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Bellefroid M, Rodari A, Galais M, Krijger PHL, Tjalsma SJD, Nestola L, Plant E, Vos ESM, Cristinelli S, Van Driessche B, Vanhulle C, Ait-Ammar A, Burny A, Ciuffi A, de Laat W, Van Lint C. Role of the cellular factor CTCF in the regulation of bovine leukemia virus latency and three-dimensional chromatin organization. Nucleic Acids Res 2022; 50:3190-3202. [PMID: 35234910 PMCID: PMC8989512 DOI: 10.1093/nar/gkac107] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 01/31/2022] [Accepted: 02/05/2022] [Indexed: 01/12/2023] Open
Abstract
Bovine leukemia virus (BLV)-induced tumoral development is a multifactorial phenomenon that remains incompletely understood. Here, we highlight the critical role of the cellular CCCTC-binding factor (CTCF) both in the regulation of BLV transcriptional activities and in the deregulation of the three-dimensional (3D) chromatin architecture surrounding the BLV integration site. We demonstrated the in vivo recruitment of CTCF to three conserved CTCF binding motifs along the provirus. Next, we showed that CTCF localized to regions of transitions in the histone modifications profile along the BLV genome and that it is implicated in the repression of the 5′Long Terminal Repeat (LTR) promoter activity, thereby contributing to viral latency, while favoring the 3′LTR promoter activity. Finally, we demonstrated that BLV integration deregulated the host cellular 3D chromatin organization through the formation of viral/host chromatin loops. Altogether, our results highlight CTCF as a new critical effector of BLV transcriptional regulation and BLV-induced physiopathology.
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Affiliation(s)
- Maxime Bellefroid
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Anthony Rodari
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Mathilde Galais
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Peter H L Krijger
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht 3584, CT, The Netherlands
| | - Sjoerd J D Tjalsma
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht 3584, CT, The Netherlands
| | - Lorena Nestola
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Estelle Plant
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Erica S M Vos
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht 3584, CT, The Netherlands
| | - Sara Cristinelli
- Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Lausanne 1011, Switzerland
| | - Benoit Van Driessche
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Caroline Vanhulle
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Amina Ait-Ammar
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Arsène Burny
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Angela Ciuffi
- Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Lausanne 1011, Switzerland
| | - Wouter de Laat
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht 3584, CT, The Netherlands
| | - Carine Van Lint
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
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2
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Ait-Ammar A, Bellefroid M, Daouad F, Martinelli V, Van Assche J, Wallet C, Rodari A, De Rovere M, Fahrenkrog B, Schwartz C, Van Lint C, Gautier V, Rohr O. Inhibition of HIV-1 gene transcription by KAP1 in myeloid lineage. Sci Rep 2021; 11:2692. [PMID: 33514850 PMCID: PMC7846785 DOI: 10.1038/s41598-021-82164-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [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: 06/05/2020] [Accepted: 01/13/2021] [Indexed: 02/08/2023] Open
Abstract
HIV-1 latency generates reservoirs that prevent viral eradication by the current therapies. To find strategies toward an HIV cure, detailed understandings of the molecular mechanisms underlying establishment and persistence of the reservoirs are needed. The cellular transcription factor KAP1 is known as a potent repressor of gene transcription. Here we report that KAP1 represses HIV-1 gene expression in myeloid cells including microglial cells, the major reservoir of the central nervous system. Mechanistically, KAP1 interacts and colocalizes with the viral transactivator Tat to promote its degradation via the proteasome pathway and repress HIV-1 gene expression. In myeloid models of latent HIV-1 infection, the depletion of KAP1 increased viral gene elongation and reactivated HIV-1 expression. Bound to the latent HIV-1 promoter, KAP1 associates and cooperates with CTIP2, a key epigenetic silencer of HIV-1 expression in microglial cells. In addition, Tat and CTIP2 compete for KAP1 binding suggesting a dynamic modulation of the KAP1 cellular partners upon HIV-1 infection. Altogether, our results suggest that KAP1 contributes to the establishment and the persistence of HIV-1 latency in myeloid cells.
