 32694646 DOI: 10.1038/s42255-019-0081-4] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 06/05/2019] [Indexed: 12/27/2022]
Abstract
Spontaneous control of human immunodeficiency virus (HIV) is generally associated with an enhanced capacity of CD8+ T cells to eliminate infected CD4+ T cells, but the molecular characteristics of these highly functional CD8+ T cells are largely unknown. In the present study, using single-cell analysis, it was shown that HIV-specific, central memory CD8+ T cells from spontaneous HIV controllers (HICs) and antiretrovirally treated non-controllers have opposing transcriptomic profiles. Genes linked to effector functions and survival are upregulated in cells from HICs. In contrast, genes associated with activation, exhaustion and glycolysis are upregulated in cells from non-controllers. It was shown that HIV-specific CD8+ T cells from non-controllers are largely glucose dependent, whereas those from HICs have more diverse metabolic resources that enhance both their survival potential and their capacity to develop anti-HIV effector functions. The functional efficiency of the HIV-specific CD8+ T cell response in HICs is thus engraved in their memory population and related to their metabolic programme. Metabolic reprogramming in vitro through interleukin-15 treatment abrogated the glucose dependency and enhanced the antiviral potency of HIV-specific CD8+ T cells from non-controllers.
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Affiliation(s)
- Mathieu Angin
- Institut Pasteur, Unité HIV Inflammation et Persistance, Paris, France
| | - Stevenn Volant
- Institut Pasteur, Hub Bioinformatique et Biostatistique, Paris, France
| | - Caroline Passaes
- Institut Pasteur, Unité HIV Inflammation et Persistance, Paris, France
| | - Camille Lecuroux
- CEA, Immunology of Viral Infections and Autoimmune Diseases, IDMIT Department/IBFJ, Université Paris Sud, Fontenay-aux-Roses, France
| | - Valérie Monceaux
- Institut Pasteur, Unité HIV Inflammation et Persistance, Paris, France
| | | | | | | | - Bruno Vaslin
- CEA, Immunology of Viral Infections and Autoimmune Diseases, IDMIT Department/IBFJ, Université Paris Sud, Fontenay-aux-Roses, France
| | - Roger Le Grand
- CEA, Immunology of Viral Infections and Autoimmune Diseases, IDMIT Department/IBFJ, Université Paris Sud, Fontenay-aux-Roses, France
| | - Laurence Weiss
- Assistance Publique Hôpitaux de Paris, Hôpital Européen Georges Pompidou, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Cecile Goujard
- Assistance Publique Hôpitaux de Paris, Hôpital Bicêtre, Service de Médecine Interne et Immunologie Clinique, Le Kremlin-Bicêtre, France
| | - Laurence Meyer
- Centre de Recherche en Epidémiologie et Santé des Populations, Université Paris Sud, Le Kremlin-Bicêtre, France
| | - Faroudy Boufassa
- Centre de Recherche en Epidémiologie et Santé des Populations, Université Paris Sud, Le Kremlin-Bicêtre, France
| | | | - Olivier Lambotte
- CEA, Immunology of Viral Infections and Autoimmune Diseases, IDMIT Department/IBFJ, Université Paris Sud, Fontenay-aux-Roses, France
- Assistance Publique Hôpitaux de Paris, Hôpital Bicêtre, Service de Médecine Interne et Immunologie Clinique, Le Kremlin-Bicêtre, France
| | - Asier Sáez-Cirión
- Institut Pasteur, Unité HIV Inflammation et Persistance, Paris, France.
