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Pimentel-Acosta CA, Ramírez-Salcedo J, Morales-Serna FN, Fajer-Ávila EJ, Chávez-Sánchez C, Lara HH, García-Gasca A. Molecular Effects of Silver Nanoparticles on Monogenean Parasites: Lessons from Caenorhabditis elegans. Int J Mol Sci 2020; 21:ijms21165889. [PMID: 32824343 PMCID: PMC7460582 DOI: 10.3390/ijms21165889] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/12/2020] [Accepted: 08/14/2020] [Indexed: 12/15/2022] Open
Abstract
The mechanisms of action of silver nanoparticles (AgNPs) in monogenean parasites of the genus Cichlidogyrus were investigated through a microarray hybridization approach using genomic information from the nematode Caenorhabditis elegans. The effects of two concentrations of AgNPs were explored, low (6 µg/L Ag) and high (36 µg/L Ag). Microarray analysis revealed that both concentrations of AgNPs activated similar biological processes, although by different mechanisms. Expression profiles included genes involved in detoxification, neurotoxicity, modulation of cell signaling, reproduction, embryonic development, and tegument organization as the main biological processes dysregulated by AgNPs. Two important processes (DNA damage and cell death) were mostly activated in parasites exposed to the lower concentration of AgNPs. To our knowledge, this is the first study providing information on the sub-cellular and molecular effects of exposure to AgNPs in metazoan parasites of fish.
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Affiliation(s)
- Citlalic A. Pimentel-Acosta
- Centro de Investigación en Alimentación y Desarrollo, Unidad Mazatlán en Acuicultura y Manejo Ambiental, Mazatlán, Sinaloa 82112, Mexico; (C.A.P.-A.); (F.N.M.-S.); (E.J.F.-Á.); (C.C.-S.)
| | - Jorge Ramírez-Salcedo
- Unidad de Microarreglos, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Mexico City 04510, Mexico;
| | - Francisco Neptalí Morales-Serna
- Centro de Investigación en Alimentación y Desarrollo, Unidad Mazatlán en Acuicultura y Manejo Ambiental, Mazatlán, Sinaloa 82112, Mexico; (C.A.P.-A.); (F.N.M.-S.); (E.J.F.-Á.); (C.C.-S.)
- CONACYT, Centro de Investigación en Alimentación y Desarrollo, Unidad Mazatlán en Acuicultura y Manejo Ambiental, Mazatlán, Sinaloa 82112, Mexico
| | - Emma J. Fajer-Ávila
- Centro de Investigación en Alimentación y Desarrollo, Unidad Mazatlán en Acuicultura y Manejo Ambiental, Mazatlán, Sinaloa 82112, Mexico; (C.A.P.-A.); (F.N.M.-S.); (E.J.F.-Á.); (C.C.-S.)
| | - Cristina Chávez-Sánchez
- Centro de Investigación en Alimentación y Desarrollo, Unidad Mazatlán en Acuicultura y Manejo Ambiental, Mazatlán, Sinaloa 82112, Mexico; (C.A.P.-A.); (F.N.M.-S.); (E.J.F.-Á.); (C.C.-S.)
| | - Humberto H. Lara
- Department of Biology and South Texas Center for Emerging Infectious Diseases, The University of Texas at San Antonio, San Antonio, TX 78249, USA;
| | - Alejandra García-Gasca
- Centro de Investigación en Alimentación y Desarrollo, Unidad Mazatlán en Acuicultura y Manejo Ambiental, Mazatlán, Sinaloa 82112, Mexico; (C.A.P.-A.); (F.N.M.-S.); (E.J.F.-Á.); (C.C.-S.)
