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Chrétienneau C, Spindola LM, Vorspan F, Lagerberg TV, Marie‐Claire C, Bellivier F, Mouly S, Laplanche J, Bloch V, Le Hellard S, Icick R. An epigenetic candidate-gene association study of parental styles in suicide attempters with substance use disorders. Addict Biol 2024; 29:e13392. [PMID: 38564607 PMCID: PMC10986931 DOI: 10.1111/adb.13392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 02/07/2024] [Accepted: 02/27/2024] [Indexed: 04/04/2024]
Abstract
Suicide attempts (SA) are prevalent in substance use disorders (SUD). Epigenetic mechanisms may play a pivotal role in the molecular mechanisms of environmental effects eliciting suicidal behaviour in this population. Hypothalamic-pituitary-adrenal axis (HPA), oxytocin and neurotrophin pathways have been consistently involved in SA, yet , their interplay with childhood adversity remains unclear, particularly in SUD. In 24 outpatients with SUDs, we examined the relation between three parental dysfunctional styles and history of SA with methylation of 32 genes from these pathways, eventually analysing 823 methylation sites. Extensive phenotypic characterization was obtained using a semi-structured interview. Parental style was patient-reported using the Measure of Parental Style (MOPS) questionnaire, analysed with and without imputation of missing items. Linear regressions were performed to adjust for possible confounders, followed by multiple testing correction. We describe both differentially methylated probes (DMPs) and regions (DMRs) for each set of analyses (with and without imputation of MOPS items). Without imputation, five DMRs in OXTR, CRH and NTF3 significantly interacted with MOPS father abuse to increase the risk for lifetime SA, thus covering the three pathways. After imputation of missing MOPS items, two other DMPs from FKBP5 and SOCS3 significantly interacted with each of the three father styles to increase the risk for SA. Although our findings must be interpreted with caution due to small sample size, they suggest implications of stress reactivity genes in the suicidal risk of SUD patients and highlight the significance of father dysfunction as a potential marker of childhood adversity in SUD patients.
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Affiliation(s)
- Clara Chrétienneau
- Département Universitaire de Psychiatrie et de Médecine Addictologique, GHU APHP. NordAssistance Publique – Hôpitaux de ParisParisFrance
- INSERM UMR‐S 1144, Optimisation Thérapeutique en Neurospsychopharmacologie, OTeNUniversité Paris CitéParisFrance
- FHU NOR‐SUD Network of Research in Substance Use DisordersParisFrance
| | - Leticia M. Spindola
- NORMENT, Department of Clinical ScienceUniversity of BergenBergenNorway
- Dr. Einar Martens Research Group for Biological Psychiatry, Department of Medical GeneticsHaukeland University HospitalBergenNorway
| | - Florence Vorspan
- Département Universitaire de Psychiatrie et de Médecine Addictologique, GHU APHP. NordAssistance Publique – Hôpitaux de ParisParisFrance
- INSERM UMR‐S 1144, Optimisation Thérapeutique en Neurospsychopharmacologie, OTeNUniversité Paris CitéParisFrance
- FHU NOR‐SUD Network of Research in Substance Use DisordersParisFrance
| | - Trine Vik Lagerberg
- Division of Mental Health and Addiction Department of Psychology, Faculty of Social SciencesOslo University Hospital | University of Oslo, Oslo, NorwayOsloNorway
| | - Cynthia Marie‐Claire
- INSERM UMR‐S 1144, Optimisation Thérapeutique en Neurospsychopharmacologie, OTeNUniversité Paris CitéParisFrance
- FHU NOR‐SUD Network of Research in Substance Use DisordersParisFrance
| | - Frank Bellivier
- Département Universitaire de Psychiatrie et de Médecine Addictologique, GHU APHP. NordAssistance Publique – Hôpitaux de ParisParisFrance
- INSERM UMR‐S 1144, Optimisation Thérapeutique en Neurospsychopharmacologie, OTeNUniversité Paris CitéParisFrance
- FHU NOR‐SUD Network of Research in Substance Use DisordersParisFrance
| | - Stéphane Mouly
- Department of Internal MedicineLariboisière Hospital, Assistance Publique‐Hôpitaux de ParisParisFrance
- Université Paris CitéParisFrance
| | - Jean‐Louis Laplanche
- INSERM UMR‐S 1144, Optimisation Thérapeutique en Neurospsychopharmacologie, OTeNUniversité Paris CitéParisFrance
- FHU NOR‐SUD Network of Research in Substance Use DisordersParisFrance
| | - Vanessa Bloch
- INSERM UMR‐S 1144, Optimisation Thérapeutique en Neurospsychopharmacologie, OTeNUniversité Paris CitéParisFrance
- FHU NOR‐SUD Network of Research in Substance Use DisordersParisFrance
- Pharmacie HospitalièreAssistance Publique – Hôpitaux de Paris, GHU APHP. NordParisFrance
| | - Stéphanie Le Hellard
- NORMENT, Department of Clinical ScienceUniversity of BergenBergenNorway
- Dr. Einar Martens Research Group for Biological Psychiatry, Department of Medical GeneticsHaukeland University HospitalBergenNorway
