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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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2
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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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3
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Ramhøj L, Svingen T, Evrard B, Chalmel F, Axelstad M. Two thyroperoxidase-inhibiting chemicals induce shared transcriptional changes in hippocampus of developing rats. Toxicology 2024; 505:153822. [PMID: 38685447 DOI: 10.1016/j.tox.2024.153822] [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] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 04/25/2024] [Accepted: 04/26/2024] [Indexed: 05/02/2024]
Abstract
Thyroid hormone (TH) system disrupting compounds can impair brain development by perturbing TH action during critical life stages. Human exposure to TH system disrupting chemicals is therefore of great concern. To better protect humans against such chemicals, sensitive test methods that can detect effects on the developing brain are critical. Worryingly, however, current test methods are not sensitive and specific towards TH-mediated effects. To address this shortcoming, we performed RNA-sequencing of rat brains developmentally exposed to two different thyroperoxidase (TPO) inhibiting compounds, the medical drug methimazole (MMI) or the pesticide amitrole. Pregnant and lactating rats were exposed to 8 and 16 mg/kg/day(d) MMI or 25 and 50 mg/kg/d amitrole from gestational day 7 until postnatal day 16. Bulk-RNA-seq was performed on hippocampus from the 16-day old male pups. MMI and amitrole caused pronounced changes to the transcriptomes; 816 genes were differentially expressed, and 425 gene transcripts were similarly affected by both chemicals. Functional terms indicate effects from key cellular functions to changes in cell development, migration and differentiation of several cell populations. Of the total number of DEGs, 106 appeared to form a consistent transcriptional fingerprint of developmental hypothyroidism as they were similarly and dose-dependently expressed across all treatment groups. Using a filtering system, we identified 20 genes that appeared to represent the most sensitive, robust and dose-dependent markers of altered TH-mediated brain development. These markers provide inputs to the adverse outcome pathway (AOP) framework where they, in the context of linking TPO inhibiting compounds to adverse cognitive function, can be used to assess altered gene expression in the hippocampus in rat toxicity studies.
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Affiliation(s)
- Louise Ramhøj
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark.
| | - Terje Svingen
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
| | - Bertrand Evrard
- 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
| | - Marta Axelstad
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
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Neyroud AS, Rolland AD, Lecuyer G, Evrard B, Alary N, Dejucq-Rainsford N, Bujan L, Ravel C, Chalmel F. Sperm DNA methylation dynamics after chemotherapy: a longitudinal study of a patient with testicular germ cell tumor treatment. Andrology 2024; 12:396-409. [PMID: 37354024 DOI: 10.1111/andr.13485] [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: 01/10/2023] [Revised: 05/26/2023] [Accepted: 06/19/2023] [Indexed: 06/25/2023]
Abstract
BACKGROUND An important issue for young men affected by testicular germ cell tumor (TGCT) is how TGCT and its treatment will affect, transiently or permanently, their future reproductive health. Previous studies have reported that xenobiotics can induce changes on human sperm epigenome and have the potential to promote epigenetic alterations in the offspring. OBJECTIVES Here, we report the first longitudinal DNA methylation profiling of frozen sperm from a TGCT patient before and up to 2 years after a bleomycin, etoposide, and cisplatin (BEP) chemotherapy. MATERIALS AND METHODS A TGCT was diagnosed in a 30-year-old patient. A cryopreservation of spermatozoa was proposed before adjuvant BEP treatment. Semen samples were collected before and after chemotherapy at 6, 9, 12, and 24 months. The DNA methylation status was determined by RRBS to detect DNA differentially methylated regions (DMRs). RESULTS The analysis revealed that among the 74 DMRs showing modified methylation status 6 months after therapy, 17 remained altered 24 months after treatment. We next associated DMRs with differentially methylated genes (DMGs), which were subsequently intersected with loci known to be important or expressed during early development. DISCUSSION AND CONCLUSION The consequences of the cancer treatment on the sperm epigenome during the recovery periods are topical issues of increasing significance as epigenetic modifications to the paternal genome may have deleterious effects on the offspring. The altered methylated status of these DMGs important for early development might modify their expression pattern and thus affect their function during key stages of embryogenesis, potentially leading to developmental disorders or miscarriages.
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Affiliation(s)
- Anne-Sophie Neyroud
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France
- CHU de Rennes, Département de Gynécologie Obstétrique Reproduction-CECOS, Rennes, France
| | - Antoine Dominique Rolland
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France
| | - Gwendoline Lecuyer
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France
| | - Bertrand Evrard
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France
| | - Nathan Alary
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France
| | - Nathalie Dejucq-Rainsford
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France
| | - Louis Bujan
- Développement Embryonnaire, Fertilité, Environnement (DEFE), UMR Inserm 1203 Université Toulouse 3 et Montpellier, Toulouse, France
- CECOS, Groupe d'activité de médecine de la reproduction, Hôpital Paule de Viguier, CHU Toulouse, Toulouse, France
| | - Célia Ravel
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France
- CHU de Rennes, Département de Gynécologie Obstétrique Reproduction-CECOS, Rennes, France
| | - Frédéric Chalmel
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France
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Blain R, Couly G, Shotar E, Blévinal J, Toupin M, Favre A, Abjaghou A, Inoue M, Hernández-Garzón E, Clarençon F, Chalmel F, Mazaud-Guittot S, Giacobini P, Gitton Y, Chédotal A. A tridimensional atlas of the developing human head. Cell 2023; 186:5910-5924.e17. [PMID: 38070509 PMCID: PMC10783631 DOI: 10.1016/j.cell.2023.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/01/2023] [Accepted: 11/09/2023] [Indexed: 12/24/2023]
Abstract
The evolution and development of the head have long captivated researchers due to the crucial role of the head as the gateway for sensory stimuli and the intricate structural complexity of the head. Although significant progress has been made in understanding head development in various vertebrate species, our knowledge of early human head ontogeny remains limited. Here, we used advanced whole-mount immunostaining and 3D imaging techniques to generate a comprehensive 3D cellular atlas of human head embryogenesis. We present detailed developmental series of diverse head tissues and cell types, including muscles, vasculature, cartilage, peripheral nerves, and exocrine glands. These datasets, accessible through a dedicated web interface, provide insights into human embryogenesis. We offer perspectives on the branching morphogenesis of human exocrine glands and unknown features of the development of neurovascular and skeletomuscular structures. These insights into human embryology have important implications for understanding craniofacial defects and neurological disorders and advancing diagnostic and therapeutic strategies.
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Affiliation(s)
- Raphael Blain
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Gérard Couly
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Eimad Shotar
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France; Department of Interventional Neuroradiology, Pitié-Salpêtrière Hospital, Sorbonne Université, Paris, France
| | | | - Maryne Toupin
- INSERM, EHESP, Univ Rennes, Institut de recherche en santé, environnement et travail (Irset), UMR_S 1085, Rennes, France
| | - Anais Favre
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Ali Abjaghou
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Megumi Inoue
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | | | - Frédéric Clarençon
- Department of Interventional Neuroradiology, Pitié-Salpêtrière Hospital, Sorbonne Université, Paris, France
| | - Frédéric Chalmel
- INSERM, EHESP, Univ Rennes, Institut de recherche en santé, environnement et travail (Irset), UMR_S 1085, Rennes, France
| | - Séverine Mazaud-Guittot
- INSERM, EHESP, Univ Rennes, Institut de recherche en santé, environnement et travail (Irset), UMR_S 1085, Rennes, France
| | - Paolo Giacobini
- University of Lille, INSERM, CHU Lille, U1172 - LilNCog - Lille Neuroscience & Cognition, 59000 Lille, France
| | - Yorick Gitton
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.
| | - Alain Chédotal
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France; Institut de pathologie, Groupe Hospitalier Est, Hospices Civils de Lyon, Lyon, France; University Claude Bernard Lyon 1, MeLiS, CNRS UMR 5284, INSERM U1314, 69008 Lyon, France.
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6
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Souali-Crespo S, Condrea D, Vernet N, Féret B, Klopfenstein M, Grandgirard E, Alunni V, Cerciat M, Jung M, Mayere C, Nef S, Mark M, Chalmel F, Ghyselinck NB. Loss of NR5A1 in mouse Sertoli cells after sex determination changes cellular identity and induces cell death by anoikis. Development 2023; 150:dev201710. [PMID: 38078651 PMCID: PMC10753587 DOI: 10.1242/dev.201710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 11/09/2023] [Indexed: 12/18/2023]
Abstract
To investigate the role of the nuclear receptor NR5A1 in the testis after sex determination, we analyzed mice lacking NR5A1 in Sertoli cells (SCs) from embryonic day (E) 13.5 onwards. Ablation of Nr5a1 impaired the expression of genes characteristic of SC identity (e.g. Sox9 and Amh), caused SC death from E14.5 onwards through a Trp53-independent mechanism related to anoikis, and induced disorganization of the testis cords. Together, these effects caused germ cells to enter meiosis and die. Single-cell RNA-sequencing experiments revealed that NR5A1-deficient SCs changed their molecular identity: some acquired a 'pre-granulosa-like' cell identity, whereas other reverted to a 'supporting progenitor-like' cell identity, most of them being 'intersex' because they expressed both testicular and ovarian genes. Fetal Leydig cells (LCs) did not display significant changes, indicating that SCs are not required beyond E14.5 for their emergence or maintenance. In contrast, adult LCs were absent from postnatal testes. In addition, adult mutant males displayed persistence of Müllerian duct derivatives, decreased anogenital distance and reduced penis length, which could be explained by the loss of AMH and testosterone synthesis due to SC failure.
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Affiliation(s)
- Sirine Souali-Crespo
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Département de Génétique Fonctionnelle et Cancer, Centre National de la Recherche Scientifique (CNRS UMR7104), Institut National de la Santé et de la Recherche Médicale (INSERM U1258), Université de Strasbourg (UNISTRA), 1 rue Laurent Fries, BP-10142, F-67404 Illkirch Cedex, France
| | - Diana Condrea
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Département de Génétique Fonctionnelle et Cancer, Centre National de la Recherche Scientifique (CNRS UMR7104), Institut National de la Santé et de la Recherche Médicale (INSERM U1258), Université de Strasbourg (UNISTRA), 1 rue Laurent Fries, BP-10142, F-67404 Illkirch Cedex, France
| | - Nadège Vernet
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Département de Génétique Fonctionnelle et Cancer, Centre National de la Recherche Scientifique (CNRS UMR7104), Institut National de la Santé et de la Recherche Médicale (INSERM U1258), Université de Strasbourg (UNISTRA), 1 rue Laurent Fries, BP-10142, F-67404 Illkirch Cedex, France
| | - Betty Féret
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Département de Génétique Fonctionnelle et Cancer, Centre National de la Recherche Scientifique (CNRS UMR7104), Institut National de la Santé et de la Recherche Médicale (INSERM U1258), Université de Strasbourg (UNISTRA), 1 rue Laurent Fries, BP-10142, F-67404 Illkirch Cedex, France
| | - Muriel Klopfenstein
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Département de Génétique Fonctionnelle et Cancer, Centre National de la Recherche Scientifique (CNRS UMR7104), Institut National de la Santé et de la Recherche Médicale (INSERM U1258), Université de Strasbourg (UNISTRA), 1 rue Laurent Fries, BP-10142, F-67404 Illkirch Cedex, France
| | - Erwan Grandgirard
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Département de Génétique Fonctionnelle et Cancer, Centre National de la Recherche Scientifique (CNRS UMR7104), Institut National de la Santé et de la Recherche Médicale (INSERM U1258), Université de Strasbourg (UNISTRA), 1 rue Laurent Fries, BP-10142, F-67404 Illkirch Cedex, France
- Imaging Center, IGBMC, F-67404 Illkirch Cedex, France
| | - Violaine Alunni
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Département de Génétique Fonctionnelle et Cancer, Centre National de la Recherche Scientifique (CNRS UMR7104), Institut National de la Santé et de la Recherche Médicale (INSERM U1258), Université de Strasbourg (UNISTRA), 1 rue Laurent Fries, BP-10142, F-67404 Illkirch Cedex, France
- GenomEast Platform, France Génomique consortium, IGBMC, 1 rue Laurent Fries, F-67404 Illkirch Cedex, France
| | - Marie Cerciat
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Département de Génétique Fonctionnelle et Cancer, Centre National de la Recherche Scientifique (CNRS UMR7104), Institut National de la Santé et de la Recherche Médicale (INSERM U1258), Université de Strasbourg (UNISTRA), 1 rue Laurent Fries, BP-10142, F-67404 Illkirch Cedex, France
- GenomEast Platform, France Génomique consortium, IGBMC, 1 rue Laurent Fries, F-67404 Illkirch Cedex, France
| | - Matthieu Jung
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Département de Génétique Fonctionnelle et Cancer, Centre National de la Recherche Scientifique (CNRS UMR7104), Institut National de la Santé et de la Recherche Médicale (INSERM U1258), Université de Strasbourg (UNISTRA), 1 rue Laurent Fries, BP-10142, F-67404 Illkirch Cedex, France
- GenomEast Platform, France Génomique consortium, IGBMC, 1 rue Laurent Fries, F-67404 Illkirch Cedex, France
| | - Chloé Mayere
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, CH-1211 Geneva 4, Switzerland
| | - Serge Nef
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, CH-1211 Geneva 4, Switzerland
| | - Manuel Mark
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Département de Génétique Fonctionnelle et Cancer, Centre National de la Recherche Scientifique (CNRS UMR7104), Institut National de la Santé et de la Recherche Médicale (INSERM U1258), Université de Strasbourg (UNISTRA), 1 rue Laurent Fries, BP-10142, F-67404 Illkirch Cedex, France
- Service de Biologie de la Reproduction, Hôpitaux Universitaires de Strasbourg (HUS), F-67000 Strasbourg, France
| | - Frédéric Chalmel
- Univ Rennes, EHESP, Inserm, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France
| | - Norbert B. Ghyselinck
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Département de Génétique Fonctionnelle et Cancer, Centre National de la Recherche Scientifique (CNRS UMR7104), Institut National de la Santé et de la Recherche Médicale (INSERM U1258), Université de Strasbourg (UNISTRA), 1 rue Laurent Fries, BP-10142, F-67404 Illkirch Cedex, France
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7
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Gregoire EP, De Cian MC, Migale R, Perea-Gomez A, Schaub S, Bellido-Carreras N, Stévant I, Mayère C, Neirijnck Y, Loubat A, Rivaud P, Sopena ML, Lachambre S, Linssen MM, Hohenstein P, Lovell-Badge R, Nef S, Chalmel F, Schedl A, Chaboissier MC. The -KTS splice variant of WT1 is essential for ovarian determination in mice. Science 2023; 382:600-606. [PMID: 37917714 PMCID: PMC7615308 DOI: 10.1126/science.add8831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 07/13/2022] [Accepted: 09/29/2023] [Indexed: 11/04/2023]
Abstract
Sex determination in mammals depends on the differentiation of the supporting lineage of the gonads into Sertoli or pregranulosa cells that govern testis and ovary development, respectively. Although the Y-linked testis-determining gene Sry has been identified, the ovarian-determining factor remains unknown. In this study, we identified -KTS, a major, alternatively spliced isoform of the Wilms tumor suppressor WT1, as a key determinant of female sex determination. Loss of -KTS variants blocked gonadal differentiation in mice, whereas increased expression, as found in Frasier syndrome, induced precocious differentiation of ovaries independently of their genetic sex. In XY embryos, this antagonized Sry expression, resulting in male-to-female sex reversal. Our results identify -KTS as an ovarian-determining factor and demonstrate that its time of activation is critical in gonadal sex differentiation.
