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Martin C, Evrard B, Percevault F, Ryder K, Darde T, Lardenois A, Zhadobov M, Sauleau R, Chalmel F, Le Dréan Y, Habauzit D. Transcriptional landscape of human keratinocyte models exposed to 60-GHz millimeter-waves. Toxicol In Vitro 2024; 97:105808. [PMID: 38484921 DOI: 10.1016/j.tiv.2024.105808] [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] [Received: 07/27/2023] [Revised: 03/05/2024] [Accepted: 03/09/2024] [Indexed: 03/19/2024]
Abstract
The use of millimeter waves (MMW) will exponentially grow in the coming years due to their future utilization in 5G/6G networks. The question of possible biological effects at these frequencies has been raised. In this present study, we aimed to investigate gene expression changes under exposure to MMW using the Bulk RNA Barcoding and sequencing (BRB-seq) technology. To address this issue, three exposure scenarios were performed aiming at: i) comparing the cellular response of two primary culture of keratinocytes (HEK and NHEK) and one keratinocyte derivate cell line (HaCaT) exposed to MMW; ii) exploring the incident power density dose-effect on gene expression in HaCaT cell line; and, iii) studying the exposure duration at the new ICNIRP exposure limit for the general population. With the exception of heat effect induced by high power MMW (over 10 mW/cm2), those exposure scenarios have not enabled us to demonstrate important gene expression changes in the different cell populations studied. Very few differentially genes were observed between MMW exposed samples and heat shock control, and most of them were significantly associated with heat shock response that may reflect small differences in the heat generation. Together these results show that acute exposure to MMW has no effects on the transcriptional landscape of human keratinocyte models under athermal conditions.
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Affiliation(s)
- Catherine Martin
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France
| | - Bertrand Evrard
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France
| | - Frédéric Percevault
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France
| | - Kate Ryder
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France
| | - Thomas Darde
- SciLicium, 10 rue de la Sauvaie, 35200 Rennes, France
| | - Aurélie Lardenois
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France
| | - Maxim Zhadobov
- Univ Rennes, CNRS, IETR (Institut d'Électronique et des Technologies du Numérique), UMR 6164, F-35000 Rennes, France
| | - Ronan Sauleau
- Univ Rennes, CNRS, IETR (Institut d'Électronique et des Technologies du Numérique), UMR 6164, F-35000 Rennes, France
| | - Frédéric Chalmel
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France
| | - Yves Le Dréan
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France
| | - Denis Habauzit
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France; ANSES (French Agency for Food, Environmental and Occupational Health & Safety), Toxicology of Contaminants Unit, Fougères, France.
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Lecuyer GCV, Lardenois A, Chalmel F. UncoVer: A Web-based Resource for Single-cell and Spatially Resolved Omics Data in Uro-oncology. Eur Urol Oncol 2024:S2588-9311(24)00100-7. [PMID: 38688769 DOI: 10.1016/j.euo.2024.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/18/2024] [Accepted: 04/17/2024] [Indexed: 05/02/2024]
Affiliation(s)
- Gwendoline C V Lecuyer
- Institut de Recherche en Santé, Environnement et Travail, University of Rennes, Rennes, France
| | - Aurélie Lardenois
- Institut de Recherche en Santé, Environnement et Travail, University of Rennes, Rennes, France
| | - Frédéric Chalmel
- Institut de Recherche en Santé, Environnement et Travail, University of Rennes, Rennes, France.
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Alhaj Hussen K, Chabaane E, Nelson E, Lekiashvili S, Diop S, Keita S, Evrard B, Lardenois A, Delord M, Verhoeyen E, Cornils K, Kasraian Z, Macintyre EA, Cumano A, Garrick D, Goodhardt M, Andrieu GP, Asnafi V, Chalmel F, Canque B. Multimodal cartography of human lymphopoiesis reveals B and T/NK/ILC lineages are subjected to differential regulation. iScience 2023; 26:107890. [PMID: 37766969 PMCID: PMC10520540 DOI: 10.1016/j.isci.2023.107890] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 08/24/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
The developmental cartography of human lymphopoiesis remains incompletely understood. Here, we establish a multimodal map demonstrating that lymphoid specification follows independent direct or stepwise hierarchic routes converging toward the emergence of newly characterized CD117lo multi-lymphoid progenitors (MLPs) that undergo a proliferation arrest before entering the CD127- (NK/ILC/T) or CD127+ (B) lymphoid pathways. While the differentiation of CD127- early lymphoid progenitors is mainly driven by Flt3 signaling, emergence of their CD127+ counterparts is regulated cell-intrinsically and depends exclusively on the divisional history of their upstream precursors, including hematopoietic stem cells. Further, transcriptional mapping of differentiation trajectories reveals that whereas myeloid granulomonocytic lineages follow continuous differentiation pathways, lymphoid trajectories are intrinsically discontinuous and characterized by sequential waves of cell proliferation allowing pre-commitment amplification of lymphoid progenitor pools. Besides identifying new lymphoid specification pathways and regulatory checkpoints, our results demonstrate that NK/ILC/T and B lineages are under fundamentally distinct modes of regulation. (149 words).
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Affiliation(s)
- Kutaiba Alhaj Hussen
- INSERM U976, Université de Paris, École Pratique des Hautes Études/PSL Research University, Institut de Recherche Saint Louis, Paris, France
- Service de Biochimie, Université de Paris Saclay, Hôpital Paul Brousse, AP-HP, Villejuif, Paris, France
| | - Emna Chabaane
- INSERM U976, Université de Paris, École Pratique des Hautes Études/PSL Research University, Institut de Recherche Saint Louis, Paris, France
| | - Elisabeth Nelson
- INSERM U976, Université de Paris, École Pratique des Hautes Études/PSL Research University, Institut de Recherche Saint Louis, Paris, France
| | - Shalva Lekiashvili
- INSERM U976, Université de Paris, École Pratique des Hautes Études/PSL Research University, Institut de Recherche Saint Louis, Paris, France
| | - Samuel Diop
- INSERM U976, Université de Paris, École Pratique des Hautes Études/PSL Research University, Institut de Recherche Saint Louis, Paris, France
| | - Seydou Keita
- INSERM U976, Université de Paris, École Pratique des Hautes Études/PSL Research University, Institut de Recherche Saint Louis, Paris, France
| | - Bertrand Evrard
- University Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France
| | - Aurélie Lardenois
- University Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France
| | - Marc Delord
- INSERM U976, Université de Paris, École Pratique des Hautes Études/PSL Research University, Institut de Recherche Saint Louis, Paris, France
| | - Els Verhoeyen
- CIRI, International Center for Infectiology Research, Université de Lyon, INSERM U1111, Lyon, France
- Centre Mediterranéen de Médecine Moléculaire (C3M), INSERM U1065, Nice, France
| | - Kerstin Cornils
- Division of Pediatric Stem Cell Transplantation and Immunology, Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf and Research Institute Children’s Cancer Center, Hamburg, Germany
| | - Zeinab Kasraian
- INSERM U976, Université de Paris, École Pratique des Hautes Études/PSL Research University, Institut de Recherche Saint Louis, Paris, France
- Institut Necker Enfants-Malades, INSERM U1151, Hôpital Necker Enfants-Malades, Laboratoire d'Onco-Hématologie, Assistance Publique-Hôpitaux de Paris (AP-HP), Université de Paris, Paris, France
| | - Elizabeth A. Macintyre
- Institut Necker Enfants-Malades, INSERM U1151, Hôpital Necker Enfants-Malades, Laboratoire d'Onco-Hématologie, Assistance Publique-Hôpitaux de Paris (AP-HP), Université de Paris, Paris, France
| | - Ana Cumano
- Unit of Lymphopoiesis, Immunology Department, Institut Pasteur, Paris, France
| | - David Garrick
- INSERM U976, Université de Paris, École Pratique des Hautes Études/PSL Research University, Institut de Recherche Saint Louis, Paris, France
| | - Michele Goodhardt
- INSERM U976, Université de Paris, École Pratique des Hautes Études/PSL Research University, Institut de Recherche Saint Louis, Paris, France
| | - Guillaume P. Andrieu
- Institut Necker Enfants-Malades, INSERM U1151, Hôpital Necker Enfants-Malades, Laboratoire d'Onco-Hématologie, Assistance Publique-Hôpitaux de Paris (AP-HP), Université de Paris, Paris, France
| | - Vahid Asnafi
- Institut Necker Enfants-Malades, INSERM U1151, Hôpital Necker Enfants-Malades, Laboratoire d'Onco-Hématologie, Assistance Publique-Hôpitaux de Paris (AP-HP), Université de Paris, Paris, France
| | - Frederic Chalmel
- University Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France
| | - Bruno Canque
- INSERM U976, Université de Paris, École Pratique des Hautes Études/PSL Research University, Institut de Recherche Saint Louis, Paris, France
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Dochez-Arnault J, Desdoits-Lethimonier C, Matias I, Evrard B, Lagarrigue M, Toupin M, Lardenois A, Chalmel F, Mazaud-Guittot S, Dejucq-Rainsford N, Gely-Pernot A. Expression of the endocannabinoid system and response to cannabinoid components by the human fetal testis. BMC Med 2023; 21:219. [PMID: 37430350 DOI: 10.1186/s12916-023-02916-5] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 05/31/2023] [Indexed: 07/12/2023] Open
Abstract
BACKGROUND Cannabis consumption by pregnant women continues to increase worldwide, raising concerns about adverse effects on fetal growth and deleterious impacts on the newborn, in connection with evidence of placental transfer of cannabis compound. Cannabis action is mediated by the endocannabinoid system (ECS), which expression is well established in the brain but unknown in the developing testis. The fetal testis, whose endocrine function orchestrates the masculinization of many distant organs, is particularly sensitive to disruption by xenobiotics. In this context, we aimed to determine whether cannabis exposure has the potential to directly impact the human fetal testis. METHODS We determined the expression of components of the ECS in the human fetal testis from 6 to 17 developmental weeks and assessed the direct effects of phytocannabinoids Δ9-trans-tetrahydrocannabinol (THC) and cannabidiol (CBD) on the testis morphology and cell functions ex vivo. RESULTS We demonstrate the presence in the human fetal testis of two key endocannabinoids, 2-arachidonylglycerol (2-AG) and to a lower level anandamide (AEA), as well as a range of enzymes and receptors for the ECS. Ex vivo exposure of first trimester testes to CBD, THC, or CBD/THC [ratio 1:1] at 10-7 to 10-5 M altered testosterone secretion by Leydig cells, AMH secretion by Sertoli cells, and impacted testicular cell proliferation and viability as early as 72 h post-exposure. Transcriptomic analysis on 72 h-exposed fetal testis explants revealed 187 differentially expressed genes (DEGs), including genes involved in steroid synthesis and toxic substance response. Depending on the molecules and testis age, highly deleterious effects of phytocannabinoid exposure were observed on testis tissue after 14 days, including Sertoli and germ cell death. CONCLUSIONS Our study is the first to evidence the presence of the ECS in the human fetal testis and to highlight the potential adverse effect of cannabis consumption by pregnant women onto the development of the male gonad.
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Affiliation(s)
- J Dochez-Arnault
- Univ Rennes, Inserm (Institut National de La Santé Et de La Recherche Médicale), EHESP, Irset (Institut de Recherche en Santé, Environnement Et Travail) - UMR_S 1085 (Institut de Recherche en Santé, environnement et travail), 9 Avenue du Professeur Léon Bernard, 35000, Rennes, CEDEX, France
| | - C Desdoits-Lethimonier
- Univ Rennes, Inserm (Institut National de La Santé Et de La Recherche Médicale), EHESP, Irset (Institut de Recherche en Santé, Environnement Et Travail) - UMR_S 1085 (Institut de Recherche en Santé, environnement et travail), 9 Avenue du Professeur Léon Bernard, 35000, Rennes, CEDEX, France
| | - I Matias
- Neurocentre Magendie - Inserm, U1215, Bordeaux, France
| | - B Evrard
- Univ Rennes, Inserm (Institut National de La Santé Et de La Recherche Médicale), EHESP, Irset (Institut de Recherche en Santé, Environnement Et Travail) - UMR_S 1085 (Institut de Recherche en Santé, environnement et travail), 9 Avenue du Professeur Léon Bernard, 35000, Rennes, CEDEX, France
| | - M Lagarrigue
- Univ Rennes, Inserm (Institut National de La Santé Et de La Recherche Médicale), EHESP, Irset (Institut de Recherche en Santé, Environnement Et Travail) - UMR_S 1085 (Institut de Recherche en Santé, environnement et travail), 9 Avenue du Professeur Léon Bernard, 35000, Rennes, CEDEX, France
| | | | - A Lardenois
- Univ Rennes, Inserm (Institut National de La Santé Et de La Recherche Médicale), EHESP, Irset (Institut de Recherche en Santé, Environnement Et Travail) - UMR_S 1085 (Institut de Recherche en Santé, environnement et travail), 9 Avenue du Professeur Léon Bernard, 35000, Rennes, CEDEX, France
| | - F Chalmel
- Univ Rennes, Inserm (Institut National de La Santé Et de La Recherche Médicale), EHESP, Irset (Institut de Recherche en Santé, Environnement Et Travail) - UMR_S 1085 (Institut de Recherche en Santé, environnement et travail), 9 Avenue du Professeur Léon Bernard, 35000, Rennes, CEDEX, France
| | - S Mazaud-Guittot
- Univ Rennes, Inserm (Institut National de La Santé Et de La Recherche Médicale), EHESP, Irset (Institut de Recherche en Santé, Environnement Et Travail) - UMR_S 1085 (Institut de Recherche en Santé, environnement et travail), 9 Avenue du Professeur Léon Bernard, 35000, Rennes, CEDEX, France
| | - N Dejucq-Rainsford
- Univ Rennes, Inserm (Institut National de La Santé Et de La Recherche Médicale), EHESP, Irset (Institut de Recherche en Santé, Environnement Et Travail) - UMR_S 1085 (Institut de Recherche en Santé, environnement et travail), 9 Avenue du Professeur Léon Bernard, 35000, Rennes, CEDEX, France
| | - A Gely-Pernot
- Univ Rennes, Inserm (Institut National de La Santé Et de La Recherche Médicale), EHESP, Irset (Institut de Recherche en Santé, Environnement Et Travail) - UMR_S 1085 (Institut de Recherche en Santé, environnement et travail), 9 Avenue du Professeur Léon Bernard, 35000, Rennes, CEDEX, France.
