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Chang YT, Prompsy P, Kimeswenger S, Tsai YC, Ignatova D, Pavlova O, Iselin C, French LE, Levesque MP, Kuonen F, Bobrowicz M, Brunner PM, Pascolo S, Hoetzenecker W, Guenova E. MHC-I upregulation safeguards neoplastic T cells in the skin against NK cell-mediated eradication in mycosis fungoides. Nat Commun 2024; 15:752. [PMID: 38272918 PMCID: PMC10810852 DOI: 10.1038/s41467-024-45083-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 01/15/2024] [Indexed: 01/27/2024] Open
Abstract
Cancer-associated immune dysfunction is a major challenge for effective therapies. The emergence of antibodies targeting tumor cell-surface antigens led to advancements in the treatment of hematopoietic malignancies, particularly blood cancers. Yet their impact is constrained against tumors of hematopoietic origin manifesting in the skin. In this study, we employ a clonality-supervised deep learning methodology to dissect key pathological features implicated in mycosis fungoides, the most common cutaneous T-cell lymphoma. Our investigations unveil the prominence of the IL-32β-major histocompatibility complex (MHC)-I axis as a critical determinant in tumor T-cell immune evasion within the skin microenvironment. In patients' skin, we find MHC-I to detrimentally impact the functionality of natural killer (NK) cells, diminishing antibody-dependent cellular cytotoxicity and promoting resistance of tumor skin T-cells to cell-surface targeting therapies. Through murine experiments in female mice, we demonstrate that disruption of the MHC-I interaction with NK cell inhibitory Ly49 receptors restores NK cell anti-tumor activity and targeted T-cell lymphoma elimination in vivo. These findings underscore the significance of attenuating the MHC-I-dependent immunosuppressive networks within skin tumors. Overall, our study introduces a strategy to reinvigorate NK cell-mediated anti-tumor responses to overcome treatment resistance to existing cell-surface targeted therapies for skin lymphoma.
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Affiliation(s)
- Yun-Tsan Chang
- Department of Dermatology, Lausanne University Hospital (CHUV) and Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Pacôme Prompsy
- Department of Dermatology, Lausanne University Hospital (CHUV) and Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Susanne Kimeswenger
- Department of Dermatology and Venerology, Medical Faculty, Johannes Kepler University, Linz, Austria
| | - Yi-Chien Tsai
- Department of Dermatology, Lausanne University Hospital (CHUV) and Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Desislava Ignatova
- Department of Dermatology, University Hospital of Zurich and Faculty of Medicine, University of Zurich, Zurich, Switzerland
| | - Olesya Pavlova
- Department of Dermatology, Lausanne University Hospital (CHUV) and Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Christoph Iselin
- Department of Dermatology, Lausanne University Hospital (CHUV) and Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Lars E French
- Department of Dermatology and Allergology, Ludwig-Maximilians-University of Munich, Munich, Germany
- Dr. Phillip Frost Department of Dermatology and Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Mitchell P Levesque
- Department of Dermatology, University Hospital of Zurich and Faculty of Medicine, University of Zurich, Zurich, Switzerland
| | - François Kuonen
- Department of Dermatology, Lausanne University Hospital (CHUV) and Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | | | - Patrick M Brunner
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Steve Pascolo
- Department of Dermatology, University Hospital of Zurich and Faculty of Medicine, University of Zurich, Zurich, Switzerland
| | - Wolfram Hoetzenecker
- Department of Dermatology and Venerology, Medical Faculty, Johannes Kepler University, Linz, Austria.
| | - Emmanuella Guenova
- Department of Dermatology, Lausanne University Hospital (CHUV) and Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.
- Department of Dermatology, University Hospital of Zurich and Faculty of Medicine, University of Zurich, Zurich, Switzerland.
- Department of Dermatology, Hospital 12 de Octubre, Medical School, University Complutense, Madrid, Spain.