- Correspondence: ; Tel.: +52-66-9989-8700
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Nicolas De Lamballerie C, Pizzorno A, Dubois J, Padey B, Julien T, Traversier A, Carbonneau J, Orcel E, Lina B, Hamelin ME, Roche M, Textoris J, Boivin G, Legras-Lachuer C, Terrier O, Rosa-Calatrava M. Human Respiratory Syncytial Virus-Induced Immune Signature of Infection Revealed by Transcriptome Analysis of Clinical Pediatric Nasopharyngeal Swab Samples. J Infect Dis 2020; 223:1052-1061. [PMID: 32726438 DOI: 10.1093/infdis/jiaa468] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 07/24/2020] [Indexed: 11/12/2022] Open
Abstract
Human respiratory syncytial virus (HRSV) constitutes one the main causes of respiratory infection in neonates and infants worldwide. Transcriptome analysis of clinical samples using high-throughput technologies remains an important tool to better understand virus-host complex interactions in the real-life setting but also to identify new diagnosis/prognosis markers or therapeutics targets. A major challenge when exploiting clinical samples such as nasal swabs, washes, or bronchoalveolar lavages is the poor quantity and integrity of nucleic acids. In this study, we applied a tailored transcriptomics workflow to exploit nasal wash samples from children who tested positive for HRSV. Our analysis revealed a characteristic immune signature as a direct reflection of HRSV pathogenesis and highlighted putative biomarkers of interest such as IP-10, TMEM190, MCEMP1, and TIMM23.
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Affiliation(s)
- Claire Nicolas De Lamballerie
- CIRI, Centre International de Recherche en Infectiologie (Team VirPath), Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Lyon, France.,Viroscan3D SAS, Lyon, France
| | - Andrés Pizzorno
- CIRI, Centre International de Recherche en Infectiologie (Team VirPath), Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Lyon, France
| | - Julia Dubois
- CIRI, Centre International de Recherche en Infectiologie (Team VirPath), Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Lyon, France
| | - Blandine Padey
- CIRI, Centre International de Recherche en Infectiologie (Team VirPath), Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Lyon, France
| | - Thomas Julien
- CIRI, Centre International de Recherche en Infectiologie (Team VirPath), Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Lyon, France.,VirNext, Faculté de Médecine RTH Laennec, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
| | - Aurélien Traversier
- CIRI, Centre International de Recherche en Infectiologie (Team VirPath), Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Lyon, France
| | - Julie Carbonneau
- Research Center in Infectious Diseases, Centre Hospitalier Universitaire de Quebec and Laval University, Quebec City, Quebec, Canada
| | | | - Bruno Lina
- CIRI, Centre International de Recherche en Infectiologie (Team VirPath), Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Lyon, France
| | - Marie-Eve Hamelin
- Research Center in Infectious Diseases, Centre Hospitalier Universitaire de Quebec and Laval University, Quebec City, Quebec, Canada
| | | | - Julien Textoris
- Pathophysiology of Injury-Induced Immunosuppression, Hospices Civils de Lyon, bioMérieux, Université Claude Bernard Lyon 1, Hôpital Edouard Herriot, Lyon, France
| | - Guy Boivin
- Research Center in Infectious Diseases, Centre Hospitalier Universitaire de Quebec and Laval University, Quebec City, Quebec, Canada
| | - Catherine Legras-Lachuer
- Viroscan3D SAS, Lyon, France.,Ecologie Microbienne, UMR CNRS 5557, USC INRA 1364, Université Claude Bernard Lyon 1, Université de Lyon, Villeurbanne, France
| | - Olivier Terrier
- CIRI, Centre International de Recherche en Infectiologie (Team VirPath), Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Lyon, France
| | - Manuel Rosa-Calatrava
- CIRI, Centre International de Recherche en Infectiologie (Team VirPath), Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Lyon, France.,VirNext, Faculté de Médecine RTH Laennec, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
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3
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Pizzorno A, Terrier O, Nicolas de Lamballerie C, Julien T, Padey B, Traversier A, Roche M, Hamelin ME, Rhéaume C, Croze S, Escuret V, Poissy J, Lina B, Legras-Lachuer C, Textoris J, Boivin G, Rosa-Calatrava M. Repurposing of Drugs as Novel Influenza Inhibitors From Clinical Gene Expression Infection Signatures. Front Immunol 2019; 10:60. [PMID: 30761132 PMCID: PMC6361841 DOI: 10.3389/fimmu.2019.00060] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 01/10/2019] [Indexed: 11/13/2022] Open
Abstract