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Saout JR, Lecuyer G, Léonard S, Evrard B, Kammerer-Jacquet SF, Noël L, Khene ZE, Mathieu R, Brunot A, Rolland AD, Bensalah K, Rioux-Leclercq N, Lardenois A, Chalmel F. Single-cell Deconvolution of a Specific Malignant Cell Population as a Poor Prognostic Biomarker in Low-risk Clear Cell Renal Cell Carcinoma Patients. Eur Urol 2023; 83:441-451. [PMID: 36801089 DOI: 10.1016/j.eururo.2023.02.008] [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] [Received: 09/12/2022] [Revised: 12/10/2022] [Accepted: 02/03/2023] [Indexed: 02/17/2023]
Abstract
BACKGROUND Intratumor heterogeneity (ITH) is a key feature in clear cell renal cell carcinomas (ccRCCs) that impacts outcomes such as aggressiveness, response to treatments, or recurrence. In particular, it may explain tumor relapse after surgery in clinically low-risk patients who did not benefit from adjuvant therapy. Recently, single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool to unravel expression ITH (eITH) and might enable better assessment of clinical outcomes in ccRCC. OBJECTIVE To explore eITH in ccRCC with a focus on malignant cells (MCs) and assess its relevance to improve prognosis for low-risk patients. DESIGN, SETTING, AND PARTICIPANTS We performed scRNA-seq on tumor samples from five untreated ccRCC patients ranging from pT1a to pT3b. Data were complemented with a published dataset composed of pairs of matched normal and ccRCC samples. INTERVENTION Radical or partial nephrectomy on untreated ccRCC patients. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS Viability and cell type proportions were determined by flow cytometry. Following scRNA-seq, a functional analysis was performed and tumor progression trajectories were inferred. A deconvolution approach was applied on an external cohort, and Kaplan-Meier survival curves were estimated with respect to the prevalence of malignant clusters. RESULTS AND LIMITATIONS We analyzed 54 812 cells and identified 35 cell subpopulations. The eITH analysis revealed that each tumor contained various degrees of clonal diversity. The transcriptomic signatures of MCs in one particularly heterogeneous sample were used to design a deconvolution-based strategy that allowed the risk stratification of 310 low-risk ccRCC patients. CONCLUSIONS We described eITH in ccRCCs, and used this information to establish significant cell population-based prognostic signatures and better discriminate ccRCC patients. This approach has the potential to improve the stratification of clinically low-risk patients and their therapeutic management. PATIENT SUMMARY We sequenced the RNA content of individual cell subpopulations composed of clear cell renal cell carcinomas and identified specific malignant cells the genetic information of which can be used to predict tumor progression.
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Affiliation(s)
- Judikael R Saout
- Inserm, EHESP, Univ Rennes, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France
| | - Gwendoline Lecuyer
- Inserm, EHESP, Univ Rennes, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France
| | - Simon Léonard
- Inserm, EHESP, Univ Rennes, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France; LabEx IGO "Immunotherapy, Graft, Oncology", Nantes, France; INSERM, EFS, UMR S1236, Univ Rennes, Rennes, France
| | - Bertrand Evrard
- Inserm, EHESP, Univ Rennes, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France
| | - Solène-Florence Kammerer-Jacquet
- Inserm, EHESP, Univ Rennes, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France; Pathology Department, University Hospital of Rennes, Rennes, France
| | - Laurence Noël
- Inserm, EHESP, Univ Rennes, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France
| | | | - Romain Mathieu
- Inserm, EHESP, Univ Rennes, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France; Urology Department, University Hospital of Rennes, Rennes, France
| | - Angélique Brunot
- Department of Medical Oncology, Centre Eugène Marquis, Unicancer, Rennes, France
| | - Antoine D Rolland
- Inserm, EHESP, Univ Rennes, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France
| | - Karim Bensalah
- Urology Department, University Hospital of Rennes, Rennes, France
| | - Nathalie Rioux-Leclercq
- Inserm, EHESP, Univ Rennes, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France; Pathology Department, University Hospital of Rennes, Rennes, France
| | - Aurélie Lardenois
- Inserm, EHESP, Univ Rennes, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France
| | - Frédéric Chalmel
- Inserm, EHESP, Univ Rennes, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France.
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Draskau MK, Schwartz CL, Evrard B, Lardenois A, Pask A, Chalmel F, Svingen T. The anti-androgenic fungicide triticonazole induces region-specific transcriptional changes in the developing rat perineum and phallus. Chemosphere 2022; 308:136346. [PMID: 36084822 DOI: 10.1016/j.chemosphere.2022.136346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 08/05/2022] [Accepted: 09/02/2022] [Indexed: 06/15/2023]
Abstract
Intrauterine exposure to endocrine disrupting chemicals can interfere with male reproductive development. This can lead to male reproductive disorders such as hypospadias, cryptorchidism and reduced fertility, as well as shorter anogenital distance (AGD) - a biomarker for incomplete androgen-dependent fetal masculinization. However, it remains challenging to predict adverse in vivo outcomes based on in vitro effect patterns for many chemicals. This is a challenge for modern toxicology, which aims to reduce animal testing for chemical safety assessments. To enable the transition towards higher reliance on alternative test methods, we need to better map underlying mechanisms leading to adverse effects. Herein, we have analyzed the transcriptome of the perineum and phallus of male fetal rats and defined the impacts of exposure to an anti-androgenic fungicide, triticonazole. Previously we have shown that developmental exposure to triticonazole can induce short male AGD, but without a marked effect on the transcriptome of the fetal testes. In contrast, we report here significant changes to the transcriptional landscape of the perineum and phallus, including regional differences between these adjacent tissues. This highlights the importance of analyzing the correct tissue when characterizing mechanisms of complex in vivo effect outcomes. Our results provide a rich resource for the spatiotemporal gene networks that are involved in the development of male external genitalia, and that can be disrupted upon exposure to chemicals that prevent normal masculinization of the perineum and phallus. Such data will be critical in the development of novel alternative test methods to determine the endocrine disrupting potential of existing and emerging chemicals.
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Affiliation(s)
- Monica Kam Draskau
- National Food Institute, Technical University of Denmark, Kemitorvet Building 202, Kongens Lyngby DK-2800, Denmark
| | - Camilla Lindgren Schwartz
- National Food Institute, Technical University of Denmark, Kemitorvet Building 202, Kongens Lyngby DK-2800, Denmark
| | - Bertrand Evrard
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085, F-35000 Rennes, France
| | - Aurélie Lardenois
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085, F-35000 Rennes, France
| | - Andrew Pask
- School of BioSciences, The University of Melbourne, Melbourne, 3010, Australia
| | - Frédéric Chalmel
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085, F-35000 Rennes, France
| | - Terje Svingen
- National Food Institute, Technical University of Denmark, Kemitorvet Building 202, Kongens Lyngby DK-2800, Denmark.
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Leonard S, Lardenois A, Tarte K, Rolland AD, Chalmel F. FlexDotPlot: a universal and modular dot plot visualization tool for complex multifaceted data. Bioinform Adv 2022; 2:vbac019. [PMID: 36699406 PMCID: PMC9710660 DOI: 10.1093/bioadv/vbac019] [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] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/14/2022] [Accepted: 03/22/2022] [Indexed: 02/01/2023]
Abstract
Motivation Dot plots are heatmap-like charts that provide a compact way to simultaneously display two quantitative information by means of dots of different sizes and colors. Despite the popularity of this visualization method, particularly in single-cell RNA-sequencing (scRNA-seq) studies, existing tools used to make dot plots are limited in terms of functionality and usability. Results We developed FlexDotPlot, an R package for generating dot plots from multifaceted data, including scRNA-seq data. It provides a universal and easy-to-use solution with a high versatility. An interactive R Shiny application is also available allowing non-R users to easily generate dot plots with several tunable parameters. Availability and implementation Source code and detailed manual are available on CRAN (stable version) and at https://github.com/Simon-Leonard/FlexDotPlot (development version). Code to reproduce figures is available at https://github.com/Simon-Leonard/FlexDotPlot_paper. A Shiny app is available as a stand-alone application within the package. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
- Simon Leonard
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail), UMR_S 1085, F-35000 Rennes, France,UMR 1236, University of Rennes, INSERM, Etablissement Français du Sang Bretagne, F-35043 Rennes, France,LabEx IGO “Immunotherapy, Graft, Oncology”, F-35043 Nantes, France
| | - Aurélie Lardenois
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail), UMR_S 1085, F-35000 Rennes, France
| | - Karin Tarte
- UMR 1236, University of Rennes, INSERM, Etablissement Français du Sang Bretagne, F-35043 Rennes, France,SITI Laboratory, Etablissement Français du Sang Bretagne, CHU Rennes, Rennes, F-35033 France
| | - Antoine D Rolland
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail), UMR_S 1085, F-35000 Rennes, France
| | - Frédéric Chalmel
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail), UMR_S 1085, F-35000 Rennes, France,To whom correspondence should be addressed.
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8
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Ramskov Tetzlaff CN, Ramhøj L, Lardenois A, Axelstad M, Evrard B, Chalmel F, Taxvig C, Svingen T. Adult female rats perinatally exposed to perfluorohexane sulfonate (PFHxS) and a mixture of endocrine disruptors display increased body/fat weights without a transcriptional footprint in fat cells. Toxicol Lett 2021; 339:78-87. [DOI: 10.1016/j.toxlet.2020.12.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 12/22/2020] [Accepted: 12/26/2020] [Indexed: 12/11/2022]
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9
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Draskau MK, Lardenois A, Evrard B, Boberg J, Chalmel F, Svingen T. Transcriptome analysis of fetal rat testis following intrauterine exposure to the azole fungicides triticonazole and flusilazole reveals subtle changes despite adverse endocrine effects. Chemosphere 2021; 264:128468. [PMID: 33032228 DOI: 10.1016/j.chemosphere.2020.128468] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 07/10/2020] [Revised: 09/11/2020] [Accepted: 09/26/2020] [Indexed: 06/11/2023]
Abstract
Azoles are used in agriculture and medicine to combat fungal infections. We have previously examined the endocrine disrupting properties of the agricultural azole fungicides triticonazole and flusilazole. Triticonazole displayed strong androgen receptor (AR) antagonism in vitro, whereas in utero exposure resulted in anti-androgenic effects in vivo evidenced by shorter anogenital distance (AGD) in fetal male rats. Flusilazole displayed strong AR antagonism, but less potent than triticonazole, and disrupted steroidogenesis in vitro, whereas in utero exposure disrupted fetal male plasma hormone levels. To elaborate on how these azole fungicides can disrupt male reproductive development by different mechanisms, and to investigate whether feminization effects such as short AGD in males can also be detected at the transcript level in fetal testes, we profiled fetal testis transcriptomes after in utero exposure to triticonazole and flusilazole by 3'Digital Gene Expression (3'DGE). The analysis revealed few transcriptional changes after exposure to either compound at gestation day 17 and 21. This suggests that the observed influence of flusilazole on hormone production may be by directly targeting steroidogenic enzyme activity in the testis at the protein level, whereas observations of shorter AGD by triticonazole may primarily be due to disturbed androgen signaling in androgen-sensitive tissues. Expression of Calb2 and Gsta2 was altered by flusilazole but not triticonazole and may pinpoint novel pathways of disrupted testicular steroid synthesis. Our findings have wider implication for how we integrate omics data in chemical testing frameworks, including selection of non-animal test methods and building of Adverse Outcome Pathways for regulatory purposes.