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21
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Dargél AA, Volant S, Saha S, Etain B, Grant R, Azorin JM, Gard S, Bellivier F, Bougerol T, Kahn JP, Roux P, Aubin V, Courtet P, Leboyer M, Scott J, Henry C. Activation Levels, Cardiovascular Risk, and Functional Impairment in Remitted Bipolar Patients: Clinical Relevance of a Dimensional Approach. Psychother Psychosom 2019; 88:45-47. [PMID: 30308490 DOI: 10.1159/000493690] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 09/11/2018] [Indexed: 11/19/2022]
Affiliation(s)
- Aroldo A Dargél
- Unité Perception et Mémoire, Centre National de la Recherche Scientifique, Institut Pasteur, Paris, France.,Centre Thérapeutique et Préventif de Jour Troubles Bipolaires, Clinique Bellevue, Meudon, France
| | - Stevenn Volant
- Bioinformatics and Biostatistics Hub (C3BI), USR 3756 IP CNRS, Institut Pasteur, Paris, France
| | - Soham Saha
- Unité Perception et Mémoire, Centre National de la Recherche Scientifique, Institut Pasteur, Paris, France
| | - Bruno Etain
- Fondation FondaMental, Fondation de Cooperation Scientifique, Créteil, France.,AP-HP, GH Saint-Louis - Lariboisière - Fernand Widal, Pôle Neurosciences Tête et Cou, INSERM UMRS 1144, University Paris Diderot, Paris, France
| | - Rebecca Grant
- Center for Global Health (CGH), Institut Pasteur, Paris, France
| | - Jean-Michel Azorin
- Fondation FondaMental, Fondation de Cooperation Scientifique, Créteil, France.,Département de Psychiatrie, Hôpital Sainte-Marguerite, Marseille, France
| | - Sebastian Gard
- Fondation FondaMental, Fondation de Cooperation Scientifique, Créteil, France.,Centre Expert Troubles Bipolaires, Service de Psychiatrie Adulte, Hôpital Charles-Perrens, Bordeaux, France
| | - Frank Bellivier
- Fondation FondaMental, Fondation de Cooperation Scientifique, Créteil, France.,AP-HP, GH Saint-Louis - Lariboisière - Fernand Widal, Pôle Neurosciences Tête et Cou, INSERM UMRS 1144, University Paris Diderot, Paris, France
| | - Thierry Bougerol
- Fondation FondaMental, Fondation de Cooperation Scientifique, Créteil, France.,Université Grenoble Alpes, CHU de Grenoble et des Alpes, Grenoble Institut des Neurosciences (GIN) Inserm U 836, Grenoble, France
| | - Jean-Pierre Kahn
- Fondation FondaMental, Fondation de Cooperation Scientifique, Créteil, France.,Centre Hospitalier Universitaire de Nancy - Hôpitaux de Brabois, Université de Lorraine, Nancy, France
| | - Paul Roux
- Fondation FondaMental, Fondation de Cooperation Scientifique, Créteil, France.,Department of Adult Psychiatry, Versailles Hospital, Le Chesnay, France.,University of Versailles Saint-Quentin-En-Yvelines, Montigny-le-Bretonneux, France
| | - Valerie Aubin
- Fondation FondaMental, Fondation de Cooperation Scientifique, Créteil, France.,Pôle de Psychiatrie, Centre Hospitalier Princesse Grace, Monaco, France
| | - Philippe Courtet
- Fondation FondaMental, Fondation de Cooperation Scientifique, Créteil, France.,Department of Emergency Psychiatry and Acute Care, CHU Montpellier, INSERM U1061, Montpellier University, Montpellier, France
| | - Marion Leboyer
- Fondation FondaMental, Fondation de Cooperation Scientifique, Créteil, France.,Pôle de Psychiatrie, AP-HP, Hôpital H. Mondor - A. Chenevier, Créteil, France.,INSERM, U955, Université Paris-Est, Créteil, France
| | | | - Jan Scott
- Department of Academic Psychiatry, Institute of Neuroscience, Newcastle University, Newcastle, United Kingdom
| | - Chantal Henry
- Unité Perception et Mémoire, Centre National de la Recherche Scientifique, Institut Pasteur, Paris, .,Fondation FondaMental, Fondation de Cooperation Scientifique, Créteil, .,Pôle de Psychiatrie, AP-HP, Hôpital H. Mondor - A. Chenevier, Créteil, .,INSERM, U955, Université Paris-Est, Créteil,
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22
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Valle-Casuso JC, Angin M, Volant S, Passaes C, Monceaux V, Mikhailova A, Bourdic K, Avettand-Fenoel V, Boufassa F, Sitbon M, Lambotte O, Thoulouze MI, Müller-Trutwin M, Chomont N, Sáez-Cirión A. Cellular Metabolism Is a Major Determinant of HIV-1 Reservoir Seeding in CD4 + T Cells and Offers an Opportunity to Tackle Infection. Cell Metab 2019; 29:611-626.e5. [PMID: 30581119 DOI: 10.1016/j.cmet.2018.11.015] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 09/04/2018] [Accepted: 11/23/2018] [Indexed: 01/01/2023]
Abstract
HIV persists in long-lived infected cells that are not affected by antiretroviral treatment. These HIV reservoirs are mainly located in CD4+ T cells, but their distribution is variable in the different subsets. Susceptibility to HIV-1 increases with CD4+ T cell differentiation. We evaluated whether the metabolic programming that supports the differentiation and function of CD4+ T cells affected their susceptibility to HIV-1. We found that differences in HIV-1 susceptibility between naive and more differentiated subsets were associated with the metabolic activity of the cells. Indeed, HIV-1 selectively infected CD4+ T cells with high oxidative phosphorylation and glycolysis, independent of their activation phenotype. Moreover, partial inhibition of glycolysis (1) impaired HIV-1 infection in vitro in all CD4+ T cell subsets, (2) decreased the viability of preinfected cells, and (3) precluded HIV-1 amplification in cells from HIV-infected individuals. Our results elucidate the link between cell metabolism and HIV-1 infection and identify a vulnerability in tackling HIV reservoirs.
