1
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Truchi M, Lacoux C, Gille C, Fassy J, Magnone V, Lopes Goncalves R, Girard-Riboulleau C, Manosalva-Pena I, Gautier-Isola M, Lebrigand K, Barbry P, Spicuglia S, Vassaux G, Rezzonico R, Barlaud M, Mari B. Detecting subtle transcriptomic perturbations induced by lncRNAs knock-down in single-cell CRISPRi screening using a new sparse supervised autoencoder neural network. Front Bioinform 2024; 4:1340339. [PMID: 38501112 PMCID: PMC10945021 DOI: 10.3389/fbinf.2024.1340339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 02/14/2024] [Indexed: 03/20/2024] Open
Abstract
Single-cell CRISPR-based transcriptome screens are potent genetic tools for concomitantly assessing the expression profiles of cells targeted by a set of guides RNA (gRNA), and inferring target gene functions from the observed perturbations. However, due to various limitations, this approach lacks sensitivity in detecting weak perturbations and is essentially reliable when studying master regulators such as transcription factors. To overcome the challenge of detecting subtle gRNA induced transcriptomic perturbations and classifying the most responsive cells, we developed a new supervised autoencoder neural network method. Our Sparse supervised autoencoder (SSAE) neural network provides selection of both relevant features (genes) and actual perturbed cells. We applied this method on an in-house single-cell CRISPR-interference-based (CRISPRi) transcriptome screening (CROP-Seq) focusing on a subset of long non-coding RNAs (lncRNAs) regulated by hypoxia, a condition that promote tumor aggressiveness and drug resistance, in the context of lung adenocarcinoma (LUAD). The CROP-seq library of validated gRNA against a subset of lncRNAs and, as positive controls, HIF1A and HIF2A, the 2 main transcription factors of the hypoxic response, was transduced in A549 LUAD cells cultured in normoxia or exposed to hypoxic conditions during 3, 6 or 24 h. We first validated the SSAE approach on HIF1A and HIF2 by confirming the specific effect of their knock-down during the temporal switch of the hypoxic response. Next, the SSAE method was able to detect stable short hypoxia-dependent transcriptomic signatures induced by the knock-down of some lncRNAs candidates, outperforming previously published machine learning approaches. This proof of concept demonstrates the relevance of the SSAE approach for deciphering weak perturbations in single-cell transcriptomic data readout as part of CRISPR-based screening.
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Affiliation(s)
- Marin Truchi
- Université Côte d’Azur, IPMC, UMR CNRS 7275 Inserm 1323, IHU RespiERA, Valbonne, France
| | - Caroline Lacoux
- Université Côte d’Azur, IPMC, UMR CNRS 7275 Inserm 1323, IHU RespiERA, Valbonne, France
| | - Cyprien Gille
- Université Côte d’Azur, I3S, CNRS UMR7271, Nice, France
| | - Julien Fassy
- Université Côte d’Azur, IPMC, UMR CNRS 7275 Inserm 1323, IHU RespiERA, Valbonne, France
| | - Virginie Magnone
- Université Côte d’Azur, IPMC, UMR CNRS 7275 Inserm 1323, IHU RespiERA, Valbonne, France
| | | | | | - Iris Manosalva-Pena
- Aix-Marseille University, Inserm, TAGC, UMR1090, Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - Marine Gautier-Isola
- Université Côte d’Azur, IPMC, UMR CNRS 7275 Inserm 1323, IHU RespiERA, Valbonne, France
| | - Kevin Lebrigand
- Université Côte d’Azur, IPMC, UMR CNRS 7275 Inserm 1323, IHU RespiERA, Valbonne, France
| | - Pascal Barbry
- Université Côte d’Azur, IPMC, UMR CNRS 7275 Inserm 1323, IHU RespiERA, Valbonne, France
| | - Salvatore Spicuglia
- Aix-Marseille University, Inserm, TAGC, UMR1090, Equipe Labélisée Ligue Contre le Cancer, Marseille, France
| | - Georges Vassaux
- Université Côte d’Azur, IPMC, UMR CNRS 7275 Inserm 1323, IHU RespiERA, Valbonne, France
| | - Roger Rezzonico
- Université Côte d’Azur, IPMC, UMR CNRS 7275 Inserm 1323, IHU RespiERA, Valbonne, France
| | | | - Bernard Mari
- Université Côte d’Azur, IPMC, UMR CNRS 7275 Inserm 1323, IHU RespiERA, Valbonne, France
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2
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Zaragosi LE, Gouleau A, Delin M, Lebrigand K, Arguel MJ, Girard-Riboulleau C, Rios G, Redman E, Plaisant M, Waldmann R, Magnone V, Marcet B, Barbry P, Ponzio G. Combination of CRISPR-Cas9-RNP and Single-Cell RNAseq to Identify Cell State-Specific FOXJ1 Functions in the Human Airway Epithelium. Methods Mol Biol 2024; 2725:1-25. [PMID: 37856015 DOI: 10.1007/978-1-0716-3507-0_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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
Abstract
The study of the airway epithelium in vitro is routinely performed using air-liquid culture (ALI) models from nasal or bronchial basal cells. These 3D experimental models allow to follow the regeneration steps of fully differentiated mucociliary epithelium and to study gene function by performing gene invalidation. Recent progress made with CRISPR-based techniques has overcome the experimental difficulty of this approach, by a direct transfection of ribonucleoprotein complexes combining a mix of synthetic small guide RNAs (sgRNAs) and recombinant Cas9. The approach shows more than 95% efficiency and does not require any selection step. A limitation of this approach is that it generates cell populations that contain heterogeneous deletions, which makes the evaluation of invalidation efficiency difficult. We have successfully used Flongle sequencing (Nanopore) to quantify the number of distinct deletions. We describe the use of CRISPR-Cas9 RNP in combination with single-cell RNA sequencing to functionally characterize the impact of gene invalidation in ALI cultures. The complex ecosystem of the airway epithelium, composed of many cell types, makes single-cell approaches particularly relevant to study cell type, or cell state-specific events. This protocol describes the invalidation of FOXJ1 in ALI cultures through the following steps: (1) Establishment of basal cell cultures from nasal turbinates, (2) CRISPR-Cas9 RNP invalidation of FOXJ1, (3) Quantification of FOXJ1 invalidation efficiency by Nanopore sequencing, (4) Dissociation of ALI cultures and single-cell RNAseq, (5) Analysis of single-cell RNAseq data from FOXJ1-invalidated cells.We confirm here that FOXJ1 invalidation impairs the final differentiation step of multiciliated cells and provides a framework to explore other gene functions.
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Affiliation(s)
| | - Alizé Gouleau
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis, France
| | - Margot Delin
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis, France
| | - Kevin Lebrigand
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis, France
| | | | | | - Geraldine Rios
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis, France
| | - Elisa Redman
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis, France
| | - Magali Plaisant
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis, France
| | - Rainer Waldmann
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis, France
| | | | - Brice Marcet
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis, France
| | - Pascal Barbry
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis, France
| | - Gilles Ponzio
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis, France
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3
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Guilbaud E, Barouillet T, Ilie M, Borowczyk C, Ivanov S, Sarrazy V, Vaillant N, Ayrault M, Castiglione A, Rignol G, Brest P, Bazioti V, Zaitsev K, Lebrigand K, Dussaud S, Magnone V, Bertolotto C, Marchetti S, Irondelle M, Goldberg I, Huby T, Westerterp M, Gautier EL, Mari B, Barbry P, Hofman P, Yvan-Charvet L. Cholesterol efflux pathways hinder KRAS-driven lung tumor progenitor cell expansion. Cell Stem Cell 2023; 30:800-817.e9. [PMID: 37267915 DOI: 10.1016/j.stem.2023.05.005] [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: 02/16/2023] [Revised: 04/13/2023] [Accepted: 05/04/2023] [Indexed: 06/04/2023]
Abstract
Cholesterol efflux pathways could be exploited in tumor biology to unravel cancer vulnerabilities. A mouse model of lung-tumor-bearing KRASG12D mutation with specific disruption of cholesterol efflux pathways in epithelial progenitor cells promoted tumor growth. Defective cholesterol efflux in epithelial progenitor cells governed their transcriptional landscape to support their expansion and create a pro-tolerogenic tumor microenvironment (TME). Overexpression of the apolipoprotein A-I, to raise HDL levels, protected these mice from tumor development and dire pathologic consequences. Mechanistically, HDL blunted a positive feedback loop between growth factor signaling pathways and cholesterol efflux pathways that cancer cells hijack to expand. Cholesterol removal therapy with cyclodextrin reduced tumor burden in progressing tumor by suppressing the proliferation and expansion of epithelial progenitor cells of tumor origin. Local and systemic perturbations of cholesterol efflux pathways were confirmed in human lung adenocarcinoma (LUAD). Our results position cholesterol removal therapy as a putative metabolic target in lung cancer progenitor cells.
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Affiliation(s)
- Emma Guilbaud
- Institut National de la Santé et de la Recherche Médicale (Inserm) U1065, Université Côte d'Azur, Centre Méditerranéen de Médecine Moléculaire (C3M), Atip-Avenir, Fédération Hospitalo-Universitaire (FHU) OncoAge, 06204 Nice, France; Department of Radiation Oncology, Weill Cornell Medical College, New York, NY, USA.
| | - Thibault Barouillet
- Institut National de la Santé et de la Recherche Médicale (Inserm) U1065, Université Côte d'Azur, Centre Méditerranéen de Médecine Moléculaire (C3M), Atip-Avenir, Fédération Hospitalo-Universitaire (FHU) OncoAge, 06204 Nice, France
| | - Marius Ilie
- Institute of Research on Cancer and Aging of Nice (IRCAN), Inserm U1081, CNRS UMR7284, Laboratory of Clinical and Experimental Pathology, Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, CHU de Nice, University Hospital Federation OncoAge, 06107 Nice, France
| | - Coraline Borowczyk
- Institut National de la Santé et de la Recherche Médicale (Inserm) U1065, Université Côte d'Azur, Centre Méditerranéen de Médecine Moléculaire (C3M), Atip-Avenir, Fédération Hospitalo-Universitaire (FHU) OncoAge, 06204 Nice, France
| | - Stoyan Ivanov
- Institut National de la Santé et de la Recherche Médicale (Inserm) U1065, Université Côte d'Azur, Centre Méditerranéen de Médecine Moléculaire (C3M), Atip-Avenir, Fédération Hospitalo-Universitaire (FHU) OncoAge, 06204 Nice, France
| | - Vincent Sarrazy
- Institut National de la Santé et de la Recherche Médicale (Inserm) U1065, Université Côte d'Azur, Centre Méditerranéen de Médecine Moléculaire (C3M), Atip-Avenir, Fédération Hospitalo-Universitaire (FHU) OncoAge, 06204 Nice, France
| | - Nathalie Vaillant
- Institut National de la Santé et de la Recherche Médicale (Inserm) U1065, Université Côte d'Azur, Centre Méditerranéen de Médecine Moléculaire (C3M), Atip-Avenir, Fédération Hospitalo-Universitaire (FHU) OncoAge, 06204 Nice, France
| | - Marion Ayrault
- Institut National de la Santé et de la Recherche Médicale (Inserm) U1065, Université Côte d'Azur, Centre Méditerranéen de Médecine Moléculaire (C3M), Atip-Avenir, Fédération Hospitalo-Universitaire (FHU) OncoAge, 06204 Nice, France
| | - Alexia Castiglione
- Institut National de la Santé et de la Recherche Médicale (Inserm) U1065, Université Côte d'Azur, Centre Méditerranéen de Médecine Moléculaire (C3M), Atip-Avenir, Fédération Hospitalo-Universitaire (FHU) OncoAge, 06204 Nice, France
| | - Guylène Rignol
- Institut National de la Santé et de la Recherche Médicale (Inserm) U1065, Université Côte d'Azur, Centre Méditerranéen de Médecine Moléculaire (C3M), Atip-Avenir, Fédération Hospitalo-Universitaire (FHU) OncoAge, 06204 Nice, France
| | - Patrick Brest
- Institute of Research on Cancer and Aging of Nice (IRCAN), Inserm U1081, CNRS UMR7284, Laboratory of Clinical and Experimental Pathology, Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, CHU de Nice, University Hospital Federation OncoAge, 06107 Nice, France
| | - Venetia Bazioti
- Department of Pediatrics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Konstantin Zaitsev
- Computer Technologies Department, ITMO University, Saint Petersburg, Russia
| | - Kevin Lebrigand
- Université Côte d'Azur, Institut de Pharmacologie Moléculaire et Cellulaire (IPMC), CNRS UMR7275, FHU-OncoAge, Nice Sophia-Antipolis, France
| | | | - Virginie Magnone
- Université Côte d'Azur, Institut de Pharmacologie Moléculaire et Cellulaire (IPMC), CNRS UMR7275, FHU-OncoAge, Nice Sophia-Antipolis, France
| | - Corine Bertolotto
- Institut National de la Santé et de la Recherche Médicale (Inserm) U1065, Université Côte d'Azur, Centre Méditerranéen de Médecine Moléculaire (C3M), Atip-Avenir, Fédération Hospitalo-Universitaire (FHU) OncoAge, 06204 Nice, France
| | - Sandrine Marchetti
- Institut National de la Santé et de la Recherche Médicale (Inserm) U1065, Université Côte d'Azur, Centre Méditerranéen de Médecine Moléculaire (C3M), Atip-Avenir, Fédération Hospitalo-Universitaire (FHU) OncoAge, 06204 Nice, France
| | - Marie Irondelle
- Institut National de la Santé et de la Recherche Médicale (Inserm) U1065, Université Côte d'Azur, Centre Méditerranéen de Médecine Moléculaire (C3M), Atip-Avenir, Fédération Hospitalo-Universitaire (FHU) OncoAge, 06204 Nice, France
| | - Ira Goldberg
- Division of Endocrinology, Diabetes and Metabolism, NYU Langone Medical Center, New York, NY, USA
| | - Thierry Huby
- Sorbonne Université, INSERM, UMR_S 1166 ICAN, 75013 Paris, France
| | - Marit Westerterp
- Department of Pediatrics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | | | - Bernard Mari
- Université Côte d'Azur, Institut de Pharmacologie Moléculaire et Cellulaire (IPMC), CNRS UMR7275, FHU-OncoAge, Nice Sophia-Antipolis, France
| | - Pascal Barbry
- Université Côte d'Azur, Institut de Pharmacologie Moléculaire et Cellulaire (IPMC), CNRS UMR7275, FHU-OncoAge, Nice Sophia-Antipolis, France
| | - Paul Hofman
- Institute of Research on Cancer and Aging of Nice (IRCAN), Inserm U1081, CNRS UMR7284, Laboratory of Clinical and Experimental Pathology, Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, CHU de Nice, University Hospital Federation OncoAge, 06107 Nice, France
| | - Laurent Yvan-Charvet
- Institut National de la Santé et de la Recherche Médicale (Inserm) U1065, Université Côte d'Azur, Centre Méditerranéen de Médecine Moléculaire (C3M), Atip-Avenir, Fédération Hospitalo-Universitaire (FHU) OncoAge, 06204 Nice, France.