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Affiliation(s)
- Amina Ait-Ammar
- grid.11843.3f0000 0001 2157 9291Université de Strasbourg, UR 7292 DHPI, FMTS, IUT Louis Pasteur, 1 Allée d’Athènes, 67300 Schiltigheim, France ,grid.7886.10000 0001 0768 2743Center for Research in Infectious Diseases (CRID), School of Medicine and Medical Science (SMMS), University College Dublin (UCD), Dublin, Ireland ,grid.4989.c0000 0001 2348 0746Service of Molecular Virology, Institute for Molecular Biology and Medicine (IBMM), Université Libre de Bruxelles (ULB), Gosselies, Belgium
| | - Maxime Bellefroid
- grid.4989.c0000 0001 2348 0746Service of Molecular Virology, Institute for Molecular Biology and Medicine (IBMM), Université Libre de Bruxelles (ULB), Gosselies, Belgium
| | - Fadoua Daouad
- grid.11843.3f0000 0001 2157 9291Université de Strasbourg, UR 7292 DHPI, FMTS, IUT Louis Pasteur, 1 Allée d’Athènes, 67300 Schiltigheim, France
| | - Valérie Martinelli
- grid.4989.c0000 0001 2348 0746Laboratory Biology of the Nucleus, Institute for Molecular Biology and Medicine, Université Libre de Bruxelles, 6041 Charleroi, Belgium
| | - Jeanne Van Assche
- grid.11843.3f0000 0001 2157 9291Université de Strasbourg, UR 7292 DHPI, FMTS, IUT Louis Pasteur, 1 Allée d’Athènes, 67300 Schiltigheim, France
| | - Clémentine Wallet
- grid.11843.3f0000 0001 2157 9291Université de Strasbourg, UR 7292 DHPI, FMTS, IUT Louis Pasteur, 1 Allée d’Athènes, 67300 Schiltigheim, France
| | - Anthony Rodari
- grid.4989.c0000 0001 2348 0746Service of Molecular Virology, Institute for Molecular Biology and Medicine (IBMM), Université Libre de Bruxelles (ULB), Gosselies, Belgium
| | - Marco De Rovere
- grid.11843.3f0000 0001 2157 9291Université de Strasbourg, UR 7292 DHPI, FMTS, IUT Louis Pasteur, 1 Allée d’Athènes, 67300 Schiltigheim, France
| | - Birthe Fahrenkrog
- grid.4989.c0000 0001 2348 0746Laboratory Biology of the Nucleus, Institute for Molecular Biology and Medicine, Université Libre de Bruxelles, 6041 Charleroi, Belgium
| | - Christian Schwartz
- grid.11843.3f0000 0001 2157 9291Université de Strasbourg, UR 7292 DHPI, FMTS, IUT Louis Pasteur, 1 Allée d’Athènes, 67300 Schiltigheim, France
| | - Carine Van Lint
- grid.4989.c0000 0001 2348 0746Service of Molecular Virology, Institute for Molecular Biology and Medicine (IBMM), Université Libre de Bruxelles (ULB), Gosselies, Belgium
| | - Virginie Gautier
- grid.7886.10000 0001 0768 2743Center for Research in Infectious Diseases (CRID), School of Medicine and Medical Science (SMMS), University College Dublin (UCD), Dublin, Ireland
| | - Olivier Rohr
- grid.11843.3f0000 0001 2157 9291Université de Strasbourg, UR 7292 DHPI, FMTS, IUT Louis Pasteur, 1 Allée d’Athènes, 67300 Schiltigheim, France
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Ait-Ammar A, Kula A, Darcis G, Verdikt R, De Wit S, Gautier V, Mallon PWG, Marcello A, Rohr O, Van Lint C. Current Status of Latency Reversing Agents Facing the Heterogeneity of HIV-1 Cellular and Tissue Reservoirs. Front Microbiol 2020; 10:3060. [PMID: 32038533 PMCID: PMC6993040 DOI: 10.3389/fmicb.2019.03060] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [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: 10/18/2019] [Accepted: 12/18/2019] [Indexed: 12/15/2022] Open
Abstract