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Affiliation(s)
- José Carlos Valle-Casuso
- Institut Pasteur, Unité HIV Inflammation et Persistance, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Mathieu Angin
- Institut Pasteur, Unité HIV Inflammation et Persistance, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Stevenn Volant
- Institut Pasteur, Hub Bioinformatique et Biostatistique - C3BI, USR 3756 IP CNRS, Paris, France
| | - Caroline Passaes
- Institut Pasteur, Unité HIV Inflammation et Persistance, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Valérie Monceaux
- Institut Pasteur, Unité HIV Inflammation et Persistance, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Anastassia Mikhailova
- Institut Pasteur, Unité HIV Inflammation et Persistance, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Katia Bourdic
- Assistance Publique Hôpitaux de Paris, Hôpital Bicêtre, Service de Médecine Interne et Immunologie Clinique, 94275 Le Kremlin-Bicêtre, France
| | - Véronique Avettand-Fenoel
- Université Paris Descartes, Sorbonne Paris Cité, 7327 Paris, France; Assistance Publique Hôpitaux de Paris, Laboratoire de Virologie, CHU Necker-Enfants Malades, Paris, France
| | - Faroudy Boufassa
- INSERM U1018, Centre de Recherche en Epidémiologie et Santé des Populations, Université Paris Sud, Le Kremlin-Bicêtre, France
| | - Marc Sitbon
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Olivier Lambotte
- Assistance Publique Hôpitaux de Paris, Hôpital Bicêtre, Service de Médecine Interne et Immunologie Clinique, 94275 Le Kremlin-Bicêtre, France; CEA, Université Paris Sud, INSERM U1184, Center for Immunology of Viral Infections and Autoimmune Diseases (IMVA), IDMIT Department/IBFJ, Fontenay-aux-Roses, France
| | | | - Michaela Müller-Trutwin
- Institut Pasteur, Unité HIV Inflammation et Persistance, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Nicolas Chomont
- Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal H2X 0A9, Canada
| | - Asier Sáez-Cirión
- Institut Pasteur, Unité HIV Inflammation et Persistance, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France.
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23
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Dargél AA, Roussel F, Volant S, Etain B, Grant R, Azorin JM, M'Bailara K, Bellivier F, Bougerol T, Kahn JP, Roux P, Aubin V, Courtet P, Leboyer M, Kapczinski F, Henry C. Emotional hyper-reactivity and cardiometabolic risk in remitted bipolar patients: a machine learning approach. Acta Psychiatr Scand 2018; 138:348-359. [PMID: 29766490 DOI: 10.1111/acps.12901] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/25/2018] [Indexed: 01/08/2023]
Abstract
OBJECTIVE Remitted bipolar disorder (BD) patients frequently present with chronic mood instability and emotional hyper-reactivity, associated with poor psychosocial functioning and low-grade inflammation. We investigated emotional hyper-reactivity as a dimension for characterization of remitted BD patients, and clinical and biological factors for identifying those with and without emotional hyper-reactivity. METHOD A total of 635 adult remitted BD patients, evaluated in the French Network of Bipolar Expert Centers from 2010-2015, were assessed for emotional reactivity using the Multidimensional Assessment of Thymic States. Machine learning algorithms were used on clinical and biological variables to enhance characterization of patients. RESULTS After adjustment, patients with emotional hyper-reactivity (n = 306) had significantly higher levels of systolic and diastolic blood pressure (P < 1.0 × 10-8 ), high-sensitivity C-reactive protein (P < 1.0 × 10-8 ), fasting glucose (P < 2.23 × 10-6 ), glycated hemoglobin (P = 0.0008) and suicide attempts (P = 1.4 × 10-8 ). Using models of combined clinical and biological factors for distinguishing BD patients with and without emotional hyper-reactivity, the strongest predictors were: systolic and diastolic blood pressure, fasting glucose, C-reactive protein and number of suicide attempts. This predictive model identified patients with emotional hyper-reactivity with 84.9% accuracy. CONCLUSION The assessment of emotional hyper-reactivity in remitted BD patients is clinically relevant, particularly for identifying those at higher risk of cardiometabolic dysfunction, chronic inflammation, and suicide.