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4
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Zapletalová M, Rancurel C, Industri B, Bardin M, Le Brigand K, Nicot P, Magnone V, Seassau A, Barbry P, Potěšil D, Zdráhal Z, Ponchet M, Lochman J. BABA-induced pathogen resistance: a multi-omics analysis of the tomato response reveals a hyper-receptive status involving ethylene. Hortic Res 2023; 10:uhad068. [PMID: 37287445 PMCID: PMC10243938 DOI: 10.1093/hr/uhad068] [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] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 04/05/2023] [Indexed: 06/09/2023]
Abstract
Prior exposure to microbial-associated molecular patterns or specific chemical compounds can promote plants into a primed state with stronger defence responses. β-aminobutyric acid (BABA) is an endogenous stress metabolite that induces resistance protecting various plants towards diverse stresses. In this study, by integrating BABA-induced changes in selected metabolites with transcriptome and proteome data, we generated a global map of the molecular processes operating in BABA-induced resistance (BABA-IR) in tomato. BABA significantly restricts the growth of the pathogens Oidium neolycopersici and Phytophthora parasitica but not Botrytis cinerea. A cluster analysis of the upregulated processes showed that BABA acts mainly as a stress factor in tomato. The main factor distinguishing BABA-IR from other stress conditions was the extensive induction of signaling and perception machinery playing a key role in effective resistance against pathogens. Interestingly, the signalling processes and immune response activated during BABA-IR in tomato differed from those in Arabidopsis with substantial enrichment of genes associated with jasmonic acid (JA) and ethylene (ET) signalling and no change in Asp levels. Our results revealed key differences between the effect of BABA on tomato and other model plants studied until now. Surprisingly, salicylic acid (SA) is not involved in BABA downstream signalization whereas ET and JA play a crucial role.
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Affiliation(s)
| | | | - Benoit Industri
- UMR Institut Sophia Agrobiotech INRAE 1355, CNRS 6254, Université Côte d’Azur, 400, Route des Chappes, 06903 Sophia Antipolis, France
| | - Marc Bardin
- Unité 407 Pathologie végétale, INRAE, Domaine Saint-Maurice, 84143 Montfavet cedex, France
| | - Kevin Le Brigand
- UMR Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d’Azur, CNRS 7275, 660 Route des Lucioles 06560 Valbonne, France
| | - Philippe Nicot
- Unité 407 Pathologie végétale, INRAE, Domaine Saint-Maurice, 84143 Montfavet cedex, France
| | - Virginie Magnone
- UMR Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d’Azur, CNRS 7275, 660 Route des Lucioles 06560 Valbonne, France
| | - Aurélie Seassau
- UMR Institut Sophia Agrobiotech INRAE 1355, CNRS 6254, Université Côte d’Azur, 400, Route des Chappes, 06903 Sophia Antipolis, France
| | - Pascal Barbry
- UMR Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d’Azur, CNRS 7275, 660 Route des Lucioles 06560 Valbonne, France
| | - David Potěšil
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Zbyněk Zdráhal
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Michel Ponchet
- UMR Institut Sophia Agrobiotech INRAE 1355, CNRS 6254, Université Côte d’Azur, 400, Route des Chappes, 06903 Sophia Antipolis, France
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5
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Cavard A, Redman E, Mercey O, Abelanet S, Plaisant M, Arguel MJ, Magnone V, García SR, Rios G, Deprez M, Lebrigand K, Ponzio G, Caballero I, Barbry P, Zaragosi LE, Marcet B. The MIR34B/C genomic region contains multiple potential regulators of multiciliogenesis. FEBS Lett 2023. [PMID: 37102425 DOI: 10.1002/1873-3468.14630] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 04/11/2023] [Accepted: 04/12/2023] [Indexed: 04/28/2023]
Abstract
The MIR449 genomic locus encompasses several regulators of multiciliated cell formation (multiciliogenesis). The miR-449 homologues miR-34b/c represent additional regulators of multiciliogenesis that are transcribed from another locus. Here, we characterized the expression of BTG4, LAYN and HOATZ, located in the MIR34B/C locus using single-cell RNA-seq and super-resolution microscopy from human, mouse or pig multiciliogenesis models. BTG4, LAYN and HOATZ transcripts were expressed in both precursors and mature multiciliated cells. The Layilin/LAYN protein was absent from primary cilia, but it was expressed in apical membrane regions or throughout motile cilia. LAYN silencing altered apical actin cap formation and multiciliogenesis. HOATZ protein was detected in primary cilia or throughout motile cilia. Altogether, our data suggest that the MIR34B/C locus may gather potential actors of multiciliogenesis.
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Affiliation(s)
- Amélie Cavard
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis, France
| | - Elisa Redman
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis, France
| | - Olivier Mercey
- Institut de Biologie de l'École Normale Supérieure, Paris, France
| | - Sophie Abelanet
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis, France
| | - Magali Plaisant
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis, France
| | | | | | | | - Géraldine Rios
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis, France
| | - Marie Deprez
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis, France
| | - Kévin Lebrigand
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis, France
| | - Gilles Ponzio
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis, France
| | | | - Pascal Barbry
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis, France
| | | | - Brice Marcet
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis, France
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6
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Truchi M, Savary G, Lebrigand K, Baeri A, Girard-Riboulleau C, Magnone V, Leroy S, Hofman V, Hofman P, Barbry P, Bellusci S, Cauffiez C, Vassaux G, Pottier N, Mari B. Single-cell RNA-seq characterization of lung fibrosis resolution reveals a delayed capillary endothelial signature associated with alveolar regeneration in aged mice. Rev Mal Respir 2023. [DOI: 10.1016/j.rmr.2022.11.063] [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] [Indexed: 02/18/2023]
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7
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Feliz Morel ÁJ, Hasanovic A, Morin A, Prunier C, Magnone V, Lebrigand K, Aouad A, Cogoluegnes S, Favier J, Pasquier C, Mus-Veteau I. Persistent Properties of a Subpopulation of Cancer Cells Overexpressing the Hedgehog Receptor Patched. Pharmaceutics 2022; 14:pharmaceutics14050988. [PMID: 35631574 PMCID: PMC9146430 DOI: 10.3390/pharmaceutics14050988] [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: 01/19/2022] [Revised: 04/22/2022] [Accepted: 04/29/2022] [Indexed: 02/01/2023] Open
Abstract
Despite the development of new therapeutic strategies, cancer remains one of the leading causes of mortality worldwide. One of the current major challenges is the resistance of cancers to chemotherapy treatments inducing metastases and relapse of the tumor. The Hedgehog receptor Patched (Ptch1) is overexpressed in many types of cancers. We showed that Ptch1 contributes to the efflux of doxorubicin and plays an important role in the resistance to chemotherapy in adrenocortical carcinoma (ACC), a rare cancer which presents strong resistance to the standard of care chemotherapy treatment. In the present study, we isolated and characterized a subpopulation of the ACC cell line H295R in which Ptch1 is overexpressed and more present at the cell surface. This cell subpopulation is more resistant to doxorubicin, grows as spheroids, and has a greater capability of clonogenicity, migration, and invasion than the parental cells. Xenograft experiments performed in mice and in ovo showed that this cell subpopulation is more tumorigenic and metastatic than the parental cells. These results suggest that this cell subpopulation has cancer stem-like or persistent cell properties which were strengthened by RNA-seq. If present in tumors from ACC patients, these cells could be responsible for therapy resistance, relapse, and metastases.
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Affiliation(s)
- Álvaro Javier Feliz Morel
- Université Côte d’Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire (IPMC), 06560 Valbonne, France; (Á.J.F.M.); (A.H.); (V.M.); (K.L.); (A.A.); (S.C.)
| | - Anida Hasanovic
- Université Côte d’Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire (IPMC), 06560 Valbonne, France; (Á.J.F.M.); (A.H.); (V.M.); (K.L.); (A.A.); (S.C.)
| | - Aurélie Morin
- Université de Paris, PARCC, INSERM, Equipe Labellisée par la Ligue Contre le Cancer, CEDEX 15, 75737 Paris, France; (A.M.); (J.F.)
| | - Chloé Prunier
- INOVOTION, Biopolis-5 Av. du Grand Sablon, 38700 La Tronche, France;
| | - Virginie Magnone
- Université Côte d’Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire (IPMC), 06560 Valbonne, France; (Á.J.F.M.); (A.H.); (V.M.); (K.L.); (A.A.); (S.C.)
| | - Kevin Lebrigand
- Université Côte d’Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire (IPMC), 06560 Valbonne, France; (Á.J.F.M.); (A.H.); (V.M.); (K.L.); (A.A.); (S.C.)
| | - Amaury Aouad
- Université Côte d’Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire (IPMC), 06560 Valbonne, France; (Á.J.F.M.); (A.H.); (V.M.); (K.L.); (A.A.); (S.C.)
| | - Sarah Cogoluegnes
- Université Côte d’Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire (IPMC), 06560 Valbonne, France; (Á.J.F.M.); (A.H.); (V.M.); (K.L.); (A.A.); (S.C.)
| | - Judith Favier
- Université de Paris, PARCC, INSERM, Equipe Labellisée par la Ligue Contre le Cancer, CEDEX 15, 75737 Paris, France; (A.M.); (J.F.)
| | - Claude Pasquier
- Université Côte d’Azur, CNRS-UMR7271, Laboratoire d’Informatique, Signaux et Systèmes de Sophia Antipolis (I3S), 06560 Valbonne, France;
| | - Isabelle Mus-Veteau
- Université Côte d’Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire (IPMC), 06560 Valbonne, France; (Á.J.F.M.); (A.H.); (V.M.); (K.L.); (A.A.); (S.C.)
- Correspondence:
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8
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Gallerand A, Stunault MI, Merlin J, Luehmann HP, Sultan DH, Firulyova MM, Magnone V, Khedher N, Jalil A, Dolfi B, Castiglione A, Dumont A, Ayrault M, Vaillant N, Gilleron J, Barbry P, Dombrowicz D, Mack M, Masson D, Bertero T, Becher B, Williams JW, Zaitsev K, Liu Y, Guinamard RR, Yvan-Charvet L, Ivanov S. Brown adipose tissue monocytes support tissue expansion. Nat Commun 2021; 12:5255. [PMID: 34489438 PMCID: PMC8421389 DOI: 10.1038/s41467-021-25616-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 01/28/2021] [Accepted: 08/12/2021] [Indexed: 12/24/2022] Open
Abstract
Monocytes are part of the mononuclear phagocytic system. Monocytes play a central role during inflammatory conditions and a better understanding of their dynamics might open therapeutic opportunities. In the present study, we focused on the characterization and impact of monocytes on brown adipose tissue (BAT) functions during tissue remodeling. Single-cell RNA sequencing analysis of BAT immune cells uncovered a large diversity in monocyte and macrophage populations. Fate-mapping experiments demonstrated that the BAT macrophage pool requires constant replenishment from monocytes. Using a genetic model of BAT expansion, we found that brown fat monocyte numbers were selectively increased in this scenario. This observation was confirmed using a CCR2-binding radiotracer and positron emission tomography. Importantly, in line with their tissue recruitment, blood monocyte counts were decreased while bone marrow hematopoiesis was not affected. Monocyte depletion prevented brown adipose tissue expansion and altered its architecture. Podoplanin engagement is strictly required for BAT expansion. Together, these data redefine the diversity of immune cells in the BAT and emphasize the role of monocyte recruitment for tissue remodeling. Adipose tissue is composed of a number of adipocytes and a number of other cells including immune cells. Here the authors use single-cell sequencing of murine brown adipose tissue immune cells and describe multiple macrophage and monocyte subsets and show that monocytes contribute to brown adipose tissue expansion.
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Affiliation(s)
| | | | | | - Hannah P Luehmann
- Department of Radiology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Deborah H Sultan
- Department of Radiology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Maria M Firulyova
- Computer Technologies Department, ITMO University, Saint Petersburg, Russia
| | | | | | - Antoine Jalil
- Université Bourgogne Franche-Comté, LNC UMR1231, Dijon, France
| | | | | | | | | | | | | | - Pascal Barbry
- Université Côte d'Azur, CNRS, IPMC, Valbonne, France
| | - David Dombrowicz
- Univ.Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, Lille, France
| | - Matthias Mack
- Department of Internal Medicine - Nephrology, University Hospital Regensburg, Regensburg, Germany
| | - David Masson
- Université Bourgogne Franche-Comté, LNC UMR1231, Dijon, France
| | | | - Burkhard Becher
- Institute of Experimental Immunology, University of Zürich, Zürich, Switzerland
| | - Jesse W Williams
- Department of Integrative Biology and Physiology, Center for Immunology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Konstantin Zaitsev
- Computer Technologies Department, ITMO University, Saint Petersburg, Russia
| | - Yongjian Liu
- Department of Radiology, Washington University School of Medicine, Saint Louis, MO, USA
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9
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Pandiani C, Strub T, Nottet N, Cheli Y, Gambi G, Bille K, Husser C, Dalmasso M, Béranger G, Lassalle S, Magnone V, Pédeutour F, Irondelle M, Maschi C, Nahon-Estève S, Martel A, Caujolle JP, Hofman P, LeBrigand K, Davidson I, Baillif S, Barbry P, Ballotti R, Bertolotto C. Single-cell RNA sequencing reveals intratumoral heterogeneity in primary uveal melanomas and identifies HES6 as a driver of the metastatic disease. Cell Death Differ 2021; 28:1990-2000. [PMID: 33462406 PMCID: PMC8185008 DOI: 10.1038/s41418-020-00730-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [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: 08/04/2020] [Revised: 12/27/2020] [Accepted: 12/29/2020] [Indexed: 01/30/2023] Open
Abstract
Intratumor heterogeneity has been recognized in numerous cancers as a major source of metastatic dissemination. In uveal melanomas, the existence and identity of specific subpopulations, their biological function and their contribution to metastasis remain unknown. Here, in multiscale analyses using single-cell RNA sequencing of six different primary uveal melanomas, we uncover an intratumoral heterogeneity at the genomic and transcriptomic level. We identify distinct transcriptional cell states and diverse tumor-associated populations in a subset of the samples. We also decipher a gene regulatory network underlying an invasive and poor prognosis state driven in part by the transcription factor HES6. HES6 heterogenous expression has been validated by RNAscope assays within primary human uveal melanomas, which further unveils the existence of these cells conveying a dismal prognosis in tumors diagnosed with a favorable outcome using bulk analyses. Depletion of HES6 impairs proliferation, migration and metastatic dissemination in vitro and in vivo using the chick chorioallantoic membrane assay, demonstrating the essential role of HES6 in uveal melanomas. Thus, single-cell analysis offers an unprecedented view of primary uveal melanoma heterogeneity, identifies bona fide biomarkers for metastatic cells in the primary tumor, and reveals targetable modules driving growth and metastasis formation. Significantly, our findings demonstrate that HES6 is a valid target to stop uveal melanoma progression.