One of the most explored therapeutic approaches aimed at eradicating HIV-1 reservoirs is the "shock and kill" strategy which is based on HIV-1 reactivation in latently-infected cells ("shock" phase) while maintaining antiretroviral therapy (ART) in order to prevent spreading of the infection by the neosynthesized virus. This kind of strategy allows for the "kill" phase, during which latently-infected cells die from viral cytopathic effects or from host cytolytic effector mechanisms following viral reactivation. Several latency reversing agents (LRAs) with distinct mechanistic classes have been characterized to reactivate HIV-1 viral gene expression. Some LRAs have been tested in terms of their potential to purge latent HIV-1 in vivo in clinical trials, showing that reversing HIV-1 latency is possible. However, LRAs alone have failed to reduce the size of the viral reservoirs. Together with the inability of the immune system to clear the LRA-activated reservoirs and the lack of specificity of these LRAs, the heterogeneity of the reservoirs largely contributes to the limited success of clinical trials using LRAs. Indeed, HIV-1 latency is established in numerous cell types that are characterized by distinct phenotypes and metabolic properties, and these are influenced by patient history. Hence, the silencing mechanisms of HIV-1 gene expression in these cellular and tissue reservoirs need to be better understood to rationally improve this cure strategy and hopefully reach clinical success.
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Affiliation(s)
- Amina Ait-Ammar
- Service of Molecular Virology, Department of Molecular Virology (DBM), Université Libre de Bruxelles (ULB), Gosselies, Belgium
| | - Anna Kula
- Malopolska Centre of Biotechnology, Laboratory of Virology, Jagiellonian University, Krakow, Poland
| | - Gilles Darcis
- Infectious Diseases Department, Liège University Hospital, Liège, Belgium
| | - Roxane Verdikt
- Service of Molecular Virology, Department of Molecular Virology (DBM), Université Libre de Bruxelles (ULB), Gosselies, Belgium
| | - Stephane De Wit
- Service des Maladies Infectieuses, CHU Saint-Pierre, Université Libre de Bruxelles, Bruxelles, Belgium
| | - Virginie Gautier
- UCD Centre for Experimental Pathogen Host Research (CEPHR), School of Medicine, University College Dublin, Dublin, Ireland
| | - Patrick W G Mallon
- UCD Centre for Experimental Pathogen Host Research (CEPHR), School of Medicine, University College Dublin, Dublin, Ireland
| | - Alessandro Marcello
- Laboratory of Molecular Virology, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Olivier Rohr
- Université de Strasbourg, EA7292, FMTS, IUT Louis Pasteur, Schiltigheim, France
| | - Carine Van Lint
- Service of Molecular Virology, Department of Molecular Virology (DBM), Université Libre de Bruxelles (ULB), Gosselies, Belgium
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Verdikt R, Darcis G, Ait-Ammar A, Van Lint C. Applications of CRISPR/Cas9 tools in deciphering the mechanisms of HIV-1 persistence. Curr Opin Virol 2019; 38:63-69. [PMID: 31509794 DOI: 10.1016/j.coviro.2019.07.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 07/03/2019] [Accepted: 07/08/2019] [Indexed: 12/27/2022]
Abstract
HIV-1 infection can be controlled but not cured by combination antiretroviral therapy. Indeed, the virus persists in treated individuals in viral reservoirs, the best described of which consisting in latently infected central memory CD4+ T cells. However, other cell types in other body compartments than in the peripheral blood contribute to HIV-1 persistence. Addressing the molecular mechanisms of HIV-1 persistence and their cell-specific and tissue-specific variations is thus crucial to develop HIV-1 curative strategies. CRISPR/Cas9 editing technologies have revolutionized genetic engineering by their high specificity and their versatility. Multiple applications now allow to investigate the molecular mechanisms of HIV-1 persistence. Here, we review recent advances in CRISPR-based technologies in deciphering HIV-1 gene expression regulation during persistence.