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Affiliation(s)
- A A Dargél
- Institut Pasteur, Unité Perception et Mémoire, Paris, France.,Centre National de la Recherche Scientifique, Unité Mixte de Recherche 3571, Paris, France
| | - F Roussel
- Centre de Recherche Interdisciplinaire (CRI), Paris, France
| | - S Volant
- Institut Pasteur, Bioinformatics and Biostatistics Hub (C3BI), USR 3756 IP CNRS, Paris, France
| | - B Etain
- Fondation FondaMental, Fondation de Cooperation Scientifique, Créteil, France.,AP-HP, GH Saint-Louis - Lariboisière - Fernand Widal, Pôle Neurosciences Tête et Cou, INSERM UMRS 1144, University Paris Diderot, Paris, France
| | - R Grant
- Centre for Global Health, Institut Pasteur, Paris, France
| | - J-M Azorin
- Fondation FondaMental, Fondation de Cooperation Scientifique, Créteil, France.,Département de Psychiatrie, Hôpital Sainte-Marguerite, Marseille, France
| | - K M'Bailara
- Fondation FondaMental, Fondation de Cooperation Scientifique, Créteil, France.,Laboratoire de Psychologie, EA 4139, Centre Expert Troubles Bipolaires, Pôle 3-4-7, Hôpital Charles Perrens, Université Bordeaux, Bordeaux, France
| | - F Bellivier
- Fondation FondaMental, Fondation de Cooperation Scientifique, Créteil, France.,AP-HP, GH Saint-Louis - Lariboisière - Fernand Widal, Pôle Neurosciences Tête et Cou, INSERM UMRS 1144, University Paris Diderot, Paris, France
| | - T Bougerol
- Fondation FondaMental, Fondation de Cooperation Scientifique, Créteil, France.,Université Grenoble Alpes, CHU de Grenoble et des Alpes, Grenoble Institut des Neurosciences (GIN) Inserm U 836, Grenoble, France
| | - J-P Kahn
- Fondation FondaMental, Fondation de Cooperation Scientifique, Créteil, France.,Centre Hospitalier Universitaire de Nancy - Hôpitaux de Brabois, Université de Lorraine, Nancy, France
| | - P Roux
- Fondation FondaMental, Fondation de Cooperation Scientifique, Créteil, France.,Department of Adult Psychiatry, Versailles Hospital, Le Chesnay, France.,EA4047, University of Versailles Saint-Quentin-En-Yvelines, Montigny-le-Bretonneux, France
| | - V Aubin
- Fondation FondaMental, Fondation de Cooperation Scientifique, Créteil, France.,Pôle de Psychiatrie, Centre Hospitalier Princesse Grace, Monaco, France
| | - P Courtet
- Fondation FondaMental, Fondation de Cooperation Scientifique, Créteil, France.,Department of Emergency Psychiatry and Acute Care, CHU Montpellier, INSERM U1061, Montpellier University, Montpellier, France
| | - M Leboyer
- Fondation FondaMental, Fondation de Cooperation Scientifique, Créteil, France.,AP-HP, Pôle de psychiatrie, Hôpital H. Mondor - A. Chenevier, Créteil, France.,INSERM, U955, Université Paris-Est, Créteil, France
| | | | - F Kapczinski
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON, Canada
| | - C Henry
- Institut Pasteur, Unité Perception et Mémoire, Paris, France.,Fondation FondaMental, Fondation de Cooperation Scientifique, Créteil, France.,AP-HP, Pôle de psychiatrie, Hôpital H. Mondor - A. Chenevier, Créteil, France.,INSERM, U955, Université Paris-Est, Créteil, France
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24
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Angebault C, Ghozlane A, Volant S, Botterel F, d’Enfert C, Bougnoux ME. Combined bacterial and fungal intestinal microbiota analyses: Impact of storage conditions and DNA extraction protocols. PLoS One 2018; 13:e0201174. [PMID: 30074988 PMCID: PMC6075747 DOI: 10.1371/journal.pone.0201174] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [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: 03/20/2018] [Accepted: 07/10/2018] [Indexed: 12/19/2022] Open
Abstract
Background The human intestinal microbiota contains a vast community of microorganisms increasingly studied using high-throughput DNA sequencing. Standardized protocols for storage and DNA extraction from fecal samples have been established mostly for bacterial microbiota analysis. Here, we investigated the impact of storage and DNA extraction on bacterial and fungal community structures detected concomitantly. Methods Fecal samples from healthy adults were stored at -80°C as such or diluted in RNAlater® and subjected to 2 extraction protocols with mechanical lysis: the Powersoil® MoBio kit or the International Human Microbiota Standard (IHMS) Protocol Q. Libraries of the 12 samples targeting the V3-V4 16S and the ITS1 regions were prepared using Metabiote® (Genoscreen) and sequenced on GS-FLX-454. Sequencing data were analysed using SHAMAN (http://shaman.pasteur.fr/). The bacterial and fungal microbiota were compared in terms of diversity and relative abundance. Results We obtained 171869 and 199089 quality-controlled reads for 16S and ITS, respectively. All 16S reads were assigned to 41 bacterial genera; only 52% of ITS reads were assigned to 40 fungal genera/section. Rarefaction curves were satisfactory in 3/3 and 2/3 subjects for 16S and ITS, respectively. PCoA showed important inter-individual variability of intestinal microbiota largely overweighing the effect of storage or extraction. Storage in RNAlater® impacted (downward trend) the relative abundances of 7/41 bacterial and 6/40 fungal taxa, while extraction impacted randomly 18/41 bacterial taxa and 1/40 fungal taxon. Conclusion Our results showed that RNAlater® moderately impacts bacterial or fungal community structures, while extraction significantly influences the bacterial composition. For combined bacterial and fungal intestinal microbiota analysis, immediate sample freezing should be preferred when feasible, but storage in RNAlater® remains an option under unfavourable conditions or for concomitant metatranscriptomic analysis; and extraction should rely on protocols validated for bacterial analysis, such as IHMS Protocol Q, and including a powerful mechanical lysis, essential for fungal extraction.