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Affiliation(s)
- Elodie P Gregoire
- Université Côte d’Azur, Inserm, CNRS, Institut de Biologie Valrose (iBV), 06108 Nice, France
| | - Marie-Cécile De Cian
- Université Côte d’Azur, Inserm, CNRS, Institut de Biologie Valrose (iBV), 06108 Nice, France
| | - Roberta Migale
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Aitana Perea-Gomez
- Université Côte d’Azur, Inserm, CNRS, Institut de Biologie Valrose (iBV), 06108 Nice, France
| | - Sébastien Schaub
- Sorbonne Université, CNRS, Development Biology Laboratory (LBDV), 06234 Villefranche sur Mer, France
| | | | - Isabelle Stévant
- Department of Genetic Medicine and Development, University of Geneva, 1211 Geneva, Switzerland
- iGE3, Institute of Genetics and Genomics of Geneva, University of Geneva, 1211 Geneva Switzerland
| | - Chloé Mayère
- Department of Genetic Medicine and Development, University of Geneva, 1211 Geneva, Switzerland
- iGE3, Institute of Genetics and Genomics of Geneva, University of Geneva, 1211 Geneva Switzerland
| | - Yasmine Neirijnck
- Université Côte d’Azur, Inserm, CNRS, Institut de Biologie Valrose (iBV), 06108 Nice, France
| | - Agnès Loubat
- Université Côte d’Azur, Inserm, CNRS, Institut de Biologie Valrose (iBV), 06108 Nice, France
| | - Paul Rivaud
- Univ Rennes, Inserm, EHESP, IRSET (Institut de Recherche en Santé, Environnement et Travail)-UMR_S 1085, 35000 Rennes, France
| | | | - Simon Lachambre
- Infinity, Inserm, CNRS, University Toulouse III, 31024 Toulouse, France
| | - Margot M. Linssen
- Central Animal and Transgenic Facility and Dept. Human Genetics, Leiden University Medical Center, 2333ZA Leiden, the Netherlands
| | - Peter Hohenstein
- Central Animal and Transgenic Facility and Dept. Human Genetics, Leiden University Medical Center, 2333ZA Leiden, the Netherlands
| | | | - Serge Nef
- Department of Genetic Medicine and Development, University of Geneva, 1211 Geneva, Switzerland
- iGE3, Institute of Genetics and Genomics of Geneva, University of Geneva, 1211 Geneva Switzerland
| | - Frédéric Chalmel
- Univ Rennes, Inserm, EHESP, IRSET (Institut de Recherche en Santé, Environnement et Travail)-UMR_S 1085, 35000 Rennes, France
| | - Andreas Schedl
- Université Côte d’Azur, Inserm, CNRS, Institut de Biologie Valrose (iBV), 06108 Nice, France
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Lesné L, Desdoits-Lethimonier C, Hug E, Costet N, Raffenne L, Toupin M, Evrard B, Kugathas I, Lavoué V, Chalmel F, Jégou B, Mazaud-Guittot S. Antiepileptic drugs are endocrine disruptors for the human fetal testis ex vivo. Toxicol Sci 2023; 195:169-183. [PMID: 37505509 DOI: 10.1093/toxsci/kfad076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023] Open
Abstract
Valproic acid (VPA) has long been the most widely used antiepileptic drug (AED) for the treatment of epilepsy, bipolar psychiatric disorders, and migraine. However, long-term VPA treatment has several adverse effects on the male reproductive system notably on endocrine functions and/or spermatic parameters. In utero exposure of the fetus to VPA is well known to be associated with a higher risk of several congenital malformations including those of male reproductive organs. Subsequent generations of AEDs, such as carbamazepine (CARB) and lamotrigine (LAM), are considered safer and are currently recommended for women of child-bearing age with epilepsy. Because anomalies of the male genital tract mostly result from endocrine imbalance during fetal life, we hypothesized that AEDs could directly impair testis differentiation. We thus aimed at identifying and characterizing the effects of VPA, CARB, and LAM on the differentiation and function of the different testicular cell types, and at understanding the mechanisms underlying these effects. By using ex vivo culture of first-trimester human fetal testes, we show that VPA induces multiple endocrine disruptive effects, compared with the milder ones caused by CARB and LAM. AED also subtly altered the germ cell lineage in distinct manners. Transcriptomic analysis of VPA-induced alterations highlighted a very broad range of effects on the fetal testis. Overall, our results show that AEDs can behave as endocrine disruptors for the human fetal testis ex vivo. This is consistent with, and likely underlies, the VPA-induced male genital tract masculinization abnormalities observed in patients.
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Affiliation(s)
- Laurianne Lesné
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail)-UMR_S 1085, 35000 Rennes, France
| | - Christèle Desdoits-Lethimonier
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail)-UMR_S 1085, 35000 Rennes, France
| | - Elisa Hug
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail)-UMR_S 1085, 35000 Rennes, France
| | - Nathalie Costet
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail)-UMR_S 1085, 35000 Rennes, France
| | - Léo Raffenne
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail)-UMR_S 1085, 35000 Rennes, France
| | - Maryne Toupin
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail)-UMR_S 1085, 35000 Rennes, France
| | - Bertrand Evrard
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail)-UMR_S 1085, 35000 Rennes, France
| | - Indusha Kugathas
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail)-UMR_S 1085, 35000 Rennes, France
| | - Vincent Lavoué
- Univ Rennes, CHU Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail)-UMR_S 1085, 35000 Rennes, France
| | - Frédéric Chalmel
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail)-UMR_S 1085, 35000 Rennes, France
| | - Bernard Jégou
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail)-UMR_S 1085, 35000 Rennes, France
- EHESP-School of Public Health, 35043 Rennes, France
| | - Séverine Mazaud-Guittot
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail)-UMR_S 1085, 35000 Rennes, France
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9
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Séraudie I, Pillet C, Cesana B, Bazelle P, Jeanneret F, Evrard B, Chalmel F, Bouzit A, Battail C, Long JA, Descotes JL, Cochet C, Filhol O. A new scaffold-free tumoroid model provides a robust preclinical tool to investigate invasion and drug response in Renal Cell Carcinoma. Cell Death Dis 2023; 14:622. [PMID: 37736770 PMCID: PMC10517165 DOI: 10.1038/s41419-023-06133-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 08/24/2023] [Accepted: 09/07/2023] [Indexed: 09/23/2023]
Abstract
Clear cell Renal Cell Carcinoma (ccRCC) is one of the most prevalent kidney cancers, which is often asymptomatic and thus discovered at a metastatic state (mRCC). mRCC are highly heterogeneous tumors composed of subclonal populations that lead to poor treatment response rate. Several recent works explored the potential of ccRCC tumoroids culture derived from patients. However, these models were produced following a scaffold-based method using collagen I or Matrigel that exhibit lot variability and whose complexity could induce treatment response modifications and phenotypic alterations. Following the observation that ccRCC tumoroids can create their own niche by secreting extracellular matrix components, we developed the first scaffold-free tumoroid model of ccRCC tumors. Tumoroids from mice as well as from human tumors were generated with high success rate (≥90%) using a magnetic suspension method and standard culture media. Immunofluorescence analysis revealed their self-organization capacities to maintain multiple tumor-resident cell types, including endothelial progenitor cells. Transcriptomic analysis showed the reproducibility of the method highlighting that the majority of gene expression patterns was conserved in tumoroids compared to their matching tumor tissue. Moreover, this model enables to evaluate drug effects and invasiveness of renal cancer cells in a 3D context, providing a robust preclinical tool for drug screening and biomarker assessment in line with alternative ex vivo methods like tumor tissue slice culture or in vivo xenograft models.
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Grants
- EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)
- INSERM, CEA, Ligue Comité de l’Isère, University Grenoble Alpes, Centre Hospitalier Universitaire de Grenoble-Alpes (CHUGA), Groupement des Entreprises Françaises dans la Lutte contre le Cancer (GEFLUC)
- CEA, UGA
- CEA, Inserm
- UGA, Inserm, CEA
- CHU, Ligue Comité de l’Isère
- Inserm, Ligue Comité de l’Isère
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Affiliation(s)
- Irinka Séraudie
- University Grenoble Alpes, Inserm, CEA, IRIG-Biosanté, UMR 1292, F-38000, Grenoble, France
| | - Catherine Pillet
- University Grenoble Alpes, Inserm, CEA, IRIG-Biosanté, UMR 1292, F-38000, Grenoble, France
| | - Beatrice Cesana
- University Grenoble Alpes, Inserm, CEA, IRIG-Biosanté, UMR 1292, F-38000, Grenoble, France
| | - Pauline Bazelle
- University Grenoble Alpes, Inserm, CEA, IRIG-Biosanté, UMR 1292, F-38000, Grenoble, France
| | - Florian Jeanneret
- University Grenoble Alpes, Inserm, CEA, IRIG-Biosanté, UMR 1292, F-38000, Grenoble, France
- University Grenoble Alpes, Inserm, CEA, IRIG-Biosanté, UA 13, F-38000, Grenoble, France
| | - Bertrand Evrard
- University Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085, F-35000, Rennes, France
| | - Frédéric Chalmel
- University Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085, F-35000, Rennes, France
| | - Assilah Bouzit
- Centre hospitalier universitaire Grenoble Alpes, CS 10217, 38043, Grenoble, cedex 9, France
| | - Christophe Battail
- University Grenoble Alpes, Inserm, CEA, IRIG-Biosanté, UMR 1292, F-38000, Grenoble, France
- University Grenoble Alpes, Inserm, CEA, IRIG-Biosanté, UA 13, F-38000, Grenoble, France
| | - Jean-Alexandre Long
- Centre hospitalier universitaire Grenoble Alpes, CS 10217, 38043, Grenoble, cedex 9, France
| | - Jean Luc Descotes
- Centre hospitalier universitaire Grenoble Alpes, CS 10217, 38043, Grenoble, cedex 9, France
| | - Claude Cochet
- University Grenoble Alpes, Inserm, CEA, IRIG-Biosanté, UMR 1292, F-38000, Grenoble, France
| | - Odile Filhol
- University Grenoble Alpes, Inserm, CEA, IRIG-Biosanté, UMR 1292, F-38000, Grenoble, France.
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Petit FG, Kervarrec C, Allais-Bonnet A, Evrard B, Chalmel F, Deng C, Jamin SP. Uterine defects and estradiol-dependent development of oviductal diverticula in mice lacking the SMAD4 C-terminal Mad homology 2 domain. FASEB J 2023; 37:e23073. [PMID: 37402125 DOI: 10.1096/fj.202300737r] [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] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 06/08/2023] [Accepted: 06/21/2023] [Indexed: 07/05/2023]
Abstract
In female mammals, the oviduct and uterus are essential sites for female and male gamete transport, fertilization, implantation, and maintenance of a successful pregnancy. To delineate the reproductive function of Mothers against decapentaplegic homolog 4 (Smad4), we specifically inactivated Smad4 in ovarian granulosa cells and, oviduct and uterine mesenchymal cells using the Amhr2-cre mouse line. Deletion of exon 8 of Smad4 results in the production of an MH2-truncated SMAD4 protein. These mutant mice are infertile due to the development of oviductal diverticula and defects during the implantation process. The ovaries are fully functional as demonstrated in an ovary transfer experiment. The development of oviductal diverticula occurs shortly after puberty and is dependent on estradiol. The diverticula interfere with sperm migration and embryo transit to the uterus, reducing the number of implantation sites. Analysis of the uterus shows that, even if implantation occurs, decidualization and vascularization are defective resulting in embryo resorption as early as the seventh day of pregnancy. Thus, Smad4 plays an important function in female reproduction by controlling the structural and functional integrity of the oviduct and uterus.