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Affiliation(s)
- Roxane Verdikt
- Service of Molecular Virology, Department of Molecular Virology (DBM), Université Libre de Bruxelles (ULB), 6041 Gosselies, Belgium
| | - Gilles Darcis
- Infectious Diseases Department, Liège University Hospital, 4000 Liège, Belgium
| | - Amina Ait-Ammar
- Service of Molecular Virology, Department of Molecular Virology (DBM), Université Libre de Bruxelles (ULB), 6041 Gosselies, Belgium
| | - Carine Van Lint
- Service of Molecular Virology, Department of Molecular Virology (DBM), Université Libre de Bruxelles (ULB), 6041 Gosselies, Belgium.
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5
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Le Douce V, Forouzanfar F, Eilebrecht S, Van Driessche B, Ait-Ammar A, Verdikt R, Kurashige Y, Marban C, Gautier V, Candolfi E, Benecke AG, Van Lint C, Rohr O, Schwartz C. Erratum: Corrigendum: HIC1 controls cellular- and HIV-1- gene transcription via interactions with CTIP2 and HMGA1. Sci Rep 2017; 7:39569. [PMID: 28184044 PMCID: PMC5301224 DOI: 10.1038/srep39569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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6
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Le Douce V, Forouzanfar F, Eilebrecht S, Van Driessche B, Ait-Ammar A, Verdikt R, Kurashige Y, Marban C, Gautier V, Candolfi E, Benecke AG, Van Lint C, Rohr O, Schwartz C. HIC1 controls cellular- and HIV-1- gene transcription via interactions with CTIP2 and HMGA1. Sci Rep 2016; 6:34920. [PMID: 27725726 PMCID: PMC5057145 DOI: 10.1038/srep34920] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 09/21/2016] [Indexed: 02/06/2023] Open
Abstract
Among many cellular transcriptional regulators, Bcl11b/CTIP2 and HGMA1 have been described to control the establishment and the persistence of HIV-1 latency in microglial cells, the main viral reservoir in the brain. In this present work, we identify and characterize a transcription factor i.e. HIC1, which physically interacts with both Bcl11b/CTIP2 and HMGA1 to co-regulate specific subsets of cellular genes and the viral HIV-1 gene. Our results suggest that HIC1 represses Tat dependent HIV-1 transcription. Interestingly, this repression of Tat function is linked to HIC1 K314 acetylation status and to SIRT1 deacetylase activity. Finally, we show that HIC1 interacts and cooperates with HGMA1 to regulate Tat dependent HIV-1 transcription. Our results also suggest that HIC1 repression of Tat function happens in a TAR dependent manner and that this TAR element may serve as HIC1 reservoir at the viral promoter to facilitate HIC1/TAT interaction.
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Affiliation(s)
- Valentin Le Douce
- University of Strasbourg, EA7292, DHPI, Institut of Parasitology and tropical pathology Strasbourg, France.,University of Strasbourg, IUT Louis Pasteur, Schiltigheim, France.,Institut des Hautes Etudes Scientifiques-Centre National de la Recherche Scientifique, 35 route de Chartres, 91440 Bures sur Yvette, France
| | - Faezeh Forouzanfar
- University of Strasbourg, EA7292, DHPI, Institut of Parasitology and tropical pathology Strasbourg, France
| | - Sebastian Eilebrecht
- Institut Universitaire de France, Paris, France.,Université Libre de Bruxelles (ULB), Service of Molecular Virology, Institute for Molecular Biology and Medicine (IBMM), 12 rue des Profs Jeener et Brachet, 6041 Gosselies, Belgium
| | - Benoit Van Driessche
- Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 242, Heidelberg 69120, Germany
| | - Amina Ait-Ammar
- University of Strasbourg, EA7292, DHPI, Institut of Parasitology and tropical pathology Strasbourg, France
| | - Roxane Verdikt
- Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 242, Heidelberg 69120, Germany
| | - Yoshihito Kurashige
- CNRS UMR 7224, Université Pierre et Marie Curie, 7 quai Saint Bernard, 75005 Paris, France
| | - Céline Marban
- CNRS UMR 7224, Université Pierre et Marie Curie, 7 quai Saint Bernard, 75005 Paris, France