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Affiliation(s)
- Monica Kam Draskau
- Division of Diet, Disease Prevention and Toxicology, National Food Institute, Technical University of Denmark, Kemitorvet Building 202, Kongens Lyngby, DK 2800, Denmark
| | - Aurélie Lardenois
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail), UMR_S 1085, F-35000, Rennes, France
| | - Bertrand Evrard
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail), UMR_S 1085, F-35000, Rennes, France
| | - Julie Boberg
- Division of Diet, Disease Prevention and Toxicology, National Food Institute, Technical University of Denmark, Kemitorvet Building 202, Kongens Lyngby, DK 2800, Denmark
| | - Frédéric Chalmel
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail), UMR_S 1085, F-35000, Rennes, France
| | - Terje Svingen
- Division of Diet, Disease Prevention and Toxicology, National Food Institute, Technical University of Denmark, Kemitorvet Building 202, Kongens Lyngby, DK 2800, Denmark.
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10
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Darde TA, Lecluze E, Lardenois A, Stévant I, Alary N, Tüttelmann F, Collin O, Nef S, Jégou B, Rolland AD, Chalmel F. The ReproGenomics Viewer: a multi-omics and cross-species resource compatible with single-cell studies for the reproductive science community. Bioinformatics 2020; 35:3133-3139. [PMID: 30668675 DOI: 10.1093/bioinformatics/btz047] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 01/07/2019] [Accepted: 01/17/2019] [Indexed: 12/22/2022] Open
Abstract
MOTIVATION Recent advances in transcriptomics have enabled unprecedented insight into gene expression analysis at a single-cell resolution. While it is anticipated that the number of publications based on such technologies will increase in the next decade, there is currently no public resource to centralize and enable scientists to explore single-cell datasets published in the field of reproductive biology. RESULTS Here, we present a major update of the ReproGenomics Viewer, a cross-species and cross-technology web-based resource of manually-curated sequencing datasets related to reproduction. The redesign of the ReproGenomics Viewer's architecture is accompanied by significant growth of the database content including several landmark single-cell RNA-sequencing datasets. The implementation of additional tools enables users to visualize and browse the complex, high-dimensional data now being generated in the reproductive field. AVAILABILITY AND IMPLEMENTATION The ReproGenomics Viewer resource is freely accessible at http://rgv.genouest.org. The website is implemented in Python, JavaScript and MongoDB, and is compatible with all major browsers. Source codes can be downloaded from https://github.com/fchalmel/RGV. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Thomas A Darde
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes F-35000, France
| | - Estelle Lecluze
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes F-35000, France
| | - Aurélie Lardenois
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes F-35000, France
| | - Isabelle Stévant
- Department of Genetic Medicine and Development, University of Geneva, Geneva 1211, Switzerland
| | - Nathan Alary
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes F-35000, France
| | - Frank Tüttelmann
- Institute of Human Genetics, University of Münster, Münster, Germany
| | - Olivier Collin
- Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA/INRIA) - GenOuest platform, Université de Rennes 1, Rennes F-35042, France
| | - Serge Nef
- Department of Genetic Medicine and Development, University of Geneva, Geneva 1211, Switzerland
| | - Bernard Jégou
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes F-35000, France
| | - Antoine D Rolland
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes F-35000, France
| | - Frédéric Chalmel
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes F-35000, France
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11
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Pham TH, Lecomte S, Le Guevel R, Lardenois A, Evrard B, Chalmel F, Ferriere F, Balaguer P, Efstathiou T, Pakdel F. Characterization of Glyceollins as Novel Aryl Hydrocarbon Receptor Ligands and Their Role in Cell Migration. Int J Mol Sci 2020; 21:ijms21041368. [PMID: 32085612 PMCID: PMC7072876 DOI: 10.3390/ijms21041368] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 02/05/2020] [Accepted: 02/14/2020] [Indexed: 12/31/2022] Open
Abstract
Recent studies strongly support the use of the aryl hydrocarbon receptor (AhR) as a therapeutic target in breast cancer. Glyceollins, a group of soybean phytoalexins, are known to exert therapeutic effects in chronic human diseases and also in cancer. To investigate the interaction between glyceollin I (GI), glyceollin II (GII) and AhR, a computational docking analysis, luciferase assays, immunofluorescence and transcriptome analyses were performed with different cancer cell lines. The docking experiments predicted that GI and GII can enter into the AhR binding pocket, but their interactions with the amino acids of the binding site differ, in part, from those interacting with 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Both GI and GII were able to weakly and partially activate AhR, with GII being more potent. The results from the transcriptome assays showed that approximately 10% of the genes regulated by TCDD were also modified by both GI and GII, which could have either antagonistic or synergistic effects upon TCDD activation. In addition, we report here, on the basis of phenotype, that GI and GII inhibit the migration of triple-negative (ER-, PgR-, HER2NEU-) MDA-MB-231 breast cancer cells, and that they inhibit the expression of genes which code for important regulators of cell migration and invasion in cancer tissues. In conclusion, GI and GII are AhR ligands that should be further investigated to determine their usefulness in cancer treatments.
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Affiliation(s)
- Thu Ha Pham
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) -UMR_S1085, F-35000 Rennes, France; (T.H.P.); (S.L.); (A.L.); (B.E.); (F.C.); (F.F.)
| | - Sylvain Lecomte
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) -UMR_S1085, F-35000 Rennes, France; (T.H.P.); (S.L.); (A.L.); (B.E.); (F.C.); (F.F.)
| | - Remy Le Guevel
- ImPACcell platform (SFR Biosit), Univ Rennes, 35000 Rennes, France;
| | - Aurélie Lardenois
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) -UMR_S1085, F-35000 Rennes, France; (T.H.P.); (S.L.); (A.L.); (B.E.); (F.C.); (F.F.)
| | - Bertrand Evrard
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) -UMR_S1085, F-35000 Rennes, France; (T.H.P.); (S.L.); (A.L.); (B.E.); (F.C.); (F.F.)
| | - Frédéric Chalmel
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) -UMR_S1085, F-35000 Rennes, France; (T.H.P.); (S.L.); (A.L.); (B.E.); (F.C.); (F.F.)
| | - François Ferriere
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) -UMR_S1085, F-35000 Rennes, France; (T.H.P.); (S.L.); (A.L.); (B.E.); (F.C.); (F.F.)
| | - Patrick Balaguer
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM U1194, ICM, Univ. Montpellier, 34090 Montpellier, France;
| | - Theo Efstathiou
- Laboratoire Nutrinov, Technopole Atalante Champeaux, 8 Rue Jules Maillard de la Gournerie, 35012 Rennes CEDEX, France;
| | - Farzad Pakdel
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) -UMR_S1085, F-35000 Rennes, France; (T.H.P.); (S.L.); (A.L.); (B.E.); (F.C.); (F.F.)
- Correspondence: ; Tel.: +33-(0)22-323-5132
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12
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Lorant J, Larcher T, Jaulin N, Hedan B, Lardenois A, Leroux I, Dubreil L, Ledevin M, Goubin H, Moullec S, Deschamps JY, Thorin C, André C, Adjali O, Rouger K. Vascular Delivery of Allogeneic MuStem Cells in Dystrophic Dogs Requires Only Short-Term Immunosuppression to Avoid Host Immunity and Generate Clinical/Tissue Benefits. Cell Transplant 2018; 27:1096-1110. [PMID: 29871519 PMCID: PMC6158548 DOI: 10.1177/0963689718776306] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 04/05/2018] [Accepted: 04/17/2018] [Indexed: 01/15/2023] Open
Abstract
Growing demonstrations of regenerative potential for some stem cells led recently to promising therapeutic proposals for neuromuscular diseases. We have shown that allogeneic MuStem cell transplantation into Golden Retriever muscular dystrophy (GRMD) dogs under continuous immunosuppression (IS) leads to persistent clinical stabilization and muscle repair. However, long-term IS in medical practice is associated with adverse effects raising safety concerns. Here, we investigate whether the IS removal or its restriction to the transplantation period could be considered. Dogs aged 4-5 months old received vascular infusions of allogeneic MuStem cells without IS (GRMDMU/no-IS) or under transient IS (GRMDMU/tr-IS). At 5 months post-infusion, persisting clinical status improvement of the GRMDMU/tr-IS dogs was observed while GRMDMU/no-IS dogs exhibited no benefit. Histologically, only 9-month-old GRMDMU/tr-IS dogs showed an increased muscle regenerative activity. A mixed cell reaction with the host peripheral blood mononucleated cells (PBMCs) and corresponding donor cells revealed undetectable to weak lymphocyte proliferation in GRMDMU/tr-IS dogs compared with a significant proliferation in GRMDMU/no-IS dogs. Importantly, any dog group showed neither cellular nor humoral anti-dystrophin responses. Our results show that transient IS is necessary and sufficient to sustain allogeneic MuStem cell transplantation benefits and prevent host immunity. These findings provide useful critical insight to designing therapeutic strategies.
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Affiliation(s)
- Judith Lorant
- PAnTher, INRA, École Nationale Vétérinaire, Agro-alimentaire et de l’Alimentation Nantes-Atlantique (Oniris), Université Bretagne Loire (UBL), Nantes, F-44307, France
- Judith Lorant and Thibaut Larcher both contributed equally to this work
| | - Thibaut Larcher
- PAnTher, INRA, École Nationale Vétérinaire, Agro-alimentaire et de l’Alimentation Nantes-Atlantique (Oniris), Université Bretagne Loire (UBL), Nantes, F-44307, France
- Judith Lorant and Thibaut Larcher both contributed equally to this work
| | - Nicolas Jaulin
- INSERM, UMR1089, Centre Hospitalier Universitaire, Nantes, France
| | - Benoît Hedan
- CNRS, UMR6290, Institut de Génétique et Développement de Rennes, Université Rennes 1, Rennes, France
- Université Rennes 1, UEB, IFR140, Faculté de Médecine, Rennes, France
| | - Aurélie Lardenois
- PAnTher, INRA, École Nationale Vétérinaire, Agro-alimentaire et de l’Alimentation Nantes-Atlantique (Oniris), Université Bretagne Loire (UBL), Nantes, F-44307, France
| | - Isabelle Leroux
- PAnTher, INRA, École Nationale Vétérinaire, Agro-alimentaire et de l’Alimentation Nantes-Atlantique (Oniris), Université Bretagne Loire (UBL), Nantes, F-44307, France
| | - Laurence Dubreil
- PAnTher, INRA, École Nationale Vétérinaire, Agro-alimentaire et de l’Alimentation Nantes-Atlantique (Oniris), Université Bretagne Loire (UBL), Nantes, F-44307, France
| | - Mireille Ledevin
- PAnTher, INRA, École Nationale Vétérinaire, Agro-alimentaire et de l’Alimentation Nantes-Atlantique (Oniris), Université Bretagne Loire (UBL), Nantes, F-44307, France
| | - Hélicia Goubin
- PAnTher, INRA, École Nationale Vétérinaire, Agro-alimentaire et de l’Alimentation Nantes-Atlantique (Oniris), Université Bretagne Loire (UBL), Nantes, F-44307, France
| | | | - Jack-Yves Deschamps
- PAnTher, INRA, École Nationale Vétérinaire, Agro-alimentaire et de l’Alimentation Nantes-Atlantique (Oniris), Université Bretagne Loire (UBL), Nantes, F-44307, France
- Centre de Boisbonne, Oniris, Nantes, France
| | - Chantal Thorin
- Laboratoire de Physiopathologie Animale et Pharmacologie Fonctionnelle, Oniris, Nantes, France
| | - Catherine André
- CNRS, UMR6290, Institut de Génétique et Développement de Rennes, Université Rennes 1, Rennes, France
- Université Rennes 1, UEB, IFR140, Faculté de Médecine, Rennes, France
| | - Oumeya Adjali
- INSERM, UMR1089, Centre Hospitalier Universitaire, Nantes, France
| | - Karl Rouger
- PAnTher, INRA, École Nationale Vétérinaire, Agro-alimentaire et de l’Alimentation Nantes-Atlantique (Oniris), Université Bretagne Loire (UBL), Nantes, F-44307, France
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13
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Saury C, Lardenois A, Schleder C, Leroux I, Lieubeau B, David L, Charrier M, Guével L, Viau S, Delorme B, Rouger K. Human serum and platelet lysate are appropriate xeno-free alternatives for clinical-grade production of human MuStem cell batches. Stem Cell Res Ther 2018; 9:128. [PMID: 29720259 PMCID: PMC5932844 DOI: 10.1186/s13287-018-0852-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [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: 11/21/2017] [Revised: 02/16/2018] [Accepted: 03/20/2018] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Canine MuStem cells have demonstrated regenerative efficacy in a dog model of muscular dystrophy, and the recent characterization of human counterparts (hMuStem) has highlighted the therapeutic potential of this muscle-derived stem cell population. To date, these cells have only been generated in research-grade conditions. However, evaluation of the clinical efficacy of any such therapy will require the production of hMuStem cells in compliance with good manufacturing practices (GMPs). Because the current use of fetal bovine serum (FBS) to isolate and expand hMuStem cells raises several ethical, safety, and supply concerns, we assessed the use of two alternative xeno-free blood derivatives: human serum (HS) and a human platelet lysate (hPL). METHODS hMuStem cells were isolated and expanded in vitro in either HS-supplemented or hPL-supplemented media and the proliferation rate, clonogenicity, myogenic commitment potential, and oligopotency compared with that observed in FBS-supplemented medium. Flow cytometry and high-throughput 3'-digital gene expression RNA sequencing were used to characterize the phenotype and global gene expression pattern of hMuStem cells cultured with HS or hPL. RESULTS HS-supplemented and hPL-supplemented media both supported the isolation and long-term proliferation of hMuStem cells. Compared with FBS-based medium, both supplements enhanced clonogenicity and allowed for a reduction in growth factor supplementation. Neither supplement altered the cell lineage pattern of hMuStem cells. In vitro differentiation assays revealed a decrease in myogenic commitment and in the fusion ability of hMuStem cells when cultured with hPL. In return, this reduction of myogenic potential in hPL-supplemented cultures was rapidly reversed by substitution of hPL with HS or fibrinogen-depleted hPL. Moreover, culture of hMuStem cells in hPL hydrogel and fibrinogen-depleted hPL demonstrated that myogenic differentiation potential is maintained in heparin-free hPL derivatives. CONCLUSIONS Our findings indicate that HS and hPL are efficient and viable alternatives to FBS for the preparation of hMuStem cell batches in compliance with GMPs.