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Affiliation(s)
- Charlotte Pandiani
- grid.460782.f0000 0004 4910 6551Université Côte d’Azur, Nice, France ,grid.462370.40000 0004 0620 5402Inserm, Biology and Pathologies of melanocytes, team1, Equipe labellisée Ligue 2020 and Equipe labellisée ARC 2019, Centre Méditerranéen de Médecine Moléculaire, Nice, France
| | - Thomas Strub
- grid.460782.f0000 0004 4910 6551Université Côte d’Azur, Nice, France ,grid.462370.40000 0004 0620 5402Inserm, Biology and Pathologies of melanocytes, team1, Equipe labellisée Ligue 2020 and Equipe labellisée ARC 2019, Centre Méditerranéen de Médecine Moléculaire, Nice, France
| | - Nicolas Nottet
- grid.460782.f0000 0004 4910 6551Université Côte d’Azur, Nice, France ,grid.462370.40000 0004 0620 5402Inserm, Biology and Pathologies of melanocytes, team1, Equipe labellisée Ligue 2020 and Equipe labellisée ARC 2019, Centre Méditerranéen de Médecine Moléculaire, Nice, France
| | - Yann Cheli
- grid.460782.f0000 0004 4910 6551Université Côte d’Azur, Nice, France ,grid.462370.40000 0004 0620 5402Inserm, Biology and Pathologies of melanocytes, team1, Equipe labellisée Ligue 2020 and Equipe labellisée ARC 2019, Centre Méditerranéen de Médecine Moléculaire, Nice, France
| | - Giovanni Gambi
- grid.420255.40000 0004 0638 2716Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
| | - Karine Bille
- grid.460782.f0000 0004 4910 6551Université Côte d’Azur, Nice, France ,grid.462370.40000 0004 0620 5402Inserm, Biology and Pathologies of melanocytes, team1, Equipe labellisée Ligue 2020 and Equipe labellisée ARC 2019, Centre Méditerranéen de Médecine Moléculaire, Nice, France
| | - Chrystel Husser
- grid.460782.f0000 0004 4910 6551Université Côte d’Azur, Nice, France ,grid.462370.40000 0004 0620 5402Inserm, Biology and Pathologies of melanocytes, team1, Equipe labellisée Ligue 2020 and Equipe labellisée ARC 2019, Centre Méditerranéen de Médecine Moléculaire, Nice, France
| | - Mélanie Dalmasso
- grid.460782.f0000 0004 4910 6551Université Côte d’Azur, Nice, France ,grid.462370.40000 0004 0620 5402Inserm, Biology and Pathologies of melanocytes, team1, Equipe labellisée Ligue 2020 and Equipe labellisée ARC 2019, Centre Méditerranéen de Médecine Moléculaire, Nice, France
| | - Guillaume Béranger
- grid.460782.f0000 0004 4910 6551Université Côte d’Azur, Nice, France ,grid.462370.40000 0004 0620 5402Inserm, Biology and Pathologies of melanocytes, team1, Equipe labellisée Ligue 2020 and Equipe labellisée ARC 2019, Centre Méditerranéen de Médecine Moléculaire, Nice, France
| | - Sandra Lassalle
- grid.460782.f0000 0004 4910 6551Université Côte d’Azur, Nice, France ,Laboratoire de Pathologie clinique et expérimentale, biobanque BB-0033-00025, and IRCAN team 4, FHU OncoAge, Nice, France
| | - Virginie Magnone
- grid.460782.f0000 0004 4910 6551Université Côte d’Azur, Nice, France ,grid.429194.30000 0004 0638 0649CNRS, Institut de Pharmacologie Moléculaire et Cellulaire (IPMC), Valbonne, France
| | - Florence Pédeutour
- grid.460782.f0000 0004 4910 6551Université Côte d’Azur, Nice, France ,grid.464719.90000 0004 0639 4696Laboratoire de Génétique des tumeurs solides and IRCAN, Nice, France
| | - Marie Irondelle
- grid.460782.f0000 0004 4910 6551Université Côte d’Azur, Nice, France ,grid.462370.40000 0004 0620 5402Inserm, Imagery platform, Centre Méditerranéen de Médecine Moléculaire, Nice, France
| | - Célia Maschi
- grid.460782.f0000 0004 4910 6551Université Côte d’Azur, Nice, France ,Pasteur 2 Teaching Hospital, Department of Ophthalmology, Nice, France
| | - Sacha Nahon-Estève
- grid.460782.f0000 0004 4910 6551Université Côte d’Azur, Nice, France ,Pasteur 2 Teaching Hospital, Department of Ophthalmology, Nice, France
| | - Arnaud Martel
- grid.460782.f0000 0004 4910 6551Université Côte d’Azur, Nice, France ,Pasteur 2 Teaching Hospital, Department of Ophthalmology, Nice, France
| | - Jean-Pierre Caujolle
- grid.460782.f0000 0004 4910 6551Université Côte d’Azur, Nice, France ,Pasteur 2 Teaching Hospital, Department of Ophthalmology, Nice, France
| | - Paul Hofman
- grid.460782.f0000 0004 4910 6551Université Côte d’Azur, Nice, France ,Laboratoire de Pathologie clinique et expérimentale, biobanque BB-0033-00025, and IRCAN team 4, FHU OncoAge, Nice, France
| | - Kévin LeBrigand
- grid.460782.f0000 0004 4910 6551Université Côte d’Azur, Nice, France ,grid.429194.30000 0004 0638 0649CNRS, Institut de Pharmacologie Moléculaire et Cellulaire (IPMC), Valbonne, France
| | - Irwin Davidson
- grid.420255.40000 0004 0638 2716Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
| | - Stéphanie Baillif
- grid.460782.f0000 0004 4910 6551Université Côte d’Azur, Nice, France ,Pasteur 2 Teaching Hospital, Department of Ophthalmology, Nice, France
| | - Pascal Barbry
- grid.460782.f0000 0004 4910 6551Université Côte d’Azur, Nice, France ,grid.429194.30000 0004 0638 0649CNRS, Institut de Pharmacologie Moléculaire et Cellulaire (IPMC), Valbonne, France
| | - Robert Ballotti
- grid.460782.f0000 0004 4910 6551Université Côte d’Azur, Nice, France ,grid.462370.40000 0004 0620 5402Inserm, Biology and Pathologies of melanocytes, team1, Equipe labellisée Ligue 2020 and Equipe labellisée ARC 2019, Centre Méditerranéen de Médecine Moléculaire, Nice, France
| | - Corine Bertolotto
- grid.460782.f0000 0004 4910 6551Université Côte d’Azur, Nice, France ,grid.462370.40000 0004 0620 5402Inserm, Biology and Pathologies of melanocytes, team1, Equipe labellisée Ligue 2020 and Equipe labellisée ARC 2019, Centre Méditerranéen de Médecine Moléculaire, Nice, France
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10
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Baranek T, Lebrigand K, de Amat Herbozo C, Gonzalez L, Bogard G, Dietrich C, Magnone V, Boisseau C, Jouan Y, Trottein F, Si-Tahar M, Leite-de-Moraes M, Mallevaey T, Paget C. High Dimensional Single-Cell Analysis Reveals iNKT Cell Developmental Trajectories and Effector Fate Decision. Cell Rep 2021; 32:108116. [PMID: 32905761 DOI: 10.1016/j.celrep.2020.108116] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [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: 05/12/2020] [Revised: 07/24/2020] [Accepted: 08/17/2020] [Indexed: 02/02/2023] Open
Abstract
CD1d-restricted invariant Natural Killer T (iNKT) cells represent a unique class of T lymphocytes endowed with potent regulatory and effector immune functions. Although these functions are acquired during thymic ontogeny, the sequence of events that gives rise to discrete effector subsets remains unclear. Using an unbiased single-cell transcriptomic analysis combined with functional assays, we reveal an unappreciated diversity among thymic iNKT cells, especially among iNKT1 cells. Mathematical modeling and biological methods unravel a developmental map whereby iNKT2 cells constitute a transient branching point toward the generation of iNKT1 and iNKT17 cells, which reconciles the two previously proposed models. In addition, we identify the transcription co-factor Four-and-a-half LIM domains protein 2 (FHL2) as a critical cell-intrinsic regulator of iNKT1 specification. Thus, these data illustrate the changing transcriptional network that guides iNKT cell effector fate.
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Affiliation(s)
- Thomas Baranek
- INSERM, Centre d'Etude des Pathologies Respiratoires (CEPR), UMR 1100, Tours, France; Université de Tours, Faculté de Médecine de Tours, Tours, France.
| | - Kevin Lebrigand
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis, France
| | | | - Loïc Gonzalez
- INSERM, Centre d'Etude des Pathologies Respiratoires (CEPR), UMR 1100, Tours, France; Université de Tours, Faculté de Médecine de Tours, Tours, France
| | - Gemma Bogard
- INSERM, Centre d'Etude des Pathologies Respiratoires (CEPR), UMR 1100, Tours, France; Université de Tours, Faculté de Médecine de Tours, Tours, France
| | - Céline Dietrich
- Université de Paris, Paris, France; Laboratory of Immunoregulation and Immunopathology, INEM (Institut Necker-Enfants Malades), CNRS UMR8253 and INSERM UMR1151, Paris, France
| | | | - Chloé Boisseau
- INSERM, Centre d'Etude des Pathologies Respiratoires (CEPR), UMR 1100, Tours, France; Université de Tours, Faculté de Médecine de Tours, Tours, France
| | - Youenn Jouan
- INSERM, Centre d'Etude des Pathologies Respiratoires (CEPR), UMR 1100, Tours, France; Université de Tours, Faculté de Médecine de Tours, Tours, France; Service de Médecine Intensive et Réanimation, Centre Hospitalier Régional Universitaire, Tours, France
| | - François Trottein
- Centre d'Infection et d'Immunité de Lille, Inserm U1019, CNRS UMR 9017, University of Lille, CHU Lille- Institut Pasteur de Lille, 59000 Lille, France
| | - Mustapha Si-Tahar
- INSERM, Centre d'Etude des Pathologies Respiratoires (CEPR), UMR 1100, Tours, France; Université de Tours, Faculté de Médecine de Tours, Tours, France
| | - Maria Leite-de-Moraes
- Université de Paris, Paris, France; Laboratory of Immunoregulation and Immunopathology, INEM (Institut Necker-Enfants Malades), CNRS UMR8253 and INSERM UMR1151, Paris, France
| | - Thierry Mallevaey
- Department of Immunology, University of Toronto, Toronto, ON M5S 1A8, Canada; Institute of Biomaterials & Biomedical Engineering, Toronto, ON M5S 1A8, Canada
| | - Christophe Paget
- INSERM, Centre d'Etude des Pathologies Respiratoires (CEPR), UMR 1100, Tours, France; Université de Tours, Faculté de Médecine de Tours, Tours, France.
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11
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Leon LM, Gautier M, Allan R, Ilié M, Nottet N, Pons N, Paquet A, Lebrigand K, Truchi M, Fassy J, Magnone V, Kinnebrew G, Radovich M, Cheok MHC, Barbry P, Vassaux G, Marquette CH, Ponzio G, Ivan M, Pottier N, Hofman P, Mari B, Rezzonico R. Correction: The nuclear hypoxia-regulated NLUCAT1 long non-coding RNA contributes to an aggressive phenotype in lung adenocarcinoma through regulation of oxidative stress. Oncogene 2021; 40:2621. [PMID: 33686243 DOI: 10.1038/s41388-021-01670-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Lung cancer is the leading cause of cancer death worldwide, with poor prognosis and a high rate of recurrence despite early surgical removal. Hypoxic regions within tumors represent sources of aggressiveness and resistance to therapy. Although long non-coding RNAs (lncRNAs) are increasingly recognized as major gene expression regulators, their regulation and function following hypoxic stress are still largely unexplored. Combining profiling studies on early-stage lung adenocarcinoma (LUAD) biopsies and on A549 LUAD cell lines cultured in normoxic or hypoxic conditions, we identified a subset of lncRNAs that are both correlated with the hypoxic status of tumors and regulated by hypoxia in vitro. We focused on a new transcript, Nuclear LUCAT1 (NLUCAT1), which is strongly upregulated by hypoxia in vitro and correlated with hypoxic markers and poor prognosis in LUADs. Full molecular characterization showed that NLUCAT1 is a large nuclear transcript composed of six exons and mainly regulated by NF-κB and NRF2 transcription factors. CRISPR-Cas9-mediated invalidation of NLUCAT1 revealed a decrease in proliferative and invasive properties, an increase in oxidative stress and a higher sensitivity to cisplatin-induced apoptosis. Transcriptome analysis of NLUCAT1-deficient cells showed repressed genes within the antioxidant and/or cisplatin-response networks. We demonstrated that the concomitant knockdown of four of these genes products, GPX2, GLRX, ALDH3A1, and PDK4, significantly increased ROS-dependent caspase activation, thus partially mimicking the consequences of NLUCAT1 inactivation in LUAD cells. Overall, we demonstrate that NLUCAT1 contributes to an aggressive phenotype in early-stage hypoxic tumors, suggesting it may represent a new potential therapeutic target in LUADs.