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Ettinger M, Burner T, Sharma A, Chang YT, Lackner A, Prompsy P, Deli IM, Traxler J, Wahl G, Altrichter S, Langer R, Tsai YC, Varkhande SR, Schoeftner LC, Iselin C, Gratz IK, Kimeswenger S, Guenova E, Hoetzenecker W. Th17-associated cytokines IL-17 and IL-23 in inflamed skin of Darier disease patients as potential therapeutic targets. Nat Commun 2023; 14:7470. [PMID: 37978298 PMCID: PMC10656568 DOI: 10.1038/s41467-023-43210-5] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 11/02/2023] [Indexed: 11/19/2023] Open
Abstract
Darier disease (DD) is a rare, inherited multi-organ disorder associated with mutations in the ATP2A2 gene. DD patients often have skin involvement characterized by malodorous, inflamed skin and recurrent, severe infections. Therapeutic options are limited and inadequate for the long-term management of this chronic disease. The aim of this study was to characterize the cutaneous immune infiltrate in DD skin lesions in detail and to identify new therapeutic targets. Using gene and protein expression profiling assays including scRNA sequencing, we demonstrate enhanced expression of Th17-related genes and cytokines and increased numbers of Th17 cells in six DD patients. We provide evidence that targeting the IL-17/IL-23 axis in a case series of three DD patients with monoclonal antibodies is efficacious with significant clinical improvement. As DD is a chronic, relapsing disease, our findings might pave the way toward additional options for the long-term management of skin inflammation in patients with DD.
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Affiliation(s)
- Monika Ettinger
- Department of Dermatology and Venereology, Kepler University Hospital Linz, Linz, Austria
- Department of Dermatology and Venereology, Medical Faculty, Johannes Kepler University Linz, Linz, Austria
| | - Teresa Burner
- Department of Dermatology and Venereology, Medical Faculty, Johannes Kepler University Linz, Linz, Austria
| | - Anshu Sharma
- Department of Biosciences and Molecular Biology, University of Salzburg, Salzburg, Austria
| | - Yun-Tsan Chang
- Department of Dermatology, University of Lausanne and Faculty of Biology and Medicine, Lausanne, Switzerland
| | - Angelika Lackner
- Department of Dermatology and Venereology, Medical Faculty, Johannes Kepler University Linz, Linz, Austria
| | - Pacôme Prompsy
- Department of Dermatology, University of Lausanne and Faculty of Biology and Medicine, Lausanne, Switzerland
| | - Isabella M Deli
- Department of Dermatology and Venereology, Kepler University Hospital Linz, Linz, Austria
| | - Judith Traxler
- Department of Dermatology and Venereology, Kepler University Hospital Linz, Linz, Austria
| | - Gerald Wahl
- Department of Dermatology and Venereology, Kepler University Hospital Linz, Linz, Austria
| | - Sabine Altrichter
- Department of Dermatology and Venereology, Kepler University Hospital Linz, Linz, Austria
- Department of Dermatology and Venereology, Medical Faculty, Johannes Kepler University Linz, Linz, Austria
| | - Rupert Langer
- Institute of Pathology and Molecular Pathology, Kepler University Hospital Linz, Linz, Austria
- Institute of Pathology and Molecular Pathology, Medical Faculty, Johannes Kepler University Linz, Linz, Austria
| | - Yi-Chien Tsai
- Department of Dermatology, University of Lausanne and Faculty of Biology and Medicine, Lausanne, Switzerland
| | - Suraj R Varkhande
- Department of Biosciences and Molecular Biology, University of Salzburg, Salzburg, Austria
| | - Leonie C Schoeftner
- Department of Biosciences and Molecular Biology, University of Salzburg, Salzburg, Austria
| | - Christoph Iselin
- Department of Dermatology, University of Lausanne and Faculty of Biology and Medicine, Lausanne, Switzerland
| | - Iris K Gratz
- Department of Biosciences and Molecular Biology, University of Salzburg, Salzburg, Austria
| | - Susanne Kimeswenger
- Department of Dermatology and Venereology, Medical Faculty, Johannes Kepler University Linz, Linz, Austria
| | - Emmanuella Guenova
- Department of Dermatology, University of Lausanne and Faculty of Biology and Medicine, Lausanne, Switzerland
- Department of Dermatology, Hospital 12 de octubre, Medical school, University Complutense, Madrid, Spain
| | - Wolfram Hoetzenecker
- Department of Dermatology and Venereology, Kepler University Hospital Linz, Linz, Austria.
- Department of Dermatology and Venereology, Medical Faculty, Johannes Kepler University Linz, Linz, Austria.