| | - Romain Icick
- Département Universitaire de Psychiatrie et de Médecine Addictologique, GHU APHP. NordAssistance Publique – Hôpitaux de ParisParisFrance
- INSERM UMR‐S 1144, Optimisation Thérapeutique en Neurospsychopharmacologie, OTeNUniversité Paris CitéParisFrance
- FHU NOR‐SUD Network of Research in Substance Use DisordersParisFrance
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Morillo L, Paternina T, Alasseur Q, Genovesio A, Schwartz S, Le Hir H. Comprehensive mapping of exon junction complex binding sites reveals universal EJC deposition in Drosophila. BMC Biol 2023; 21:246. [PMID: 37936138 PMCID: PMC10630996 DOI: 10.1186/s12915-023-01749-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/26/2023] [Indexed: 11/09/2023] Open
Abstract
BACKGROUND The exon junction complex (EJC) is involved in most steps of the mRNA life cycle, ranging from splicing to nonsense-mediated mRNA decay (NMD). It is assembled by the splicing machinery onto mRNA in a sequence-independent manner. A fundamental open question is whether the EJC is deposited onto all exon‒exon junctions or only on a subset of them. Several previous studies have made observations supportive of the latter, yet these have been limited by methodological constraints. RESULTS In this study, we sought to overcome these limitations via the integration of two different approaches for transcriptome-wide mapping of EJCs. Our results revealed that nearly all, if not all, internal exons consistently harbor an EJC in Drosophila, demonstrating that EJC presence is an inherent consequence of the splicing reaction. Furthermore, our study underscores the limitations of eCLIP methods in fully elucidating the landscape of RBP binding sites. Our findings highlight how highly specific (low false positive) methodologies can lead to erroneous interpretations due to partial sensitivity (high false negatives). CONCLUSIONS This study contributes to our understanding of EJC deposition and its association with pre-mRNA splicing. The universal presence of EJC on internal exons underscores its significance in ensuring proper mRNA processing. Additionally, our observations highlight the need to consider both specificity and sensitivity in RBP mapping methodologies.
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Affiliation(s)
- Lucía Morillo
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
| | - Toni Paternina
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
| | - Quentin Alasseur
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
| | - Auguste Genovesio
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
| | - Schraga Schwartz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7630031, Israel
| | - Hervé Le Hir
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France.
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Marchet C, Limasset A. Scalable sequence database search using partitioned aggregated Bloom comb trees. Bioinformatics 2023; 39:i252-i259. [PMID: 37387170 DOI: 10.1093/bioinformatics/btad225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2023] Open
Abstract
MOTIVATION The Sequence Read Archive public database has reached 45 petabytes of raw sequences and doubles its nucleotide content every 2 years. Although BLAST-like methods can routinely search for a sequence in a small collection of genomes, making searchable immense public resources accessible is beyond the reach of alignment-based strategies. In recent years, abundant literature tackled the task of finding a sequence in extensive sequence collections using k-mer-based strategies. At present, the most scalable methods are approximate membership query data structures that combine the ability to query small signatures or variants while being scalable to collections up to 10 000 eukaryotic samples. Results. Here, we present PAC, a novel approximate membership query data structure for querying collections of sequence datasets. PAC index construction works in a streaming fashion without any disk footprint besides the index itself. It shows a 3-6 fold improvement in construction time compared to other compressed methods for comparable index size. A PAC query can need single random access and be performed in constant time in favorable instances. Using limited computation resources, we built PAC for very large collections. They include 32 000 human RNA-seq samples in 5 days, the entire GenBank bacterial genome collection in a single day for an index size of 3.5 TB. The latter is, to our knowledge, the largest sequence collection ever indexed using an approximate membership query structure. We also showed that PAC's ability to query 500 000 transcript sequences in less than an hour. AVAILABILITY AND IMPLEMENTATION PAC's open-source software is available at https://github.com/Malfoy/PAC.