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Affiliation(s)
- Laura Moreno Leon
- Université Côte d'Azur, CNRS UMR7275, IPMC, Valbonne, France.,FHU-OncoAge, Nice, France
| | - Marine Gautier
- Université Côte d'Azur, CNRS UMR7275, IPMC, Valbonne, France.,FHU-OncoAge, Nice, France
| | - Richard Allan
- Université Côte d'Azur, CNRS UMR7275, IPMC, Valbonne, France.,FHU-OncoAge, Nice, France
| | - Marius Ilié
- FHU-OncoAge, Nice, France.,Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France.,Hospital-Related Biobank (BB-0033-00025), Pasteur Hospital, Nice, France
| | - Nicolas Nottet
- Université Côte d'Azur, CNRS UMR7275, IPMC, Valbonne, France.,FHU-OncoAge, Nice, France
| | - Nicolas Pons
- Université Côte d'Azur, CNRS UMR7275, IPMC, Valbonne, France.,FHU-OncoAge, Nice, France
| | - Agnes Paquet
- Université Côte d'Azur, CNRS UMR7275, IPMC, Valbonne, France.,FHU-OncoAge, Nice, France
| | - Kévin Lebrigand
- Université Côte d'Azur, CNRS UMR7275, IPMC, Valbonne, France.,FHU-OncoAge, Nice, France
| | - Marin Truchi
- Université Côte d'Azur, CNRS UMR7275, IPMC, Valbonne, France.,FHU-OncoAge, Nice, France
| | - Julien Fassy
- Université Côte d'Azur, CNRS UMR7275, IPMC, Valbonne, France.,FHU-OncoAge, Nice, France
| | - Virginie Magnone
- Université Côte d'Azur, CNRS UMR7275, IPMC, Valbonne, France.,FHU-OncoAge, Nice, France
| | - Garrett Kinnebrew
- Department of Surgery, Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Milan Radovich
- Department of Surgery, Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Meyling Hua-Chen Cheok
- INSERM UMR-S1172, Institute for Cancer Research of Lille, Factors of Leukemia Cell Persistence, Lille, Cedex, France
| | - Pascal Barbry
- Université Côte d'Azur, CNRS UMR7275, IPMC, Valbonne, France.,FHU-OncoAge, Nice, France
| | - Georges Vassaux
- FHU-OncoAge, Nice, France.,Université Côte d'Azur, INSERM, CNRS UMR7275, IPMC, Valbonne, France
| | - Charles-Hugo Marquette
- FHU-OncoAge, Nice, France.,Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France.,Department of Pneumology, CHU-Nice, Nice, France
| | - Gilles Ponzio
- Université Côte d'Azur, CNRS UMR7275, IPMC, Valbonne, France.,FHU-OncoAge, Nice, France
| | - Mircea Ivan
- Department of Medicine and Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Nicolas Pottier
- EA4483, Faculté de Médecine de Lille, Pole Recherche, Lille, France
| | - Paul Hofman
- FHU-OncoAge, Nice, France.,Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France.,Hospital-Related Biobank (BB-0033-00025), Pasteur Hospital, Nice, France
| | - Bernard Mari
- Université Côte d'Azur, CNRS UMR7275, IPMC, Valbonne, France. .,FHU-OncoAge, Nice, France.
| | - Roger Rezzonico
- FHU-OncoAge, Nice, France. .,Université Côte d'Azur, INSERM, CNRS UMR7275, IPMC, Valbonne, France.
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12
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Deprez M, Zaragosi LE, Truchi M, Becavin C, Ruiz García S, Arguel MJ, Plaisant M, Magnone V, Lebrigand K, Abelanet S, Brau F, Paquet A, Pe'er D, Marquette CH, Leroy S, Barbry P. A Single-Cell Atlas of the Human Healthy Airways. Am J Respir Crit Care Med 2021; 202:1636-1645. [PMID: 32726565 DOI: 10.1164/rccm.201911-2199oc] [Citation(s) in RCA: 207] [Impact Index Per Article: 69.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Rationale: The respiratory tract constitutes an elaborate line of defense that is based on a unique cellular ecosystem.Objectives: We aimed to investigate cell population distributions and transcriptional changes along the airways by using single-cell RNA profiling.Methods: We have explored the cellular heterogeneity of the human airway epithelium in 10 healthy living volunteers by single-cell RNA profiling. A total of 77,969 cells were collected at 35 distinct locations, from the nose to the 12th division of the airway tree.Measurements and Main Results: The resulting atlas is composed of a high percentage of epithelial cells (89.1%) but also immune (6.2%) and stromal (4.7%) cells with distinct cellular proportions in different regions of the airways. It reveals differential gene expression between identical cell types (suprabasal, secretory, and multiciliated cells) from the nose (MUC4, PI3, SIX3) and tracheobronchial (SCGB1A1, TFF3) airways. By contrast, cell-type-specific gene expression is stable across all tracheobronchial samples. Our atlas improves the description of ionocytes, pulmonary neuroendocrine cells, and brush cells and identifies a related population of NREP-positive cells. We also report the association of KRT13 with dividing cells that are reminiscent of previously described mouse "hillock" cells and with squamous cells expressing SCEL and SPRR1A/B.Conclusions: Robust characterization of a single-cell cohort in healthy airways establishes a valuable resource for future investigations. The precise description of the continuum existing from the nasal epithelium to successive divisions of the airways and the stable gene expression profile of these regions better defines conditions under which relevant tracheobronchial proxies of human respiratory diseases can be developed.
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Affiliation(s)
- Marie Deprez
- Université Côte d'Azur, CNRS, Institut Pharmacologie Moléculaire et Cellulaire, Sophia-Antipolis, France
| | - Laure-Emmanuelle Zaragosi
- Université Côte d'Azur, CNRS, Institut Pharmacologie Moléculaire et Cellulaire, Sophia-Antipolis, France
| | - Marin Truchi
- Université Côte d'Azur, CNRS, Institut Pharmacologie Moléculaire et Cellulaire, Sophia-Antipolis, France
| | - Christophe Becavin
- Université Côte d'Azur, CNRS, Institut Pharmacologie Moléculaire et Cellulaire, Sophia-Antipolis, France
| | - Sandra Ruiz García
- Université Côte d'Azur, CNRS, Institut Pharmacologie Moléculaire et Cellulaire, Sophia-Antipolis, France
| | - Marie-Jeanne Arguel
- Université Côte d'Azur, CNRS, Institut Pharmacologie Moléculaire et Cellulaire, Sophia-Antipolis, France
| | - Magali Plaisant
- Université Côte d'Azur, CNRS, Institut Pharmacologie Moléculaire et Cellulaire, Sophia-Antipolis, France
| | - Virginie Magnone
- Université Côte d'Azur, CNRS, Institut Pharmacologie Moléculaire et Cellulaire, Sophia-Antipolis, France
| | - Kevin Lebrigand
- Université Côte d'Azur, CNRS, Institut Pharmacologie Moléculaire et Cellulaire, Sophia-Antipolis, France
| | - Sophie Abelanet
- Université Côte d'Azur, CNRS, Institut Pharmacologie Moléculaire et Cellulaire, Sophia-Antipolis, France
| | - Frédéric Brau
- Université Côte d'Azur, CNRS, Institut Pharmacologie Moléculaire et Cellulaire, Sophia-Antipolis, France
| | - Agnès Paquet
- Université Côte d'Azur, CNRS, Institut Pharmacologie Moléculaire et Cellulaire, Sophia-Antipolis, France
| | - Dana Pe'er
- Memorial Sloan Kettering Cancer Center, New York, New York; and
| | - Charles-Hugo Marquette
- Université Côte d'Azur, Centre Hospitalier Universitaire de Nice, Fédération Hospitalo-Universitaire OncoAge, CNRS, Inserm, Institute for Research on Cancer and Aging Nice Team 3, Pulmonology Department, Nice, France
| | - Sylvie Leroy
- Université Côte d'Azur, CNRS, Institut Pharmacologie Moléculaire et Cellulaire, Sophia-Antipolis, France.,Université Côte d'Azur, Centre Hospitalier Universitaire de Nice, Fédération Hospitalo-Universitaire OncoAge, CNRS, Inserm, Institute for Research on Cancer and Aging Nice Team 3, Pulmonology Department, Nice, France
| | - Pascal Barbry
- Université Côte d'Azur, CNRS, Institut Pharmacologie Moléculaire et Cellulaire, Sophia-Antipolis, France
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13
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Cambien B, Lebrigand K, Baeri A, Nottet N, Compin C, Lamit A, Ferraris O, Peyrefitte CN, Magnone V, Henriques J, Zaragosi LE, Giorgetti-Peraldi S, Bost F, Gautier-Isola M, Rezzonico R, Barbry P, Barthel R, Mari B, Vassaux G. Identification of oncolytic vaccinia restriction factors in canine high-grade mammary tumor cells using single-cell transcriptomics. PLoS Pathog 2020; 16:e1008660. [PMID: 33075093 PMCID: PMC7595618 DOI: 10.1371/journal.ppat.1008660] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 05/23/2020] [Revised: 10/29/2020] [Accepted: 09/01/2020] [Indexed: 01/13/2023] Open
Abstract
Mammary carcinoma, including triple-negative breast carcinomas (TNBC) are tumor-types for which human and canine pathologies are closely related at the molecular level. The efficacy of an oncolytic vaccinia virus (VV) was compared in low-passage primary carcinoma cells from TNBC versus non-TNBC. Non-TNBC cells were 28 fold more sensitive to VV than TNBC cells in which VV replication is impaired. Single-cell RNA-seq performed on two different TNBC cell samples, infected or not with VV, highlighted three distinct populations: naïve cells, bystander cells, defined as cells exposed to the virus but not infected and infected cells. The transcriptomes of these three populations showed striking variations in the modulation of pathways regulated by cytokines and growth factors. We hypothesized that the pool of genes expressed in the bystander populations was enriched in antiviral genes. Bioinformatic analysis suggested that the reduced activity of the virus was associated with a higher mesenchymal status of the cells. In addition, we demonstrated experimentally that high expression of one gene, DDIT4, is detrimental to VV production. Considering that DDIT4 is associated with a poor prognosis in various cancers including TNBC, our data highlight DDIT4 as a candidate resistance marker for oncolytic poxvirus therapy. This information could be used to design new generations of oncolytic poxviruses. Beyond the field of gene therapy, this study demonstrates that single-cell transcriptomics can be used to identify cellular factors influencing viral replication. The identification of cellular genes influencing viral replication/propagation has been studied using hypothesis-driven approaches and/or high-throughput RNA interference screens. In the present report, we propose a methodology based on single-cell transcriptomics. We have studied, in the context of oncolytic virotherapy, the susceptibility of different grades of primary low-passage mammary carcinoma cells of canine origin to an oncolytic vaccinia virus (VV). We highlight a fault in replication of VV in cells that originated from high-grade triple-negative breast carcinomas (TNBC). Single-cell RNA-seq performed on TNBC cell samples infected with VV suggested that the reduced activity of the virus was associated with a higher mesenchymal status of the cells. We also demonstrate that high expression of one gene, DDIT4, is detrimental to VV production. Considering that DDIT4 is associated with a poor prognosis in various cancers including TNBC, our data highlight DDIT4 as a candidate resistance marker for oncolytic poxvirus therapy. Beyond the field of cancer gene therapy, we demonstrate here that single-cell transcriptomics increases the arsenal of tools available to identify cellular factors influencing viral replication.
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Affiliation(s)
| | - Kevin Lebrigand
- Université Côte d'Azur, CNRS, IPMC, FHU-OncoAge, Valbonne, France
| | - Alberto Baeri
- Université Côte d'Azur, CNRS, IPMC, FHU-OncoAge, Valbonne, France
| | - Nicolas Nottet
- Université Côte d'Azur, CNRS, IPMC, FHU-OncoAge, Valbonne, France
| | | | - Audrey Lamit
- Université Côte d'Azur, CEA, Laboratoire TIRO, Nice France
| | - Olivier Ferraris
- Institut de recherche biomédicale des armées, Université de Lyon, Lyon, France
| | | | - Virginie Magnone
- Université Côte d'Azur, CNRS, IPMC, FHU-OncoAge, Valbonne, France
| | | | | | | | | | | | - Roger Rezzonico
- Université Côte d'Azur, INSERM, CNRS, IPMC, Valbonne, France
| | - Pascal Barbry
- Université Côte d'Azur, CNRS, IPMC, FHU-OncoAge, Valbonne, France
| | | | - Bernard Mari
- Université Côte d'Azur, CNRS, IPMC, FHU-OncoAge, Valbonne, France
| | - Georges Vassaux
- Université Côte d'Azur, INSERM, CNRS, IPMC, Valbonne, France
- * E-mail:
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14
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Castagnola S, Cazareth J, Lebrigand K, Jarjat M, Magnone V, Delhaye S, Brau F, Bardoni B, Maurin T. Agonist-induced functional analysis and cell sorting associated with single-cell transcriptomics characterizes cell subtypes in normal and pathological brain. Genome Res 2020; 30:1633-1642. [PMID: 32973039 PMCID: PMC7605246 DOI: 10.1101/gr.262717.120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 09/23/2020] [Indexed: 12/31/2022]
Abstract
To gain better insight into the dynamic interaction between cells and their environment, we developed the agonist-induced functional analysis and cell sorting (aiFACS) technique, which allows the simultaneous recording and sorting of cells in real-time according to their immediate and individual response to a stimulus. By modulating the aiFACS selection parameters, testing different developmental times, using various stimuli, and multiplying the analysis of readouts, it is possible to analyze cell populations of any normal or pathological tissue. The association of aiFACS with single-cell transcriptomics allows the construction of functional tissue cartography based on specific pharmacological responses of cells. As a proof of concept, we used aiFACS on the dissociated mouse brain, a highly heterogeneous tissue, enriching it in interneurons by stimulation with KCl or with AMPA, an agonist of the glutamate receptors, followed by sorting based on calcium levels. After AMPA stimulus, single-cell transcriptomics of these aiFACS-selected interneurons resulted in a nine-cluster classification. Furthermore, we used aiFACS on interneurons derived from the brain of the Fmr1-KO mouse, a rodent model of fragile X syndrome. We showed that these interneurons manifest a generalized defective response to AMPA compared with wild-type cells, affecting all the analyzed cell clusters at one specific postnatal developmental time.
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Affiliation(s)
- Sara Castagnola
- Université Côte d'Azur, CNRS, Institute of Molecular Cellular Pharmacology, F-06560 Valbonne, France
| | - Julie Cazareth
- Université Côte d'Azur, CNRS, Institute of Molecular Cellular Pharmacology, F-06560 Valbonne, France
| | - Kevin Lebrigand
- Université Côte d'Azur, CNRS, Institute of Molecular Cellular Pharmacology, F-06560 Valbonne, France
| | - Marielle Jarjat
- Université Côte d'Azur, CNRS, Institute of Molecular Cellular Pharmacology, F-06560 Valbonne, France
| | - Virginie Magnone
- Université Côte d'Azur, CNRS, Institute of Molecular Cellular Pharmacology, F-06560 Valbonne, France
| | - Sébastien Delhaye
- Université Côte d'Azur, CNRS, Institute of Molecular Cellular Pharmacology, F-06560 Valbonne, France
| | - Frederic Brau
- Université Côte d'Azur, CNRS, Institute of Molecular Cellular Pharmacology, F-06560 Valbonne, France
| | - Barbara Bardoni
- Université Côte d'Azur, INSERM, CNRS, Institute of Molecular Cellular Pharmacology, F-06560 Valbonne, France
| | - Thomas Maurin
- Université Côte d'Azur, CNRS, Institute of Molecular Cellular Pharmacology, F-06560 Valbonne, France
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15
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Savary G, Dewaeles E, Diazzi S, Buscot M, Nottet N, Fassy J, Courcot E, Henaoui IS, Lemaire J, Martis N, Van der Hauwaert C, Pons N, Magnone V, Leroy S, Hofman V, Plantier L, Lebrigand K, Paquet A, Lino Cardenas CL, Vassaux G, Hofman P, Günther A, Crestani B, Wallaert B, Rezzonico R, Brousseau T, Glowacki F, Bellusci S, Perrais M, Broly F, Barbry P, Marquette CH, Cauffiez C, Mari B, Pottier N. The Long Noncoding RNA DNM3OS Is a Reservoir of FibromiRs with Major Functions in Lung Fibroblast Response to TGF-β and Pulmonary Fibrosis. Am J Respir Crit Care Med 2020; 200:184-198. [PMID: 30964696 DOI: 10.1164/rccm.201807-1237oc] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Rationale: Given the paucity of effective treatments for idiopathic pulmonary fibrosis (IPF), new insights into the deleterious mechanisms controlling lung fibroblast activation, the key cell type driving the fibrogenic process, are essential to develop new therapeutic strategies. TGF-β (transforming growth factor-β) is the main profibrotic factor, but its inhibition is associated with severe side effects because of its pleiotropic role. Objectives: To determine if downstream noncoding effectors of TGF-β in fibroblasts may represent new effective therapeutic targets whose modulation may be well tolerated. Methods: We investigated the whole noncoding fraction of TGF-β-stimulated lung fibroblast transcriptome to identify new genomic determinants of lung fibroblast differentiation into myofibroblasts. Differential expression of the long noncoding RNA (lncRNA) DNM3OS (dynamin 3 opposite strand) and its associated microRNAs (miRNAs) was validated in a murine model of pulmonary fibrosis and in IPF tissue samples. Distinct and complementary antisense oligonucleotide-based strategies aiming at interfering with DNM3OS were used to elucidate the role of DNM3OS and its associated miRNAs in IPF pathogenesis. Measurements and Main Results: We identified DNM3OS as a fibroblast-specific critical downstream effector of TGF-β-induced lung myofibroblast activation. Mechanistically, DNM3OS regulates this process in trans by giving rise to three distinct profibrotic mature miRNAs (i.e., miR-199a-5p/3p and miR-214-3p), which influence SMAD and non-SMAD components of TGF-β signaling in a multifaceted way. In vivo, we showed that interfering with DNM3OS function not only prevents lung fibrosis but also improves established pulmonary fibrosis. Conclusions: Pharmacological approaches aiming at interfering with the lncRNA DNM3OS may represent new effective therapeutic strategies in IPF.