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Affiliation(s)
- Fabrice G Petit
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S1085, Rennes, France
- Univ Paris-Sud, Inserm, UMR_S0782, Clamart, France
| | - Christine Kervarrec
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S1085, Rennes, France
| | | | - Bertrand Evrard
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S1085, Rennes, France
| | - Frédéric Chalmel
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S1085, Rennes, France
| | - Chuxia Deng
- Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Soazik P Jamin
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S1085, Rennes, France
- Univ Paris-Sud, Inserm, UMR_S0782, Clamart, France
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11
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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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12
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Ramhøj L, Axelstad M, Baert Y, Cañas-Portilla AI, Chalmel F, Dahmen L, De La Vieja A, Evrard B, Haigis AC, Hamers T, Heikamp K, Holbech H, Iglesias-Hernandez P, Knapen D, Marchandise L, Morthorst JE, Nikolov NG, Nissen ACVE, Oelgeschlaeger M, Renko K, Rogiers V, Schüürmann G, Stinckens E, Stub MH, Torres-Ruiz M, Van Duursen M, Vanhaecke T, Vergauwen L, Wedebye EB, Svingen T. New approach methods to improve human health risk assessment of thyroid hormone system disruption-a PARC project. Front Toxicol 2023; 5:1189303. [PMID: 37265663 PMCID: PMC10229837 DOI: 10.3389/ftox.2023.1189303] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 05/05/2023] [Indexed: 06/03/2023] Open
Abstract
Current test strategies to identify thyroid hormone (TH) system disruptors are inadequate for conducting robust chemical risk assessment required for regulation. The tests rely heavily on histopathological changes in rodent thyroid glands or measuring changes in systemic TH levels, but they lack specific new approach methodologies (NAMs) that can adequately detect TH-mediated effects. Such alternative test methods are needed to infer a causal relationship between molecular initiating events and adverse outcomes such as perturbed brain development. Although some NAMs that are relevant for TH system disruption are available-and are currently in the process of regulatory validation-there is still a need to develop more extensive alternative test batteries to cover the range of potential key events along the causal pathway between initial chemical disruption and adverse outcomes in humans. This project, funded under the Partnership for the Assessment of Risk from Chemicals (PARC) initiative, aims to facilitate the development of NAMs that are specific for TH system disruption by characterizing in vivo mechanisms of action that can be targeted by in embryo/in vitro/in silico/in chemico testing strategies. We will develop and improve human-relevant in vitro test systems to capture effects on important areas of the TH system. Furthermore, we will elaborate on important species differences in TH system disruption by incorporating non-mammalian vertebrate test species alongside classical laboratory rat species and human-derived in vitro assays.
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Affiliation(s)
- Louise Ramhøj
- Research Group for Molecular and Reproductive Toxicology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Marta Axelstad
- Research Group for Molecular and Reproductive Toxicology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Yoni Baert
- Department In Vitro Toxicology and Dermato-cosmetology (IVTD), Vrije Universiteit Brussel, Jette, Belgium
| | - Ana I. Cañas-Portilla
- Environmental Toxicology Unit from National Center for Environmental Health (CNSA), Endocrine Tumor Unit from UFIEC, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Frédéric Chalmel
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail), Rennes, France
| | - Lars Dahmen
- Department Experimental Toxicology and ZEBET, German Centre for the Protection of Laboratory Animals (Bf3R), German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Antonio De La Vieja
- Environmental Toxicology Unit from National Center for Environmental Health (CNSA), Endocrine Tumor Unit from UFIEC, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Bertrand Evrard
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail), Rennes, France
| | - Ann-Cathrin Haigis
- Zebrafishlab, Veterinary Physiology and Biochemistry, Department of Veterinary Sciences, University of Antwerp, Wilrijk, Belgium
| | - Timo Hamers
- Amsterdam Institute for Life and Environment (A-LIFE), Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Kim Heikamp
- Amsterdam Institute for Life and Environment (A-LIFE), Vrije Universiteit Amsterdam, Amsterdam, Netherlands
- Centre for Health Protection (GZB), National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Henrik Holbech
- Department of Biology, University of Southern Denmark, Odense, Denmark
| | - Patricia Iglesias-Hernandez
- Environmental Toxicology Unit from National Center for Environmental Health (CNSA), Endocrine Tumor Unit from UFIEC, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Dries Knapen
- Zebrafishlab, Veterinary Physiology and Biochemistry, Department of Veterinary Sciences, University of Antwerp, Wilrijk, Belgium
| | - Lorna Marchandise
- Department In Vitro Toxicology and Dermato-cosmetology (IVTD), Vrije Universiteit Brussel, Jette, Belgium
| | - Jane E. Morthorst
- Department of Biology, University of Southern Denmark, Odense, Denmark
| | - Nikolai Georgiev Nikolov
- Group for Chemical Risk Assessment and GMO, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Ana C. V. E. Nissen
- Group for Chemical Risk Assessment and GMO, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Michael Oelgeschlaeger
- Department Experimental Toxicology and ZEBET, German Centre for the Protection of Laboratory Animals (Bf3R), German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Kostja Renko
- Department Experimental Toxicology and ZEBET, German Centre for the Protection of Laboratory Animals (Bf3R), German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Vera Rogiers
- Department In Vitro Toxicology and Dermato-cosmetology (IVTD), Vrije Universiteit Brussel, Jette, Belgium
| | - Gerrit Schüürmann
- UFZ Department of Ecological Chemistry, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Evelyn Stinckens
- Zebrafishlab, Veterinary Physiology and Biochemistry, Department of Veterinary Sciences, University of Antwerp, Wilrijk, Belgium
| | - Mette H. Stub
- Research Group for Molecular and Reproductive Toxicology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Monica Torres-Ruiz
- Environmental Toxicology Unit from National Center for Environmental Health (CNSA), Endocrine Tumor Unit from UFIEC, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Majorie Van Duursen
- Amsterdam Institute for Life and Environment (A-LIFE), Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Tamara Vanhaecke
- Department In Vitro Toxicology and Dermato-cosmetology (IVTD), Vrije Universiteit Brussel, Jette, Belgium
| | - Lucia Vergauwen
- Zebrafishlab, Veterinary Physiology and Biochemistry, Department of Veterinary Sciences, University of Antwerp, Wilrijk, Belgium
| | - Eva Bay Wedebye
- Group for Chemical Risk Assessment and GMO, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Terje Svingen
- Research Group for Molecular and Reproductive Toxicology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
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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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Kugathas I, Johansson HKL, Chan Sock Peng E, Toupin M, Evrard B, Darde TA, Boberg J, Draskau MK, Rolland AD, Mazaud-Guittot S, Chalmel F, Svingen T. Transcriptional profiling of the developing rat ovary following intrauterine exposure to the endocrine disruptors diethylstilbestrol and ketoconazole. Arch Toxicol 2023; 97:849-863. [PMID: 36653537 PMCID: PMC9968686 DOI: 10.1007/s00204-023-03442-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 01/09/2023] [Indexed: 01/20/2023]
Abstract
Exposure to endocrine-disrupting chemicals (EDCs) during development may cause reproductive disorders in women. Although female reproductive endpoints are assessed in rodent toxicity studies, a concern is that typical endpoints are not sensitive enough to detect chemicals of concern to human health. If so, measured endpoints must be improved or new biomarkers of effects included. Herein, we have characterized the dynamic transcriptional landscape of developing rat ovaries exposed to two well-known EDCs, diethylstilbestrol (DES) and ketoconazole (KTZ), by 3' RNA sequencing. Rats were orally exposed from day 7 of gestation until birth, and from postnatal day 1 until days 6, 14 or 22. Three exposure doses for each chemical were used: 3, 6 and 12 µg/kg bw/day of DES; 3, 6, 12 mg/kg bw/day of KTZ. The transcriptome changed dynamically during perinatal development in control ovaries, with 1137 differentially expressed genes (DEGs) partitioned into 3 broad expression patterns. A cross-species deconvolution strategy based on a mouse ovary developmental cell atlas was used to map any changes to ovarian cellularity across the perinatal period to allow for characterization of actual changes to gene transcript levels. A total of 184 DEGs were observed across dose groups and developmental stages in DES-exposed ovaries, and 111 DEGs in KTZ-exposed ovaries across dose groups and developmental stages. Based on our analyses, we have identified new candidate biomarkers for female reproductive toxicity induced by EDC, including Kcne2, Calb2 and Insl3.
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Affiliation(s)
- Indusha Kugathas
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085, 9 avenue du Professeur Léon Bernard, 35000 Rennes, France
| | - Hanna K. L. Johansson
- National Food Institute, Technical University of Denmark, Kemitorvet, Building 202, 2800 Kongens Lyngby, Denmark
| | - Edith Chan Sock Peng
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085, 9 avenue du Professeur Léon Bernard, 35000 Rennes, France
| | - Maryne Toupin
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085, 9 avenue du Professeur Léon Bernard, 35000 Rennes, France
| | - Bertrand Evrard
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085, 9 avenue du Professeur Léon Bernard, 35000 Rennes, France
| | | | - Julie Boberg
- National Food Institute, Technical University of Denmark, Kemitorvet, Building 202, 2800 Kongens Lyngby, Denmark
| | - Monica K. Draskau
- National Food Institute, Technical University of Denmark, Kemitorvet, Building 202, 2800 Kongens Lyngby, Denmark
| | - Antoine D. Rolland
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085, 9 avenue du Professeur Léon Bernard, 35000 Rennes, France
| | - Séverine Mazaud-Guittot
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085, 9 avenue du Professeur Léon Bernard, 35000 Rennes, France
| | - Frédéric Chalmel
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085, 9 avenue du Professeur Léon Bernard, 35000, Rennes, France.
| | - Terje Svingen
- National Food Institute, Technical University of Denmark, Kemitorvet, Building 202, 2800, Kongens Lyngby, Denmark.
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15
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Dumont L, Lopez Maestre H, Chalmel F, Huber L, Rives-Feraille A, Moutard L, Bateux F, Rondanino C, Rives N. Throughout in vitro first spermatogenic wave: Next-generation sequencing gene expression patterns of fresh and cryopreserved prepubertal mice testicular tissue explants. Front Endocrinol (Lausanne) 2023; 14:1112834. [PMID: 37008933 PMCID: PMC10063980 DOI: 10.3389/fendo.2023.1112834] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 02/22/2023] [Indexed: 03/19/2023] Open
Abstract
INTRODUCTION Suitable cryopreservation procedures of pre-pubertal testicular tissue associated with efficient culture conditions are crucial in the fields of fertility preservation and restoration. In vitro spermatogenesis remains a challenging technical procedure to undergo a complete spermatogenesis.The number of haploid cells and more specifically the spermatic yield produced in vitro in mice is still extremely low compared to age-matched in vivo controls and this procedure has never yet been successfully transferred to humans. METHODS To evaluate the impact of in vitro culture and freezing procedure, pre-pubertal testicular mice testes were directly cultured until day 4 (D4), D16 and D30 or cryopreserved by controlled slow freezing then cultured until D30. Testes composed of a panel of 6.5 dpp (days postpartum), 10.5 dpp, 22.5 dpp, and 36.5 dpp mice were used as in vivo controls. Testicular tissues were assessed by histological (HES) and immunofluorescence (stimulated by retinoic acid gene 8, STRA8) analyses. Moreover, a detailed transcriptome evaluation study has been carried out to study the gene expression patterns throughout the first in vitro spermatogenic wave. RESULTS Transcriptomic analyses reveal that cultured tissues expression profiles are almost comparable between D16 and D30; highlighting an abnormal kinetic throughout the second half of the first spermatogenesis during in vitro cultures. In addition, testicular explants have shown dysregulation of their transcriptomic profile compared to controls with genes related to inflammation response, insulin-like growth factor and genes involved in steroidogenesis. DISCUSSION The present work first shows that cryopreservation had very little impact on gene expression in testicular tissue, either directly after thawing or after 30 days in culture. Transcriptomic analysis of testis tissue samples is highly informative due to the large number of expressed genes and identified isoforms. This study provides a very valuable basis for future studies concerning in vitro spermatogenesis in mice.
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Affiliation(s)
- Ludovic Dumont
- Univ Rouen Normandie, INSERM, NORDIC UMR 1239 – Team Adrenal and Gonadal Pathophysiology (AGoPath), Rouen, France
- Normandie, Institute for Research and Innovation in Biomedicine (IRIB), Rouen, France
- *Correspondence: Ludovic Dumont,
| | - Hélène Lopez Maestre
- Univ Rouen Normandie, INSERM, PANTHER UMR 1234, Rouen, France
- Institut Pasteur, Hub de Bioinformatique et Biostatistique – Département Biologie Computationnelle, USR 3756, CNRS, Paris, France
| | | | - Louise Huber
- Univ Rouen Normandie, INSERM, NORDIC UMR 1239 – Team Adrenal and Gonadal Pathophysiology (AGoPath), Rouen, France
- Normandie, Institute for Research and Innovation in Biomedicine (IRIB), Rouen, France
| | - Aurélie Rives-Feraille
- Univ Rouen Normandie, INSERM, NORDIC UMR 1239 – Team Adrenal and Gonadal Pathophysiology (AGoPath), Rouen, France
- Normandie, Institute for Research and Innovation in Biomedicine (IRIB), Rouen, France
| | - Laura Moutard
- Univ Rouen Normandie, INSERM, NORDIC UMR 1239 – Team Adrenal and Gonadal Pathophysiology (AGoPath), Rouen, France
- Normandie, Institute for Research and Innovation in Biomedicine (IRIB), Rouen, France
| | - Frédérique Bateux
- Univ Rouen Normandie, INSERM, NORDIC UMR 1239 – Team Adrenal and Gonadal Pathophysiology (AGoPath), Rouen, France
- Normandie, Institute for Research and Innovation in Biomedicine (IRIB), Rouen, France
| | - Christine Rondanino
- Univ Rouen Normandie, INSERM, NORDIC UMR 1239 – Team Adrenal and Gonadal Pathophysiology (AGoPath), Rouen, France
- Normandie, Institute for Research and Innovation in Biomedicine (IRIB), Rouen, France
| | - Nathalie Rives
- Univ Rouen Normandie, INSERM, NORDIC UMR 1239 – Team Adrenal and Gonadal Pathophysiology (AGoPath), Rouen, France
- Normandie, Institute for Research and Innovation in Biomedicine (IRIB), Rouen, France
- Rouen University Hospital, Biology of Reproduction-CECOS laboratory, Rouen, 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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Lehtiniemi T, Bourgery M, Ma L, Ahmedani A, Mäkelä M, Asteljoki J, Olotu O, Laasanen S, Zhang FP, Tan K, Chousal JN, Burow D, Koskinen S, Laiho A, Elo L, Chalmel F, Wilkinson M, Kotaja N. SMG6 localizes to the chromatoid body and shapes the male germ cell transcriptome to drive spermatogenesis. Nucleic Acids Res 2022; 50:11470-11491. [PMID: 36259644 PMCID: PMC9723633 DOI: 10.1093/nar/gkac900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 09/23/2022] [Accepted: 10/03/2022] [Indexed: 12/24/2022] Open
Abstract
Nonsense-mediated RNA decay (NMD) is a highly conserved and selective RNA turnover pathway that depends on the endonuclease SMG6. Here, we show that SMG6 is essential for male germ cell differentiation in mice. Germ-cell conditional knockout (cKO) of Smg6 induces extensive transcriptome misregulation, including a failure to eliminate meiotically expressed transcripts in early haploid cells, and accumulation of NMD target mRNAs with long 3' untranslated regions (UTRs). Loss of SMG6 in the male germline results in complete arrest of spermatogenesis at the early haploid cell stage. We find that SMG6 is strikingly enriched in the chromatoid body (CB), a specialized cytoplasmic granule in male germ cells also harboring PIWI-interacting RNAs (piRNAs) and the piRNA-binding protein PIWIL1. This raises the possibility that SMG6 and the piRNA pathway function together, which is supported by several findings, including that Piwil1-KO mice phenocopy Smg6-cKO mice and that SMG6 and PIWIL1 co-regulate many genes in round spermatids. Together, our results demonstrate that SMG6 is an essential regulator of the male germline transcriptome, and highlight the CB as a molecular platform coordinating RNA regulatory pathways to control sperm production and fertility.