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Affiliation(s)
- Camille Marchet
- University of Lille, CNRS, Centrale Lille, UMR 9189 CRIStAL, F-59000 Lille, France
| | - Antoine Limasset
- University of Lille, CNRS, Centrale Lille, UMR 9189 CRIStAL, F-59000 Lille, France
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Drommi M, Rulmont C, Esmieu C, Hureau C. Hybrid Bis-Histidine Phenanthroline-Based Ligands to Lessen Aβ-Bound Cu ROS Production: An Illustration of Cu(I) Significance. Molecules 2021; 26:7630. [PMID: 34946712 PMCID: PMC8707446 DOI: 10.3390/molecules26247630] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 12/10/2021] [Indexed: 11/23/2022] Open
Abstract
We here report the synthesis of three new hybrid ligands built around the phenanthroline scaffold and encompassing two histidine-like moieties: phenHH, phenHGH and H'phenH', where H correspond to histidine and H' to histamine. These ligands were designed to capture Cu(I/II) from the amyloid-β peptide and to prevent the formation of reactive oxygen species produced by amyloid-β bound copper in presence of physiological reductant (e.g., ascorbate) and dioxygen. The amyloid-β peptide is a well-known key player in Alzheimer's disease, a debilitating and devasting neurological disorder the mankind has to fight against. The Cu-Aβ complex does participate in the oxidative stress observed in the disease, due to the redox ability of the Cu(I/II) ions. The complete characterization of the copper complexes made with phenHH, phenHGH and H'phenH' is reported, along with the ability of ligands to remove Cu from Aβ, and to prevent the formation of reactive oxygen species catalyzed by Cu and Cu-Aβ, including in presence of zinc, the second metal ions important in the etiology of Alzheimer's disease. The importance of the reduced state of copper, Cu(I), in the prevention and arrest of ROS is mechanistically described with the help of cyclic voltammetry experiments.
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Affiliation(s)
| | | | | | - Christelle Hureau
- CNRS, LCC (Laboratoire de Chimie de Coordination), 205 Route de Narbonne, CEDEX 4, 31077 Toulouse, France; (M.D.); (C.R.); (C.E.)
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Abstract
Abscisic acid (ABA) is a key hormone that promotes dormancy during seed development on the mother plant and after seed dispersal participates in the control of dormancy release and germination in response to environmental signals. The modulation of ABA endogenous levels is largely achieved by fine-tuning, in the different seed tissues, hormone synthesis by cleavage of carotenoid precursors and inactivation by 8'-hydroxylation. In this review, we provide an overview of the current knowledge on ABA metabolism in developing and germinating seeds; notably, how environmental signals such as light, temperature and nitrate control seed dormancy through the adjustment of hormone levels. A number of regulatory factors have been recently identified which functional relationships with major transcription factors, such as ABA INSENSITIVE3 (ABI3), ABI4 and ABI5, have an essential role in the control of seed ABA levels. The increasing importance of epigenetic mechanisms in the regulation of ABA metabolism gene expression is also described. In the last section, we give an overview of natural variations of ABA metabolism genes and their effects on seed germination, which could be useful both in future studies to better understand the regulation of ABA metabolism and to identify candidates as breeding materials for improving germination properties.