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Raimundo F, Prompsy P, Vert JP, Vallot C. A benchmark of computational pipelines for single-cell histone modification data. Genome Biol 2023; 24:143. [PMID: 37340307 PMCID: PMC10280832 DOI: 10.1186/s13059-023-02981-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 06/07/2023] [Indexed: 06/22/2023] Open
Abstract
BACKGROUND Single-cell histone post translational modification (scHPTM) assays such as scCUT&Tag or scChIP-seq allow single-cell mapping of diverse epigenomic landscapes within complex tissues and are likely to unlock our understanding of various mechanisms involved in development or diseases. Running scHTPM experiments and analyzing the data produced remains challenging since few consensus guidelines currently exist regarding good practices for experimental design and data analysis pipelines. RESULTS We perform a computational benchmark to assess the impact of experimental parameters and data analysis pipelines on the ability of the cell representation to recapitulate known biological similarities. We run more than ten thousand experiments to systematically study the impact of coverage and number of cells, of the count matrix construction method, of feature selection and normalization, and of the dimension reduction algorithm used. This allows us to identify key experimental parameters and computational choices to obtain a good representation of single-cell HPTM data. We show in particular that the count matrix construction step has a strong influence on the quality of the representation and that using fixed-size bin counts outperforms annotation-based binning. Dimension reduction methods based on latent semantic indexing outperform others, and feature selection is detrimental, while keeping only high-quality cells has little influence on the final representation as long as enough cells are analyzed. CONCLUSIONS This benchmark provides a comprehensive study on how experimental parameters and computational choices affect the representation of single-cell HPTM data. We propose a series of recommendations regarding matrix construction, feature and cell selection, and dimensionality reduction algorithms.
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Affiliation(s)
- Félix Raimundo
- Google Research, Brain team, 75009, Paris, France
- Translational Research Department, Institut Curie, PSL Research University, 75005, Paris, France
| | - Pacôme Prompsy
- Translational Research Department, Institut Curie, PSL Research University, 75005, Paris, France
- CNRS UMR3244, Institut Curie, PSL Research University, 75005, Paris, France
| | - Jean-Philippe Vert
- Google Research, Brain team, 75009, Paris, France.
- Owkin, Inc, NY, New York, USA.
| | - Céline Vallot
- Translational Research Department, Institut Curie, PSL Research University, 75005, Paris, France.
- CNRS UMR3244, Institut Curie, PSL Research University, 75005, Paris, France.
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Marsolier J, Prompsy P, Durand A, Lyne AM, Landragin C, Trouchet A, Bento ST, Eisele A, Foulon S, Baudre L, Grosselin K, Bohec M, Baulande S, Dahmani A, Sourd L, Letouzé E, Salomon AV, Marangoni E, Perié L, Vallot C. H3K27me3 conditions chemotolerance in triple-negative breast cancer. Nat Genet 2022; 54:459-468. [PMID: 35410383 PMCID: PMC7612638 DOI: 10.1038/s41588-022-01047-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [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: 12/21/2021] [Accepted: 03/04/2022] [Indexed: 12/11/2022]
Abstract
The persistence of cancer cells resistant to therapy remains a major clinical challenge. In triple-negative breast cancer, resistance to chemotherapy results in the highest recurrence risk among breast cancer subtypes. The drug-tolerant state seems largely defined by nongenetic features, but the underlying mechanisms are poorly understood. Here, by monitoring epigenomes, transcriptomes and lineages with single-cell resolution, we show that the repressive histone mark H3K27me3 (trimethylation of histone H3 at lysine 27) regulates cell fate at the onset of chemotherapy. We report that a persister expression program is primed with both H3K4me3 (trimethylation of histone H3 at lysine 4) and H3K27me3 in unchallenged cells, with H3K27me3 being the lock to its transcriptional activation. We further demonstrate that depleting H3K27me3 enhances the potential of cancer cells to tolerate chemotherapy. Conversely, preventing H3K27me3 demethylation simultaneously to chemotherapy inhibits the transition to a drug-tolerant state, and delays tumor recurrence in vivo. Our results highlight how chromatin landscapes shape the potential of cancer cells to respond to initial therapy.