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Affiliation(s)
- Tiina Lehtiniemi
- Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, Turku, Finland
| | - Matthieu Bourgery
- Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, Turku, Finland
| | - Lin Ma
- Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, Turku, Finland
| | - Ammar Ahmedani
- Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, Turku, Finland
| | - Margareeta Mäkelä
- Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, Turku, Finland
| | - Juho Asteljoki
- Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, Turku, Finland
| | - Opeyemi Olotu
- Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, Turku, Finland
| | - Samuli Laasanen
- Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, Turku, Finland
| | - Fu-Ping Zhang
- Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, Turku, Finland
- Turku Center for Disease Modeling, University of Turku, Turku, Finland
- GM-Unit, Helsinki Institute of Life Science, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Kun Tan
- Department of Obstetrics, Gynecology, and Reproductive Sciences, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Jennifer N Chousal
- Department of Obstetrics, Gynecology, and Reproductive Sciences, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Dana Burow
- Department of Obstetrics, Gynecology, and Reproductive Sciences, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Satu Koskinen
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Asta Laiho
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Laura L Elo
- Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, Turku, Finland
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Frédéric Chalmel
- University of Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000, Rennes, France
| | - Miles F Wilkinson
- Department of Obstetrics, Gynecology, and Reproductive Sciences, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Institute for Genomic Medicine (IGM), University of California, San Diego, La Jolla, CA 92093, USA
| | - Noora Kotaja
- Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, Turku, Finland
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18
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Davidsen N, Ramhøj L, Kugathas I, Evrard B, Darde TA, Chalmel F, Svingen T, Rosenmai AK. PFOS disrupts key developmental pathways during hiPSC-derived cardiomyocyte differentiation in vitro. Toxicol In Vitro 2022; 85:105475. [PMID: 36116746 DOI: 10.1016/j.tiv.2022.105475] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 08/17/2022] [Accepted: 09/12/2022] [Indexed: 11/26/2022]
Abstract
Exposure to perfluorooctanesulfonic acid (PFOS) has been associated with congenital heart disease (CHD) and decreased birth weight. PFOS exposure can disrupt signaling pathways relevant for cardiac development in stem cell-derived cardiomyocyte assays, such as the PluriBeat assay, where spheroids of human induced pluripotent stem cells (hiPSCs) differentiate into contracting cardiomyocytes. Notably, cell line origin can also affect how the assay responds to chemical exposure. Herein, we examined the effect of PFOS on cardiomyocyte differentiation by transcriptomics profiling of two different hiPSC lines to see if they exhibit a common pattern of disruption. Two stages of differentiation were investigated: the cardiac progenitor stage and the cardiomyocyte stage. Many differentially expressed genes (DEGs) were observed between cell lines independent of exposure. However, 135 DEGs were identified as common between the two cell lines. Of these, 10 DEGs were associated with GO-terms related to the heart. PFOS exposure disrupted multiple signaling pathways relevant to cardiac development, including WNT, TGF, HH, and EGF. Of these pathways, genes related to the non-canonical WNTCa2+ signaling was particularly affected. PFOS thus has the capacity to disrupt pathways important for cardiac development and function.
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Affiliation(s)
- Nichlas Davidsen
- National Food Institute, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark.
| | - Louise Ramhøj
- National Food Institute, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark
| | - Indusha Kugathas
- 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 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, Kgs. Lyngby DK-2800, Denmark
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Lesne L, Desdoits C, Hug E, Toupin M, Kugathas I, Raffenne L, Costet N, Lavoué V, Chalmel F, Jégou B, Mazaud-Guittot S. P06-03 Effects of antiepileptic drugs on the human fetal testis ex vivo. Toxicol Lett 2022. [DOI: 10.1016/j.toxlet.2022.07.321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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20
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Keppner A, Correia M, Santambrogio S, Koay TW, Maric D, Osterhof C, Winter DV, Clerc A, Stumpe M, Chalmel F, Dewilde S, Odermatt A, Kressler D, Hankeln T, Wenger RH, Hoogewijs D. Androglobin, a chimeric mammalian globin, is required for male fertility. eLife 2022; 11:72374. [PMID: 35700329 PMCID: PMC9249397 DOI: 10.7554/elife.72374] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 06/13/2022] [Indexed: 11/13/2022] Open
Abstract
Spermatogenesis is a highly specialized differentiation process driven by a dynamic gene expression program and ending with the production of mature spermatozoa. Whereas hundreds of genes are known to be essential for male germline proliferation and differentiation, the contribution of several genes remains uncharacterized. The predominant expression of the latest globin family member, androglobin (Adgb), in mammalian testis tissue prompted us to assess its physiological function in spermatogenesis. Adgb knockout mice display male infertility, reduced testis weight, impaired maturation of elongating spermatids, abnormal sperm shape, and ultrastructural defects in microtubule and mitochondrial organization. Epididymal sperm from Adgb knockout animals display multiple flagellar malformations including coiled, bifid or shortened flagella, and erratic acrosomal development. Following immunoprecipitation and mass spectrometry, we could identify septin 10 (Sept10) as interactor of Adgb. The Sept10-Adgb interaction was confirmed both in vivo using testis lysates and in vitro by reciprocal co-immunoprecipitation experiments. Furthermore, the absence of Adgb leads to mislocalization of Sept10 in sperm, indicating defective manchette and sperm annulus formation. Finally, in vitro data suggest that Adgb contributes to Sept10 proteolysis in a calmodulin-dependent manner. Collectively, our results provide evidence that Adgb is essential for murine spermatogenesis and further suggest that Adgb is required for sperm head shaping via the manchette and proper flagellum formation.
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Affiliation(s)
- Anna Keppner
- Department of Endocrinology, Metabolism and Cardiovascular system, University of Fribourg, Fribourg, Switzerland
| | - Miguel Correia
- Department of Endocrinology, Metabolism and Cardiovascular system, University of Fribourg, Fribourg, Switzerland
| | | | - Teng Wei Koay
- Department of Endocrinology, Metabolism and Cardiovascular system, University of Fribourg, Fribourg, Switzerland
| | - Darko Maric
- Department of Endocrinology, Metabolism and Cardiovascular system, University of Fribourg, Fribourg, Switzerland
| | - Carina Osterhof
- Institute for Organismic and Molecular Evolutionary Biology, University of Mainz, Mainz, Germany
| | - Denise V Winter
- Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Angèle Clerc
- Department of Endocrinology, Metabolism and Cardiovascular system, University of Fribourg, Fribourg, Switzerland
| | - Michael Stumpe
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | | | - Sylvia Dewilde
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Alex Odermatt
- Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Dieter Kressler
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Thomas Hankeln
- Institute for Organismic and Molecular Evolutionary Biology, University of Mainz, Mainz, Germany
| | - Roland H Wenger
- Institute of Physiology, University of Zurich, Zurich, Switzerland
| | - David Hoogewijs
- Department of Endocrinology, Metabolism and Cardiovascular system, University of Fribourg, Fribourg, Switzerland
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21
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Imran M, Chalmel F, Sergent O, Evrard B, Le Mentec H, Legrand A, Dupont A, Bescher M, Bucher S, Fromenty B, Huc L, Sparfel L, Lagadic-Gossmann D, Podechard N. Transcriptomic analysis in zebrafish larvae identifies iron-dependent mitochondrial dysfunction as a possible key event of NAFLD progression induced by benzo[a]pyrene/ethanol co-exposure. Cell Biol Toxicol 2022:10.1007/s10565-022-09706-4. [PMID: 35412187 DOI: 10.1007/s10565-022-09706-4] [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] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 02/28/2022] [Indexed: 11/02/2022]
Abstract
Non-alcoholic fatty liver disease (NAFLD) is a worldwide epidemic for which environmental contaminants are increasingly recognized as important etiological factors. Among them, the combination of benzo[a]pyrene (B[a]P), a potent environmental carcinogen, with ethanol, was shown to induce the transition of steatosis toward steatohepatitis. However, the underlying mechanisms involved remain to be deciphered. In this context, we used high-fat diet fed zebrafish model, in which we previously observed progression of steatosis to a steatohepatitis-like state following a 7-day-co-exposure to 43 mM ethanol and 25 nM B[a]P. Transcriptomic analysis highlighted the potent role of mitochondrial dysfunction, alterations in heme and iron homeostasis, involvement of aryl hydrocarbon receptor (AhR) signaling, and oxidative stress. Most of these mRNA dysregulations were validated by RT-qPCR. Moreover, similar changes were observed using a human in vitro hepatocyte model, HepaRG cells. The mitochondria structural and functional alterations were confirmed by transmission electronic microscopy and Seahorse technology, respectively. Involvement of AhR signaling was evidenced by using in vivo an AhR antagonist, CH223191, and in vitro in AhR-knock-out HepaRG cells. Furthermore, as co-exposure was found to increase the levels of both heme and hemin, we investigated if mitochondrial iron could induce oxidative stress. We found that mitochondrial labile iron content was raised in toxicant-exposed larvae. This increase was prevented by the iron chelator, deferoxamine, which also inhibited liver co-exposure toxicity. Overall, these results suggest that the increase in mitochondrial iron content induced by B[a]P/ethanol co-exposure causes mitochondrial dysfunction that contributes to the pathological progression of NAFLD.
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Affiliation(s)
- Muhammad Imran
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé environnement et travail) - UMR_S 1085, F-35000, Rennes, France.,Iqra University, Karachi, Pakistan
| | - Frédéric Chalmel
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé environnement et travail) - UMR_S 1085, F-35000, Rennes, France
| | - Odile Sergent
- 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
| | - Hélène Le Mentec
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé environnement et travail) - UMR_S 1085, F-35000, Rennes, France
| | - Antoine Legrand
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé environnement et travail) - UMR_S 1085, F-35000, Rennes, France
| | - Aurélien Dupont
- Univ Rennes, Biosit - UMS 3480, US_S 018, F-35000, Rennes, France
| | - Maëlle Bescher
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé environnement et travail) - UMR_S 1085, F-35000, Rennes, France
| | - Simon Bucher
- Univ Rennes, Inserm, Inrae, Institut NUMECAN (Nutrition Metabolisms and Cancer)-UMR_S 13 1241, and UMR_A 1341, 35000, Rennes, France
| | - Bernard Fromenty
- Univ Rennes, Inserm, Inrae, Institut NUMECAN (Nutrition Metabolisms and Cancer)-UMR_S 13 1241, and UMR_A 1341, 35000, Rennes, France
| | - Laurence Huc
- Université de Toulouse, Inrae, ENVT, INP-Purpan, UPS, Toxalim (Research Centre in Food Toxicology), 31027, Toulouse, France
| | - Lydie Sparfel
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé environnement et travail) - UMR_S 1085, F-35000, Rennes, France
| | - Dominique Lagadic-Gossmann
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé environnement et travail) - UMR_S 1085, F-35000, Rennes, France
| | - Normand Podechard
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé environnement et travail) - UMR_S 1085, F-35000, Rennes, France.
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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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23
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Neyroud AS, Rolland A, Evrard B, Alary N, Dejucq-Rainsford N, Jégou B, Bujan L, Ravel C, Chalmel F. P–055 Methylation dynamics of the sperm epigenome after chemotherapy: a case study. Hum Reprod 2021. [DOI: 10.1093/humrep/deab130.054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Study question
What is the evolution of the sperm epigenome after chemotherapy in a patient with testicular cancer (TC)?
Summary answer
These new data on epigenetic recovery profil after TC are useful tools for counseling and reassuring these patients.
What is known already
An important issue for young men affected TC is how TC and its treatment will affect, transiently or permanently, their future reproductive health. The consequences of cancer treatment on the sperm epigenome during the recovery periods are topical issues of ascendant significance as epigenetic modifications to the paternal genome may have deleterious effects on the offspring.
Study design, size, duration
Here we report the epigenomic profiling of frozen sperm from a TC patient before and after the treatment at different time points (6, 9, 12 and 24 months) by using RRBS analysis (Reduced representation bisulfite sequencing method).
Participants/materials, setting, methods
A testicular tumor (testicular germ cell tumor) was diagnosed in a 30 years old patient. A cryopreservation of spermatozoa was proposed before treatment.Semen samples were obtained 2 times before treatment and 4 times after treatment (6, 9, 12 and 24 months following the initiation of treatment).
Main results and the role of chance
Upon collection, sampling after chemotherapy ranged from 0,6 to 4,2 million per sperm straw between 6 and 24 months after the treatment, always increasing.
In order to capture the direct effect of the treatment on the methylation changes, the DMR detection has been operated between pre-chemotherapy samples (pair-wise) and the time point of 6 months. Among the 179 hqDMRs, 74 are differentially methylated between the PreCT and PostCT6m samples (16 hyper- and 68 hypo-methylated) associated with 49 DMGs (15 hyper- and 34 hypo-methylated).