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Affiliation(s)
| | - Annie Marion-Poll
- IJPB Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France;
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Rousselle M, Simion P, Tilak MK, Figuet E, Nabholz B, Galtier N. Is adaptation limited by mutation? A timescale-dependent effect of genetic diversity on the adaptive substitution rate in animals. PLoS Genet 2020; 16:e1008668. [PMID: 32251427 PMCID: PMC7162527 DOI: 10.1371/journal.pgen.1008668] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [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: 12/18/2019] [Revised: 04/16/2020] [Accepted: 02/14/2020] [Indexed: 12/16/2022] Open
Abstract
Whether adaptation is limited by the beneficial mutation supply is a long-standing question of evolutionary genetics, which is more generally related to the determination of the adaptive substitution rate and its relationship with species effective population size (Ne) and genetic diversity. Empirical evidence reported so far is equivocal, with some but not all studies supporting a higher adaptive substitution rate in large-Ne than in small-Ne species. We gathered coding sequence polymorphism data and estimated the adaptive amino-acid substitution rate ωa, in 50 species from ten distant groups of animals with markedly different population mutation rate θ. We reveal the existence of a complex, timescale dependent relationship between species adaptive substitution rate and genetic diversity. We find a positive relationship between ωa and θ among closely related species, indicating that adaptation is indeed limited by the mutation supply, but this was only true in relatively low-θ taxa. In contrast, we uncover no significant correlation between ωa and θ at a larger taxonomic scale, suggesting that the proportion of beneficial mutations scales negatively with species' long-term Ne.
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Affiliation(s)
| | - Paul Simion
- ISEM, Univ. Montpellier, CNRS, EPHE, IRD, Montpellier, France
- LEGE, Department of Biology, University of Namur, Namur, Belgium
| | - Marie-Ka Tilak
- ISEM, Univ. Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Emeric Figuet
- ISEM, Univ. Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Benoit Nabholz
- ISEM, Univ. Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Nicolas Galtier
- ISEM, Univ. Montpellier, CNRS, EPHE, IRD, Montpellier, France
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Abstract
Spinocerebellar ataxia type 7 (SCA7) is a rare autosomal dominant neurodegenerative disorder characterized by progressive neuronal loss in the cerebellum, brainstem, and retina, leading to cerebellar ataxia and blindness as major symptoms. SCA7 is due to the expansion of a CAG triplet repeat that is translated into a polyglutamine tract in ATXN7. Larger SCA7 expansions are associated with earlier onset of symptoms and more severe and rapid disease progression. Here, we summarize the pathological and genetic aspects of SCA7, compile the current knowledge about ATXN7 functions, and then focus on recent advances in understanding the pathogenesis and in developing biomarkers and therapeutic strategies. ATXN7 is a bona fide subunit of the multiprotein SAGA complex, a transcriptional coactivator harboring chromatin remodeling activities, and plays a role in the differentiation of photoreceptors and Purkinje neurons, two highly vulnerable neuronal cell types in SCA7. Polyglutamine expansion in ATXN7 causes its misfolding and intranuclear accumulation, leading to changes in interactions with native partners and/or partners sequestration in insoluble nuclear inclusions. Studies of cellular and animal models of SCA7 have been crucial to unveil pathomechanistic aspects of the disease, including gene deregulation, mitochondrial and metabolic dysfunctions, cell and non-cell autonomous protein toxicity, loss of neuronal identity, and cell death mechanisms. However, a better understanding of the principal molecular mechanisms by which mutant ATXN7 elicits neurotoxicity, and how interconnected pathogenic cascades lead to neurodegeneration is needed for the development of effective therapies. At present, therapeutic strategies using nucleic acid-based molecules to silence mutant ATXN7 gene expression are under development for SCA7.
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Affiliation(s)
- Anna Niewiadomska-Cimicka
- Institute of Genetic and Molecular and Cellular Biology (IGBMC), Centre National de la Recherche Scientifique (UMR7104), Institut National de la Santé et de la Recherche Médicale (U1258), University of Strasbourg, Illkirch, France
| | - Yvon Trottier
- Institute of Genetic and Molecular and Cellular Biology (IGBMC), Centre National de la Recherche Scientifique (UMR7104), Institut National de la Santé et de la Recherche Médicale (U1258), University of Strasbourg, Illkirch, France.