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Affiliation(s)
- Charlotte Saury
- Macopharma, Biotherapy Division, F-59420, Mouvaux, France.,PAnTher, INRA, École Nationale Vétérinaire, Agro-alimentaire et de l'alimentation Nantes-Atlantique (Oniris), Université Bretagne Loire (UBL), F-44307, Nantes, France
| | - Aurélie Lardenois
- PAnTher, INRA, École Nationale Vétérinaire, Agro-alimentaire et de l'alimentation Nantes-Atlantique (Oniris), Université Bretagne Loire (UBL), F-44307, Nantes, France
| | - Cindy Schleder
- PAnTher, INRA, École Nationale Vétérinaire, Agro-alimentaire et de l'alimentation Nantes-Atlantique (Oniris), Université Bretagne Loire (UBL), F-44307, Nantes, France
| | - Isabelle Leroux
- PAnTher, INRA, École Nationale Vétérinaire, Agro-alimentaire et de l'alimentation Nantes-Atlantique (Oniris), Université Bretagne Loire (UBL), F-44307, Nantes, France
| | | | - Laurent David
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, UBL, F-44093, Nantes, France.,Institut de Transplantation Urologie Néphrologie (ITUN), CHU Nantes, F-44093, Nantes, France.,Inserm UMS016, SFR François Bonamy, iPSC Core Facility, Nantes, France.,CNRS UMS 3556, Nantes, France.,Université de Nantes, Nantes, France.,CHU Nantes, Nantes, France
| | - Marine Charrier
- PAnTher, INRA, École Nationale Vétérinaire, Agro-alimentaire et de l'alimentation Nantes-Atlantique (Oniris), Université Bretagne Loire (UBL), F-44307, Nantes, France.,Institut du thorax, INSERM, CNRS, Université de Nantes, Nantes, France.,Université de Nantes, F-44000, Nantes, France
| | - Laëtitia Guével
- PAnTher, INRA, École Nationale Vétérinaire, Agro-alimentaire et de l'alimentation Nantes-Atlantique (Oniris), Université Bretagne Loire (UBL), F-44307, Nantes, France.,Université de Nantes, F-44000, Nantes, France
| | - Sabrina Viau
- Macopharma, Biotherapy Division, F-59420, Mouvaux, France
| | - Bruno Delorme
- Macopharma, Biotherapy Division, F-59420, Mouvaux, France
| | - Karl Rouger
- PAnTher, INRA, École Nationale Vétérinaire, Agro-alimentaire et de l'alimentation Nantes-Atlantique (Oniris), Université Bretagne Loire (UBL), F-44307, Nantes, France. .,INRA, UMR 703, École Nationale Vétérinaire, Agroalimentaire et de l'Alimentation Nantes-Atlantique (Oniris), Route de Gachet, CS. 40706, F-44307, Nantes, France.
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14
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Lardenois A, Jagot S, Lagarrigue M, Guével B, Ledevin M, Larcher T, Dubreil L, Pineau C, Rouger K, Guével L. Quantitative proteome profiling of dystrophic dog skeletal muscle reveals a stabilized muscular architecture and protection against oxidative stress after systemic delivery of MuStem cells. Proteomics 2017; 16:2028-42. [PMID: 27246553 DOI: 10.1002/pmic.201600002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [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: 01/05/2016] [Revised: 05/02/2016] [Accepted: 05/30/2016] [Indexed: 12/23/2022]
Abstract
Proteomic profiling plays a decisive role in the elucidation of molecular signatures representative of a specific clinical context. MuStem cell based therapy represents a promising approach for clinical applications to cure Duchenne muscular dystrophy (DMD). To expand our previous studies collected in the clinically relevant DMD animal model, we decided to investigate the skeletal muscle proteome 4 months after systemic delivery of allogenic MuStem cells. Quantitative proteomics with isotope-coded protein labeling was used to compile quantitative changes in the protein expression profiles of muscle in transplanted Golden Retriever muscular dystrophy (GRMD) dogs as compared to Golden Retriever muscular dystrophy dogs. A total of 492 proteins were quantified, including 25 that were overrepresented and 46 that were underrepresented after MuStem cell transplantation. Interestingly, this study demonstrates that somatic stem cell therapy impacts on the structural integrity of the muscle fascicle by acting on fibers and its connections with the extracellular matrix. We also show that cell infusion promotes protective mechanisms against oxidative stress and favors the initial phase of muscle repair. This study allows us to identify putative candidates for tissue markers that might be of great value in objectively exploring the clinical benefits resulting from our cell-based therapy for DMD. All MS data have been deposited in the ProteomeXchange with identifier PXD001768 (http://proteomecentral.proteomexchange.org/dataset/PXD001768).
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Affiliation(s)
- Aurélie Lardenois
- INRA, UMR703 PAnTher, Nantes, France.,LUNAM Université, Oniris, École nationale vétérinaire, agro-alimentaire et de l'alimentation Nantes-Atlantique, Nantes, France
| | - Sabrina Jagot
- INRA, UMR703 PAnTher, Nantes, France.,LUNAM Université, Oniris, École nationale vétérinaire, agro-alimentaire et de l'alimentation Nantes-Atlantique, Nantes, France.,Université de Nantes, Nantes, France
| | - Mélanie Lagarrigue
- Protim, Irset Inserm UMR 1085, Campus de Beaulieu, Rennes, France.,Université de Rennes I, Campus de Beaulieu, Rennes, France
| | - Blandine Guével
- Protim, Irset Inserm UMR 1085, Campus de Beaulieu, Rennes, France.,Université de Rennes I, Campus de Beaulieu, Rennes, France
| | - Mireille Ledevin
- INRA, UMR703 PAnTher, Nantes, France.,LUNAM Université, Oniris, École nationale vétérinaire, agro-alimentaire et de l'alimentation Nantes-Atlantique, Nantes, France
| | - Thibaut Larcher
- INRA, UMR703 PAnTher, Nantes, France.,LUNAM Université, Oniris, École nationale vétérinaire, agro-alimentaire et de l'alimentation Nantes-Atlantique, Nantes, France
| | - Laurence Dubreil
- INRA, UMR703 PAnTher, Nantes, France.,LUNAM Université, Oniris, École nationale vétérinaire, agro-alimentaire et de l'alimentation Nantes-Atlantique, Nantes, France
| | - Charles Pineau
- Protim, Irset Inserm UMR 1085, Campus de Beaulieu, Rennes, France.,Université de Rennes I, Campus de Beaulieu, Rennes, France
| | - Karl Rouger
- INRA, UMR703 PAnTher, Nantes, France.,LUNAM Université, Oniris, École nationale vétérinaire, agro-alimentaire et de l'alimentation Nantes-Atlantique, Nantes, France
| | - Laëtitia Guével
- INRA, UMR703 PAnTher, Nantes, France.,LUNAM Université, Oniris, École nationale vétérinaire, agro-alimentaire et de l'alimentation Nantes-Atlantique, Nantes, France.,Université de Nantes, Nantes, France
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15
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Robriquet F, Lardenois A, Babarit C, Larcher T, Dubreil L, Leroux I, Zuber C, Ledevin M, Deschamps JY, Fromes Y, Cherel Y, Guevel L, Rouger K. Differential Gene Expression Profiling of Dystrophic Dog Muscle after MuStem Cell Transplantation. PLoS One 2015; 10:e0123336. [PMID: 25955839 PMCID: PMC4425432 DOI: 10.1371/journal.pone.0123336] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [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: 09/24/2014] [Accepted: 03/02/2015] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Several adult stem cell populations exhibit myogenic regenerative potential, thus representing attractive candidates for therapeutic approaches of neuromuscular diseases such as Duchenne Muscular Dystrophy (DMD). We have recently shown that systemic delivery of MuStem cells, skeletal muscle-resident stem cells isolated in healthy dog, generates the remodelling of muscle tissue and gives rise to striking clinical benefits in Golden Retriever Muscular Dystrophy (GRMD) dog. This global effect, which is observed in the clinically relevant DMD animal model, leads us to question here the molecular pathways that are impacted by MuStem cell transplantation. To address this issue, we compare the global gene expression profile between healthy, GRMD and MuStem cell treated GRMD dog muscle, four months after allogenic MuStem cell transplantation. RESULTS In the dystrophic context of the GRMD dog, disease-related deregulation is observed in the case of 282 genes related to various processes such as inflammatory response, regeneration, calcium ion binding, extracellular matrix organization, metabolism and apoptosis regulation. Importantly, we reveal the impact of MuStem cell transplantation on several molecular and cellular pathways based on a selection of 31 genes displaying signals specifically modulated by the treatment. Concomitant with a diffuse dystrophin expression, a histological remodelling and a stabilization of GRMD dog clinical status, we show that cell delivery is associated with an up-regulation of genes reflecting a sustained enhancement of muscle regeneration. We also identify a decreased mRNA expression of a set of genes having metabolic functions associated with lipid homeostasis and energy. Interestingly, ubiquitin-mediated protein degradation is highly enhanced in GRMD dog muscle after systemic delivery of MuStem cells. CONCLUSIONS Overall, our results provide the first high-throughput characterization of GRMD dog muscle and throw new light on the complex molecular/cellular effects associated with muscle repair and the clinical efficacy of MuStem cell-based therapy.