We further sub-clustered the 74 hqDMRs between PreCT and PostCT6m into 6 patterns, 3 hyper- and 3 hypo-methylated. Briefly, patterns P1 and P4 include hqDMRs that quickly get back to their pre-treatment methylation status just after 9th months onwards. Patterns P2 and P5 include hqDMRs that slowly get back to their pre-treatment methylation status between 12 and 24 months after treatment. Patterns P3 and P6 include hqDMRs that remain hyper- or hypo-methylated even after 24 months.
We have intersected the genes (DMGs) associated with the detected hqDMRs with those known to be important or expressed during embryogenesis. We thus detected that 7 hyper-methylated and 6 hypomethylated DMGs were involved (or expressed) during embryonic / fetal development.
Limitations, reasons for caution
This study involves a single patient. As the patient made no major changes in his personal way of life, we hypothesized that sperm parameter variations may be attributable to the BEP treatment.
Wider implications of the findings: The altered methylated status of those DMGs important for early development might modify their expression pattern and thus affect their function during key stages of embryogenesis leading to potential developmental disorders. It is important to notice that among the 110 DMGs none of them correspond to known imprinted genes.
Trial registration number
Not applicable
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Affiliation(s)
- A S Neyroud
- CHU de Rennes, Biology of reproduction, rennes, France
| | - A Rolland
- Univ Rennes- Inserm- EHESP- Irset Institut de recherche en santé- environnement et travail - UMR_S 1085- F–35000 Rennes- France., Inserm, Rennes, France
| | - B Evrard
- Univ Rennes- Inserm- EHESP- Irset Institut de recherche en santé- environnement et travail - UMR_S 1085- F–35000 Rennes- France., Inserm, Rennes, France
| | - N Alary
- Univ Rennes- Inserm- EHESP- Irset Institut de recherche en santé- environnement et travail - UMR_S 1085- F–35000 Rennes- France., Inserm, Rennes, France
| | - N Dejucq-Rainsford
- Univ Rennes- Inserm- EHESP- Irset Institut de recherche en santé- environnement et travail - UMR_S 1085- F–35000 Rennes- France., Inserm, Rennes, France
| | - B Jégou
- Univ Rennes- Inserm- EHESP- Irset Institut de recherche en santé- environnement et travail - UMR_S 1085- F–35000 Rennes- France., Inserm, Rennes, France
| | - L Bujan
- CHU de Toulouse, Biology of reproduction, Toulouse, France
| | - C Ravel
- CHU de Rennes, Biology of reproduction, rennes, France
| | - F Chalmel
- Univ Rennes- Inserm- EHESP- Irset Institut de recherche en santé- environnement et travail - UMR_S 1085- F–35000 Rennes- France., Inserm, Rennes, France
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Chalmel F, Giwercman A, Huhtaniemi I, Jouannet P, Robaire B, Spira A. In memoriam: Bernard Jégou, humanist scientist. Andrology 2021; 9:1023-1024. [PMID: 34019734 DOI: 10.1111/andr.13049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 05/18/2021] [Indexed: 11/28/2022]
Affiliation(s)
- Frédéric Chalmel
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail), Rennes, France
| | | | - Ilpo Huhtaniemi
- Imperial College London, Surgery & Cancer, Hammersmith Hospital, London, UK
| | | | - Bernard Robaire
- Pharmacology and Therapeutics, 3655 Promenade Sir William Osler, McGill University, Montreal, Quebec, Canada
| | - Alfred Spira
- Department of Epidemiology and Public Health, University Paris Saclay, Paris, France
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Lecluze E, Rolland AD, Filis P, Evrard B, Leverrier-Penna S, Maamar MB, Coiffec I, Lavoué V, Fowler PA, Mazaud-Guittot S, Jégou B, Chalmel F. Dynamics of the transcriptional landscape during human fetal testis and ovary development. Hum Reprod 2021; 35:1099-1119. [PMID: 32412604 DOI: 10.1093/humrep/deaa041] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 02/10/2020] [Indexed: 12/17/2022] Open
Abstract
STUDY QUESTION Which transcriptional program triggers sex differentiation in bipotential gonads and downstream cellular events governing fetal testis and ovary development in humans? SUMMARY ANSWER The characterization of a dynamically regulated protein-coding and non-coding transcriptional landscape in developing human gonads of both sexes highlights a large number of potential key regulators that show an early sexually dimorphic expression pattern. WHAT IS KNOWN ALREADY Gonadal sex differentiation is orchestrated by a sexually dimorphic gene expression program in XX and XY developing fetal gonads. A comprehensive characterization of its non-coding counterpart offers promising perspectives for deciphering the molecular events underpinning gonad development and for a complete understanding of the etiology of disorders of sex development in humans. STUDY DESIGN, SIZE, DURATION To further investigate the protein-coding and non-coding transcriptional landscape during gonad differentiation, we used RNA-sequencing (RNA-seq) and characterized the RNA content of human fetal testis (N = 24) and ovaries (N = 24) from 6 to 17 postconceptional week (PCW), a key period in sex determination and gonad development. PARTICIPANTS/MATERIALS, SETTING, METHODS First trimester fetuses (6-12 PCW) and second trimester fetuses (13-14 and 17 PCW) were obtained from legally induced normally progressing terminations of pregnancy. Total RNA was extracted from whole human fetal gonads and sequenced as paired-end 2 × 50 base reads. Resulting sequences were mapped to the human genome, allowing for the assembly and quantification of corresponding transcripts. MAIN RESULTS AND THE ROLE OF CHANCE This RNA-seq analysis of human fetal testes and ovaries at seven key developmental stages led to the reconstruction of 22 080 transcripts differentially expressed during testicular and/or ovarian development. In addition to 8935 transcripts displaying sex-independent differential expression during gonad development, the comparison of testes and ovaries enabled the discrimination of 13 145 transcripts that show a sexually dimorphic expression profile. The latter include 1479 transcripts differentially expressed as early as 6 PCW, including 39 transcription factors, 40 long non-coding RNAs and 20 novel genes. Despite the use of stringent filtration criteria (expression cut-off of at least 1 fragment per kilobase of exon model per million reads mapped, fold change of at least 2 and false discovery rate adjusted P values of less than <1%), the possibility of assembly artifacts and of false-positive differentially expressed transcripts cannot be fully ruled out. LARGE-SCALE DATA Raw data files (fastq) and a searchable table (.xlss) containing information on genomic features and expression data for all refined transcripts have been submitted to the NCBI GEO under accession number GSE116278. LIMITATIONS, REASONS FOR CAUTION The intrinsic nature of this bulk analysis, i.e. the sequencing of transcripts from whole gonads, does not allow direct identification of the cellular origin(s) of the transcripts characterized. Potential cellular dilution effects (e.g. as a result of distinct proliferation rates in XX and XY gonads) may account for a few of the expression profiles identified as being sexually dimorphic. Finally, transcriptome alterations that would result from exposure to pre-abortive drugs cannot be completely excluded. Although we demonstrated the high quality of the sorted cell populations used for experimental validations using quantitative RT-PCR, it cannot be totally excluded that some germline expression may correspond to cell contamination by, for example, macrophages. WIDER IMPLICATIONS OF THE FINDINGS For the first time, this study has led to the identification of 1000 protein-coding and non-coding candidate genes showing an early, sexually dimorphic, expression pattern that have not previously been associated with sex differentiation. Collectively, these results increase our understanding of gonad development in humans, and contribute significantly to the identification of new candidate genes involved in fetal gonad differentiation. The results also provide a unique resource that may improve our understanding of the fetal origin of testicular and ovarian dysgenesis syndromes, including cryptorchidism and testicular cancers. STUDY FUNDING/COMPETING INTEREST(S) This work was supported by the French National Institute of Health and Medical Research (Inserm), the University of Rennes 1, the French School of Public Health (EHESP), the Swiss National Science Foundation [SNF n° CRS115_171007 to B.J.], the French National Research Agency [ANR n° 16-CE14-0017-02 and n° 18-CE14-0038-02 to F.C.], the Medical Research Council [MR/L010011/1 to P.A.F.] and the European Community's Seventh Framework Programme (FP7/2007-2013) [under grant agreement no 212885 to P.A.F.] and from the European Union's Horizon 2020 Research and Innovation Programme [under grant agreement no 825100 to P.A.F. and S.M.G.]. There are no competing interests related to this study.
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Affiliation(s)
- Estelle Lecluze
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France
| | - Antoine D Rolland
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France
| | - Panagiotis Filis
- Institute of Medical Sciences, School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK
| | - Bertrand Evrard
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France
| | - Sabrina Leverrier-Penna
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France.,Univ Poitiers, STIM, CNRS ERL7003, Poitiers Cedex 9, CNRS ERL7003, France
| | - Millissia Ben Maamar
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France
| | - Isabelle Coiffec
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France
| | - Vincent Lavoué
- Service Gynécologie et Obstétrique, CHU Rennes, F-35000 Rennes, France
| | - Paul A Fowler
- Institute of Medical Sciences, School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK
| | - Séverine Mazaud-Guittot
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France
| | - Bernard Jégou
- 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
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Dagher J, Brunot A, Evrard B, Kammerer-Jacquet SF, Beaumont M, Cornevin L, Derquin F, Verhoest G, Bensalah K, Lespagnol A, Dugay F, Belaud-Rotureau MA, Chalmel F, Rioux-Leclercq N. Multiple metastatic clones assessed by an integrative multiomics strategy in clear cell renal carcinoma: a case study. J Clin Pathol 2021; 75:426-430. [PMID: 33766955 DOI: 10.1136/jclinpath-2020-207326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/17/2021] [Accepted: 02/22/2021] [Indexed: 11/03/2022]
Abstract
The dynamics of metastatic evolution in clear cell renal cell carcinoma (ccRCC) are complex. We report a case study where tumour heterogeneity resulting from clonal evolution is a frequent feature and could play a role in metastatic dissemination.We used an integrative multiomics strategy combining genomic and transcriptomic data to classify fourteen specimens from spatially different areas of a kidney tumour and three non-primary sites including a vein thrombus and two adrenal metastases.All sites were heterogeneous and polyclonal, each tumour site containing two different aggressive subclonal populations, with differentially expressed genes implicated in distinct biological functions. These are rare primary metastatic samples prior to any medical treatment, where we showed a multiple metastatic seeding of two subclonal populations.Multiple interdependent lineages could be the source of metastatic heterogeneity in ccRCC. By sampling metastases, patients with resistance to therapies could benefit a combination of targeted therapies based on more than one aggressive clone.
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Affiliation(s)
- Julien Dagher
- Univ Rennes, Inserm, EHESP, Irset - UMR_S1085, F-35000, Rennes 1 University, Rennes, Bretagne, France.,Department of Pathology, University Hospital, Rennes, Bretagne, France
| | - Angelique Brunot
- Univ Rennes, Inserm, EHESP, Irset - UMR_S1085, F-35000, Rennes 1 University, Rennes, Bretagne, France.,Department of Oncology, University Hospital of Rennes, Rennes, France
| | - Bertrand Evrard
- Univ Rennes, Inserm, EHESP, Irset - UMR_S1085, F-35000, Rennes 1 University, Rennes, Bretagne, France
| | | | - Marion Beaumont
- Department of Cytogenetics and Cell Biology, CHU de Rennes, Rennes, France
| | - Laurence Cornevin
- Department of Cytogenetics and Cell Biology, CHU de Rennes, Rennes, France
| | - Fanny Derquin
- Department of Oncology, University Hospital of Rennes, Rennes, France
| | - Gregory Verhoest
- Department of Urology, University Hospital of Rennes, Rennes, France
| | - Karim Bensalah
- Department of Urology, University Hospital of Rennes, Rennes, France
| | | | - Frederic Dugay
- Department of Cytogenetics and Cell Biology, CHU de Rennes, Rennes, France
| | - Marc-Antoine Belaud-Rotureau
- Univ Rennes, Inserm, EHESP, Irset - UMR_S1085, F-35000, Rennes 1 University, Rennes, Bretagne, France.,Department of Cytogenetics and Cell Biology, CHU de Rennes, Rennes, France
| | - Frédéric Chalmel
- Univ Rennes, Inserm, EHESP, Irset - UMR_S1085, F-35000, Rennes 1 University, Rennes, Bretagne, France
| | - Nathalie Rioux-Leclercq
- Univ Rennes, Inserm, EHESP, Irset - UMR_S1085, F-35000, Rennes 1 University, Rennes, Bretagne, France.,Department of Pathology, University Hospital, Rennes, Bretagne, France
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27
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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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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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29
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Jamin SP, Hikmet F, Mathieu R, Jégou B, Lindskog C, Chalmel F, Primig M. Combined RNA/tissue profiling identifies novel Cancer/testis genes. Mol Oncol 2021; 15:3003-3023. [PMID: 33426787 PMCID: PMC8564638 DOI: 10.1002/1878-0261.12900] [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: 07/20/2020] [Revised: 11/19/2020] [Accepted: 12/24/2020] [Indexed: 11/14/2022] Open
Abstract
Cancer/Testis (CT) genes are induced in germ cells, repressed in somatic cells, and derepressed in somatic tumors, where these genes can contribute to cancer progression. CT gene identification requires data obtained using standardized protocols and technologies. This is a challenge because data for germ cells, gonads, normal somatic tissues, and a wide range of cancer samples stem from multiple sources and were generated over substantial periods of time. We carried out a GeneChip‐based RNA profiling analysis using our own data for testis and enriched germ cells, data for somatic cancers from the Expression Project for Oncology, and data for normal somatic tissues from the Gene Omnibus Repository. We identified 478 candidate loci that include known CT genes, numerous genes associated with oncogenic processes, and novel candidates that are not referenced in the Cancer/Testis Database (www.cta.lncc.br). We complemented RNA expression data at the protein level for SPESP1, GALNTL5, PDCL2, and C11orf42 using cancer tissue microarrays covering malignant tumors of breast, uterus, thyroid, and kidney, as well as published RNA profiling and immunohistochemical data provided by the Human Protein Atlas (www.proteinatlas.org). We report that combined RNA/tissue profiling identifies novel CT genes that may be of clinical interest as therapeutical targets or biomarkers. Our findings also highlight the challenges of detecting truly germ cell‐specific mRNAs and the proteins they encode in highly heterogenous testicular, somatic, and tumor tissues.