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Lesne E, Coutte L, Solans L, Slupek S, Debrie AS, Dhennin V, Froguel P, Hot D, Locht C, Antoine R, Jacob-Dubuisson F. Distinct virulence ranges for infection of mice by Bordetella pertussis revealed by engineering of the sensor-kinase BvgS. PLoS One 2018; 13:e0204861. [PMID: 30307950 PMCID: PMC6181320 DOI: 10.1371/journal.pone.0204861] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 09/14/2018] [Indexed: 12/30/2022] Open
Abstract
The whooping cough agent Bordetella pertussis coordinately regulates the expression of its virulence factors with the two-component system BvgAS. In laboratory conditions, specific chemical modulators are used to trigger phenotypic modulation of B. pertussis from its default virulent Bvg+ phase to avirulent Bvg- or intermediate Bvgi phases, in which no virulence factors or only a subset of them are produced, respectively. Whether phenotypic modulation occurs in the host remains unknown. In this work, recombinant B. pertussis strains harboring BvgS variants were tested in a mouse model of infection and analyzed using transcriptomic approaches. Recombinant BP-BvgΔ65, which is in the Bvgi phase by default and can be up-modulated to the Bvg+ phase in vitro, could colonize the mouse nose but was rapidly cleared from the lungs, while Bvg+-phase strains colonized both organs for up to four weeks. These results indicated that phenotypic modulation, which might have restored the full virulence capability of BP-BvgΔ65, does not occur in mice or is temporally or spatially restricted and has no effect in those conditions. Transcriptomic analyses of this and other recombinant Bvgi and Bvg+-phase strains revealed that two distinct ranges of virulence gene expression allow colonization of the mouse nose and lungs, respectively. We also showed that a recombinant strain expressing moderately lower levels of the virulence genes than its wild type parent was as efficient at colonizing both organs. Altogether, genetic modifications of BvgS generate a range of phenotypic phases, which are useful tools to decipher host-pathogen interactions.
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Affiliation(s)
- Elodie Lesne
- Univ. Lille, Lille, France
- CNRS UMR 8204, Lille, France
- Inserm U1019, Lille, France
- CHU Lille, Lille, France
- Institut Pasteur de Lille, Centre d’Infection et d’Immunité de Lille, Lille, France
| | - Loic Coutte
- Univ. Lille, Lille, France
- CNRS UMR 8204, Lille, France
- Inserm U1019, Lille, France
- CHU Lille, Lille, France
- Institut Pasteur de Lille, Centre d’Infection et d’Immunité de Lille, Lille, France
| | - Luis Solans
- Univ. Lille, Lille, France
- CNRS UMR 8204, Lille, France
- Inserm U1019, Lille, France
- CHU Lille, Lille, France
- Institut Pasteur de Lille, Centre d’Infection et d’Immunité de Lille, Lille, France
| | - Stephanie Slupek
- Univ. Lille, Lille, France
- CNRS UMR 8204, Lille, France
- Inserm U1019, Lille, France
- CHU Lille, Lille, France
- Institut Pasteur de Lille, Centre d’Infection et d’Immunité de Lille, Lille, France
| | - Anne-Sophie Debrie
- Univ. Lille, Lille, France
- CNRS UMR 8204, Lille, France
- Inserm U1019, Lille, France
- CHU Lille, Lille, France
- Institut Pasteur de Lille, Centre d’Infection et d’Immunité de Lille, Lille, France
| | - Véronique Dhennin
- Univ. Lille, Lille, France
- CNRS UMR 8199, European Genomic Institute for Diabetes, Lille, France
| | - Philippe Froguel
- Univ. Lille, Lille, France
- CNRS UMR 8199, European Genomic Institute for Diabetes, Lille, France
| | - David Hot
- Univ. Lille, Lille, France
- CNRS UMR 8204, Lille, France
- Inserm U1019, Lille, France
- CHU Lille, Lille, France
- Institut Pasteur de Lille, Centre d’Infection et d’Immunité de Lille, Lille, France
| | - Camille Locht
- Univ. Lille, Lille, France
- CNRS UMR 8204, Lille, France
- Inserm U1019, Lille, France
- CHU Lille, Lille, France
- Institut Pasteur de Lille, Centre d’Infection et d’Immunité de Lille, Lille, France
| | - Rudy Antoine
- Univ. Lille, Lille, France
- CNRS UMR 8204, Lille, France
- Inserm U1019, Lille, France
- CHU Lille, Lille, France
- Institut Pasteur de Lille, Centre d’Infection et d’Immunité de Lille, Lille, France
- * E-mail: (RA); (FJD)
| | - Françoise Jacob-Dubuisson
- Univ. Lille, Lille, France
- CNRS UMR 8204, Lille, France
- Inserm U1019, Lille, France
- CHU Lille, Lille, France
- Institut Pasteur de Lille, Centre d’Infection et d’Immunité de Lille, Lille, France
- * E-mail: (RA); (FJD)
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