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Affiliation(s)
- Florence Robriquet
- INRA, UMR703 PAnTher, Nantes, France
- LUNAM Université, Oniris, École nationale vétérinaire, agro-alimentaire et de l’alimentation Nantes-Atlantique, Nantes, France
- Université de Nantes, Nantes, France
| | - Aurélie Lardenois
- INRA, UMR703 PAnTher, Nantes, France
- LUNAM Université, Oniris, École nationale vétérinaire, agro-alimentaire et de l’alimentation Nantes-Atlantique, Nantes, France
| | - Candice Babarit
- INRA, UMR703 PAnTher, Nantes, France
- LUNAM Université, Oniris, École nationale vétérinaire, agro-alimentaire et de l’alimentation Nantes-Atlantique, Nantes, France
| | - Thibaut Larcher
- INRA, UMR703 PAnTher, Nantes, France
- LUNAM Université, Oniris, École nationale vétérinaire, agro-alimentaire et de l’alimentation Nantes-Atlantique, Nantes, France
| | - Laurence Dubreil
- INRA, UMR703 PAnTher, Nantes, France
- LUNAM Université, Oniris, École nationale vétérinaire, agro-alimentaire et de l’alimentation Nantes-Atlantique, Nantes, France
| | - Isabelle Leroux
- INRA, UMR703 PAnTher, Nantes, France
- LUNAM Université, Oniris, École nationale vétérinaire, agro-alimentaire et de l’alimentation Nantes-Atlantique, Nantes, France
| | - Céline Zuber
- INRA, UMR703 PAnTher, Nantes, France
- LUNAM Université, Oniris, École nationale vétérinaire, agro-alimentaire et de l’alimentation Nantes-Atlantique, Nantes, France
| | - Mireille Ledevin
- INRA, UMR703 PAnTher, Nantes, France
- LUNAM Université, Oniris, École nationale vétérinaire, agro-alimentaire et de l’alimentation Nantes-Atlantique, Nantes, France
| | - Jack-Yves Deschamps
- INRA, UMR703 PAnTher, Nantes, France
- LUNAM Université, Oniris, École nationale vétérinaire, agro-alimentaire et de l’alimentation Nantes-Atlantique, Nantes, France
| | - Yves Fromes
- LUNAM Université, Oniris, École nationale vétérinaire, agro-alimentaire et de l’alimentation Nantes-Atlantique, Nantes, France
- Laboratoire RMN AIM-CEA, Institut de Myologie, Hôpital Pitié-Salpêtrière, Paris, France
| | - Yan Cherel
- INRA, UMR703 PAnTher, Nantes, France
- LUNAM Université, Oniris, École nationale vétérinaire, agro-alimentaire et de l’alimentation Nantes-Atlantique, Nantes, France
| | - Laetitia Guevel
- INRA, UMR703 PAnTher, Nantes, France
- LUNAM Université, Oniris, École nationale vétérinaire, agro-alimentaire et de l’alimentation Nantes-Atlantique, Nantes, France
- Université de Nantes, Nantes, France
- * E-mail:
| | - Karl Rouger
- INRA, UMR703 PAnTher, Nantes, France
- LUNAM Université, Oniris, École nationale vétérinaire, agro-alimentaire et de l’alimentation Nantes-Atlantique, Nantes, France
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16
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Becker E, Liu Y, Lardenois A, Walther T, Horecka J, Stuparevic I, Law MJ, Lavigne R, Evrard B, Demougin P, Riffle M, Strich R, Davis RW, Pineau C, Primig M. Integrated RNA- and protein profiling of fermentation and respiration in diploid budding yeast provides insight into nutrient control of cell growth and development. J Proteomics 2015; 119:30-44. [PMID: 25662576 DOI: 10.1016/j.jprot.2015.01.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [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: 09/30/2014] [Revised: 01/16/2015] [Accepted: 01/25/2015] [Indexed: 12/29/2022]
Abstract
UNLABELLED Diploid budding yeast undergoes rapid mitosis when it ferments glucose, and in the presence of a non-fermentable carbon source and the absence of a nitrogen source it triggers sporulation. Rich medium with acetate is a commonly used pre-sporulation medium, but our understanding of the molecular events underlying the acetate-driven transition from mitosis to meiosis is still incomplete. We identified 263 proteins for which mRNA and protein synthesis are linked or uncoupled in fermenting and respiring cells. Using motif predictions, interaction data and RNA profiling we find among them 28 likely targets for Ume6, a subunit of the conserved Rpd3/Sin3 histone deacetylase-complex regulating genes involved in metabolism, stress response and meiosis. Finally, we identify 14 genes for which both RNA and proteins are detected exclusively in respiring cells but not in fermenting cells in our sample set, including CSM4, SPR1, SPS4 and RIM4, which were thought to be meiosis-specific. Our work reveals intertwined transcriptional and post-transcriptional control mechanisms acting when a MATa/α strain responds to nutritional signals, and provides molecular clues how the carbon source primes yeast cells for entering meiosis. BIOLOGICAL SIGNIFICANCE Our integrated genomics study provides insight into the interplay between the transcriptome and the proteome in diploid yeast cells undergoing vegetative growth in the presence of glucose (fermentation) or acetate (respiration). Furthermore, it reveals novel target genes involved in these processes for Ume6, the DNA binding subunit of the conserved histone deacetylase Rpd3 and the co-repressor Sin3. We have combined data from an RNA profiling experiment using tiling arrays that cover the entire yeast genome, and a large-scale protein detection analysis based on mass spectrometry in diploid MATa/α cells. This distinguishes our study from most others in the field-which investigate haploid yeast strains-because only diploid cells can undergo meiotic development in the simultaneous absence of a non-fermentable carbon source and nitrogen. Indeed, we report molecular clues how respiration of acetate might prime diploid cells for efficient spore formation, a phenomenon that is well known but poorly understood.
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Affiliation(s)
| | - Yuchen Liu
- Inserm U1085 IRSET, Université de Rennes 1, 35042 Rennes, France
| | | | - Thomas Walther
- Inserm U1085 IRSET, Université de Rennes 1, 35042 Rennes, France
| | - Joe Horecka
- Stanford Genome Technology Center, Palo Alto, CA 94304, USA
| | - Igor Stuparevic
- Inserm U1085 IRSET, Université de Rennes 1, 35042 Rennes, France
| | - Michael J Law
- Rowan University, School of Osteopathic Medicine, Stratford, NJ 08084, USA
| | - Régis Lavigne
- Inserm U1085 IRSET, Proteomics Core Facility Biogenouest, Université de Rennes 1, 35042 Rennes, France
| | - Bertrand Evrard
- Inserm U1085 IRSET, Université de Rennes 1, 35042 Rennes, France
| | | | - Michael Riffle
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Randy Strich
- Rowan University, School of Osteopathic Medicine, Stratford, NJ 08084, USA
| | - Ronald W Davis
- Stanford Genome Technology Center, Palo Alto, CA 94304, USA; Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Charles Pineau
- Inserm U1085 IRSET, Université de Rennes 1, 35042 Rennes, France; Inserm U1085 IRSET, Proteomics Core Facility Biogenouest, Université de Rennes 1, 35042 Rennes, France
| | - Michael Primig
- Inserm U1085 IRSET, Université de Rennes 1, 35042 Rennes, France.
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17
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Lardenois A, Stuparevic I, Liu Y, Law MJ, Becker E, Smagulova F, Waern K, Guilleux MH, Horecka J, Chu A, Kervarrec C, Strich R, Snyder M, Davis RW, Steinmetz LM, Primig M. The conserved histone deacetylase Rpd3 and its DNA binding subunit Ume6 control dynamic transcript architecture during mitotic growth and meiotic development. Nucleic Acids Res 2014; 43:115-28. [PMID: 25477386 PMCID: PMC4288150 DOI: 10.1093/nar/gku1185] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [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] [Indexed: 01/16/2023] Open
Abstract
It was recently reported that the sizes of many mRNAs change when budding yeast cells exit mitosis and enter the meiotic differentiation pathway. These differences were attributed to length variations of their untranslated regions. The function of UTRs in protein translation is well established. However, the mechanism controlling the expression of distinct transcript isoforms during mitotic growth and meiotic development is unknown. In this study, we order developmentally regulated transcript isoforms according to their expression at specific stages during meiosis and gametogenesis, as compared to vegetative growth and starvation. We employ regulatory motif prediction, in vivo protein-DNA binding assays, genetic analyses and monitoring of epigenetic amino acid modification patterns to identify a novel role for Rpd3 and Ume6, two components of a histone deacetylase complex already known to repress early meiosis-specific genes in dividing cells, in mitotic repression of meiosis-specific transcript isoforms. Our findings classify developmental stage-specific early, middle and late meiotic transcript isoforms, and they point to a novel HDAC-dependent control mechanism for flexible transcript architecture during cell growth and differentiation. Since Rpd3 is highly conserved and ubiquitously expressed in many tissues, our results are likely relevant for development and disease in higher eukaryotes.
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Affiliation(s)
| | - Igor Stuparevic
- Inserm U1085-Irset, Université de Rennes 1, Rennes, F-35042, France
| | - Yuchen Liu
- Inserm U1085-Irset, Université de Rennes 1, Rennes, F-35042, France
| | - Michael J Law
- School of Osteopathic Medicine, Rowan University, Stratford, NJ 08084, USA
| | | | - Fatima Smagulova
- Inserm U1085-Irset, Université de Rennes 1, Rennes, F-35042, France
| | - Karl Waern
- Department of Genetics, Stanford University, Stanford, CA 94395, USA
| | | | - Joe Horecka
- Stanford Genome Technology Center, Palo Alto, CA 94304, USA
| | - Angela Chu
- Stanford Genome Technology Center, Palo Alto, CA 94304, USA
| | | | - Randy Strich
- School of Osteopathic Medicine, Rowan University, Stratford, NJ 08084, USA
| | - Mike Snyder
- Department of Genetics, Stanford University, Stanford, CA 94395, USA
| | - Ronald W Davis
- Stanford Genome Technology Center, Palo Alto, CA 94304, USA Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Lars M Steinmetz
- European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Michael Primig
- Inserm U1085-Irset, Université de Rennes 1, Rennes, F-35042, France
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18
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Walther T, Létisse F, Peyriga L, Alkim C, Liu Y, Lardenois A, Martin-Yken H, Portais JC, Primig M, François J. Developmental stage dependent metabolic regulation during meiotic differentiation in budding yeast. BMC Biol 2014; 12:60. [PMID: 25178389 PMCID: PMC4176597 DOI: 10.1186/s12915-014-0060-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Indexed: 12/12/2022] Open
Abstract
Background The meiotic developmental pathway in yeast enables both differentiation of vegetative cells into haploid spores that ensure long-term survival, and recombination of the parental DNA to create genetic diversity. Despite the importance of proper metabolic regulation for the supply of building blocks and energy, little is known about the reprogramming of central metabolic pathways in meiotically differentiating cells during passage through successive developmental stages. Results Metabolic regulation during meiotic differentiation in budding yeast was analyzed by integrating information on genome-wide transcriptional activity, 26 enzymatic activities in the central metabolism, the dynamics of 67 metabolites, and a metabolic flux analysis at mid-stage meiosis. Analyses of mutants arresting sporulation at defined stages demonstrated that metabolic reprogramming is tightly controlled by the progression through the developmental pathway. The correlation between transcript levels and enzymatic activities in the central metabolism varies significantly in a developmental stage-dependent manner. The complete loss of phosphofructokinase activity at mid-stage meiosis enables a unique setup of the glycolytic pathway which facilitates carbon flux repartitioning into synthesis of spore wall precursors during the co-assimilation of glycogen and acetate. The need for correct homeostasis of purine nucleotides during the meiotic differentiation was demonstrated by the sporulation defect of the AMP deaminase mutant amd1, which exhibited hyper-accumulation of ATP accompanied by depletion of guanosine nucleotides. Conclusions Our systems-level analysis shows that reprogramming of the central metabolism during the meiotic differentiation is controlled at different hierarchical levels to meet the metabolic and energetic needs at successive developmental stages. Electronic supplementary material The online version of this article (doi:10.1186/s12915-014-0060-x) contains supplementary material, which is available to authorized users.
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19
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Chalmel F, Lardenois A, Evrard B, Rolland AD, Sallou O, Dumargne MC, Coiffec I, Collin O, Primig M, Jégou B. High-resolution profiling of novel transcribed regions during rat spermatogenesis. Biol Reprod 2014; 91:5. [PMID: 24740603 DOI: 10.1095/biolreprod.114.118166] [Citation(s) in RCA: 40] [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] [Indexed: 12/16/2022] Open
Abstract
Mammalian spermatogenesis is a complex and highly orchestrated combination of processes in which male germline proliferation and differentiation result in the production of mature spermatozoa. If recent genome-wide studies have contributed to the in-depth analysis of the male germline protein-encoding transcriptome, little effort has yet been devoted to the systematic identification of novel unannotated transcribed regions expressed during mammalian spermatogenesis. We report high-resolution expression profiling of male germ cells in rat, using next-generation sequencing technology and highly enriched testicular cell populations. Among 20 424 high-confidence transcripts reconstructed, we defined a stringent set of 1419 long multi-exonic unannotated transcripts expressed in the testis (testis-expressed unannotated transcripts [TUTs]). TUTs were divided into 7 groups with different expression patterns. Most TUTs share many of the characteristics of vertebrate long noncoding RNAs (lncRNAs). We also markedly reinforced the finding that TUTs and known lncRNAs accumulate during the meiotic and postmeiotic stages of spermatogenesis in mammals and that X-linked meiotic TUTs do not escape the silencing effects of meiotic sex chromosome inactivation. Importantly, we discovered that TUTs and known lncRNAs with a peak expression during meiosis define a distinct class of noncoding transcripts that exhibit exons twice as long as those of other transcripts. Our study provides new insights in transcriptional profiling of the male germline and represents a high-quality resource for novel loci expressed during spermatogenesis that significantly contributes to rat genome annotation.