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Affiliation(s)
- Cécile Angebault
- Unité de Parasitologie-Mycologie, Service de Microbiologie clinique, Hôpital Necker-Enfants-Malades, Assistance Publique des Hôpitaux de Paris (APHP), Paris, France
- Université Paris Descartes, Sorbonne Paris-Cité, Paris, France
- Unité de Parasitologie-Mycologie, Département de Virologie, Bactériologie-Hygiène, Mycologie-Parasitologie, Unité transversale du traitement des infections (VBHMP–UT2I), DHU-VIC, CHU Henri Mondor, Assistance Publique des Hôpitaux de Paris (APHP), Créteil, France
- EA Dynamyc 7380 UPEC, ENVA, Faculté de Médecine de Créteil, Créteil
| | - Amine Ghozlane
- Institut Pasteur, Bioinformatics and Biostatistics Hub—C3BI—USR 3756 IP CNRS, Paris, France
| | - Stevenn Volant
- Institut Pasteur, Bioinformatics and Biostatistics Hub—C3BI—USR 3756 IP CNRS, Paris, France
| | - Françoise Botterel
- Unité de Parasitologie-Mycologie, Département de Virologie, Bactériologie-Hygiène, Mycologie-Parasitologie, Unité transversale du traitement des infections (VBHMP–UT2I), DHU-VIC, CHU Henri Mondor, Assistance Publique des Hôpitaux de Paris (APHP), Créteil, France
- EA Dynamyc 7380 UPEC, ENVA, Faculté de Médecine de Créteil, Créteil
| | - Christophe d’Enfert
- Institut Pasteur, INRA, Unité Biologie et Pathogénicité Fongiques, Département Mycologie, Paris, France
| | - Marie-Elisabeth Bougnoux
- Unité de Parasitologie-Mycologie, Service de Microbiologie clinique, Hôpital Necker-Enfants-Malades, Assistance Publique des Hôpitaux de Paris (APHP), Paris, France
- Université Paris Descartes, Sorbonne Paris-Cité, Paris, France
- Institut Pasteur, INRA, Unité Biologie et Pathogénicité Fongiques, Département Mycologie, Paris, France
- * E-mail: ,
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25
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Dickson LB, Ghozlane A, Volant S, Bouchier C, Ma L, Vega-Rúa A, Dusfour I, Jiolle D, Paupy C, Mayanja MN, Kohl A, Lutwama JJ, Duong V, Lambrechts L. Diverse laboratory colonies of Aedes aegypti harbor the same adult midgut bacterial microbiome. Parasit Vectors 2018; 11:207. [PMID: 29587819 PMCID: PMC5870067 DOI: 10.1186/s13071-018-2780-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [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: 10/11/2017] [Accepted: 03/06/2018] [Indexed: 03/25/2023] Open
Abstract
Background Host-associated microbes, collectively known as the microbiota, play an important role in the biology of multicellular organisms. In mosquito vectors of human pathogens, the gut bacterial microbiota influences vectorial capacity and has become the subject of intense study. In laboratory studies of vector biology, genetic effects are often inferred from differences between geographically and genetically diverse colonies of mosquitoes that are reared in the same insectary. It is unclear, however, to what extent genetic effects can be confounded by uncontrolled differences in the microbiota composition among mosquito colonies. To address this question, we used 16S metagenomics to compare the midgut bacterial microbiome of six laboratory colonies of Aedes aegypti recently derived from wild populations representing the geographical range and genetic diversity of the species. Results We found that the diversity, abundance, and community structure of the midgut bacterial microbiome was remarkably similar among the six different colonies of Ae. aegypti, regardless of their geographical origin. We also confirmed the relatively low complexity of bacterial communities inhabiting the mosquito midgut. Conclusions Our finding that geographically diverse colonies of Ae. aegypti reared in the same insectary harbor a similar gut bacterial microbiome supports the conclusion that the gut microbiota of adult mosquitoes is environmentally determined regardless of the host genotype. Thus, uncontrolled differences in microbiota composition are unlikely to represent a significant confounding factor in genetic studies of vector biology. Electronic supplementary material The online version of this article (10.1186/s13071-018-2780-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Laura B Dickson
- Insect-Virus Interactions Group, Department of Genomes and Genetics, Institut Pasteur, CNRS UMR 2000, Paris, France.