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Affiliation(s)
- Soazik P Jamin
- Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S, Univ Rennes, France
| | - Feria Hikmet
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Sweden
| | - Romain Mathieu
- Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S, Univ Rennes, France.,Department of Urology, University Hospital, Rennes, France
| | - Bernard Jégou
- Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S, Univ Rennes, France
| | - Cecilia Lindskog
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Sweden
| | - Frédéric Chalmel
- Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S, Univ Rennes, France
| | - Michael Primig
- Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S, Univ Rennes, France
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Rolland AD, Evrard B, Darde TA, Le Béguec C, Le Bras Y, Bensalah K, Lavoué S, Jost B, Primig M, Dejucq-Rainsford N, Chalmel F, Jégou B. RNA profiling of human testicular cells identifies syntenic lncRNAs associated with spermatogenesis. Hum Reprod 2020; 34:1278-1290. [PMID: 31247106 DOI: 10.1093/humrep/dez063] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 03/15/2019] [Indexed: 12/15/2022] Open
Abstract
STUDY QUESTION Is the noncoding transcriptional landscape during spermatogenesis conserved between human and rodents? SUMMARY ANSWER We identified a core group of 113 long noncoding RNAs (lncRNAs) and 20 novel genes dynamically and syntenically transcribed during spermatogenesis. WHAT IS KNOWN ALREADY Spermatogenesis is a complex differentiation process driven by a tightly regulated and highly specific gene expression program. Recently, several studies in various species have established that a large proportion of known lncRNAs are preferentially expressed during meiosis and spermiogenesis in a testis-specific manner. STUDY DESIGN, SIZE, DURATION To further investigate lncRNA expression in human spermatogenesis, we carried out a cross-species RNA profiling study using isolated testicular cells. PARTICIPANTS/MATERIALS, SETTING, METHODS Human testes were obtained from post-mortem donors (N = 8, 51 years old on average) or from prostate cancer patients with no hormonal treatment (N = 9, 80 years old on average) and only patients with full spermatogenesis were used to prepare enriched populations of spermatocytes, spermatids, Leydig cells, peritubular cells and Sertoli cells. To minimize potential biases linked to inter-patient variations, RNAs from two or three donors were pooled prior to RNA-sequencing (paired-end, strand-specific). Resulting reads were mapped to the human genome, allowing for assembly and quantification of corresponding transcripts. MAIN RESULTS AND THE ROLE OF CHANCE Our RNA-sequencing analysis of pools of isolated human testicular cells enabled us to reconstruct over 25 000 transcripts. Among them we identified thousands of lncRNAs, as well as many previously unidentified genes (novel unannotated transcripts) that share many properties of lncRNAs. Of note is that although noncoding genes showed much lower synteny than protein-coding ones, a significant fraction of syntenic lncRNAs displayed conserved expression during spermatogenesis. LARGE SCALE DATA Raw data files (fastq) and a searchable table (.xlss) containing information on genomic features and expression data for all refined transcripts have been submitted to the NCBI Gene Expression Omnibus under accession number GSE74896. LIMITATIONS, REASONS FOR CAUTION Isolation procedures may alter the physiological state of testicular cells, especially for somatic cells, leading to substantial changes at the transcriptome level. We therefore cross-validated our findings with three previously published transcriptomic analyses of human spermatogenesis. Despite the use of stringent filtration criteria, i.e. expression cut-off of at least three fragments per kilobase of exon model per million reads mapped, fold-change of at least three and false discovery rate adjusted P-values of less than <1%, the possibility of assembly artifacts and false-positive transcripts cannot be fully ruled out. WIDER IMPLICATIONS OF THE FINDINGS For the first time, this study has led to the identification of a large number of conserved germline-associated lncRNAs that are potentially important for spermatogenesis and sexual reproduction. In addition to further substantiating the basis of the human testicular physiology, our study provides new candidate genes for male infertility of genetic origin. This is likely to be relevant for identifying interesting diagnostic and prognostic biomarkers and also potential novel therapeutic targets for male contraception. STUDY FUNDING/COMPETING INTEREST(S) This work was supported by l'Institut national de la santé et de la recherche médicale (Inserm); l'Université de Rennes 1; l'Ecole des hautes études en santé publique (EHESP); INERIS-STORM to B.J. [N 10028NN]; Rennes Métropole 'Défis scientifiques émergents' to F.C (2011) and A.D.R (2013). The authors have no competing financial interests.
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Affiliation(s)
- A D Rolland
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail)-UMR_S1085, Rennes, France
| | - B Evrard
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail)-UMR_S1085, Rennes, France
| | - T A Darde
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail)-UMR_S1085, Rennes, France.,Univ Rennes, Inria, CNRS, IRISA, Rennes, France
| | - C Le Béguec
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail)-UMR_S1085, Rennes, France
| | - Y Le Bras
- Univ Rennes, Inria, CNRS, IRISA, Rennes, France
| | - K Bensalah
- Urology Department, University of Rennes, Rennes, France
| | - S Lavoué
- Unité de Coordination Hospitalière des Prélèvements d'organes et de Tissus, Centre Hospitalier Universitaire de Rennes, Rennes, France
| | - B Jost
- Plateforme GenomEast-Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964, CNRS UMR 7104, Université de Strasbourg, Illkirch, France
| | - M Primig
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail)-UMR_S1085, Rennes, France
| | - N Dejucq-Rainsford
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail)-UMR_S1085, Rennes, France
| | - F Chalmel
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail)-UMR_S1085, Rennes, France
| | - B Jégou
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail)-UMR_S1085, Rennes, France
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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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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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Debaize L, Jakobczyk H, Avner S, Gaudichon J, Rio AG, Sérandour AA, Dorsheimer L, Chalmel F, Carroll JS, Zörnig M, Rieger MA, Delalande O, Salbert G, Galibert MD, Gandemer V, Troadec MB. Interplay between transcription regulators RUNX1 and FUBP1 activates an enhancer of the oncogene c-KIT and amplifies cell proliferation. Nucleic Acids Res 2018; 46:11214-11228. [PMID: 30500954 PMCID: PMC6265458 DOI: 10.1093/nar/gky756] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 08/07/2018] [Accepted: 08/10/2018] [Indexed: 12/31/2022] Open
Abstract
Runt-related transcription factor 1 (RUNX1) is a well-known master regulator of hematopoietic lineages but its mechanisms of action are still not fully understood. Here, we found that RUNX1 localizes on active chromatin together with Far Upstream Binding Protein 1 (FUBP1) in human B-cell precursor lymphoblasts, and that both factors interact in the same transcriptional regulatory complex. RUNX1 and FUBP1 chromatin localization identified c-KIT as a common target gene. We characterized two regulatory regions, at +700 bp and +30 kb within the first intron of c-KIT, bound by both RUNX1 and FUBP1, and that present active histone marks. Based on these regions, we proposed a novel FUBP1 FUSE-like DNA-binding sequence on the +30 kb enhancer. We demonstrated that FUBP1 and RUNX1 cooperate for the regulation of the expression of the oncogene c-KIT. Notably, upregulation of c-KIT expression by FUBP1 and RUNX1 promotes cell proliferation and renders cells more resistant to the c-KIT inhibitor imatinib mesylate, a common therapeutic drug. These results reveal a new mechanism of action of RUNX1 that implicates FUBP1, as a facilitator, to trigger transcriptional regulation of c-KIT and to regulate cell proliferation. Deregulation of this regulatory mechanism may explain some oncogenic function of RUNX1 and FUBP1.
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Affiliation(s)
- Lydie Debaize
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) – UMR 6290, F-35000 Rennes, France
| | - Hélène Jakobczyk
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) – UMR 6290, F-35000 Rennes, France
| | - Stéphane Avner
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) – UMR 6290, F-35000 Rennes, France
| | - Jérémie Gaudichon
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) – UMR 6290, F-35000 Rennes, France
| | - Anne-Gaëlle Rio
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) – UMR 6290, F-35000 Rennes, France
| | - Aurélien A Sérandour
- CRCINA, INSERM, CNRS, Université d’Angers, Université de Nantes, 44035 Nantes, France
- Ecole Centrale de Nantes, Nantes, France
| | - Lena Dorsheimer
- Department of Medicine, Hematology/Oncology, Goethe University Frankfurt, Frankfurt, Germany
| | - Frédéric Chalmel
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) – UMR_S 1085, F-35000 Rennes, France
| | - Jason S Carroll
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Martin Zörnig
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, D-60528 Frankfurt, Germany
| | - Michael A Rieger
- Department of Medicine, Hematology/Oncology, Goethe University Frankfurt, Frankfurt, Germany
| | - Olivier Delalande
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) – UMR 6290, F-35000 Rennes, France
| | - Gilles Salbert
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) – UMR 6290, F-35000 Rennes, France
| | - Marie-Dominique Galibert
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) – UMR 6290, F-35000 Rennes, France
- Génétique Somatique des Cancers, Centre Hospitalier Universitaire, 35033 Rennes, France
| | - Virginie Gandemer
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) – UMR 6290, F-35000 Rennes, France
- Department of pediatric oncohematology, Centre Hospitalier Universitaire, 35203 Rennes, France
| | - Marie-Bérengère Troadec
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) – UMR 6290, F-35000 Rennes, France
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35
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Lecluze E, Jégou B, Rolland AD, Chalmel F. New transcriptomic tools to understand testis development and functions. Mol Cell Endocrinol 2018; 468:47-59. [PMID: 29501799 DOI: 10.1016/j.mce.2018.02.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 02/26/2018] [Accepted: 02/27/2018] [Indexed: 12/16/2022]
Abstract
The testis plays a central role in the male reproductive system - secreting several hormones including male steroids and producing male gametes. A complex and coordinated molecular program is required for the proper differentiation of testicular cell types and maintenance of their functions in adulthood. The testicular transcriptome displays the highest levels of complexity and specificity across all tissues in a wide range of species. Many studies have used high-throughput sequencing technologies to define the molecular dynamics and regulatory networks in the testis as well as to identify novel genes or gene isoforms expressed in this organ. This review intends to highlight the complementarity of these transcriptomic studies and to show how the use of different sequencing protocols contribute to improve our global understanding of testicular biology.
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Affiliation(s)
- Estelle Lecluze
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, Environnement et travail) - UMR_S1085, F-35000 Rennes, France
| | - Bernard Jégou
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, Environnement et travail) - UMR_S1085, F-35000 Rennes, France
| | - Antoine D Rolland
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, Environnement et travail) - UMR_S1085, F-35000 Rennes, France
| | - Frédéric Chalmel
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, Environnement et travail) - UMR_S1085, F-35000 Rennes, France.
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36
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Bonvallot N, David A, Chalmel F, Chevrier C, Cordier S, Cravedi JP, Zalko D. Metabolomics as a powerful tool to decipher the biological effects of environmental contaminants in humans. Current Opinion in Toxicology 2018. [DOI: 10.1016/j.cotox.2017.12.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Abstract
About 1-6% of the genetic ancestry of modern humans today originates from admixture with archaic humans. It has recently been shown that autosomal genomic regions with a reduced proportion of Neanderthal and Denisovan ancestries (NA and DA) are significantly enriched in genes that are more expressed in testis than in other tissues. To determine whether a cellular segregation pattern would exist, we combined maps of archaic introgression with a cross-analysis of three transcriptomic datasets deciphering the transcriptional landscape of human gonadal cell types. We reveal that the regions deficient in both NA and DA contain a significant enrichment of genes transcribed in meiotic germ cells. The interbreeding of anatomically modern humans with archaic humans may have introduced archaic-derived alleles that contributed to genetic incompatibilities affecting meiosis that were subsequently purged by natural selection.
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Affiliation(s)
- B Jégou
- Inserm U1085-IRSET, Université de Rennes 1, Rennes, France.,Université Sorbonne Paris Cité (USPC), Paris, France.,EHESP - School of Public Health, Rennes, France
| | - S Sankararaman
- Department of Computer Science, UCLA, Los Angeles, CA.,Department of Human Genetics, UCLA, Los Angeles, CA
| | - A D Rolland
- Inserm U1085-IRSET, Université de Rennes 1, Rennes, France
| | - D Reich
- Department of Genetics, Harvard Medical School, Boston, MA.,Broad Institute of Harvard and MIT, Cambridge, MA.,Harvard Medical School, Howard Hughes Medical Institute, Boston, MA
| | - F Chalmel
- Inserm U1085-IRSET, Université de Rennes 1, Rennes, France
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Darde TA, Gaudriault P, Beranger R, Lancien C, Caillarec-Joly A, Sallou O, Bonvallot N, Chevrier C, Mazaud-Guittot S, Jégou B, Collin O, Becker E, Rolland AD, Chalmel F. TOXsIgN: a cross-species repository for toxicogenomic signatures. Bioinformatics 2018; 34:2116-2122. [DOI: 10.1093/bioinformatics/bty040] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 01/24/2018] [Indexed: 02/02/2023] Open
Affiliation(s)
- Thomas A Darde
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S1085, F-35000 Rennes, France
- Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA/INRIA) – GenOuest Platform, Université de Rennes 1, F-35042 Rennes, France
| | - Pierre Gaudriault
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S1085, F-35000 Rennes, France
| | - Rémi Beranger
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S1085, F-35000 Rennes, France
| | - Clément Lancien
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S1085, F-35000 Rennes, France
| | - Annaëlle Caillarec-Joly
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S1085, F-35000 Rennes, France
| | - Olivier Sallou
- Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA/INRIA) – GenOuest Platform, Université de Rennes 1, F-35042 Rennes, France
| | - Nathalie Bonvallot
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S1085, F-35000 Rennes, France
| | - Cécile Chevrier
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S1085, F-35000 Rennes, France
| | - Séverine Mazaud-Guittot
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S1085, F-35000 Rennes, France
| | - Bernard Jégou
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S1085, F-35000 Rennes, France
| | - Olivier Collin
- Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA/INRIA) – GenOuest Platform, Université de Rennes 1, F-35042 Rennes, France
| | - Emmanuelle Becker
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S1085, F-35000 Rennes, France
| | - Antoine D Rolland
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S1085, F-35000 Rennes, France
| | - Frédéric Chalmel
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S1085, F-35000 Rennes, France
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Jumeau F, Chalmel F, Fernandez-Gomez FJ, Carpentier C, Obriot H, Tardivel M, Caillet-Boudin ML, Rigot JM, Rives N, Buée L, Sergeant N, Mitchell V. Defining the human sperm microtubulome: an integrated genomics approach. Biol Reprod 2017; 96:93-106. [PMID: 28395323 DOI: 10.1095/biolreprod.116.143479] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [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: 07/19/2016] [Accepted: 11/10/2016] [Indexed: 11/01/2022] Open
Abstract
Sperm motility notably depends on the structural integrity of the flagellum and the regulation of microtubule dynamics. Although researchers have started to use "omics" techniques to characterize the human sperm's molecular landscape, the constituents responsible for the assembly, organization, and dynamics of the flagellum microtubule have yet to be fully defined. In this study, we defined a core set of 116 gene products associated with the human sperm microtubulome (including products potentially involved in abnormal ciliary phenotypes and male infertility disorders). To this end, we designed and applied an integrated genomics workflow and combined relevant proteomics, transcriptomics, and interactomics datasets to reconstruct a dynamic interactome map. By further integrating phenotypic information, we defined a disease-interaction network; this enabled us to highlight a number of novel factors potentially associated with altered sperm motility and male fertility. Lastly, we experimentally validated the expression pattern of two candidate genes (CUL3 and DCDC2C) that had never previously been associated with male germline differentiation. Our analysis suggested that CUL3 and DCDC2C's products have important roles in the sperm flagellum. Taken as a whole, our results demonstrate that an integrated genomics strategy can highlight relevant molecular factors in specific sperm components. This approach could be easily extended by including other "omics" data (from asthenozoospermic men, for example) and identifying other critical proteins from the human sperm microtubulome.