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Affiliation(s)
| | | | | | | | - Olivier Sallou
- Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA/INRIA)-GenOuest platform, Rennes, France
| | | | | | - Olivier Collin
- Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA/INRIA)-GenOuest platform, Rennes, France
| | - Michael Primig
- Inserm U1085-IRSET, Université de Rennes 1, Rennes, France
| | - Bernard Jégou
- Inserm U1085-IRSET, Université de Rennes 1, Rennes, France Ecole des Hautes Études en Santé Publique, Rennes, France
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20
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Meikar O, Vagin VV, Chalmel F, Sõstar K, Lardenois A, Hammell M, Jin Y, Da Ros M, Wasik KA, Toppari J, Hannon GJ, Kotaja N. An atlas of chromatoid body components. RNA 2014; 20:483-95. [PMID: 24554440 PMCID: PMC3964910 DOI: 10.1261/rna.043729.113] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 01/10/2014] [Indexed: 05/10/2023]
Abstract
The genome of male germ cells is actively transcribed during spermatogenesis to produce phase-specific protein-coding mRNAs and a considerable amount of different noncoding RNAs. Ribonucleoprotein (RNP) granule-mediated RNA regulation provides a powerful means to secure the quality and correct expression of the requisite transcripts. Haploid spermatids are characterized by a unique, unusually large cytoplasmic granule, the chromatoid body (CB), which emerges during the switch between the meiotic and post-meiotic phases of spermatogenesis. To better understand the role of the CB in male germ cell differentiation, we isolated CBs from mouse testes and revealed its full RNA and protein composition. We showed that the CB is mainly composed of RNA-binding proteins and other proteins involved RNA regulation. The CB was loaded with RNA, including pachytene piRNAs, a diverse set of mRNAs, and a number of uncharacterized long noncoding transcripts. The CB was demonstrated to accumulate nascent RNA during all the steps of round spermatid differentiation. Our results revealed the CB as a large germ cell-specific RNP platform that is involved in the control of the highly complex transcriptome of haploid male germ cells.
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Affiliation(s)
- Oliver Meikar
- Institute of Biomedicine, Department of Physiology, University of Turku, Turku FI-20520, Finland
| | - Vasily V. Vagin
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Frédéric Chalmel
- Inserm Unité 1085-Irset, Université de Rennes 1, IFR140, Rennes F-35042, France
| | - Karin Sõstar
- Institute of Biomedicine, Department of Physiology, University of Turku, Turku FI-20520, Finland
| | - Aurélie Lardenois
- INRA, UMR703 PAnTher, F-44307 Nantes, France
- LUNAM Université, Oniris, École national vétérinaire, agro-alimentaire et de l'alimentation Nantes-Atlantique, F-44307 Nantes, France
| | - Molly Hammell
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Ying Jin
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Matteo Da Ros
- Institute of Biomedicine, Department of Physiology, University of Turku, Turku FI-20520, Finland
| | - Kaja A. Wasik
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Jorma Toppari
- Institute of Biomedicine, Department of Physiology, University of Turku, Turku FI-20520, Finland
- Department of Pediatrics, University of Turku, Turku FI-20520, Finland
| | - Gregory J. Hannon
- Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Noora Kotaja
- Institute of Biomedicine, Department of Physiology, University of Turku, Turku FI-20520, Finland
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21
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Chalmel F, Lardenois A, Georg I, Barrionuevo F, Demougin P, Jégou B, Scherer G, Primig M. Genome-wide identification of Sox8-, and Sox9-dependent genes during early post-natal testis development in the mouse. Andrology 2013; 1:281-92. [PMID: 23315995 DOI: 10.1111/j.2047-2927.2012.00049.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Revised: 11/14/2012] [Accepted: 11/20/2012] [Indexed: 01/15/2023]
Abstract
The SOX8 and SOX9 transcription factors are involved in, among others, sex differentiation, male gonad development and adult maintenance of spermatogenesis. Sox8(-/-) mice lacking Sox9 in Sertoli cells fail to form testis cords and cannot establish spermatogenesis. Although genetic and histological data show an important role for these transcription factors in regulating spermatogenesis, it is not clear which genes depend upon them at a genome-wide level. To identify transcripts that respond to the absence of Sox8 in all cells and Sox9 in Sertoli cells we measured mRNA concentrations in testicular samples from mice at 0, 6 and 18 days post-partum. In total, 621 and 629 transcripts were found at decreased or increased levels, respectively, at different time points in the mutant as compared to the control samples. These mRNAs were categorized as preferentially expressed in Sertoli cells or germ cells using data obtained with male and female gonad samples and enriched testicular cell populations. Five candidate genes were validated at the protein level. Furthermore, we identified putative direct SOX8 and SOX9 target genes by integrating predicted SOX-binding sites present in potential regulatory regions upstream of the transcription start site. Finally, we used protein network data to gain insight into the effects on regulatory interactions that occur when Sox8 and Sox9 are absent in developing Sertoli cells. The integration of testicular samples with enriched Sertoli cells, germ cells and female gonads enabled us to broadly distinguish transcripts directly affected in Sertoli cells from others that respond to secondary events in testicular cell types. Thus, combined RNA profiling signals, motif predictions and network data identified putative SOX8/SOX9 target genes in Sertoli cells and yielded insight into regulatory interactions that depend upon these transcription factors. In addition, our results will facilitate the interpretation of genome-wide in vivo SOX8 and SOX9 DNA binding data.
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Affiliation(s)
- F Chalmel
- Inserm, U1085-Irset, University of Rennes 1, Rennes, France
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22
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Rolland AD, Lardenois A, Goupil AS, Lareyre JJ, Houlgatte R, Chalmel F, Le Gac F. Profiling of androgen response in rainbow trout pubertal testis: relevance to male gonad development and spermatogenesis. PLoS One 2013; 8:e53302. [PMID: 23301058 PMCID: PMC3536770 DOI: 10.1371/journal.pone.0053302] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [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: 07/25/2012] [Accepted: 11/27/2012] [Indexed: 12/15/2022] Open
Abstract
The capacity of testicular somatic cells to promote and sustain germ cell differentiation is largely regulated by sexual steroids and notably androgens. In fish species the importance of androgens is emphasized by their ability to induce sex reversal of the developing fries and to trigger spermatogenesis. Here we studied the influence of androgens on testicular gene expression in trout testis using microarrays. Following treatment of immature males with physiological doses of testosterone or 11-ketotestosterone, 418 genes that exhibit changes in expression were identified. Interestingly, the activity of testosterone appeared stronger than that of 11-ketotestosterone. Expression profiles of responsive genes throughout testis development and in isolated germ cells confirmed androgens to mainly affect gene expression in somatic cells. Furthermore, specific clusters of genes that exhibit regulation coincidently with changes in the natural circulating levels of androgens during the reproductive cycle were highlighted, reinforcing the physiological significance of these data. Among somatic genes, a phylogenetic footprinting study identified putative androgen response elements within the proximal promoter regions of 42 potential direct androgen target genes. Finally, androgens were also found to alter the germ line towards meiotic expression profiles, supporting the hypothesis of a role for the somatic responsive genes in driving germ cell fate. This study significantly increases our understanding of molecular pathways regulated by androgens in vertebrates. The highly cyclic testicular development in trout together with functions associated with regulated genes reveal potential mechanisms for androgen actions in tubule formation, steroid production, germ cell development and sperm secretion.
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Affiliation(s)
- Antoine D. Rolland
- INRA, UR1037 LPGP, SFR Biosit, Biogenouest, Campus de Beaulieu, Rennes, France
| | - Aurélie Lardenois
- Inserm, U1085, IRSET, Université de Rennes I, Campus de Beaulieu, Rennes, France
| | - Anne-Sophie Goupil
- INRA, UR1037 LPGP, SFR Biosit, Biogenouest, Campus de Beaulieu, Rennes, France
| | | | - Rémi Houlgatte
- Inserm, UMR1087, l’institut du thorax IRT - UN, Nantes, France
- Université de Nantes, Nantes, France
| | - Frédéric Chalmel
- Inserm, U1085, IRSET, Université de Rennes I, Campus de Beaulieu, Rennes, France
| | - Florence Le Gac
- INRA, UR1037 LPGP, SFR Biosit, Biogenouest, Campus de Beaulieu, Rennes, France
- * E-mail:
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23
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van Werven FJ, Neuert G, Hendrick N, Lardenois A, Buratowski S, van Oudenaarden A, Primig M, Amon A. Transcription of two long noncoding RNAs mediates mating-type control of gametogenesis in budding yeast. Cell 2012; 150:1170-81. [PMID: 22959267 DOI: 10.1016/j.cell.2012.06.049] [Citation(s) in RCA: 210] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Revised: 04/30/2012] [Accepted: 06/29/2012] [Indexed: 12/26/2022]
Abstract
The cell-fate decision leading to gametogenesis is essential for sexual reproduction. In S. cerevisiae, only diploid MATa/α but not haploid MATa or MATα cells undergo gametogenesis, known as sporulation. We find that transcription of two long noncoding RNAs (lncRNAs) mediates mating-type control of sporulation. In MATa or MATα haploids, expression of IME1, the central inducer of gametogenesis, is inhibited in cis by transcription of the lncRNA IRT1, located in the IME1 promoter. IRT1 transcription recruits the Set2 histone methyltransferase and the Set3 histone deacetylase complex to establish repressive chromatin at the IME1 promoter. Inhibiting expression of IRT1 and an antisense transcript that antagonizes the expression of the meiotic regulator IME4 allows cells expressing the haploid mating type to sporulate with kinetics that are indistinguishable from that of MATa/α diploids. Conversely, expression of the two lncRNAs abolishes sporulation in MATa/α diploids. Thus, transcription of two lncRNAs governs mating-type control of gametogenesis in yeast.
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Affiliation(s)
- Folkert J van Werven
- David H. Koch Institute for Integrative Cancer Research and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Chalmel F, Lardenois A, Evrard B, Mathieu R, Feig C, Demougin P, Gattiker A, Schulze W, Jégou B, Kirchhoff C, Primig M. Global human tissue profiling and protein network analysis reveals distinct levels of transcriptional germline-specificity and identifies target genes for male infertility. Hum Reprod 2012; 27:3233-48. [PMID: 22926843 DOI: 10.1093/humrep/des301] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Mammalian spermatogenesis is a process that involves a complex expression program in both somatic and germ cells present in the male gonad. A number of studies have attempted to define the transcriptome of male meiosis and gametogenesis in rodents and primates. Few human transcripts, however, have been associated with testicular somatic cells and germ cells at different post-natal developmental stages and little is known about their level of germline-specificity compared with non-testicular tissues. METHODS We quantified human transcripts using GeneChips and a total of 47 biopsies from prepubertal children diagnosed with undescended testis, infertile adult patients whose spermatogenesis is arrested at consecutive stages and fertile control individuals. These results were integrated with data from enriched normal germ cells, non-testicular expression data, phenotype information, predicted regulatory DNA-binding motifs and interactome data. RESULTS Among 3580 genes for which we found differential transcript concentrations in somatic and germ cells present in human testis, 933 were undetectable in 45 embryonic and adult non-testicular tissues, including many that were corroborated at protein level by published gene annotation data and histological high-throughput protein immunodetection assays. Using motif enrichment analyses, we identified regulatory promoter elements likely involved in germline development. Finally, we constructed a regulatory disease network for human fertility by integrating expression signals, interactome information, phenotypes and functional annotation data. CONCLUSIONS Our results provide broad insight into the post-natal human testicular transcriptome at the level of cell populations and in a global somatic tissular context. Furthermore, they yield clues for genetic causes of male infertility and will facilitate the identification of novel cancer/testis genes as targets for cancer immunotherapies.
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Affiliation(s)
- Frédéric Chalmel
- Inserm Unit 1085-IRSET, Université de Rennes 1, EHESP School of Public Health, F-35042 Rennes, France
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Lavigne R, Becker E, Liu Y, Evrard B, Lardenois A, Primig M, Pineau C. Direct iterative protein profiling (DIPP) - an innovative method for large-scale protein detection applied to budding yeast mitosis. Mol Cell Proteomics 2012; 11:M111.012682. [PMID: 21997732 PMCID: PMC3277764 DOI: 10.1074/mcp.m111.012682] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [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: 07/22/2011] [Revised: 09/24/2011] [Indexed: 11/06/2022] Open
Abstract
The budding yeast Saccharomyces cerevisiae is a major model organism for important biological processes such as mitotic growth and meiotic development, it can be a human pathogen, and it is widely used in the food-, and biotechnology industries. Consequently, the genomes of numerous strains have been sequenced and a very large amount of RNA profiling data is available. Moreover, it has recently become possible to quantitatively analyze the entire yeast proteome; however, efficient and cost-effective high-throughput protein profiling remains a challenge. We report here a new approach to direct and label-free large-scale yeast protein identification using a tandem buffer system for protein extraction, two-step protein prefractionation and enzymatic digestion, and detection of peptides by iterative mass spectrometry. Our profiling study of diploid cells undergoing rapid mitotic growth identified 86% of the known proteins and its output was found to be widely concordant with genome-wide mRNA concentrations and DNA variations between yeast strains. This paves the way for comprehensive and straightforward yeast proteome profiling across a wide variety of experimental conditions.