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Affiliation(s)
- Grégoire Savary
- 1 CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, FHU-OncoAge, Université Côte d'Azur, Valbonne, France.,2 EA 4483-IMPECS and
| | | | - Serena Diazzi
- 1 CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, FHU-OncoAge, Université Côte d'Azur, Valbonne, France
| | - Matthieu Buscot
- 1 CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, FHU-OncoAge, Université Côte d'Azur, Valbonne, France.,3 Département de Pneumologie, CHU-Nice
| | - Nicolas Nottet
- 1 CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, FHU-OncoAge, Université Côte d'Azur, Valbonne, France
| | - Julien Fassy
- 1 CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, FHU-OncoAge, Université Côte d'Azur, Valbonne, France
| | | | - Imène-Sarah Henaoui
- 1 CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, FHU-OncoAge, Université Côte d'Azur, Valbonne, France
| | | | - Nihal Martis
- 1 CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, FHU-OncoAge, Université Côte d'Azur, Valbonne, France.,3 Département de Pneumologie, CHU-Nice
| | | | - Nicolas Pons
- 1 CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, FHU-OncoAge, Université Côte d'Azur, Valbonne, France
| | - Virginie Magnone
- 1 CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, FHU-OncoAge, Université Côte d'Azur, Valbonne, France
| | - Sylvie Leroy
- 1 CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, FHU-OncoAge, Université Côte d'Azur, Valbonne, France.,3 Département de Pneumologie, CHU-Nice
| | - Véronique Hofman
- 4 Laboratory of Clinical and Experimental Pathology and Hospital-Integrated Biobank (BB-0033-00025), CHU Nice, and.,5 CNRS, INSERM, Institute for Research on Cancer and Aging, FHU-OncoAge, Université Côte d'Azur, Nice, France
| | - Laurent Plantier
- 6 Centre d'Étude des Pathologies Respiratoires-CEPR, INSERM, UMR1100, Labex Mabimprove, Université François Rabelais, Tours, France
| | - Kevin Lebrigand
- 1 CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, FHU-OncoAge, Université Côte d'Azur, Valbonne, France
| | - Agnès Paquet
- 1 CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, FHU-OncoAge, Université Côte d'Azur, Valbonne, France
| | | | - Georges Vassaux
- 1 CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, FHU-OncoAge, Université Côte d'Azur, Valbonne, France
| | - Paul Hofman
- 4 Laboratory of Clinical and Experimental Pathology and Hospital-Integrated Biobank (BB-0033-00025), CHU Nice, and.,5 CNRS, INSERM, Institute for Research on Cancer and Aging, FHU-OncoAge, Université Côte d'Azur, Nice, France
| | - Andreas Günther
- 7 Center for Interstitial and Rare Diseases and Cardiopulmonary Institute and.,8 European IPF Registry and Biobank and
| | - Bruno Crestani
- 8 European IPF Registry and Biobank and.,9 Assistance Publique-Hôpitaux de Paris, Hôpital Bichat, INSERM U1152, Université Paris Diderot, LABEX Inflamex, DHU FIRE, Paris, France; and
| | | | - Roger Rezzonico
- 1 CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, FHU-OncoAge, Université Côte d'Azur, Valbonne, France
| | - Thierry Brousseau
- 11 Service de Biochimie Automatisée, Protéines et Biologie Prédictive
| | | | - Saverio Bellusci
- 13 Excellence Cluster Cardio-Pulmonary System, German Center for Lung Research, Justus-Liebig-University Gießen, Giessen, Germany
| | | | - Franck Broly
- 2 EA 4483-IMPECS and.,15 Service de Toxicologie et Génopathies, CHU Lille, Lille, France
| | - Pascal Barbry
- 1 CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, FHU-OncoAge, Université Côte d'Azur, Valbonne, France
| | | | | | - Bernard Mari
- 1 CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, FHU-OncoAge, Université Côte d'Azur, Valbonne, France
| | - Nicolas Pottier
- 2 EA 4483-IMPECS and.,15 Service de Toxicologie et Génopathies, CHU Lille, Lille, France
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16
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Ruiz García S, Deprez M, Lebrigand K, Cavard A, Paquet A, Arguel MJ, Magnone V, Truchi M, Caballero I, Leroy S, Marquette CH, Marcet B, Barbry P, Zaragosi LE. Novel dynamics of human mucociliary differentiation revealed by single-cell RNA sequencing of nasal epithelial cultures. Development 2019; 146:dev.177428. [PMID: 31558434 PMCID: PMC6826037 DOI: 10.1242/dev.177428] [Citation(s) in RCA: 149] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 09/18/2019] [Indexed: 12/12/2022]
Abstract
The upper airway epithelium, which is mainly composed of multiciliated, goblet, club and basal cells, ensures proper mucociliary function and can regenerate in response to assaults. In chronic airway diseases, defective repair leads to tissue remodeling. Delineating key drivers of differentiation dynamics can help understand how normal or pathological regeneration occurs. Using single-cell transcriptomics and lineage inference, we have unraveled trajectories from basal to luminal cells, providing novel markers for specific populations. We report that: (1) a precursor subgroup of multiciliated cells, which we have entitled deuterosomal cells, is defined by specific markers, such as DEUP1, FOXN4, YPEL1, HES6 and CDC20B; (2) goblet cells can be precursors of multiciliated cells, thus explaining the presence of hybrid cells that co-express markers of goblet and multiciliated cells; and (3) a repertoire of molecules involved in the regeneration process, such as keratins or components of the Notch, Wnt or BMP/TGFβ pathways, can be identified. Confirmation of our results on fresh human and pig airway samples, and on mouse tracheal cells, extend and confirm our conclusions regarding the molecular and cellular choreography at work during mucociliary epithelial differentiation.
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Affiliation(s)
| | - Marie Deprez
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis 06560, France
| | - Kevin Lebrigand
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis 06560, France
| | - Amélie Cavard
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis 06560, France
| | - Agnès Paquet
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis 06560, France
| | | | - Virginie Magnone
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis 06560, France
| | - Marin Truchi
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis 06560, France
| | | | - Sylvie Leroy
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis 06560, France.,Université Côte d'Azur, CHU de Nice, Pulmonology Department, Nice 06000, France
| | | | - Brice Marcet
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis 06560, France
| | - Pascal Barbry
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis 06560, France
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17
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Giovannini-Chami L, Paquet A, Sanfiorenzo C, Pons N, Cazareth J, Magnone V, Lebrigand K, Chevalier B, Vallauri A, Julia V, Marquette CH, Marcet B, Leroy S, Barbry P. The "one airway, one disease" concept in light of Th2 inflammation. Eur Respir J 2018; 52:13993003.00437-2018. [PMID: 30190271 DOI: 10.1183/13993003.00437-2018] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 08/13/2018] [Indexed: 12/19/2022]
Abstract
In line with the pathophysiological continuum described between nose and bronchus in allergic respiratory diseases, we assessed whether nasal epithelium could mirror the Type 2 T-helper cell (Th2) status of bronchial epithelium.Nasal and bronchial cells were collected by brushing from healthy controls (C, n=13), patients with allergic rhinitis and asthma (AR, n=12), and patients with isolated allergic rhinitis (R, n=14). Cellular composition was assessed by flow cytometry, gene expression was analysed by RNA sequencing and Th2, Type 17 T-helper cell (Th17) and interferon (IFN) signatures were derived from the literature.Infiltration by polymorphonuclear neutrophils (PMN) in the nose excluded 30% of the initial cohort. All bronchial samples from the AR group were Th2-high. The gene expression profile of nasal samples from the AR group correctly predicted the paired bronchial sample Th2 status in 71% of cases. Nevertheless, nasal cells did not appear to be a reliable surrogate for the Th2 response, in particular due to a more robust influence of the IFN response in 14 out of 26 nasal samples. The Th2 scores in the nose and bronchi correlated with mast cell count (both p<0.001) and number of sensitisations (p=0.006 and 0.002), while the Th17 scores correlated with PMN count (p=0.006 and 0.003).The large variability in nasal cell composition and type of inflammation restricts its use as a surrogate for assessing bronchial Th2 inflammation in AR patients.
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Affiliation(s)
- Lisa Giovannini-Chami
- Pediatric Pulmonology and Allergology Dept, Hôpitaux Pédiatriques de Nice CHU-Lenval, Université Côte d'Azur, Nice, France.,Institut de Pharmacologie Moléculaire et Cellulaire, CNRS, Université Côte d'Azur, Sophia Antipolis, France.,These authors contributed equally to this work
| | - Agnès Paquet
- Institut de Pharmacologie Moléculaire et Cellulaire, CNRS, Université Côte d'Azur, Sophia Antipolis, France.,These authors contributed equally to this work
| | - Céline Sanfiorenzo
- Pulmonology Dept, FHU Oncoage, CHU de Nice, Université Côte d'Azur, Nice, France
| | - Nicolas Pons
- Institut de Pharmacologie Moléculaire et Cellulaire, CNRS, Université Côte d'Azur, Sophia Antipolis, France
| | - Julie Cazareth
- Institut de Pharmacologie Moléculaire et Cellulaire, CNRS, Université Côte d'Azur, Sophia Antipolis, France
| | - Virginie Magnone
- Institut de Pharmacologie Moléculaire et Cellulaire, CNRS, Université Côte d'Azur, Sophia Antipolis, France
| | - Kévin Lebrigand
- Institut de Pharmacologie Moléculaire et Cellulaire, CNRS, Université Côte d'Azur, Sophia Antipolis, France
| | - Benoit Chevalier
- Institut de Pharmacologie Moléculaire et Cellulaire, CNRS, Université Côte d'Azur, Sophia Antipolis, France
| | - Ambre Vallauri
- Institut de Pharmacologie Moléculaire et Cellulaire, CNRS, Université Côte d'Azur, Sophia Antipolis, France
| | - Valérie Julia
- Institut de Pharmacologie Moléculaire et Cellulaire, CNRS, Université Côte d'Azur, Sophia Antipolis, France
| | | | - Brice Marcet
- Institut de Pharmacologie Moléculaire et Cellulaire, CNRS, Université Côte d'Azur, Sophia Antipolis, France
| | - Sylvie Leroy
- Pulmonology Dept, FHU Oncoage, CHU de Nice, Université Côte d'Azur, Nice, France.,These authors contributed equally to this work
| | - Pascal Barbry
- Institut de Pharmacologie Moléculaire et Cellulaire, CNRS, Université Côte d'Azur, Sophia Antipolis, France.,These authors contributed equally to this work
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18
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Paquet A, Giovannini-Chami L, Sanfiorenzo C, Pons N, Cazaret J, Magnone V, Lebrigand K, Chevalier B, Vallauri A, Julia V, Hugo C, Marcet B, Leroy S, Barbry P. The “one airway, one disease” concept in light of Th2 inflammation. Rev Epidemiol Sante Publique 2018. [DOI: 10.1016/j.respe.2018.03.290] [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] [Indexed: 10/17/2022] Open
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19
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Medina C, da Rocha M, Magliano M, Ratpopoulo A, Revel B, Marteu N, Magnone V, Lebrigand K, Cabrera J, Barcala M, Silva AC, Millar A, Escobar C, Abad P, Favery B, Jaubert-Possamai S. Characterization of microRNAs from Arabidopsis galls highlights a role for miR159 in the plant response to the root-knot nematode Meloidogyne incognita. New Phytol 2017; 216:882-896. [PMID: 28906559 DOI: 10.1111/nph.14717] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 06/10/2017] [Indexed: 05/05/2023]
Abstract
Root knot nematodes (RKN) are root parasites that induce the genetic reprogramming of vascular cells into giant feeding cells and the development of root galls. MicroRNAs (miRNAs) regulate gene expression during development and plant responses to various stresses. Disruption of post-transcriptional gene silencing in Arabidopsis ago1 or ago2 mutants decrease the infection rate of RKN suggesting a role for this mechanism in the plant-nematode interaction. By sequencing small RNAs from uninfected Arabidopsis roots and from galls 7 and 14 d post infection with Meloidogyne incognita, we identified 24 miRNAs differentially expressed in gall as putative regulators of gall development. Moreover, strong activity within galls was detected for five miRNA promoters. Analyses of nematode development in an Arabidopsis miR159abc mutant had a lower susceptibility to RKN, suggesting a role for the miR159 family in the plant response to M. incognita. Localization of mature miR159 within the giant and surrounding cells suggested a role in giant cell and gall. Finally, overexpression of miR159 in galls at 14 d post inoculation was associated with the repression of the miR159 target MYB33 which expression is restricted to the early stages of infection. Overall, these results implicate the miR159 in plant responses to RKN.