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Affiliation(s)
- Fanny Jumeau
- EA 4308, Department of Reproductive Biology and Spermiology-CECOS, Lille University Medical Center, Lille, France.,INSERM UMR 837-1, Alzheimer & Tauopathies, Jean-Pierre Aubert Research Center, Lille, France
| | - Frédéric Chalmel
- INSERM U1085-IRSET, 9 avenue du Professeur Léon Bernard, Rennes, France
| | | | - Céline Carpentier
- INSERM UMR 837-1, Alzheimer & Tauopathies, Jean-Pierre Aubert Research Center, Lille, France
| | - Hélène Obriot
- INSERM UMR 837-1, Alzheimer & Tauopathies, Jean-Pierre Aubert Research Center, Lille, France
| | - Meryem Tardivel
- BioImaging Center Lille-Nord de France, School of Medicine, University of Lille 2, Lille, France
| | | | - Jean-Marc Rigot
- EA 4308, Andrology Unit, Lille University Medical Center, Lille, France
| | - Nathalie Rives
- EA 4308, Reproductive Biology Laboratory-CECOS, Rouen University Medical Center, and Institute for Biomedical Research, University of Rouen, Rouen, France
| | - Luc Buée
- INSERM UMR 837-1, Alzheimer & Tauopathies, Jean-Pierre Aubert Research Center, Lille, France
| | - Nicolas Sergeant
- INSERM UMR 837-1, Alzheimer & Tauopathies, Jean-Pierre Aubert Research Center, Lille, France
| | - Valérie Mitchell
- EA 4308, Department of Reproductive Biology and Spermiology-CECOS, Lille University Medical Center, Lille, France
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40
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Beaumont M, Dagher J, Dugay F, Kammerer-Jacquet S, Becker E, Cornevin L, Jaillard S, Mathieu R, Chalmel F, Bensalah K, Rioux-Leclercq N, Belaud-Rotureau M. Étude comparative des profils génétiques des métastases de carcinomes rénaux à cellules claires. Prog Urol 2017. [DOI: 10.1016/j.purol.2017.07.216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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41
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Dumont L, Chalmel F, Oblette A, Berby B, Rives A, Duchesne V, Rondanino C, Rives N. Evaluation of apoptotic- and autophagic-related protein expressions before and after IVM of fresh, slow-frozen and vitrified pre-pubertal mouse testicular tissue. Mol Hum Reprod 2017; 23:738-754. [DOI: 10.1093/molehr/gax054] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 10/09/2017] [Indexed: 12/12/2022] Open
Affiliation(s)
- L Dumont
- Normandie Univ, UNIROUEN, EA 4308 ‘Gametogenesis and Gamete Quality’, Rouen University Hospital, Department of Reproductive Biology—CECOS, F 76000 Rouen, France
- Institute for Research and Innovation in Biomedicine (IRIB), France
| | - F Chalmel
- Inserm U1085-IRSET, Université de Rennes 1, Rennes, France
| | - A Oblette
- Normandie Univ, UNIROUEN, EA 4308 ‘Gametogenesis and Gamete Quality’, Rouen University Hospital, Department of Reproductive Biology—CECOS, F 76000 Rouen, France
- Institute for Research and Innovation in Biomedicine (IRIB), France
| | - B Berby
- Normandie Univ, UNIROUEN, EA 4308 ‘Gametogenesis and Gamete Quality’, Rouen University Hospital, Department of Reproductive Biology—CECOS, F 76000 Rouen, France
- Institute for Research and Innovation in Biomedicine (IRIB), France
| | - A Rives
- Normandie Univ, UNIROUEN, EA 4308 ‘Gametogenesis and Gamete Quality’, Rouen University Hospital, Department of Reproductive Biology—CECOS, F 76000 Rouen, France
- Institute for Research and Innovation in Biomedicine (IRIB), France
| | - V Duchesne
- Normandie Univ, UNIROUEN, EA 4308 ‘Gametogenesis and Gamete Quality’, Rouen University Hospital, Department of Reproductive Biology—CECOS, F 76000 Rouen, France
- Institute for Research and Innovation in Biomedicine (IRIB), France
| | - C Rondanino
- Normandie Univ, UNIROUEN, EA 4308 ‘Gametogenesis and Gamete Quality’, Rouen University Hospital, Department of Reproductive Biology—CECOS, F 76000 Rouen, France
- Institute for Research and Innovation in Biomedicine (IRIB), France
| | - N Rives
- Normandie Univ, UNIROUEN, EA 4308 ‘Gametogenesis and Gamete Quality’, Rouen University Hospital, Department of Reproductive Biology—CECOS, F 76000 Rouen, France
- Institute for Research and Innovation in Biomedicine (IRIB), France
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Mahé EA, Madigou T, Sérandour AA, Bizot M, Avner S, Chalmel F, Palierne G, Métivier R, Salbert G. Cytosine modifications modulate the chromatin architecture of transcriptional enhancers. Genome Res 2017; 27:947-958. [PMID: 28396520 PMCID: PMC5453328 DOI: 10.1101/gr.211466.116] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 04/05/2017] [Indexed: 12/19/2022]
Abstract
Epigenetic mechanisms are believed to play key roles in the establishment of cell-specific transcription programs. Accordingly, the modified bases 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) have been observed in DNA of genomic regulatory regions such as enhancers, and oxidation of 5mC into 5hmC by Ten-eleven translocation (TET) proteins correlates with enhancer activation. However, the functional relationship between cytosine modifications and the chromatin architecture of enhancers remains elusive. To gain insights into their function, 5mC and 5hmC levels were perturbed by inhibiting DNA methyltransferases and TETs during differentiation of mouse embryonal carcinoma cells into neural progenitors, and chromatin characteristics of enhancers bound by the pioneer transcription factors FOXA1, MEIS1, and PBX1 were interrogated. In a large fraction of the tested enhancers, inhibition of DNA methylation was associated with a significant increase in monomethylation of H3K4, a characteristic mark of enhancer priming. In addition, at some specific enhancers, 5mC oxidation by TETs facilitated chromatin opening, a process that may stabilize MEIS1 binding to these genomic regions.
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Affiliation(s)
- Elise A Mahé
- CNRS UMR6290, Equipe SP@RTE, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, 35042 Rennes Cedex, France.,Université de Rennes 1, Campus de Beaulieu, 35042 Rennes Cedex, France
| | - Thierry Madigou
- CNRS UMR6290, Equipe SP@RTE, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, 35042 Rennes Cedex, France.,Université de Rennes 1, Campus de Beaulieu, 35042 Rennes Cedex, France
| | | | - Maud Bizot
- CNRS UMR6290, Equipe SP@RTE, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, 35042 Rennes Cedex, France.,Université de Rennes 1, Campus de Beaulieu, 35042 Rennes Cedex, France
| | - Stéphane Avner
- CNRS UMR6290, Equipe SP@RTE, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, 35042 Rennes Cedex, France.,Université de Rennes 1, Campus de Beaulieu, 35042 Rennes Cedex, France
| | - Frédéric Chalmel
- Inserm U1085-IRSET, Université de Rennes 1, F-35042 Rennes, France
| | - Gaëlle Palierne
- CNRS UMR6290, Equipe SP@RTE, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, 35042 Rennes Cedex, France.,Université de Rennes 1, Campus de Beaulieu, 35042 Rennes Cedex, France
| | - Raphaël Métivier
- CNRS UMR6290, Equipe SP@RTE, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, 35042 Rennes Cedex, France.,Université de Rennes 1, Campus de Beaulieu, 35042 Rennes Cedex, France
| | - Gilles Salbert
- CNRS UMR6290, Equipe SP@RTE, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, 35042 Rennes Cedex, France.,Université de Rennes 1, Campus de Beaulieu, 35042 Rennes Cedex, France
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43
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Borowiec AS, Sion B, Chalmel F, D Rolland A, Lemonnier L, De Clerck T, Bokhobza A, Derouiche S, Dewailly E, Slomianny C, Mauduit C, Benahmed M, Roudbaraki M, Jégou B, Prevarskaya N, Bidaux G. Cold/menthol TRPM8 receptors initiate the cold-shock response and protect germ cells from cold-shock-induced oxidation. FASEB J 2016; 30:3155-70. [PMID: 27317670 PMCID: PMC5001517 DOI: 10.1096/fj.201600257r] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 05/23/2016] [Indexed: 12/21/2022]
Abstract
Testes of most male mammals present the particularity of being externalized from the body and are consequently slightly cooler than core body temperature (4-8°C below). Although, hypothermia of the testis is known to increase germ cells apoptosis, little is known about the underlying molecular mechanisms, including cold sensors, transduction pathways, and apoptosis triggers. In this study, using a functional knockout mouse model of the cold and menthol receptors, dubbed transient receptor potential melastatine 8 (TRPM8) channels, we found that TRPM8 initiated the cold-shock response by differentially modulating cold- and heat-shock proteins. Besides, apoptosis of germ cells increased in proportion to the cooling level in control mice but was independent of temperature in knockout mice. We also observed that the rate of germ cell death correlated positively with the reactive oxygen species level and negatively with the expression of the detoxifying enzymes. This result suggests that the TRPM8 sensor is a key determinant of germ cell fate under hypothermic stimulation.-Borowiec, A.-S., Sion, B., Chalmel, F., Rolland, A. D., Lemonnier, L., De Clerck, T., Bokhobza, A., Derouiche, S., Dewailly, E., Slomianny, C., Mauduit, C., Benahmed, M., Roudbaraki, M., Jégou, B., Prevarskaya, N., Bidaux, G. Cold/menthol TRPM8 receptors initiate the cold-shock response and protect germ cells from cold-shock-induced oxidation.
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Affiliation(s)
| | - Benoit Sion
- Pharmacologie Fondamentale et Clinique de la Douleur, INSERM, U1107, Neuro-Dol, Clermont Université, Université d'Auvergne, Clermont-Ferrand, France
| | | | | | - Loïc Lemonnier
- Physiologie Cellulaire (PHYCEL), INSERM, U1003, Université Lille, Lille, France
| | - Tatiana De Clerck
- Physiologie Cellulaire (PHYCEL), INSERM, U1003, Université Lille, Lille, France
| | - Alexandre Bokhobza
- Physiologie Cellulaire (PHYCEL), INSERM, U1003, Université Lille, Lille, France
| | - Sandra Derouiche
- Physiologie Cellulaire (PHYCEL), INSERM, U1003, Université Lille, Lille, France
| | - Etienne Dewailly
- Physiologie Cellulaire (PHYCEL), INSERM, U1003, Université Lille, Lille, France
| | - Christian Slomianny
- Physiologie Cellulaire (PHYCEL), INSERM, U1003, Université Lille, Lille, France
| | - Claire Mauduit
- Centre Méditerranéen de Médecine Moléculaire (C3M), Team 5, INSERM, U1065, Nice, France; and
| | - Mohamed Benahmed
- Centre Méditerranéen de Médecine Moléculaire (C3M), Team 5, INSERM, U1065, Nice, France; and
| | - Morad Roudbaraki
- Physiologie Cellulaire (PHYCEL), INSERM, U1003, Université Lille, Lille, France
| | - Bernard Jégou
- INSERM, U1085-Irset, Campus de Beaulieu, Rennes, France
| | - Natalia Prevarskaya
- Physiologie Cellulaire (PHYCEL), INSERM, U1003, Université Lille, Lille, France
| | - Gabriel Bidaux
- Physiologie Cellulaire (PHYCEL), INSERM, U1003, Université Lille, Lille, France; Laboratoire de Physique des Lasers, Atomes et Molécules (PhLAM), UMR8523, Biophotonic Team, Villeneuve d'Ascq, France
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44
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Abstract
Spermatogenesis is a complex and tightly regulated process leading to the continuous production of male gametes, the spermatozoa. This developmental process requires the sequential and coordinated expression of thousands of genes, including many that are testis-specific. The molecular networks underlying normal and pathological spermatogenesis have been widely investigated in recent decades, and many high-throughput expression studies have studied genes and proteins involved in male fertility. In this review, we focus on studies that have attempted to correlate transcription and translation during spermatogenesis by comparing the testicular transcriptome and proteome. We also discuss the recent development and use of new transcriptomic approaches that provide a better proxy for the proteome, from both qualitative and quantitative perspectives. Finally, we provide illustrations of how testis-derived transcriptomic and proteomic data can be integrated to address new questions and how the 'proteomics informed by transcriptomics' technique, by combining RNA-seq and MS-based proteomics, can contribute significantly to the discovery of new protein-coding genes or new protein isoforms expressed during spermatogenesis.