| | - Amine Ghozlane
- Bioinformatics and Biostatistics Hub, C3BI, USR 3756 CNRS, Institut Pasteur, Paris, France.,Genomics Facility - Biomics Pole, CITECH, Institut Pasteur, Paris, France
| | - Stevenn Volant
- Bioinformatics and Biostatistics Hub, C3BI, USR 3756 CNRS, Institut Pasteur, Paris, France
| | | | - Laurence Ma
- Genomics Facility - Biomics Pole, CITECH, Institut Pasteur, Paris, France
| | - Anubis Vega-Rúa
- Laboratory of Medical Entomology, Environment and Health Unit, Institut Pasteur de la Guadeloupe, Guadeloupe, France
| | - Isabelle Dusfour
- Vector Control and Adaptation, Institut Pasteur de la Guyane, Vectopole Amazonien Emile Abonnenc, Cayenne, French Guiana
| | - Davy Jiolle
- MIVEGEC, IRD, CNRS, University of Montpellier, Montpellier, France.,Centre International de Recherches Médicales de Franceville, Franceville, Gabon
| | - Christophe Paupy
- MIVEGEC, IRD, CNRS, University of Montpellier, Montpellier, France.,Centre International de Recherches Médicales de Franceville, Franceville, Gabon
| | - Martin N Mayanja
- Department of Arbovirology, Uganda Virus Research Institute, Entebbe, Uganda
| | - Alain Kohl
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Julius J Lutwama
- Department of Arbovirology, Uganda Virus Research Institute, Entebbe, Uganda
| | - Veasna Duong
- Virology Unit, Institut Pasteur in Cambodia, Phnom Penh, Cambodia
| | - Louis Lambrechts
- Insect-Virus Interactions Group, Department of Genomes and Genetics, Institut Pasteur, CNRS UMR 2000, Paris, France.
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26
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Dickson LB, Jiolle D, Minard G, Moltini-Conclois I, Volant S, Ghozlane A, Bouchier C, Ayala D, Paupy C, Moro CV, Lambrechts L. Carryover effects of larval exposure to different environmental bacteria drive adult trait variation in a mosquito vector. Sci Adv 2017; 3:e1700585. [PMID: 28835919 PMCID: PMC5559213 DOI: 10.1126/sciadv.1700585] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 07/05/2017] [Indexed: 05/19/2023]
Abstract
Conditions experienced during larval development of holometabolous insects can affect adult traits, but whether differences in the bacterial communities of larval development sites contribute to variation in the ability of insect vectors to transmit human pathogens is unknown. We addressed this question in the mosquito Aedes aegypti, a major arbovirus vector breeding in both sylvatic and domestic habitats in Sub-Saharan Africa. Targeted metagenomics revealed differing bacterial communities in the water of natural breeding sites in Gabon. Experimental exposure to different native bacterial isolates during larval development resulted in significant differences in pupation rate and adult body size but not life span. Larval exposure to an Enterobacteriaceae isolate resulted in decreased antibacterial activity in adult hemolymph and reduced dengue virus dissemination titer. Together, these data provide the proof of concept that larval exposure to different bacteria can drive variation in adult traits underlying vectorial capacity. Our study establishes a functional link between larval ecology, environmental microbes, and adult phenotypic variation in a holometabolous insect vector.
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Affiliation(s)
- Laura B. Dickson
- Insect-Virus Interactions Group, Department of Genomes and Genetics, Institut Pasteur, CNRS URA 3012, Paris, France
- Corresponding author. (L.B.D.); (L.L.)
| | - Davy Jiolle
- Insect-Virus Interactions Group, Department of Genomes and Genetics, Institut Pasteur, CNRS URA 3012, Paris, France
- MIVEGEC, UMR IRD 224-CNRS 5290-UM, Montpellier, France
- Centre International de Recherches Médicales de Franceville, Franceville, Gabon
| | - Guillaume Minard
- Université de Lyon, Lyon, France
- Université Lyon 1, CNRS UMR 5557 Ecologie Microbienne, INRA UMR 1418, Villeurbanne, France
- Metapopulation Research Center, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Isabelle Moltini-Conclois
- Insect-Virus Interactions Group, Department of Genomes and Genetics, Institut Pasteur, CNRS URA 3012, Paris, France
| | - Stevenn Volant
- Bioinformatics and Biostatistics Hub, C3BI, Institut Pasteur, USR 3756 IP CNRS, Paris, France
| | - Amine Ghozlane
- Bioinformatics and Biostatistics Hub, C3BI, Institut Pasteur, USR 3756 IP CNRS, Paris, France
- Genomics Facility, Biomics Pole, CITECH, Institut Pasteur, Paris, France
| | | | - Diego Ayala
- MIVEGEC, UMR IRD 224-CNRS 5290-UM, Montpellier, France
- Centre International de Recherches Médicales de Franceville, Franceville, Gabon
| | - Christophe Paupy
- MIVEGEC, UMR IRD 224-CNRS 5290-UM, Montpellier, France
- Centre International de Recherches Médicales de Franceville, Franceville, Gabon
| | - Claire Valiente Moro
- Université de Lyon, Lyon, France
- Université Lyon 1, CNRS UMR 5557 Ecologie Microbienne, INRA UMR 1418, Villeurbanne, France
| | - Louis Lambrechts
- Insect-Virus Interactions Group, Department of Genomes and Genetics, Institut Pasteur, CNRS URA 3012, Paris, France
- Corresponding author. (L.B.D.); (L.L.)