| | - Virginie Gautier
- Institut des Hautes Etudes Scientifiques-Centre National de la Recherche Scientifique, 35 route de Chartres, 91440 Bures sur Yvette, France
| | - Ermanno Candolfi
- University of Strasbourg, EA7292, DHPI, Institut of Parasitology and tropical pathology Strasbourg, France
| | - Arndt G Benecke
- Université Libre de Bruxelles (ULB), Service of Molecular Virology, Institute for Molecular Biology and Medicine (IBMM), 12 rue des Profs Jeener et Brachet, 6041 Gosselies, Belgium.,UCD Centre for Research in Infectious Diseases (CRID) School of Medicine and Medical Science University College Dublin, Ireland
| | - Carine Van Lint
- Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 242, Heidelberg 69120, Germany
| | - Olivier Rohr
- University of Strasbourg, EA7292, DHPI, Institut of Parasitology and tropical pathology Strasbourg, France.,University of Strasbourg, IUT Louis Pasteur, Schiltigheim, France.,Inserm UMR 1121 Faculté de Chirurgie Dentaire Pavillon Leriche 1, place de l'Hôpital Strasbourg, France
| | - Christian Schwartz
- University of Strasbourg, EA7292, DHPI, Institut of Parasitology and tropical pathology Strasbourg, France.,University of Strasbourg, IUT Louis Pasteur, Schiltigheim, France
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Marban C, Forouzanfar F, Ait-Ammar A, Fahmi F, El Mekdad H, Daouad F, Rohr O, Schwartz C. Targeting the Brain Reservoirs: Toward an HIV Cure. Front Immunol 2016; 7:397. [PMID: 27746784 PMCID: PMC5044677 DOI: 10.3389/fimmu.2016.00397] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 09/20/2016] [Indexed: 12/23/2022] Open
Abstract
One of the top research priorities of the international AIDS society by the action “Towards an HIV Cure” is the purge or the decrease of the pool of all latently infected cells. This strategy is based on reactivation of latently reservoirs (the shock) followed by an intensifying combination antiretroviral therapy (cART) to kill them (the kill). The central nervous system (CNS) has potential latently infected cells, i.e., perivascular macrophages, microglial cells, and astrocytes that will need to be eliminated. However, the CNS has several characteristics that may preclude the achievement of a cure. In this review, we discuss several limitations to the eradication of brain reservoirs and how we could circumvent these limitations by making it efforts in four directions: (i) designing efficient latency-reversal agents for CNS-cell types, (ii) improving cART by targeting HIV transcription, (iii) improving delivery of HIV drugs in the CNS and in the CNS-cell types, and (iv) developing therapeutic immunization. As a prerequisite to these efforts, we also believe that a better comprehension of molecular mechanisms involved in establishment and persistence of HIV latency in brain reservoirs are essential to design new molecules for strategies aiming to achieve a cure for instance the “shock and kill” strategy.
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Affiliation(s)
- Céline Marban
- INSERM UMR 1121 Faculté de Chirurgie Dentaire, Université de Strasbourg , Strasbourg , France
| | | | - Amina Ait-Ammar
- EA7292, DHPI, Université de Strasbourg , Strasbourg , France
| | - Faiza Fahmi
- EA7292, DHPI, Université de Strasbourg , Strasbourg , France
| | - Hala El Mekdad
- EA7292, DHPI, Université de Strasbourg, Strasbourg, France; IUT Louis Pasteur de Schiltigheim, Université de Strasbourg, Schiltigheim, France
| | - Fadoua Daouad
- EA7292, DHPI, Université de Strasbourg , Strasbourg , France
| | - Olivier Rohr
- EA7292, DHPI, Université de Strasbourg, Strasbourg, France; IUT Louis Pasteur de Schiltigheim, Université de Strasbourg, Schiltigheim, France; Institut Universitaire de France, Paris, France
| | - Christian Schwartz
- EA7292, DHPI, Université de Strasbourg, Strasbourg, France; IUT Louis Pasteur de Schiltigheim, Université de Strasbourg, Schiltigheim, France
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