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Affiliation(s)
- Justine Marsolier
- CNRS UMR3244, Institut Curie, PSL University, Paris, France,Translational Research Department, Institut Curie, PSL University, Paris, France
| | - Pacôme Prompsy
- CNRS UMR3244, Institut Curie, PSL University, Paris, France,Translational Research Department, Institut Curie, PSL University, Paris, France
| | - Adeline Durand
- CNRS UMR3244, Institut Curie, PSL University, Paris, France,Translational Research Department, Institut Curie, PSL University, Paris, France
| | - Anne-Marie Lyne
- CNRS UMR168, Institut Curie, PSL University, Sorbonne University, Paris, France
| | - Camille Landragin
- CNRS UMR3244, Institut Curie, PSL University, Paris, France,Translational Research Department, Institut Curie, PSL University, Paris, France
| | - Amandine Trouchet
- CNRS UMR3244, Institut Curie, PSL University, Paris, France,Single Cell Initiative, Institut Curie, PSL University, Paris, France
| | | | - Almut Eisele
- CNRS UMR168, Institut Curie, PSL University, Sorbonne University, Paris, France
| | - Sophie Foulon
- CNRS UMR8231, ESPCI Paris, PSL University, Paris, France
| | - Léa Baudre
- CNRS UMR3244, Institut Curie, PSL University, Paris, France,Translational Research Department, Institut Curie, PSL University, Paris, France
| | - Kevin Grosselin
- CNRS UMR8231, ESPCI Paris, PSL University, Paris, France,HiFiBio SAS, Paris, France,Current Affiliation: Broad Institute of MIT and Harvard, Cambridge MA, USA
| | - Mylène Bohec
- Single Cell Initiative, Institut Curie, PSL University, Paris, France,Genomics of Excellence (ICGex) Platform, Institut Curie, PSL University, Paris, France
| | - Sylvain Baulande
- Single Cell Initiative, Institut Curie, PSL University, Paris, France,Genomics of Excellence (ICGex) Platform, Institut Curie, PSL University, Paris, France
| | - Ahmed Dahmani
- Translational Research Department, Institut Curie, PSL University, Paris, France
| | - Laura Sourd
- Translational Research Department, Institut Curie, PSL University, Paris, France
| | - Eric Letouzé
- Functional Genomics of Solid Tumors laboratory, Centre de Recherche des Cordeliers, Sorbonne University, Inserm, USPC, Paris Descartes University, Paris Diderot University, Paris, France
| | - Anne-Vincent Salomon
- Pathology-Genetics-Immunology Department, Institut Curie, PSL Research University, Paris, France,INSERM U934, Institut Curie, PSL Research University, Paris, France
| | - Elisabetta Marangoni
- Translational Research Department, Institut Curie, PSL University, Paris, France
| | - Leïla Perié
- CNRS UMR168, Institut Curie, PSL University, Sorbonne University, Paris, France
| | - Céline Vallot
- CNRS UMR3244, Institut Curie, PSL University, Paris, France. .,Translational Research Department, Institut Curie, PSL University, Paris, France.
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Prompsy P, Kirchmeier P, Marsolier J, Deloger M, Servant N, Vallot C. Interactive analysis of single-cell epigenomic landscapes with ChromSCape. Nat Commun 2020; 11:5702. [PMID: 33177523 PMCID: PMC7658988 DOI: 10.1038/s41467-020-19542-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 10/21/2020] [Indexed: 01/05/2023] Open
Abstract
Chromatin modifications orchestrate the dynamic regulation of gene expression during development and in disease. Bulk approaches have characterized the wide repertoire of histone modifications across cell types, detailing their role in shaping cell identity. However, these population-based methods do not capture cell-to-cell heterogeneity of chromatin landscapes, limiting our appreciation of the role of chromatin in dynamic biological processes. Recent technological developments enable the mapping of histone marks at single-cell resolution, opening up perspectives to characterize the heterogeneity of chromatin marks in complex biological systems over time. Yet, existing tools used to analyze bulk histone modifications profiles are not fit for the low coverage and sparsity of single-cell epigenomic datasets. Here, we present ChromSCape, a user-friendly interactive Shiny/R application distributed as a Bioconductor package, that processes single-cell epigenomic data to assist the biological interpretation of chromatin landscapes within cell populations. ChromSCape analyses the distribution of repressive and active histone modifications as well as chromatin accessibility landscapes from single-cell datasets. Using ChromSCape, we deconvolve chromatin landscapes within the tumor micro-environment, identifying distinct H3K27me3 landscapes associated with cell identity and breast tumor subtype.
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Affiliation(s)
- Pacôme Prompsy
- CNRS UMR3244, Institut Curie, PSL Research University, 26 rue d'Ulm, 75005, Paris, France.