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27
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Pasi M, Mornico D, Volant S, Juchet A, Batisse J, Bouchier C, Parissi V, Ruff M, Lavery R, Lavigne M. DNA minicircles clarify the specific role of DNA structure on retroviral integration. Nucleic Acids Res 2016; 44:7830-47. [PMID: 27439712 PMCID: PMC5027509 DOI: 10.1093/nar/gkw651] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [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: 05/25/2016] [Accepted: 07/11/2016] [Indexed: 01/26/2023] Open
Abstract
Chromatin regulates the selectivity of retroviral integration into the genome of infected cells. At the nucleosome level, both histones and DNA structure are involved in this regulation. We propose a strategy that allows to specifically study a single factor: the DNA distortion induced by the nucleosome. This strategy relies on mimicking this distortion using DNA minicircles (MCs) having a fixed rotational orientation of DNA curvature, coupled with atomic-resolution modeling. Contrasting MCs with linear DNA fragments having identical sequences enabled us to analyze the impact of DNA distortion on the efficiency and selectivity of integration. We observed a global enhancement of HIV-1 integration in MCs and an enrichment of integration sites in the outward-facing DNA major grooves. Both of these changes are favored by LEDGF/p75, revealing a new, histone-independent role of this integration cofactor. PFV integration is also enhanced in MCs, but is not associated with a periodic redistribution of integration sites, thus highlighting its distinct catalytic properties. MCs help to separate the roles of target DNA structure, histone modifications and integrase (IN) cofactors during retroviral integration and to reveal IN-specific regulation mechanisms.
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Affiliation(s)
- Marco Pasi
- MMSB UMR5086 University of Lyon I/CNRS, Institut de Biologie et Chimie des Protéines, 7 passage du Vercors, Lyon 69367, France
| | - Damien Mornico
- Institut Pasteur-Bioinformatics and Biostatistics Hub-C3BI, USR 3756 IP-CNRS, Paris 75015, France
| | - Stevenn Volant
- Institut Pasteur-Bioinformatics and Biostatistics Hub-C3BI, USR 3756 IP-CNRS, Paris 75015, France
| | - Anna Juchet
- Institut Pasteur, Unité de Virologie Moléculaire et Vaccinologie, UMR 3569 IP-CNRS, Paris 75015, France
| | - Julien Batisse
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Dpt de Biologie Structurale Intégrative, UDS, U596 INSERM, UMR7104 CNRS, Illkirch 67400, France
| | - Christiane Bouchier
- Institut Pasteur, PF1, Plate-forme Génomique-Pôle Biomics, Citech, Paris 75015, France
| | - Vincent Parissi
- Laboratoire de Microbiologie Fondamentale et Pathogénicité, UMR 5234 CNRS-Université de Bordeaux, Bordeaux 33000, France
| | - Marc Ruff
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Dpt de Biologie Structurale Intégrative, UDS, U596 INSERM, UMR7104 CNRS, Illkirch 67400, France
| | - Richard Lavery
- MMSB UMR5086 University of Lyon I/CNRS, Institut de Biologie et Chimie des Protéines, 7 passage du Vercors, Lyon 69367, France
| | - Marc Lavigne
- Institut Pasteur, Unité de Virologie Moléculaire et Vaccinologie, UMR 3569 IP-CNRS, Paris 75015, France
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28
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Hourdel V, Volant S, O'Brien DP, Chenal A, Chamot-Rooke J, Dillies MA, Brier S. MEMHDX: an interactive tool to expedite the statistical validation and visualization of large HDX-MS datasets. Bioinformatics 2016; 32:3413-3419. [PMID: 27412089 PMCID: PMC5181559 DOI: 10.1093/bioinformatics/btw420] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [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: 03/03/2016] [Revised: 06/21/2016] [Accepted: 06/27/2016] [Indexed: 11/17/2022] Open
Abstract
Motivation: With the continued improvement of requisite mass spectrometers and UHPLC systems, Hydrogen/Deuterium eXchange Mass Spectrometry (HDX-MS) workflows are rapidly evolving towards the investigation of more challenging biological systems, including large protein complexes and membrane proteins. The analysis of such extensive systems results in very large HDX-MS datasets for which specific analysis tools are required to speed up data validation and interpretation. Results: We introduce a web application and a new R-package named ‘MEMHDX’ to help users analyze, validate and visualize large HDX-MS datasets. MEMHDX is composed of two elements. A statistical tool aids in the validation of the results by applying a mixed-effects model for each peptide, in each experimental condition, and at each time point, taking into account the time dependency of the HDX reaction and number of independent replicates. Two adjusted P-values are generated per peptide, one for the ‘Change in dynamics’ and one for the ‘Magnitude of ΔD’, and are used to classify the data by means of a ‘Logit’ representation. A user-friendly interface developed with Shiny by RStudio facilitates the use of the package. This interactive tool allows the user to easily and rapidly validate, visualize and compare the relative deuterium incorporation on the amino acid sequence and 3D structure, providing both spatial and temporal information. Availability and Implementation: MEMHDX is freely available as a web tool at the project home page http://memhdx.c3bi.pasteur.fr Contact:marie-agnes.dillies@pasteur.fr or sebastien.brier@pasteur.fr Supplementary information:Supplementary data is available at Bioinformatics online.