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Affiliation(s)
- Régis Lavigne
- From the ‡Inserm U1085, IRSET, Proteomics Core Facility Biogenouest, Université de Rennes 1, F-35042 Rennes, France
| | | | - Yuchen Liu
- §Inserm U625, Université de Rennes 1, F-35042 Rennes, France
| | - Bertrand Evrard
- §Inserm U625, Université de Rennes 1, F-35042 Rennes, France
| | | | - Michael Primig
- §Inserm U625, Université de Rennes 1, F-35042 Rennes, France
| | - Charles Pineau
- From the ‡Inserm U1085, IRSET, Proteomics Core Facility Biogenouest, Université de Rennes 1, F-35042 Rennes, France
- §Inserm U625, Université de Rennes 1, F-35042 Rennes, France
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Lavery R, Lardenois A, Ranc-Jianmotamedi F, Pauper E, Gregoire EP, Vigier C, Moreilhon C, Primig M, Chaboissier MC. XY Sox9 embryonic loss-of-function mouse mutants show complete sex reversal and produce partially fertile XY oocytes. Dev Biol 2011; 354:111-22. [DOI: 10.1016/j.ydbio.2011.03.029] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Revised: 03/18/2011] [Accepted: 03/28/2011] [Indexed: 10/18/2022]
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Lardenois A, Chalmel F, Barrionuevo F, Demougin P, Scherer G, Primig M. Profiling spermatogenic failure in adult testes bearing Sox9-deficient Sertoli cells identifies genes involved in feminization, inflammation and stress. Reprod Biol Endocrinol 2010; 8:154. [PMID: 21182756 PMCID: PMC3024295 DOI: 10.1186/1477-7827-8-154] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2010] [Accepted: 12/23/2010] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Sox9 (Sry box containing gene 9) is a DNA-binding transcription factor involved in chondrocyte development and sex determination. The protein's absence in testicular Sertoli nurse cells has been shown to disrupt testicular function in adults but little is known at the genome-wide level about molecular events concomitant with testicular break-down. METHODS To determine the genome-wide effect on mRNA concentrations triggered by the absence of Sox9 in Sertoli cells we analysed adult testicular tissue from wild-type versus mutant mice with high-density oligonucleotide microarrays and integrated the output of this experiment with regulatory motif predictions and protein-protein network data. RESULTS We report the genome-wide mRNA signature of adult testes lacking Sox9 in Sertoli cells before and after the onset of late spermatogenic failure as compared to fertile controls. The GeneChip data integrated with evolutionarily conserved Sox9 DNA binding motifs and regulatory network data identified genes involved in feminization, stress response and inflammation. CONCLUSIONS Our results extend previous observations that genes required for female gonadogenesis are up-regulated in the absence of Sox9 in fetal Sertoli cells to the adult stage. Importantly, we identify gene networks involved in immunological processes and stress response which is reminiscent of a phenomenon occurring in a sub-group of infertile men. This suggests mice lacking Sox9 in their Sertoli cells to be a potentially useful model for adult human testicular failure.
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Affiliation(s)
- Aurélie Lardenois
- Inserm, U625, Université de Rennes 1, IFR140, Rennes, F-35042, France
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Lardenois A, Gattiker A, Collin O, Chalmel F, Primig M. GermOnline 4.0 is a genomics gateway for germline development, meiosis and the mitotic cell cycle. Database (Oxford) 2010; 2010:baq030. [PMID: 21149299 PMCID: PMC3004465 DOI: 10.1093/database/baq030] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
GermOnline 4.0 is a cross-species database portal focusing on high-throughput expression data relevant for germline development, the meiotic cell cycle and mitosis in healthy versus malignant cells. It is thus a source of information for life scientists as well as clinicians who are interested in gene expression and regulatory networks. The GermOnline gateway provides unlimited access to information produced with high-density oligonucleotide microarrays (3'-UTR GeneChips), genome-wide protein-DNA binding assays and protein-protein interaction studies in the context of Ensembl genome annotation. Samples used to produce high-throughput expression data and to carry out genome-wide in vivo DNA binding assays are annotated via the MIAME-compliant Multiomics Information Management and Annotation System (MIMAS 3.0). Furthermore, the Saccharomyces Genomics Viewer (SGV) was developed and integrated into the gateway. SGV is a visualization tool that outputs genome annotation and DNA-strand specific expression data produced with high-density oligonucleotide tiling microarrays (Sc_tlg GeneChips) which cover the complete budding yeast genome on both DNA strands. It facilitates the interpretation of expression levels and transcript structures determined for various cell types cultured under different growth and differentiation conditions. Database URL: www.germonline.org/
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Affiliation(s)
- Aurélie Lardenois
- Inserm, U625, GERHM, IFR-140, Université de Rennes 1, F-35042 Rennes, France
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Trépos-Pouplard M, Lardenois A, Staub C, Guitton N, Dorval-Coiffec I, Pineau C, Primig M, Jégou B. Proteome analysis and genome-wide regulatory motif prediction identify novel potentially sex-hormone regulated proteins in rat efferent ducts. Int J Androl 2010; 33:661-74. [PMID: 19906187 DOI: 10.1111/j.1365-2605.2009.01006.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The efferent ducts are a series of tubules that conduct sperm from the rete testis to the epididymis. They absorb most fluid and proteins originating from the rete testis during concentration of spermatozoa prior to their entry into the epididymis. Proteome analysis of micro-dissected efferent duct samples from adult rats was combined with genome-wide computational prediction of conserved hormone response elements to identify factors likely regulated by oestrogens and androgens. We identified 165 proteins and found subsets of the promoters controlling their corresponding genes to contain androgen- and oestrogen response elements (ARE/EREs) at similar frequencies. Moreover, EREs were significantly enriched among the loci identified compared with their genome-wide occurrence. The expression and localization of Anxa6, Ckb, Krt19, Park7, Pdzk1 and Tpt1 in the efferent ducts and other related hormone controlled tissues was further validated at the RNA or protein level. This study identifies many novel proteins predicted to play roles in sperm maturation and male fertility and provides significant computational evidence that the efferent ducts express genes transcriptionally controlled by sex hormones.
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Lardenois A, Chalmel F, Demougin P, Kotaja N, Sassone-Corsi P, Primig M. Fhl5/Act, a CREM-binding transcriptional activator required for normal sperm maturation and morphology, is not essential for testicular gene expression. Reprod Biol Endocrinol 2009; 7:133. [PMID: 19930692 PMCID: PMC2788571 DOI: 10.1186/1477-7827-7-133] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2009] [Accepted: 11/24/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The LIM domain protein Fhl5 was previously found to interact with CREM, a DNA binding transcriptional regulator necessary for spermiogenesis in mammals. Co-transfection experiments using heterologous promoter constructs indicated a role for Fhl5 in transcriptional up-regulation of CREM-dependent testicular genes. Male mice lacking Fhl5 were reported to be fertile but displayed partially abnormal sperm maturation and morphology. METHODS To identify Fhl5 testicular target genes we carried out two whole-genome expression profiling experiments using high-density oligonucleotide microarrays and total testis samples from Fhl5 wild-type versus homozygous mutant mice first in different and then in isogenic strain backgrounds. RESULTS Weak signal differences were detected in non-isogenic samples but no statistically significant expression changes were observed when isogenic Fhl5 mutant and wild-type samples were compared. CONCLUSION The outcome of these experiments suggests that testicular expression profiling is extremely sensitive to the genetic background and that Fhl5 is not essential for testicular gene expression to a level detected by microarray-based measurements. This might be due to redundant function of the related and similarly expressed protein Fhl4.
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Affiliation(s)
| | - Frédéric Chalmel
- Inserm, U625, Université Rennes 1, IFR140, Rennes, F-35042, France
| | | | - Noora Kotaja
- University of Turku, Kiinamyllynkatu 10, FIN-20520 Turku, Finland
| | | | - Michael Primig
- Inserm, U625, Université Rennes 1, IFR140, Rennes, F-35042, France
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Reichman S, Kalathur RKR, Lambard S, Aït-Ali N, Yang Y, Lardenois A, Ripp R, Poch O, Zack DJ, Sahel JA, Léveillard T. The homeobox gene CHX10/VSX2 regulates RdCVF promoter activity in the inner retina. Hum Mol Genet 2009; 19:250-61. [PMID: 19843539 DOI: 10.1093/hmg/ddp484] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Rod-derived Cone Viability Factor (RdCVF) is a trophic factor with therapeutic potential for the treatment of retinitis pigmentosa, a retinal disease that commonly results in blindness. RdCVF is encoded by Nucleoredoxin-like 1 (Nxnl1), a gene homologous with the family of thioredoxins that participate in the defense against oxidative stress. RdCVF expression is lost after rod degeneration in the first phase of retinitis pigmentosa, and this loss has been implicated in the more clinically significant secondary cone degeneration that often occurs. Here, we describe a study of the Nxnl1 promoter using an approach that combines promoter and transcriptomic analysis. By transfection of selected candidate transcription factors, chosen based upon their expression pattern, we identified the homeodomain proteins CHX10/VSX2, VSX1 and PAX4, as well as the zinc finger protein SP3, as factors that can stimulate both the mouse and human Nxnl1 promoter. In addition, CHX10/VSX2 binds to the Nxnl1 promoter in vivo. Since CHX10/VSX2 is expressed predominantly in the inner retina, this finding motivated us to demonstrate that RdCVF is expressed in the inner as well as the outer retina. Interestingly, the loss of rods in the rd1 mouse, a model of retinitis pigmentosa, is associated with decreased expression of RdCVF by inner retinal cells as well as by rods. Based upon these results, we propose an alternative therapeutic strategy aimed at recapitulating RdCVF expression in the inner retina, where cell loss is not significant, to prevent secondary cone death and central vision loss in patients suffering from retinitis pigmentosa.
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Affiliation(s)
- Sacha Reichman
- Department of Genetics, Institut de la Vision, INSERM Université Pierre et Marie Curie-Paris 6, UMR-S 968, Paris, France
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Befort K, Filliol D, Ghate A, Darcq E, Matifas A, Muller J, Lardenois A, Thibault C, Dembele D, Le Merrer J, Becker JAJ, Poch O, Kieffer BL. Mu-opioid receptor activation induces transcriptional plasticity in the central extended amygdala. Eur J Neurosci 2008; 27:2973-84. [PMID: 18588537 DOI: 10.1111/j.1460-9568.2008.06273.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Addiction develops from the gradual adaptation of the brain to chronic drug exposure, and involves genetic reprogramming of neuronal function. The central extended amygdala (EAc) is a network formed by the central amygdala and the bed nucleus of the stria terminalis. This key site controls drug craving and seeking behaviors, and has not been investigated at the gene regulation level. We used Affymetrix microarrays to analyze transcriptional activity in the murine EAc, with a focus on mu-opioid receptor-associated events because these receptors mediate drug reward and dependence. We identified 132 genes whose expression is regulated by a chronic escalating morphine regimen in the EAc from wild-type but not mu-opioid receptor knockout mice. These modifications are mostly EAc-specific. Gene ontology analysis reveals an overrepresentation of neurogenesis, cell growth and signaling protein categories. A separate quantitative PCR analysis of genes in the last of these groups confirms the dysregulation of both orphan (Gpr88) and known (DrD1A, Adora2A, Cnr1, Grm5, Gpr6) G protein-coupled receptors, scaffolding (PSD95, Homer1) and signaling (Sgk, Cap1) proteins, and neuropeptides (CCK, galanin). These transcriptional modifications do not occur following a single morphine injection, and hence result from long-term adaptation to excessive mu receptor activation. Proteins encoded by these genes are classically associated with spine modules function in other brain areas, and therefore our data suggest a remodeling of EAc circuits at sites where glutamatergic and monoaminergic afferences interact. Together, mu receptor-dependent genes identified in this study potentially contribute to drug-induced neural plasticity, and provide a unique molecular repertoire towards understanding drug craving and relapse.
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Affiliation(s)
- K Befort
- IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), Département Neurobiologie et Génétique, Illkirch, F-67400 France.
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Becker JAJ, Befort K, Blad C, Filliol D, Ghate A, Dembele D, Thibault C, Koch M, Muller J, Lardenois A, Poch O, Kieffer BL. Transcriptome analysis identifies genes with enriched expression in the mouse central extended amygdala. Neuroscience 2008; 156:950-65. [PMID: 18786617 DOI: 10.1016/j.neuroscience.2008.07.070] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2008] [Revised: 07/18/2008] [Accepted: 07/30/2008] [Indexed: 01/18/2023]
Abstract
The central extended amygdala (EAc) is an ensemble of highly interconnected limbic structures of the anterior brain, and forms a cellular continuum including the bed nucleus of the stria terminalis (BNST), the central nucleus of the amygdala (CeA) and the nucleus accumbens shell (AcbSh). This neural network is a key site for interactions between brain reward and stress systems, and has been implicated in several aspects of drug abuse. In order to increase our understanding of EAc function at the molecular level, we undertook a genome-wide screen (Affymetrix) to identify genes whose expression is enriched in the mouse EAc. We focused on the less-well known BNST-CeA areas of the EAc, and identified 121 genes that exhibit more than twofold higher expression level in the EAc compared with whole brain. Among these, 43 genes have never been described to be expressed in the EAc. We mapped these genes throughout the brain, using non-radioactive in situ hybridization, and identified eight genes with a unique and distinct rostro-caudal expression pattern along AcbSh, BNST and CeA. Q-PCR analysis performed in brain and peripheral organ tissues indicated that, with the exception of one (Spata13), all these genes are predominantly expressed in brain. These genes encode signaling proteins (Adora2, GPR88, Arpp21 and Rem2), a transcription factor (Limh6) or proteins of unknown function (Rik130, Spata13 and Wfs1). The identification of genes with enriched expression expands our knowledge of EAc at a molecular level, and provides useful information to toward genetic manipulations within the EAc.