- Translational Research Department, Institut Curie, PSL Research University, 26 rue d'Ulm, 75005, Paris, France.
| | - Pia Kirchmeier
- CNRS UMR3244, Institut Curie, PSL Research University, 26 rue d'Ulm, 75005, Paris, France
- Translational Research Department, Institut Curie, PSL Research University, 26 rue d'Ulm, 75005, Paris, France
| | - Justine Marsolier
- CNRS UMR3244, Institut Curie, PSL Research University, 26 rue d'Ulm, 75005, Paris, France
- Translational Research Department, Institut Curie, PSL Research University, 26 rue d'Ulm, 75005, Paris, France
| | - Marc Deloger
- INSERM U900, Institut Curie, PSL Research University, Mines ParisTech, 26 rue d'Ulm, 75005, Paris, France
| | - Nicolas Servant
- INSERM U900, Institut Curie, PSL Research University, Mines ParisTech, 26 rue d'Ulm, 75005, Paris, France
| | - Céline Vallot
- CNRS UMR3244, Institut Curie, PSL Research University, 26 rue d'Ulm, 75005, Paris, France.
- Translational Research Department, Institut Curie, PSL Research University, 26 rue d'Ulm, 75005, Paris, France.
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Marone A, Trably E, Carrère H, Prompsy P, Guillon F, Joseph-Aimé M, Barakat A, Fayoud N, Bernet N, Escudié R. Enhancement of corn stover conversion to carboxylates by extrusion and biotic triggers in solid-state fermentation. Appl Microbiol Biotechnol 2018; 103:489-503. [PMID: 30406449 DOI: 10.1007/s00253-018-9463-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 10/02/2018] [Accepted: 10/08/2018] [Indexed: 11/24/2022]
Abstract
Solid-state fermentation is a potential technology for developing lignocellulosic biomass-based biorefineries. This work dealt with solid-state fermentation for carboxylates production from corn stover, as building blocks for a lignocellulosic feedstock-based biorefinery. The effect of extrusion pretreatment, together with the action of a microbial consortia and hydrolytic enzymes as biotic triggers, was investigated on corn stover conversion, microbial metabolic pathways, and populations. The extrusion caused changes in the physical and morphological characteristics, without altering the biochemical composition of the corn stover. Extrusion also led to remarkable differences in the composition of the indigenous microbial population of the substrate. Consequently, it affected the structure of community developed after fermentation and the substrate conversion yield, which increased by 118% (from 23 ± 4 gCOD/kgVSi obtained with raw substrate to 51 ± 1 gCOD/kgVSi with extruded corn stover) with regard to self-fermentation experiments. The use of activated sludge as inoculum further increased the total substrate conversion into carboxylates, up to 60 ± 2 gCOD/kgVSi, and shaped the microbial communities (mainly composed of bacteria from the Clostridia and Bacteroidia classes) with subsequent homogenization of the fermentation pathways. The addition of hydrolytic enzymes into the reactors further increased the corn stover conversion, leading to a maximum yield of 142 ± 1 gCOD/kgVSi. Thus, extrusion pretreatment combined with the use of an inoculum and enzyme addition increased by 506% corn stover conversion into carboxylates. Beside biomass pretreatment, the results of this study indicated that biotic factor greatly impacted solid-state fermentation by shaping the microbial communities and related metabolic pathways.
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Affiliation(s)
- Antonella Marone
- LBE, INRA, Univ Montpellier, 102 Avenue des Etangs, F-11100, Narbonne, France.,GENOCOV, Departament d'Enginyeria Química, Biològica i Ambiental, Escola d'Enginyeria, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Eric Trably
- LBE, INRA, Univ Montpellier, 102 Avenue des Etangs, F-11100, Narbonne, France.
| | - Hélène Carrère
- LBE, INRA, Univ Montpellier, 102 Avenue des Etangs, F-11100, Narbonne, France
| | - Pacôme Prompsy
- LBE, INRA, Univ Montpellier, 102 Avenue des Etangs, F-11100, Narbonne, France
| | | | | | - Abdellatif Barakat
- UMR, IATE, CIRAD, Montpellier SupAgro, INRA, Université de Montpellier, 34060, Montpellier, France
| | - Nour Fayoud
- UMR, IATE, CIRAD, Montpellier SupAgro, INRA, Université de Montpellier, 34060, Montpellier, France.,Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Nicolas Bernet
- LBE, INRA, Univ Montpellier, 102 Avenue des Etangs, F-11100, Narbonne, France
| | - Renaud Escudié
- LBE, INRA, Univ Montpellier, 102 Avenue des Etangs, F-11100, Narbonne, France
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