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Affiliation(s)
- Véronique Hourdel
- Department of Chemistry and Structural Biology, Institut Pasteur, UMR CNRS, Paris 3528, France
| | - Stevenn Volant
- Hub Bioinformatique Et Biostatistique, Institut Pasteur, C3bi, USR 3756 IP CNRS Paris 3528, France
| | - Darragh P O'Brien
- Department of Chemistry and Structural Biology, Institut Pasteur, UMR CNRS, Paris 3528, France
| | - Alexandre Chenal
- Department of Chemistry and Structural Biology, Institut Pasteur, UMR CNRS, Paris 3528, France
| | - Julia Chamot-Rooke
- Department of Chemistry and Structural Biology, Institut Pasteur, UMR CNRS, Paris 3528, France
| | - Marie-Agnès Dillies
- Hub Bioinformatique Et Biostatistique, Institut Pasteur, C3bi, USR 3756 IP CNRS Paris 3528, France
| | - Sébastien Brier
- Department of Chemistry and Structural Biology, Institut Pasteur, UMR CNRS, Paris 3528, France
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Galtier M, De Sordi L, Maura D, Arachchi H, Volant S, Dillies MA, Debarbieux L. Bacteriophages to reduce gut carriage of antibiotic resistant uropathogens with low impact on microbiota composition. Environ Microbiol 2016; 18:2237-45. [PMID: 26971586 DOI: 10.1111/1462-2920.13284] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 02/26/2016] [Indexed: 12/30/2022]
Abstract
Uropathogenic Escherichia coli (UPEC) is the leading cause of urinary tract infections (UTIs) worldwide, causing over 150 million clinical cases annually. There is currently no specific treatment addressing the asymptomatic carriage in the gut of UPEC before they initiate UTIs. This study investigates the efficacy of virulent bacteriophages to decrease carriage of gut pathogens. Three virulent bacteriophages infecting an antibiotic-resistant UPEC strain were isolated and characterized both in vitro and in vivo. A new experimental murine model of gut carriage of E. coli was elaborated and the impact of virulent bacteriophages on colonization levels and microbiota diversity was assessed. A single dose of a cocktail of the three bacteriophages led to a sharp decrease in E. coli levels throughout the gut. We also observed that microbiota diversity was much less affected by bacteriophages than by antibiotics. Therefore, virulent bacteriophages can efficiently target UPEC strains residing in the gut, with potentially profound public health and economic impacts. These results open a new area with the possibility to manipulate specifically the microbiota using virulent bacteriophages, which could have broad applications in many gut-related disorders/diseases and beyond.
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Affiliation(s)
- Matthieu Galtier
- Department of Microbiology, Institut Pasteur, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, Paris, France
| | - Luisa De Sordi
- Department of Microbiology, Institut Pasteur, Paris, France
| | - Damien Maura
- Department of Microbiology, Institut Pasteur, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, Paris, France
| | - Harindra Arachchi
- Institut Pasteur Hub Bioinformatique et Biostatistique - C3BI, USR 3756 IP CNRS - Paris, France
| | - Stevenn Volant
- Institut Pasteur Hub Bioinformatique et Biostatistique - C3BI, USR 3756 IP CNRS - Paris, France
| | - Marie-Agnès Dillies
- Institut Pasteur Hub Bioinformatique et Biostatistique - C3BI, USR 3756 IP CNRS - Paris, France
| | - Laurent Debarbieux
- Institut Pasteur Hub Bioinformatique et Biostatistique - C3BI, USR 3756 IP CNRS - Paris, France
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