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Affiliation(s)
- Frédéric Chalmel
- Inserm U1085-IrsetUniversité de Rennes 1, F-35042 Rennes, France
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45
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Sallou O, Duek PD, Darde TA, Collin O, Lane L, Chalmel F. PepPSy: a web server to prioritize gene products in experimental and biocuration workflows. Database (Oxford) 2016; 2016:baw070. [PMID: 27173522 PMCID: PMC4865363 DOI: 10.1093/database/baw070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 04/13/2016] [Indexed: 12/03/2022]
Abstract
Among the 20 000 human gene products predicted from genome annotation, about 3000 still lack validation at protein level. We developed PepPSy, a user-friendly gene expression-based prioritization system, to help investigators to determine in which human tissues they should look for an unseen protein. PepPSy can also be used by biocurators to revisit the annotation of specific categories of proteins based on the ‘omics’ data housed by the system. In this study, it was used to prioritize 21 dubious protein-coding genes among the 616 annotated in neXtProt for reannotation. PepPSy is freely available at http://peppsy.genouest.org. Database URL:http://peppsy.genouest.org.
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Affiliation(s)
- Olivier Sallou
- Genouest Bioinformatics Platform, IRISA, Campus de Beaulieu, Rennes 35042, France
| | - Paula D Duek
- CALIPHO Group, SIB Swiss Institute of Bioinformatics, CMU, Michel Servet 1, Geneva 1211, Switzerland
| | - Thomas A Darde
- Genouest Bioinformatics Platform, IRISA, Campus de Beaulieu, Rennes 35042, France IRSET, Inserm U1085, 9 avenue du Professeur Léon Bernard, Rennes 35000, France
| | - Olivier Collin
- Genouest Bioinformatics Platform, IRISA, Campus de Beaulieu, Rennes 35042, France
| | - Lydie Lane
- CALIPHO Group, SIB Swiss Institute of Bioinformatics, CMU, Michel Servet 1, Geneva 1211, Switzerland Department of Human Protein Sciences, Faculty of Medicine, University of Geneva, CMU, Michel Servet 1, Geneva 1211, Switzerland
| | - Frédéric Chalmel
- IRSET, Inserm U1085, 9 avenue du Professeur Léon Bernard, Rennes 35000, France
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46
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Korhonen HM, Yadav RP, Da Ros M, Chalmel F, Zimmermann C, Toppari J, Nef S, Kotaja N. DICER Regulates the Formation and Maintenance of Cell-Cell Junctions in the Mouse Seminiferous Epithelium. Biol Reprod 2015; 93:139. [PMID: 26510868 DOI: 10.1095/biolreprod.115.131938] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 10/26/2015] [Indexed: 01/09/2023] Open
Abstract
The endonuclease DICER that processes micro-RNAs and small interfering RNAs is essential for normal spermatogenesis and male fertility. We previously showed that the deletion of Dicer1 gene in postnatal spermatogonia in mice using Ngn3 promoter-driven Cre expression caused severe defects in the morphogenesis of haploid spermatid to mature spermatozoon, including problems in cell polarization and nuclear elongation. In this study, we further analyzed the same mouse model and revealed that absence of functional DICER in differentiating male germ cells induces disorganization of the cell-cell junctions in the seminiferous epithelium. We detected discontinuous and irregular apical ectoplasmic specializations between elongating spermatids and Sertoli cells. The defective anchoring of spermatids to Sertoli cells caused a premature release of spermatids into the lumen. Our findings may help also explain the abnormal elongation process of remaining spermatids because these junctions and the correct positioning of germ cells in the epithelium are critically important for the progression of spermiogenesis. Interestingly, cell adhesion-related genes were generally upregulated in Dicer1 knockout germ cells. Claudin 5 ( Cldn5 ) was among the most upregulated genes and we show that the polarized localization of CLAUDIN5 in the apical ectoplasmic specializations was lost in Dicer1 knockout spermatids. Our results suggest that DICER-dependent pathways control the formation and organization of cell-cell junctions in the seminiferous epithelium via the regulation of cell adhesion-related genes.
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Affiliation(s)
- Hanna Maria Korhonen
- Institute of Biomedicine, Department of Physiology, University of Turku, Turku, Finland
| | - Ram Prakash Yadav
- Institute of Biomedicine, Department of Physiology, University of Turku, Turku, Finland
| | - Matteo Da Ros
- Institute of Biomedicine, Department of Physiology, University of Turku, Turku, Finland
| | | | - Céline Zimmermann
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland iGE3, Institute of Genetics and Genomics of Geneva, University of Geneva, Geneva, Switzerland
| | - Jorma Toppari
- Institute of Biomedicine, Department of Physiology, University of Turku, Turku, Finland Department of Pediatrics, University of Turku, Turku, Finland
| | - Serge Nef
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland iGE3, Institute of Genetics and Genomics of Geneva, University of Geneva, Geneva, Switzerland
| | - Noora Kotaja
- Institute of Biomedicine, Department of Physiology, University of Turku, Turku, Finland
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47
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Darde TA, Sallou O, Becker E, Evrard B, Monjeaud C, Le Bras Y, Jégou B, Collin O, Rolland AD, Chalmel F. The ReproGenomics Viewer: an integrative cross-species toolbox for the reproductive science community. Nucleic Acids Res 2015; 43:W109-16. [PMID: 25883147 PMCID: PMC4489245 DOI: 10.1093/nar/gkv345] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 04/06/2015] [Indexed: 12/23/2022] Open
Abstract
We report the development of the ReproGenomics Viewer (RGV), a multi- and cross-species working environment for the visualization, mining and comparison of published omics data sets for the reproductive science community. The system currently embeds 15 published data sets related to gametogenesis from nine model organisms. Data sets have been curated and conveniently organized into broad categories including biological topics, technologies, species and publications. RGV's modular design for both organisms and genomic tools enables users to upload and compare their data with that from the data sets embedded in the system in a cross-species manner. The RGV is freely available at http://rgv.genouest.org.
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Affiliation(s)
- Thomas A Darde
- Inserm U1085-Irset, Université de Rennes 1, F-35042 Rennes, France Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA/INRIA) - GenOuest platform, Université de Rennes 1, F-35042 Rennes, France
| | - Olivier Sallou
- Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA/INRIA) - GenOuest platform, Université de Rennes 1, F-35042 Rennes, France
| | | | - Bertrand Evrard
- Inserm U1085-Irset, Université de Rennes 1, F-35042 Rennes, France
| | - Cyril Monjeaud
- Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA/INRIA) - GenOuest platform, Université de Rennes 1, F-35042 Rennes, France
| | - Yvan Le Bras
- Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA/INRIA) - GenOuest platform, Université de Rennes 1, F-35042 Rennes, France
| | - Bernard Jégou
- Inserm U1085-Irset, Université de Rennes 1, F-35042 Rennes, France Ecole des Hautes Études en Santé Publique, Avenue du Professeur Léon-Bernard, F-35043 Rennes, France
| | - Olivier Collin
- Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA/INRIA) - GenOuest platform, Université de Rennes 1, F-35042 Rennes, France
| | | | - Frédéric Chalmel
- Inserm U1085-Irset, Université de Rennes 1, F-35042 Rennes, France
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48
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Zimmermann C, Stévant I, Borel C, Conne B, Pitetti JL, Calvel P, Kaessmann H, Jégou B, Chalmel F, Nef S. Research resource: the dynamic transcriptional profile of sertoli cells during the progression of spermatogenesis. Mol Endocrinol 2015; 29:627-42. [PMID: 25710594 DOI: 10.1210/me.2014-1356] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Sertoli cells (SCs), the only somatic cells within seminiferous tubules, associate intimately with developing germ cells. They not only provide physical and nutritional support but also secrete factors essential to the complex developmental processes of germ cell proliferation and differentiation. The SC transcriptome must therefore adapt rapidly during the different stages of spermatogenesis. We report comprehensive genome-wide expression profiles of pure populations of SCs isolated at 5 distinct stages of the first wave of mouse spermatogenesis, using RNA sequencing technology. We were able to reconstruct about 13 901 high-confidence, nonredundant coding and noncoding transcripts, characterized by complex alternative splicing patterns with more than 45% comprising novel isoforms of known genes. Interestingly, roughly one-fifth (2939) of these genes exhibited a dynamic expression profile reflecting the evolving role of SCs during the progression of spermatogenesis, with stage-specific expression of genes involved in biological processes such as cell cycle regulation, metabolism and energy production, retinoic acid synthesis, and blood-testis barrier biogenesis. Finally, regulatory network analysis identified the transcription factors endothelial PAS domain-containing protein 1 (EPAS1/Hif2α), aryl hydrocarbon receptor nuclear translocator (ARNT/Hif1β), and signal transducer and activator of transcription 1 (STAT1) as potential master regulators driving the SC transcriptional program. Our results highlight the plastic transcriptional landscape of SCs during the progression of spermatogenesis and provide valuable resources to better understand SC function and spermatogenesis and its related disorders, such as male infertility.
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Affiliation(s)
- Céline Zimmermann
- Department of Genetic Medicine and Development (C.Z., I.S., C.B., B.C., J.-L.P., P.C., S.N.), University of Geneva Medical School, 1211 Geneva 4, Switzerland; Center for Integrative Genomics (H.K.), University of Lausanne, Génopode, CH-1015 Lausanne, Switzerland; and Inserm U1085-IRSET (B.J., F.C.), Université de Rennes 1, Campus de Beaulieu, F-35042 Rennes, France
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49
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Petit FG, Kervarrec C, Jamin SP, Smagulova F, Hao C, Becker E, Jégou B, Chalmel F, Primig M. Combining RNA and protein profiling data with network interactions identifies genes associated with spermatogenesis in mouse and human. Biol Reprod 2015; 92:71. [PMID: 25609838 DOI: 10.1095/biolreprod.114.126250] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [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: 11/01/2022] Open
Abstract
Genome-wide RNA profiling studies have identified hundreds of transcripts that are highly expressed in mammalian male germ cells, including many that are undetectable in somatic control tissues. Among them, genes important for spermatogenesis are significantly enriched. Information about mRNAs and their cognate proteins facilitates the identification of novel conserved target genes for functional studies in the mouse. By inspecting genome-wide RNA profiling data, we manually selected 81 genes for which RNA is detected almost exclusively in the human male germline and, in most cases, in rodent testicular germ cells. We observed corresponding mRNA/protein patterns in 43 cases using immunohistochemical data from the Human Protein Atlas and large-scale human protein profiling data obtained via mass spectroscopy. Protein network information enabled us to establish an interaction map of 38 proteins that points to potentially important testicular roles for some of them. We further characterized six candidate genes at the protein level in the mouse. We conclude that conserved genes induced in testis tend to show similar mRNA/protein expression patterns across species. Specifically, our results suggest roles during embryogenesis and adult spermatogenesis for Foxr1 and Sox30 and during spermiogenesis and fertility for Fam71b, 1700019N19Rik, Hmgb4, and Zfp597.
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Affiliation(s)
| | | | - Soazik P Jamin
- Inserm U1085-IRSET, Université de Rennes 1, Rennes, France
| | | | - Chunxiang Hao
- Inserm U1085-IRSET, Université de Rennes 1, Rennes, France
| | | | - Bernard Jégou
- Inserm U1085-IRSET, Université de Rennes 1, Rennes, France EHESP-School of Public Health, Rennes, France
| | | | - Michael Primig
- Inserm U1085-IRSET, Université de Rennes 1, Rennes, France EHESP-School of Public Health, Rennes, France
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Chocu S, Evrard B, Lavigne R, Rolland AD, Aubry F, Jégou B, Chalmel F, Pineau C. Forty-four novel protein-coding loci discovered using a proteomics informed by transcriptomics (PIT) approach in rat male germ cells. Biol Reprod 2014; 91:123. [PMID: 25210130 DOI: 10.1095/biolreprod.114.122416] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Spermatogenesis is a complex process, dependent upon the successive activation and/or repression of thousands of gene products, and ends with the production of haploid male gametes. RNA sequencing of male germ cells in the rat identified thousands of novel testicular unannotated transcripts (TUTs). Although such RNAs are usually annotated as long noncoding RNAs (lncRNAs), it is possible that some of these TUTs code for protein. To test this possibility, we used a "proteomics informed by transcriptomics" (PIT) strategy combining RNA sequencing data with shotgun proteomics analyses of spermatocytes and spermatids in the rat. Among 3559 TUTs and 506 lncRNAs found in meiotic and postmeiotic germ cells, 44 encoded at least one peptide. We showed that these novel high-confidence protein-coding loci exhibit several genomic features intermediate between those of lncRNAs and mRNAs. We experimentally validated the testicular expression pattern of two of these novel protein-coding gene candidates, both highly conserved in mammals: one for a vesicle-associated membrane protein we named VAMP-9, and the other for an enolase domain-containing protein. This study confirms the potential of PIT approaches for the discovery of protein-coding transcripts initially thought to be untranslated or unknown transcripts. Our results contribute to the understanding of spermatogenesis by characterizing two novel proteins, implicated by their strong expression in germ cells. The mass spectrometry proteomics data have been deposited with the ProteomeXchange Consortium under the data set identifier PXD000872.
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Affiliation(s)
- Sophie Chocu
- Proteomics Core Facility Biogenouest, Inserm U1085, IRSET, Campus de Beaulieu, Rennes, France Inserm U1085, IRSET, Université de Rennes 1, Rennes, France
| | | | - Régis Lavigne
- Proteomics Core Facility Biogenouest, Inserm U1085, IRSET, Campus de Beaulieu, Rennes, France Inserm U1085, IRSET, Université de Rennes 1, Rennes, France
| | | | - Florence Aubry
- Inserm U1085, IRSET, Université de Rennes 1, Rennes, France
| | - Bernard Jégou
- Inserm U1085, IRSET, Université de Rennes 1, Rennes, France
| | | | - Charles Pineau
- Proteomics Core Facility Biogenouest, Inserm U1085, IRSET, Campus de Beaulieu, Rennes, France Inserm U1085, IRSET, Université de Rennes 1, Rennes, France
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