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Affiliation(s)
- Clémence Medina
- INRA, Université Côte d'Azur, CNRS, ISA, 400 route des Chappes, BP167, 06903, Sophia Antipolis, France
| | - Martine da Rocha
- INRA, Université Côte d'Azur, CNRS, ISA, 400 route des Chappes, BP167, 06903, Sophia Antipolis, France
| | - Marc Magliano
- INRA, Université Côte d'Azur, CNRS, ISA, 400 route des Chappes, BP167, 06903, Sophia Antipolis, France
| | - Alizée Ratpopoulo
- INRA, Université Côte d'Azur, CNRS, ISA, 400 route des Chappes, BP167, 06903, Sophia Antipolis, France
| | - Benoît Revel
- INRA, Université Côte d'Azur, CNRS, ISA, 400 route des Chappes, BP167, 06903, Sophia Antipolis, France
| | - Nathalie Marteu
- INRA, Université Côte d'Azur, CNRS, ISA, 400 route des Chappes, BP167, 06903, Sophia Antipolis, France
| | - Virginie Magnone
- UCA Genomix, Institut de Pharmacologie Moléculaire et Cellulaire, CNRS UMR6097, Sophia Antipolis, France
| | - Kevin Lebrigand
- UCA Genomix, Institut de Pharmacologie Moléculaire et Cellulaire, CNRS UMR6097, Sophia Antipolis, France
| | - Javier Cabrera
- Facultad de Ciencias Ambientales y Bioquímica, Universidad de Castilla-La Mancha, Avda. Carlos III S/N, Edificio Sabatini, E-45071, Toledo, Spain
| | - Marta Barcala
- Facultad de Ciencias Ambientales y Bioquímica, Universidad de Castilla-La Mancha, Avda. Carlos III S/N, Edificio Sabatini, E-45071, Toledo, Spain
| | - Ana Cláudia Silva
- Facultad de Ciencias Ambientales y Bioquímica, Universidad de Castilla-La Mancha, Avda. Carlos III S/N, Edificio Sabatini, E-45071, Toledo, Spain
| | - Anthony Millar
- Plant Science Division, Research School of Biology, Australian National University, Canberra, 2601, ACT, Australia
| | - Carolina Escobar
- Facultad de Ciencias Ambientales y Bioquímica, Universidad de Castilla-La Mancha, Avda. Carlos III S/N, Edificio Sabatini, E-45071, Toledo, Spain
| | - Pierre Abad
- INRA, Université Côte d'Azur, CNRS, ISA, 400 route des Chappes, BP167, 06903, Sophia Antipolis, France
| | - Bruno Favery
- INRA, Université Côte d'Azur, CNRS, ISA, 400 route des Chappes, BP167, 06903, Sophia Antipolis, France
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20
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Ponzio G, Rezzonico R, Bourget I, Allan R, Nottet N, Popa A, Magnone V, Rios G, Mari B, Barbry P. A new long noncoding RNA (lncRNA) is induced in cutaneous squamous cell carcinoma and down-regulates several anticancer and cell differentiation genes in mouse. J Biol Chem 2017; 292:12483-12495. [PMID: 28596382 DOI: 10.1074/jbc.m117.776260] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [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: 01/12/2017] [Revised: 06/05/2017] [Indexed: 01/17/2023] Open
Abstract
Keratinocyte-derived cutaneous squamous cell carcinoma (cSCC) is the most common metastatic skin cancer. Although some of the early events involved in this pathology have been identified, the subsequent steps leading to tumor development are poorly defined. We demonstrate here that the development of mouse tumors induced by the concomitant application of a carcinogen and a tumor promoter (7,12-dimethylbenz[a]anthracene (DMBA) and 12-O-tetradecanoylphorbol-13-acetate (TPA), respectively) is associated with the up-regulation of a previously uncharacterized long noncoding RNA (lncRNA), termed AK144841. We found that AK144841 expression was absent from normal skin and was specifically stimulated in tumors and highly tumorigenic cells. We also found that AK144841 exists in two variants, one consisting of a large 2-kb transcript composed of four exons and one consisting of a 1.8-kb transcript lacking the second exon. Gain- and loss-of-function studies indicated that AK144841 mainly inhibited gene expression, specifically down-regulating the expression of genes of the late cornified envelope-1 (Lce1) family involved in epidermal terminal differentiation and of anticancer genes such as Cgref1, Brsk1, Basp1, Dusp5, Btg2, Anpep, Dhrs9, Stfa2, Tpm1, SerpinB2, Cpa4, Crct1, Cryab, Il24, Csf2, and Rgs16 Interestingly, the lack of the second exon significantly decreased AK144841's inhibitory effect on gene expression. We also noted that high AK144841 expression correlated with a low expression of the aforementioned genes and with the tumorigenic potential of cell lines. These findings suggest that AK144841 could contribute to the dedifferentiation program of tumor-forming keratinocytes and to molecular cascades leading to tumor development.
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Affiliation(s)
- Gilles Ponzio
- Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, 06560 Valbonne, France and.
| | - Roger Rezzonico
- Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, 06560 Valbonne, France and
| | - Isabelle Bourget
- Université Côte d'Azur, CNRS, INSERM, Institute for Research on Cancer and Aging, 06000 Nice, France
| | - Richard Allan
- Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, 06560 Valbonne, France and
| | - Nicolas Nottet
- Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, 06560 Valbonne, France and
| | - Alexandra Popa
- Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, 06560 Valbonne, France and
| | - Virginie Magnone
- Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, 06560 Valbonne, France and
| | - Géraldine Rios
- Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, 06560 Valbonne, France and
| | - Bernard Mari
- Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, 06560 Valbonne, France and
| | - Pascal Barbry
- Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, 06560 Valbonne, France and
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21
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Saintamand A, Vincent-Fabert C, Marquet M, Ghazzaui N, Magnone V, Pinaud E, Cogné M, Denizot Y. E μ and 3'RR IgH enhancers show hierarchic unilateral dependence in mature B-cells. Sci Rep 2017; 7:442. [PMID: 28348365 PMCID: PMC5428668 DOI: 10.1038/s41598-017-00575-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 03/03/2017] [Indexed: 01/18/2023] Open
Abstract
Enhancer and super-enhancers are master regulators of cell fate. While they act at long-distances on adjacent genes, it is unclear whether they also act on one another. The immunoglobulin heavy chain (IgH) locus is unique in carrying two super-enhancers at both ends of the constant gene cluster: the 5'Eμ super-enhancer promotes VDJ recombination during the earliest steps of B-cell ontogeny while the 3' regulatory region (3'RR) is essential for late differentiation. Since they carry functional synergies in mature B-cells and physically interact during IgH locus DNA looping, we investigated if they were independent engines of locus remodelling or if their function was more intimately intermingled, their optimal activation then requiring physical contact with each other. Analysis of chromatin marks, enhancer RNA transcription and accessibility in Eμ- and 3'RR-deficient mice show, in mature activated B-cells, an unilateral dependence of this pair of enhancers: while the 3'RR acts in autonomy, Eμ in contrast likely falls under control of the 3'RR.
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Affiliation(s)
- A Saintamand
- CNRS UMR 7276, CRIBL, Université de Limoges, Limoges, France. .,INSERM U1236, Université Rennes 1, Rennes, France.
| | | | - M Marquet
- CNRS UMR 7276, CRIBL, Université de Limoges, Limoges, France
| | - N Ghazzaui
- CNRS UMR 7276, CRIBL, Université de Limoges, Limoges, France
| | - V Magnone
- CNRS et Université de Nice Sophia Antipolis, Institut de Pharmacologie Moléculaire et Cellulaire, UMR 6097, Sophia, Antipolis, France
| | - E Pinaud
- CNRS UMR 7276, CRIBL, Université de Limoges, Limoges, France
| | - M Cogné
- CNRS UMR 7276, CRIBL, Université de Limoges, Limoges, France
| | - Y Denizot
- CNRS UMR 7276, CRIBL, Université de Limoges, Limoges, France.
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22
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Mercey O, Popa A, Cavard A, Paquet A, Chevalier B, Pons N, Magnone V, Zangari J, Brest P, Zaragosi LE, Ponzio G, Lebrigand K, Barbry P, Marcet B. Characterizing isomiR variants within the microRNA-34/449 family. FEBS Lett 2017; 591:693-705. [PMID: 28192603 PMCID: PMC5363356 DOI: 10.1002/1873-3468.12595] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [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: 12/16/2016] [Revised: 01/26/2017] [Accepted: 02/08/2017] [Indexed: 01/13/2023]
Abstract
miR‐34/449 microRNAs are conserved regulators of multiciliated cell differentiation. Here, we evidence and characterize expression of two isomiR variant sequences from the miR‐34/449 family in human airway epithelial cells. These isomiRs differ from their canonical counterparts miR‐34b and miR‐449c by one supplemental uridine at their 5′‐end, leading to a one‐base shift in their seed region. Overexpression of canonical miR‐34/449 or 5′‐isomiR‐34/449 induces distinct gene expression profiles and biological effects. However, some target transcripts and functional activities are shared by both canonical microRNAs and isomiRs. Indeed, both repress important targets that result in cell cycle blockage and Notch pathway inhibition. Our findings suggest that 5′‐isomiR‐34/449 may represent additional mechanisms by which miR‐34/449 family finely controls several pathways to drive multiciliogenesis.
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Affiliation(s)
- Olivier Mercey
- CNRS, IPMC, Université Côte d'Azur, Sophia-Antipolis, Valbonne, France
| | - Alexandra Popa
- CNRS, IPMC, Université Côte d'Azur, Sophia-Antipolis, Valbonne, France
| | - Amélie Cavard
- CNRS, IPMC, Université Côte d'Azur, Sophia-Antipolis, Valbonne, France
| | - Agnès Paquet
- CNRS, IPMC, Université Côte d'Azur, Sophia-Antipolis, Valbonne, France
| | - Benoît Chevalier
- CNRS, IPMC, Université Côte d'Azur, Sophia-Antipolis, Valbonne, France
| | - Nicolas Pons
- CNRS, IPMC, Université Côte d'Azur, Sophia-Antipolis, Valbonne, France
| | - Virginie Magnone
- CNRS, IPMC, Université Côte d'Azur, Sophia-Antipolis, Valbonne, France
| | - Joséphine Zangari
- CNRS, INSERM, IRCAN, FHU-OncoAge, Université Côte d'Azur, Sophia-Antipolis, Valbonne, France
| | - Patrick Brest
- CNRS, INSERM, IRCAN, FHU-OncoAge, Université Côte d'Azur, Sophia-Antipolis, Valbonne, France
| | | | - Gilles Ponzio
- CNRS, IPMC, Université Côte d'Azur, Sophia-Antipolis, Valbonne, France
| | - Kevin Lebrigand
- CNRS, IPMC, Université Côte d'Azur, Sophia-Antipolis, Valbonne, France
| | - Pascal Barbry
- CNRS, IPMC, Université Côte d'Azur, Sophia-Antipolis, Valbonne, France
| | - Brice Marcet
- CNRS, IPMC, Université Côte d'Azur, Sophia-Antipolis, Valbonne, France
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23
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Beclin C, Follert P, Stappers E, Barral S, Coré N, Chevigny AD, Magnone V, Lebrigand K, Bissels U, Huylebroeck D, Bosio A, Barbry P, Seuntjens E, Cremer H. Corrigendum: miR-200 family controls late steps of postnatal forebrain neurogenesis via Zeb2 inhibition. Sci Rep 2016; 6:39368. [PMID: 28000724 PMCID: PMC5175142 DOI: 10.1038/srep39368] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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24
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Beclin C, Follert P, Stappers E, Barral S, Coré N, de Chevigny A, Magnone V, Lebrigand K, Bissels U, Huylebroeck D, Bosio A, Barbry P, Seuntjens E, Cremer H. miR-200 family controls late steps of postnatal forebrain neurogenesis via Zeb2 inhibition. Sci Rep 2016; 6:35729. [PMID: 27767083 PMCID: PMC5073329 DOI: 10.1038/srep35729] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 10/04/2016] [Indexed: 12/28/2022] Open
Abstract
During neurogenesis, generation, migration and integration of the correct numbers of each neuron sub-type depends on complex molecular interactions in space and time. MicroRNAs represent a key control level allowing the flexibility and stability needed for this process. Insight into the role of this regulatory pathway in the brain is still limited. We performed a sequential experimental approach using postnatal olfactory bulb neurogenesis in mice, starting from global expression analyses to the investigation of functional interactions between defined microRNAs and their targets. Deep sequencing of small RNAs extracted from defined compartments of the postnatal neurogenic system demonstrated that the miR-200 family is specifically induced during late neuronal differentiation stages. Using in vivo strategies we interfered with the entire miR-200 family in loss- and gain-of-function settings, showing a role of miR-200 in neuronal maturation. This function is mediated by targeting the transcription factor Zeb2. Interestingly, so far functional interaction between miR-200 and Zeb2 has been exclusively reported in cancer or cultured stem cells. Our data demonstrate that this regulatory interaction is also active during normal neurogenesis.
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Affiliation(s)
- Christophe Beclin
- IBDM, Aix-Marseille Université, CNRS, UMR7288, 13288 Marseille, France
| | - Philipp Follert
- IBDM, Aix-Marseille Université, CNRS, UMR7288, 13288 Marseille, France
| | - Elke Stappers
- Laboratory of Molecular Biology, Dept Development and Regeneration, KULeuven, 3000 Leuven, Belgium
| | - Serena Barral
- IBDM, Aix-Marseille Université, CNRS, UMR7288, 13288 Marseille, France.,Miltenyi Biotec GmbH, Bergisch Gladbach, Germany
| | - Nathalie Coré
- IBDM, Aix-Marseille Université, CNRS, UMR7288, 13288 Marseille, France
| | | | - Virginie Magnone
- CNRS and University Nice Sophia Antipolis, IPMC, Sophia Antipolis, France
| | - Kévin Lebrigand
- CNRS and University Nice Sophia Antipolis, IPMC, Sophia Antipolis, France
| | - Ute Bissels
- Miltenyi Biotec GmbH, Bergisch Gladbach, Germany
| | - Danny Huylebroeck
- Laboratory of Molecular Biology, Dept Development and Regeneration, KULeuven, 3000 Leuven, Belgium.,Dept Cell Biology, Erasmus MC, 3015 CN Rotterdam, The Netherlands
| | | | - Pascal Barbry
- CNRS and University Nice Sophia Antipolis, IPMC, Sophia Antipolis, France
| | - Eve Seuntjens
- Laboratory of Molecular Biology, Dept Development and Regeneration, KULeuven, 3000 Leuven, Belgium.,GIGA-Neurosciences, Université de Liège, 4000 Liège, Belgium
| | - Harold Cremer
- IBDM, Aix-Marseille Université, CNRS, UMR7288, 13288 Marseille, France
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25
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Saintamand A, Vincent-Fabert C, Garot A, Rouaud P, Oruc Z, Magnone V, Cogné M, Denizot Y. Deciphering the importance of the palindromic architecture of the immunoglobulin heavy-chain 3' regulatory region. Nat Commun 2016; 7:10730. [PMID: 26883548 PMCID: PMC4757795 DOI: 10.1038/ncomms10730] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 01/15/2016] [Indexed: 01/16/2023] Open
Abstract
The IgH 3' regulatory region (3'RR) controls class switch recombination (CSR) and somatic hypermutation (SHM) in B cells. The mouse 3'RR contains four enhancer elements with hs1,2 flanked by inverted repeated sequences and the centre of a 25-kb palindrome bounded by two hs3 enhancer inverted copies (hs3a and hs3b). hs4 lies downstream of the palindrome. In mammals, evolution maintained this unique palindromic arrangement, suggesting that it is functionally significant. Here we report that deconstructing the palindromic IgH 3'RR strongly affects its function even when enhancers are preserved. CSR and IgH transcription appear to be poorly dependent on the 3'RR architecture and it is more or less preserved, provided 3'RR enhancers are present. By contrast, a ‘palindromic effect' significantly lowers VH germline transcription, AID recruitment and SHM. In conclusion, this work indicates that the IgH 3'RR does not simply pile up enhancer units but also optimally exposes them into a functional architecture of crucial importance. The IgH 3' regulatory region contains an evolutionarily conserved palindromic sequence flanking important enhancer elements. Here the authors show that the palindrome is required for generating antibody diversity.