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Affiliation(s)
- J A J Becker
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Département Neurobiologie et Génétique, Illkirch, France.
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Befort K, Filliol D, Darcq E, Ghate A, Matifas A, Lardenois A, Muller J, Thibault C, Dembele D, Poch O, Kieffer BL. Gene expression is altered in the lateral hypothalamus upon activation of the mu opioid receptor. Ann N Y Acad Sci 2008; 1129:175-84. [PMID: 18591478 DOI: 10.1196/annals.1417.028] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The lateral hypothalamus (LH) is a brain structure that controls hedonic properties of both natural rewards and drugs of abuse. Mu opioid receptors are known to mediate drug reward, but whether overstimulation of these receptors impacts on LH function has not been studied. Here we have used a genome-wide microarray approach to identify LH responses to chronic mu opioid receptor activation at the transcriptional level. We have subjected wild-type and mu opioid receptor knockout mice to an escalating morphine regimen, which produces severe physical dependence in wild-type but not mutant animals. We have analyzed gene profiles in LH samples using the 430A.2 Affymetrix array and identified a set of 25 genes whose expression is altered by morphine in wild-type mice only. The regulation was confirmed for a subset of these genes using real-time quantitative PCR on samples from independent treatments. Altered expression of aquaporin 4, apolipoprotein D, and prostaglandin synthase is indicative of modified LH physiology. The regulation of two signaling genes (the serum glucocorticoid kinase and the regulator of G protein signaling 4) suggests that neurotransmission is altered in LH circuitry. Finally, the downregulation of apelin may indicate a potential role for this neuropeptide in opioid signaling and hedonic homeostasis. Altogether, our study shows that chronic mu opioid receptor stimulation induces gene expression plasticity in the LH and provides a unique collection of mu opioid receptor-dependent genes that potentially contribute to alter reward processes in addictive diseases.
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Affiliation(s)
- K Befort
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Département Neurobiologie et Génétique, Illkirch, France.
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Fadloun A, Kobi D, Delacroix L, Dembélé D, Michel I, Lardenois A, Tisserand J, Losson R, Mengus G, Davidson I. Retinoic acid induces TGFbeta-dependent autocrine fibroblast growth. Oncogene 2008; 27:477-89. [PMID: 17637747 DOI: 10.1038/sj.onc.1210657] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2006] [Revised: 05/29/2007] [Accepted: 06/07/2007] [Indexed: 01/22/2023]
Abstract
To evaluate the role of murine TFIID subunit TAF4 in activation of cellular genes by all-trans retinoic acid (T-RA), we have characterized the T-RA response of taf4(lox/-) and taf4(-/-) embryonic fibroblasts. T-RA regulates almost 1000 genes in taf4(lox/-) cells, but less than 300 in taf4(-/-) cells showing that TAF4 is required for T-RA regulation of most, but not all cellular genes. We further show that T-RA-treated taf4(lox/-) cells exhibit transforming growth factor (TGF)beta-dependent autocrine growth and identify a set of genes regulated by loss of TAF4 and by T-RA corresponding to key mediators of the TGFbeta signalling pathway. T-RA rapidly and potently induces expression of connective tissue growth factor (CTGF) via a conserved DR2 type response element in its proximal promoter leading to serum-free autocrine growth. These results highlight the role of TAF4 as a cofactor in the cellular response to T-RA and identify the genetic programme of a novel cross talk between the T-RA and TGFbeta pathways that leads to deregulated cell growth.
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Affiliation(s)
- A Fadloun
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP. UMR7104, 1 Rue Laurent Fries, Illkirch Cédex, France
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36
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Chalmel F, Léveillard T, Jaillard C, Lardenois A, Berdugo N, Morel E, Koehl P, Lambrou G, Holmgren A, Sahel JA, Poch O. Rod-derived Cone Viability Factor-2 is a novel bifunctional-thioredoxin-like protein with therapeutic potential. BMC Mol Biol 2007; 8:74. [PMID: 17764561 PMCID: PMC2064930 DOI: 10.1186/1471-2199-8-74] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2007] [Accepted: 08/31/2007] [Indexed: 11/10/2022] Open
Abstract
Background Cone degeneration is the hallmark of the inherited retinal disease retinitis pigmentosa. We have previously identified a trophic factor "Rod-derived Cone Viability Factor (RdCVF) that is secreted by rods and promote cone viability in a mouse model of the disease. Results Here we report the bioinformatic identification and the experimental analysis of RdCVF2, a second trophic factor belonging to the Rod-derived Cone Viability Factor family. The mouse RdCVF gene is known to be bifunctional, encoding both a long thioredoxin-like isoform (RdCVF-L) and a short isoform with trophic cone photoreceptor viability activity (RdCVF-S). RdCVF2 shares many similarities with RdCVF in terms of gene structure, expression in a rod-dependent manner and protein 3D structure. Furthermore, like RdCVF, the RdCVF2 short isoform exhibits cone rescue activity that is independent of its putative thiol-oxydoreductase activity. Conclusion Taken together, these findings define a new family of bifunctional genes which are: expressed in vertebrate retina, encode trophic cone viability factors, and have major therapeutic potential for human retinal neurodegenerative diseases such as retinitis pigmentosa.
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Affiliation(s)
- Frédéric Chalmel
- Divisions of Bioinformatics and Biochemistry, Swiss Institute of Bioinformatics, University of Basel, CH-4056 Basel, Switzerland
| | - Thierry Léveillard
- Laboratoire de Physiopathologie Cellulaire et Moléculaire de la Rétine, Inserm U592, Université Pierre et Marie Curie, 75571 Paris, France
| | - Céline Jaillard
- Laboratoire de Physiopathologie Cellulaire et Moléculaire de la Rétine, Inserm U592, Université Pierre et Marie Curie, 75571 Paris, France
| | - Aurélie Lardenois
- Laboratoire de Biologie et Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, BP 163, 67404 Illkirch cedex, France
| | - Naomi Berdugo
- Laboratoire de Physiopathologie Cellulaire et Moléculaire de la Rétine, Inserm U592, Université Pierre et Marie Curie, 75571 Paris, France
- Fovea-Pharmaceuticals – 12 rue Jean Antoine Le Baif – 75013 Paris
| | - Emmanuelle Morel
- Laboratoire de Physiopathologie Cellulaire et Moléculaire de la Rétine, Inserm U592, Université Pierre et Marie Curie, 75571 Paris, France
| | - Patrice Koehl
- Department of Computer Science, Genome Center, University of California, Davis, CA 95616, USA
| | - George Lambrou
- Novartis Institutes for Biomedical Research, Basel 4002, Switzerland
| | - Arne Holmgren
- Medical Nobel Institute for Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - José A Sahel
- Laboratoire de Physiopathologie Cellulaire et Moléculaire de la Rétine, Inserm U592, Université Pierre et Marie Curie, 75571 Paris, France
- Institute of Ophthalmology, University College of London, UK
| | - Olivier Poch
- Laboratoire de Biologie et Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, BP 163, 67404 Illkirch cedex, France
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Lardenois A, Chalmel F, Bianchetti L, Sahel JA, Léveillard T, Poch O. PromAn: an integrated knowledge-based web server dedicated to promoter analysis. Nucleic Acids Res 2006; 34:W578-83. [PMID: 16845074 PMCID: PMC1538850 DOI: 10.1093/nar/gkl193] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [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] [Indexed: 11/13/2022] Open
Abstract
PromAn is a modular web-based tool dedicated to promoter analysis that integrates distinct complementary databases, methods and programs. PromAn provides automatic analysis of a genomic region with minimal prior knowledge of the genomic sequence. Prediction programs and experimental databases are combined to locate the transcription start site (TSS) and the promoter region within a large genomic input sequence. Transcription factor binding sites (TFBSs) can be predicted using several public databases and user-defined motifs. Also, a phylogenetic footprinting strategy, combining multiple alignment of large genomic sequences and assignment of various scores reflecting the evolutionary selection pressure, allows for evaluation and ranking of TFBS predictions. PromAn results can be displayed in an interactive graphical user interface, PromAnGUI. It integrates all of this information to highlight active promoter regions, to identify among the huge number of TFBS predictions those which are the most likely to be potentially functional and to facilitate user refined analysis. Such an integrative approach is essential in the face of a growing number of tools dedicated to promoter analysis in order to propose hypotheses to direct further experimental validations. PromAn is publicly available at http://bips.u-strasbg.fr/PromAn.
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Affiliation(s)
| | - Frédéric Chalmel
- Biozentrum and Swiss Institute of BioinformaticsKlingelbergstrasse 50-70, CH-4056 Basel, Switzerland
| | - Laurent Bianchetti
- Plate-Forme de Bioinformatique de Strasbourg, Institut de Génétique et de Biologie Moléculaire et CellulaireCNRS/INSERM/ULP BP 163, 67404 Illkirch Cedex, France
| | - José-Alain Sahel
- Laboratoire de Physiopathologie Cellulaire et Moléculaire de la Rétine, Inserm U592, Université Pierre et Marie Curie75571 Paris, France
| | - Thierry Léveillard
- Laboratoire de Physiopathologie Cellulaire et Moléculaire de la Rétine, Inserm U592, Université Pierre et Marie Curie75571 Paris, France
| | - Olivier Poch
- To whom correspondence should be adressed. Tel: +33 388653294; Fax: +33 388653201;
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Abou-Sleymane G, Chalmel F, Helmlinger D, Lardenois A, Thibault C, Weber C, Mérienne K, Mandel JL, Poch O, Devys D, Trottier Y. Polyglutamine expansion causes neurodegeneration by altering the neuronal differentiation program. Hum Mol Genet 2006; 15:691-703. [PMID: 16434483 DOI: 10.1093/hmg/ddi483] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [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: 12/31/2022] Open
Abstract
Huntington's disease (HD) and spinocerebellar ataxia type 7 (SCA7) belong to a group of inherited neurodegenerative diseases caused by polyglutamine (polyQ) expansion in corresponding proteins. Transcriptional alteration is a unifying feature of polyQ disorders; however, the relationship between polyQ-induced gene expression deregulation and degenerative processes remains unclear. R6/2 and R7E mouse models of HD and SCA7, respectively, present a comparable retinal degeneration characterized by progressive reduction of electroretinograph activity and important morphological changes of rod photoreceptors. The retina, which is a simple central nervous system tissue, allows correlating functional, morphological and molecular defects. Taking advantage of comparing polyQ-induced degeneration in two retina models, we combined gene expression profiling and molecular biology techniques to decipher the molecular pathways underlying polyQ expansion toxicity. We show that R7E and R6/2 retinal phenotype strongly correlates with loss of expression of a large cohort of genes specifically involved in phototransduction function and morphogenesis of differentiated rod photoreceptors. Accordingly, three key transcription factors (Nrl, Crx and Nr2e3) controlling rod differentiation genes, hence expression of photoreceptor specific traits, are down-regulated. Interestingly, other transcription factors known to cause inhibitory effects on photoreceptor differentiation when mis-expressed, such as Stat3, are aberrantly re-activated. Thus, our results suggest that independently from the protein context, polyQ expansion overrides the control of neuronal differentiation and maintenance, thereby causing dysfunction and degeneration.
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Affiliation(s)
- Gretta Abou-Sleymane
- Department of Molecular Pathology, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), CNRS/INSERM/ULP, BP10142, 67404 Illkirch Cédex, CU de Strasbourg, France
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Abstract
UNLABELLED GOAnno is a web tool that automatically annotates proteins according to the Gene Ontology (GO) using evolutionary information available in hierarchized multiple alignments. GO terms present in the aligned functional subfamily can be cross-validated and propagated to obtain highly reliable predicted GO annotation based on the GOAnno algorithm. AVAILABILITY The web tool and a reduced version for local installation are freely available at http://igbmc.u-strasbg.fr/GOAnno/GOAnno.html SUPPLEMENTARY INFORMATION The website supplies a detailed explanation and illustration of the algorithm at http://igbmc.u-strasbg.fr/GOAnno/GOAnnoHelp.html.
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Affiliation(s)
- F Chalmel
- Laboratoire de Biologie et Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP BP 163, Illkirch , France.
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