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Affiliation(s)
| | | | - Armand Garot
- Université de Limoges, CRIBL, UMR CNRS 7276, Limoges 87025, France
| | - Pauline Rouaud
- Université de Limoges, CRIBL, UMR CNRS 7276, Limoges 87025, France
| | - Zeliha Oruc
- Université de Limoges, CRIBL, UMR CNRS 7276, Limoges 87025, France
| | - Virginie Magnone
- CNRS et Université de Nice Sophia Antipolis, Institut de Pharmacologie Moléculaire et Cellulaire, UMR 6097, Sophia Antipolis 06560, France
| | - Michel Cogné
- Université de Limoges, CRIBL, UMR CNRS 7276, Limoges 87025, France.,Institut Universitaire de France, Paris 75231, France
| | - Yves Denizot
- Université de Limoges, CRIBL, UMR CNRS 7276, Limoges 87025, France
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26
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Rouaud P, Fiancette R, Vincent-Fabert C, Magnone V, Cogné M, Dubus P, Denizot Y. Mantle cell lymphoma-like lymphomas in c-myc-3'RR/p53+/- mice and c-myc-3'RR/Cdk4R24C mice: differential oncogenic mechanisms but similar cellular origin. Oncotarget 2012; 3:586-93. [PMID: 22592113 PMCID: PMC3388189 DOI: 10.18632/oncotarget.474] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [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: 12/26/2022] Open
Abstract
Mantle cell lymphoma (MCL) is a malignant lymphoproliferative B-cell disorder that does not occur spontaneously in mice but experimental mice model have been developed. Recently two different mice models prone to develop MCL-like lymphomas were generated: c-myc-3'RR/Cdk4(R24C) mice and c-myc-3'RR/p53+/- mice. Comparison of their gene expression profiles does not highlight specific differences other than those in relation with their specific mutational status (i.e., Cdk4(R24C) mutation or p53 mutations). We propose that similarly to typical human MCL and its blastoid or cyclin-D1 variants that correspond to the same genetic entity, MCL-like lymphomas of c-myc-3'RR/ p53+/- mice and c-myc-3'RR/Cdk4(R24C) mice represent a spectrum of the same entity.
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27
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Fiancette R, Rouaud P, Vincent-Fabert C, Laffleur B, Magnone V, Cogné M, Denizot Y. A p53 defect sensitizes various stages of B cell development to lymphomagenesis in mice carrying an IgH 3' regulatory region-driven c-myc transgene. J Immunol 2011; 187:5772-82. [PMID: 22039300 DOI: 10.4049/jimmunol.1102059] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Although c-myc is classically described as the driving oncogene in Burkitt's lymphoma (BL), deregulation and mutations of c-myc have been reported in multiple solid tumors and in other mature B cell malignancies such as mantle cell lymphoma (MCL), myeloma, and plasma cell lymphoma (PCL). After translocation into the IgH locus, c-myc is constitutively expressed under the control of active IgH enhancers. Those located in the IgH 3' regulatory region (3'RR) are master control elements of class switch recombination and of the transcriptional burst associated with plasma cell differentiation. c-myc-3'RR mice are prone to lymphomas with rather homogeneous, most often BL-like, phenotypes with incomplete penetrance (75% tumor incidence) and long latencies (10-12 mo). To reproduce c-myc-induced mature B cell lymphomagenesis in the context of an additional defect often observed in human lymphomas, we intercrossed c-myc-3'RR with p53(+/-) mice. Double transgenic c-myc-3'RR/p53(+/-) mice developed lymphoma with short latency (2-4 mo) and full penetrance (100% tumor incidence). The spectrum of B lymphomas occurring in c-myc-3'RR/p53(+/-) mice was widened, including nonactivated (CD43(-)) BL, activated (CD43(+)) BL, MCL-like lymphoma, and PCL, thus showing that 3'RR-mediated deregulation of c-myc can promote various types of B lymphoproliferation in cells that first acquired a p53 defect. c-myc/p53(+/-) mice closely reproduce many features of BL, MCL, and PCL and provide a novel and efficient model to dissect the molecular events leading to c-myc-induced lymphomagenesis and an important tool to test potential therapeutic agents on malignant B cells featuring various maturation stages.
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Affiliation(s)
- Rémi Fiancette
- Faculté de Médecine, Unité Mixte de Recherche 6101, Centre National de la Recherche Scientifique, 87025 Limoges, France
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28
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Ganot P, Moya A, Magnone V, Allemand D, Furla P, Sabourault C. Adaptations to endosymbiosis in a cnidarian-dinoflagellate association: differential gene expression and specific gene duplications. PLoS Genet 2011; 7:e1002187. [PMID: 21811417 PMCID: PMC3141003 DOI: 10.1371/journal.pgen.1002187] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [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: 12/29/2010] [Accepted: 06/01/2011] [Indexed: 12/23/2022] Open
Abstract
Trophic endosymbiosis between anthozoans and photosynthetic dinoflagellates forms the key foundation of reef ecosystems. Dysfunction and collapse of symbiosis lead to bleaching (symbiont expulsion), which is responsible for the severe worldwide decline of coral reefs. Molecular signals are central to the stability of this partnership and are therefore closely related to coral health. To decipher inter-partner signaling, we developed genomic resources (cDNA library and microarrays) from the symbiotic sea anemone Anemonia viridis. Here we describe differential expression between symbiotic (also called zooxanthellate anemones) or aposymbiotic (also called bleached) A. viridis specimens, using microarray hybridizations and qPCR experiments. We mapped, for the first time, transcript abundance separately in the epidermal cell layer and the gastrodermal cells that host photosynthetic symbionts. Transcriptomic profiles showed large inter-individual variability, indicating that aposymbiosis could be induced by different pathways. We defined a restricted subset of 39 common genes that are characteristic of the symbiotic or aposymbiotic states. We demonstrated that transcription of many genes belonging to this set is specifically enhanced in the symbiotic cells (gastroderm). A model is proposed where the aposymbiotic and therefore heterotrophic state triggers vesicular trafficking, whereas the symbiotic and therefore autotrophic state favors metabolic exchanges between host and symbiont. Several genetic pathways were investigated in more detail: i) a key vitamin K-dependant process involved in the dinoflagellate-cnidarian recognition; ii) two cnidarian tissue-specific carbonic anhydrases involved in the carbon transfer from the environment to the intracellular symbionts; iii) host collagen synthesis, mostly supported by the symbiotic tissue. Further, we identified specific gene duplications and showed that the cnidarian-specific isoform was also up-regulated both in the symbiotic state and in the gastroderm. Our results thus offer new insight into the inter-partner signaling required for the physiological mechanisms of the symbiosis that is crucial for coral health.
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Affiliation(s)
- Philippe Ganot
- Université de Nice-Sophia-Antipolis, Nice, France
- Université Pierre et Marie Curie, Paris, France
- Centre National de la Recherche Scientifique, Roscoff, France
- UMR7138 Systématique, Adaptation, Evolution, Nice, France
| | - Aurélie Moya
- Université de Nice-Sophia-Antipolis, Nice, France
- Université Pierre et Marie Curie, Paris, France
- Centre National de la Recherche Scientifique, Roscoff, France
- UMR7138 Systématique, Adaptation, Evolution, Nice, France
| | - Virginie Magnone
- Université de Nice-Sophia-Antipolis, Nice, France
- Centre National de la Recherche Scientifique, Roscoff, France
- Institut de Pharmacologie Moléculaire et Cellulaire, UMR 6097, Sophia Antipolis, France
| | - Denis Allemand
- Université de Nice-Sophia-Antipolis, Nice, France
- Centre Scientifique de Monaco, Monaco, Monaco
| | - Paola Furla
- Université de Nice-Sophia-Antipolis, Nice, France
- Université Pierre et Marie Curie, Paris, France
- Centre National de la Recherche Scientifique, Roscoff, France
- UMR7138 Systématique, Adaptation, Evolution, Nice, France
| | - Cécile Sabourault
- Université de Nice-Sophia-Antipolis, Nice, France
- Université Pierre et Marie Curie, Paris, France
- Centre National de la Recherche Scientifique, Roscoff, France
- UMR7138 Systématique, Adaptation, Evolution, Nice, France
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29
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Puisségur MP, Mazure NM, Bertero T, Pradelli L, Grosso S, Robbe-Sermesant K, Maurin T, Lebrigand K, Cardinaud B, Hofman V, Fourre S, Magnone V, Ricci JE, Pouysségur J, Gounon P, Hofman P, Barbry P, Mari B. miR-210 is overexpressed in late stages of lung cancer and mediates mitochondrial alterations associated with modulation of HIF-1 activity. Cell Death Differ 2010; 18:465-78. [PMID: 20885442 DOI: 10.1038/cdd.2010.119] [Citation(s) in RCA: 323] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Following the identification of a set of hypoxia-regulated microRNAs (miRNAs), recent studies have highlighted the importance of miR-210 and of its transcriptional regulation by the transcription factor hypoxia-inducible factor-1 (HIF-1). We report here that miR-210 is overexpressed at late stages of non-small cell lung cancer. Expression of miR-210 in lung adenocarcinoma A549 cells caused an alteration of cell viability associated with induction of caspase-3/7 activity. miR-210 induced a loss of mitochondrial membrane potential and the apparition of an aberrant mitochondrial phenotype. The expression profiling of cells overexpressing miR-210 revealed a specific signature characterized by enrichment for transcripts related to 'cell death' and 'mitochondrial dysfunction', including several subunits of the electron transport chain (ETC) complexes I and II. The transcript coding for one of these ETC components, SDHD, subunit D of succinate dehydrogenase complex (SDH), was validated as a bona fide miR-210 target. Moreover, SDHD knockdown mimicked miR-210-mediated mitochondrial alterations. Finally, miR-210-dependent targeting of SDHD was able to activate HIF-1, in line with previous studies linking loss-of-function SDH mutations to HIF-1 activation. miR-210 can thus regulate mitochondrial function by targeting key ETC component genes with important consequences on cell metabolism, survival and modulation of HIF-1 activity. These observations help explain contradictory data regarding miR-210 expression and its putative function in solid tumors.
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Affiliation(s)
- M-P Puisségur
- Institut de Pharmacologie Moléculaire et Cellulaire, CNRS UMR6097, Sophia Antipolis, France
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30
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Dayem MA, Moreilhon C, Turchi L, Magnone V, Christen R, Ponzio G, Barbry P. Early gene expression in wounded human keratinocytes revealed by DNA microarray analysis. Comp Funct Genomics 2010; 4:47-55. [PMID: 18629100 PMCID: PMC2447387 DOI: 10.1002/cfg.239] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2002] [Accepted: 11/21/2002] [Indexed: 11/12/2022] Open
Abstract
Wound healing involves several steps: spreading of the cells, migration and proliferation.
We have profiled gene expression during the early events of wound healing in
normal human keratinocytes with a home-made DNA microarray containing about
1000 relevant human probes. An original wounding machine was used, that allows the
wounding of up to 40% of the surface of a confluent monolayer of cultured cells grown
on a Petri dish (compared with 5% with a classical ‘scratch’ method). The two aims
of the present study were: (a) to validate a limited number of genes by comparing
the expression levels obtained with this technique with those found in the literature;
(b) to combine the use of the wounding machine with DNA microarray analysis for
large-scale detection of the molecular events triggered during the early stages of the
wound-healing process. The time-courses of RNA expression observed at 0.5, 1.5, 3,
6 and 15 h after wounding for genes such as c-Fos, c-Jun, Egr1, the plasminogen
activator PLAU (uPA) and the signal transducer and transcription activator STAT3,
were consistent with previously published data. This suggests that our methodologies
are able to perform quantitative measurement of gene expression. Transcripts encoding
two zinc finger proteins, ZFP36 and ZNF161, and the tumour necrosis factor
α-induced protein TNFAIP3, were also overexpressed after wounding. The role of
the p38 mitogen-activated protein kinase (p38MAPK) in wound healing was shown
after the inhibition of p38 by SB203580, but our results also suggest the existence of
surrogate activating pathways.
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Affiliation(s)
- Manal A Dayem
- Laboratoire de Physiologie Génomique des Eucaryotes, CNRS/UNSA UMR 6097, IPMC F-06560 Sophia Antipolis, France
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31
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Emboulé L, Daigle F, Meyer DF, Mari B, Pinarello V, Sheikboudou C, Magnone V, Frutos R, Viari A, Barbry P, Martinez D, Lefrançois T, Vachiéry N. Innovative approach for transcriptomic analysis of obligate intracellular pathogen: selective capture of transcribed sequences of Ehrlichia ruminantium. BMC Mol Biol 2009; 10:111. [PMID: 20034374 PMCID: PMC2806407 DOI: 10.1186/1471-2199-10-111] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [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: 04/09/2009] [Accepted: 12/24/2009] [Indexed: 01/25/2023] Open
Abstract
Background Whole genome transcriptomic analysis is a powerful approach to elucidate the molecular mechanisms controlling the pathogenesis of obligate intracellular bacteria. However, the major hurdle resides in the low quantity of prokaryotic mRNAs extracted from host cells. Our model Ehrlichia ruminantium (ER), the causative agent of heartwater, is transmitted by tick Amblyomma variegatum. This bacterium affects wild and domestic ruminants and is present in Sub-Saharan Africa and the Caribbean islands. Because of its strictly intracellular location, which constitutes a limitation for its extensive study, the molecular mechanisms involved in its pathogenicity are still poorly understood. Results We successfully adapted the SCOTS method (Selective Capture of Transcribed Sequences) on the model Rickettsiales ER to capture mRNAs. Southern Blots and RT-PCR revealed an enrichment of ER's cDNAs and a diminution of ribosomal contaminants after three rounds of capture. qRT-PCR and whole-genome ER microarrays hybridizations demonstrated that SCOTS method introduced only a limited bias on gene expression. Indeed, we confirmed the differential gene expression between poorly and highly expressed genes before and after SCOTS captures. The comparative gene expression obtained from ER microarrays data, on samples before and after SCOTS at 96 hpi was significantly correlated (R2 = 0.7). Moreover, SCOTS method is crucial for microarrays analysis of ER, especially for early time points post-infection. There was low detection of transcripts for untreated samples whereas 24% and 70.7% were revealed for SCOTS samples at 24 and 96 hpi respectively. Conclusions We conclude that this SCOTS method has a key importance for the transcriptomic analysis of ER and can be potentially used for other Rickettsiales. This study constitutes the first step for further gene expression analyses that will lead to a better understanding of both ER pathogenicity and the adaptation of obligate intracellular bacteria to their environment.
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Affiliation(s)
- Loïc Emboulé
- UMR 15 CIRAD-INRA, Contrôle des maladies animales exotiques et émergentes, Site de Duclos, Prise d'Eau 97170, Petit Bourg, Guadeloupe.
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32
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Vautor E, Magnone V, Rios G, Le Brigand K, Bergonier D, Lina G, Meugnier H, Barbry P, Thiéry R, Pépin M. Genetic differences among Staphylococcus aureus isolates from dairy ruminant species: a single-dye DNA microarray approach. Vet Microbiol 2008; 133:105-14. [PMID: 18640795 DOI: 10.1016/j.vetmic.2008.06.006] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2008] [Revised: 06/02/2008] [Accepted: 06/04/2008] [Indexed: 11/30/2022]
Abstract
Staphylococcus aureus is recognized worldwide as a major pathogen causing clinical or subclinical intramammary infections in lactating sheep, goats and cows. The present study was carried out to compare 65 S. aureus isolates mainly obtained from nasal carriage and subclinical mastitis in dairy sheep and 43 isolates obtained from subclinical mastitis from 22 goats and 21 cows. A DNA microarray, containing probes against 190 true or putative virulence factors, was used to detect the presence of the virulence genes. Their presence/absence was independently assessed by PCR for the genes of interest. Sheep isolates obtained from the nostrils or the udders did not show any significant tissue specific virulence factor. The dominant pulse-field electrophoresis profile (OV/OV'), associated with spa clonal complex spa-CC 1773, matched mainly with the agr group III and was only found in ovine and caprine isolates. This clone was more specifically characterized by the prevalence of the following virulence genes: lpl4, ssl6, bsaA1, bsaB, bsaP, SAV0812. Moreover, seven virulence-associated genes (lpl1, sel, sec, tst, lukF-PV-like component, lukM, SAV0876) were associated with isolates from small ruminants, while the egc cluster, fhuD1, abiF and SAV2496 with bovine isolates. This genomic study suggests the existence of lineage- and host-specific genes leading to the development of host-specific pathogenic traits of S. aureus isolates.
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Affiliation(s)
- E Vautor
- Agence Française de Sécurité Sanitaire des Aliments (AFSSA), Unité Pathologie des Petits Ruminants, Sophia-Antipolis, France.
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33
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Albrecht V, Chevallier A, Magnone V, Barbry P, Vandenbos F, Bongain A, Lefebvre JC, Giordanengo V. Easy and fast detection and genotyping of high-risk human papillomavirus by dedicated DNA microarrays. J Virol Methods 2006; 137:236-44. [PMID: 16879879 DOI: 10.1016/j.jviromet.2006.06.023] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [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: 04/03/2006] [Revised: 06/13/2006] [Accepted: 06/15/2006] [Indexed: 11/25/2022]
Abstract
Persistent cervical high-risk human papillomavirus (HPV) infection is correlated with an increased risk of developing a high-grade cervical intraepithelial lesion. A two-step method was developed for detection and genotyping of high-risk HPV. DNA was firstly amplified by asymmetrical PCR in the presence of Cy3-labelled primers and dUTP. Labelled DNA was then genotyped using DNA microarray hybridization. The current study evaluated the technical efficacy of laboratory-designed HPV DNA microarrays for high-risk HPV genotyping on 57 malignant and non-malignant cervical smears. The approach was evaluated for a broad range of cytological samples: high-grade squamous intraepithelial lesions (HSIL), low-grade squamous intraepithelial lesions (LSIL) and atypical squamous cells of high-grade (ASC-H). High-risk HPV was also detected in six atypical squamous cells of undetermined significance (ASC-US) samples; among them only one cervical specimen was found uninfected, associated with no histological lesion. The HPV oligonucleotide DNA microarray genotyping detected 36 infections with a single high-risk HPV type and 5 multiple infections with several high-risk types. Taken together, these results demonstrate the sensitivity and specificity of the HPV DNA microarray approach. This approach could improve clinical management of patients with cervical cytological abnormalities.
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Affiliation(s)
- Valérie Albrecht
- Laboratoire de Virologie, Hôpital de l'Archet, BP 3079, 151 route de Saint-Antoine de Ginestière, 06200 Nice Cedex 3, France
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Brigand KL, Russell R, Moreilhon C, Rouillard JM, Jost B, Amiot F, Magnone V, Bole-Feysot C, Rostagno P, Virolle V, Defamie V, Dessen P, Williams G, Lyons P, Rios G, Mari B, Gulari E, Kastner P, Gidrol X, Freeman TC, Barbry P. An open-access long oligonucleotide microarray resource for analysis of the human and mouse transcriptomes. Nucleic Acids Res 2006; 34:e87. [PMID: 16855282 PMCID: PMC1524919 DOI: 10.1093/nar/gkl485] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.7] [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] [Indexed: 12/28/2022] Open
Abstract
Two collections of oligonucleotides have been designed for preparing pangenomic human and mouse microarrays. A total of 148 993 and 121 703 oligonucleotides were designed against human and mouse transcripts. Quality scores were created in order to select 25 342 human and 24 109 mouse oligonucleotides. They correspond to: (i) a BLAST-specificity score; (ii) the number of expressed sequence tags matching each probe; (iii) the distance to the 3′ end of the target mRNA. Scores were also used to compare in silico the two microarrays with commercial microarrays. The sets described here, called RNG/MRC collections, appear at least as specific and sensitive as those from the commercial platforms. The RNG/MRC collections have now been used by an Anglo-French consortium to distribute more than 3500 microarrays to the academic community. Ad hoc identification of tissue-specific transcripts and a ∼80% correlation with hybridizations performed on Affymetrix GeneChip™ suggest that the RNG/MRC microarrays perform well. This work provides a comprehensive open resource for investigators working on human and mouse transcriptomes, as well as a generic method to generate new microarray collections in other organisms. All information related to these probes, as well as additional information about commercial microarrays have been stored in a freely-accessible database called MEDIANTE.
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Affiliation(s)
- Kévin Le Brigand
- CNRS, Institut de Pharmacologie Moléculaire et CellulaireUMR6097, 660, route des Lucioles F-06560 Sophia Antipolis, France
- University of Nice Sophia Antipolis, Institut de Pharmacologie Moléculaire et CellulaireUMR6097, 660, route des Lucioles F-06560 Sophia Antipolis, France
| | - Roslin Russell
- MRC Rosalind Franklin Centre for Genomics Research, Wellcome Trust Genome CampusHinxton, Cambridge CB10 1SB, UK
| | - Chimène Moreilhon
- CNRS, Institut de Pharmacologie Moléculaire et CellulaireUMR6097, 660, route des Lucioles F-06560 Sophia Antipolis, France
- University of Nice Sophia Antipolis, Institut de Pharmacologie Moléculaire et CellulaireUMR6097, 660, route des Lucioles F-06560 Sophia Antipolis, France
| | - Jean-Marie Rouillard
- Department of Chemical Engineering, University of MichiganAnn Arbor, MI 48109, USA
- Biodiscovery LLC, 3886 Penberton DrAnn Arbor, MI 48109, USA
| | | | - Franck Amiot
- CEA—Service de Génomique Fonctionnelle, Genopole d'EvryF91057 Evry Cédex, France
| | - Virginie Magnone
- CNRS, Institut de Pharmacologie Moléculaire et CellulaireUMR6097, 660, route des Lucioles F-06560 Sophia Antipolis, France
- University of Nice Sophia Antipolis, Institut de Pharmacologie Moléculaire et CellulaireUMR6097, 660, route des Lucioles F-06560 Sophia Antipolis, France
| | | | - Philippe Rostagno
- CNRS, Institut de Pharmacologie Moléculaire et CellulaireUMR6097, 660, route des Lucioles F-06560 Sophia Antipolis, France
- University of Nice Sophia Antipolis, Institut de Pharmacologie Moléculaire et CellulaireUMR6097, 660, route des Lucioles F-06560 Sophia Antipolis, France
| | - Virginie Virolle
- CNRS, Institut de Pharmacologie Moléculaire et CellulaireUMR6097, 660, route des Lucioles F-06560 Sophia Antipolis, France
- University of Nice Sophia Antipolis, Institut de Pharmacologie Moléculaire et CellulaireUMR6097, 660, route des Lucioles F-06560 Sophia Antipolis, France
| | - Virginie Defamie
- CNRS, Institut de Pharmacologie Moléculaire et CellulaireUMR6097, 660, route des Lucioles F-06560 Sophia Antipolis, France
- University of Nice Sophia Antipolis, Institut de Pharmacologie Moléculaire et CellulaireUMR6097, 660, route des Lucioles F-06560 Sophia Antipolis, France
| | - Philippe Dessen
- Laboratoire de Génétique Oncologique, UMR 1599 CNRSInstitut Gustave Roussy, F-94805 Villejuif Cedex, France
| | - Gary Williams
- MRC Rosalind Franklin Centre for Genomics Research, Wellcome Trust Genome CampusHinxton, Cambridge CB10 1SB, UK
| | - Paul Lyons
- MRC Rosalind Franklin Centre for Genomics Research, Wellcome Trust Genome CampusHinxton, Cambridge CB10 1SB, UK
| | - Géraldine Rios
- CNRS, Institut de Pharmacologie Moléculaire et CellulaireUMR6097, 660, route des Lucioles F-06560 Sophia Antipolis, France
- University of Nice Sophia Antipolis, Institut de Pharmacologie Moléculaire et CellulaireUMR6097, 660, route des Lucioles F-06560 Sophia Antipolis, France
| | - Bernard Mari
- CNRS, Institut de Pharmacologie Moléculaire et CellulaireUMR6097, 660, route des Lucioles F-06560 Sophia Antipolis, France
- University of Nice Sophia Antipolis, Institut de Pharmacologie Moléculaire et CellulaireUMR6097, 660, route des Lucioles F-06560 Sophia Antipolis, France
| | - Erdogan Gulari
- Department of Chemical Engineering, University of MichiganAnn Arbor, MI 48109, USA
- Biodiscovery LLC, 3886 Penberton DrAnn Arbor, MI 48109, USA
| | | | - Xavier Gidrol
- CEA—Service de Génomique Fonctionnelle, Genopole d'EvryF91057 Evry Cédex, France
| | - Tom C. Freeman
- MRC Rosalind Franklin Centre for Genomics Research, Wellcome Trust Genome CampusHinxton, Cambridge CB10 1SB, UK
| | - Pascal Barbry
- CNRS, Institut de Pharmacologie Moléculaire et CellulaireUMR6097, 660, route des Lucioles F-06560 Sophia Antipolis, France
- University of Nice Sophia Antipolis, Institut de Pharmacologie Moléculaire et CellulaireUMR6097, 660, route des Lucioles F-06560 Sophia Antipolis, France
- To whom correspondence should be addressed. Tel : +33 4 9395 7793; Fax: +33 4 9395 7794;
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Moreilhon C, Gras D, Hologne C, Bajolet O, Cottrez F, Magnone V, Merten M, Groux H, Puchelle E, Barbry P. LiveStaphylococcus aureusand bacterial soluble factors induce different transcriptional responses in human airway cells. Physiol Genomics 2005; 20:244-55. [PMID: 15598879 DOI: 10.1152/physiolgenomics.00135.2004] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.6] [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: 11/22/2022] Open
Abstract
To characterize the response of respiratory epithelium to infection by Staphylococcus aureus ( S. aureus), human airway cells were incubated for 1 to 24 h with a supernatant of a S. aureus culture (bacterial supernatant), then profiled with a pangenomic DNA microarray. Because an upregulation of many genes was noticed around 3 h, three independent approaches were then used to characterize the host response to a 3-h contact either with bacterial supernatant or with live bacteria: 1) a DNA microarray containing 4,200 sequence-verified probes, 2) a semiquantitative RT-PCR with a set of 537 pairs of validated primers, or 3) ELISA assay of IL-8, IL-6, TNFα, and PGE2. Among others, Fos, Jun, and EGR-1 were upregulated by the bacterial supernatant and by live bacteria. Increased expression of bhlhb2 and Mig-6, promoter regions which harbor HIF responding elements, was explained by an increased expression of the HIF-1α protein. Activation of the inducible form of cyclooxygenase, COX-2, and of the interleukins IL-1, IL-6, and IL-8, as well as of the NF-κB pathway, was observed preferentially in cells in contact with bacterial supernatant. Early infection was characterized by an upregulation of anti-apoptotic genes and a downregulation of pro-apoptotic genes. This correlated with a necrotic, rather than apoptotic cell death. Overall, this first global description of an airway epithelial infection by S. aureus demonstrates a larger global response to bacterial supernatant (in term of altered genes and variation factors) than to exponentially growing live bacteria.
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Affiliation(s)
- Chimène Moreilhon
- Institut de Pharmacologie Moléculaire et Cellulaire UMR 6097 Centre National de la Recherche Scientifique, Université de Nice-Sophia Antipolis, Valbonne, France
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Abstract
We cloned human and rat TWIK-2 and expressed this novel 2P domain K(+) channel in transiently transfected COS cells. TWIK-2 is highly expressed in the gastrointestinal tract, the vasculature, and the immune system. Rat TWIK-2 currents are about 15 times larger than human TWIK-2 currents, but both exhibit outward rectification in a physiological K(+) gradient and mild inward rectification in symmetrical K(+) conditions. TWIK-2 currents are inactivating at depolarized potentials, and the kinetic of inactivation is highly temperature-sensitive. TWIK-2 shows an extremely low conductance, which prevents the visualization of discrete single channel events. The inactivation and rectification are intrinsic properties of TWIK-2 channels. In a physiological K(+) gradient, TWIK-2 is half inhibited by 0.1 mm Ba(2+), quinine, and quinidine. Finally, cysteine 53 in the M1P1 external loop is required for functional expression of TWIK-2 but is not critical for subunit self-assembly. TWIK-2 is the first reported 2P domain K(+) channel that inactivates. The base-line, transient, and delayed activities of TWIK-2 suggest that this novel 2P domain K(+) channel may play an important functional role in cell electrogenesis.
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Affiliation(s)
- A J Patel
- Institut de Pharmacologie Moléculaire et Cellulaire, CNRS UPR 411, 660 route des Lucioles, Sophia Antipolis, 06560 Valbonne, France
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