Influenza virus infections remain a major and recurrent public health burden. The intrinsic ever-evolving nature of this virus, the suboptimal efficacy of current influenza inactivated vaccines, as well as the emergence of resistance against a limited antiviral arsenal, highlight the critical need for novel therapeutic approaches. In this context, the aim of this study was to develop and validate an innovative strategy for drug repurposing as host-targeted inhibitors of influenza viruses and the rapid evaluation of the most promising candidates in Phase II clinical trials. We exploited in vivo global transcriptomic signatures of infection directly obtained from a patient cohort to determine a shortlist of already marketed drugs with newly identified, host-targeted inhibitory properties against influenza virus. The antiviral potential of selected repurposing candidates was further evaluated in vitro, in vivo, and ex vivo. Our strategy allowed the selection of a shortlist of 35 high potential candidates out of a rationalized computational screening of 1,309 FDA-approved bioactive molecules, 31 of which were validated for their significant in vitro antiviral activity. Our in vivo and ex vivo results highlight diltiazem, a calcium channel blocker currently used in the treatment of hypertension, as a promising option for the treatment of influenza infections. Additionally, transcriptomic signature analysis further revealed the so far undescribed capacity of diltiazem to modulate the expression of specific genes related to the host antiviral response and cholesterol metabolism. Finally, combination treatment with diltiazem and virus-targeted oseltamivir neuraminidase inhibitor further increased antiviral efficacy, prompting rapid authorization for the initiation of a Phase II clinical trial. This original, host-targeted, drug repurposing strategy constitutes an effective and highly reactive process for the rapid identification of novel anti-infectious drugs, with potential major implications for the management of antimicrobial resistance and the rapid response to future epidemic or pandemic (re)emerging diseases for which we are still disarmed.
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Affiliation(s)
- Andrés Pizzorno
- Virologie et Pathologie Humaine—VirPath Team, Centre International de Recherche en Infectiologie, INSERM U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
- Research Center in Infectious Diseases of the CHU de Quebec and Laval University, Quebec City, QC, Canada
| | - Olivier Terrier
- Virologie et Pathologie Humaine—VirPath Team, Centre International de Recherche en Infectiologie, INSERM U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
| | - Claire Nicolas de Lamballerie
- Virologie et Pathologie Humaine—VirPath Team, Centre International de Recherche en Infectiologie, INSERM U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
- Viroscan3D SAS, Lyon, France
| | - Thomas Julien
- Virologie et Pathologie Humaine—VirPath Team, Centre International de Recherche en Infectiologie, INSERM U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
- VirNext, Faculté de Médecine RTH Laennec, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
| | - Blandine Padey
- Virologie et Pathologie Humaine—VirPath Team, Centre International de Recherche en Infectiologie, INSERM U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
- VirNext, Faculté de Médecine RTH Laennec, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
| | - Aurélien Traversier
- Virologie et Pathologie Humaine—VirPath Team, Centre International de Recherche en Infectiologie, INSERM U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
| | | | - Marie-Eve Hamelin
- Research Center in Infectious Diseases of the CHU de Quebec and Laval University, Quebec City, QC, Canada
| | - Chantal Rhéaume
- Research Center in Infectious Diseases of the CHU de Quebec and Laval University, Quebec City, QC, Canada
| | - Séverine Croze
- ProfileXpert, SFR-Est, CNRS UMR-S3453, INSERM US7, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
| | - Vanessa Escuret
- Virologie et Pathologie Humaine—VirPath Team, Centre International de Recherche en Infectiologie, INSERM U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
- Laboratoire de Virologie, Centre National de Référence des virus Influenza Sud, Institut des Agents Infectieux, Groupement Hospitalier Nord, Hospices Civils de Lyon, Lyon, France
| | - Julien Poissy
- Pôle de Réanimation, Hôpital Roger Salengro, Centre Hospitalier Régional et Universitaire de Lille, Université de Lille 2, Lille, France
| | - Bruno Lina
- Virologie et Pathologie Humaine—VirPath Team, Centre International de Recherche en Infectiologie, INSERM U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
- Laboratoire de Virologie, Centre National de Référence des virus Influenza Sud, Institut des Agents Infectieux, Groupement Hospitalier Nord, Hospices Civils de Lyon, Lyon, France
| | - Catherine Legras-Lachuer
- Viroscan3D SAS, Lyon, France
- Ecologie Microbienne, UMR CNRS 5557, USC INRA 1364, Université Claude Bernard Lyon 1, Université de Lyon, Villeurbanne, France
| | - Julien Textoris
- Service d'Anesthésie et de Réanimation, Hôpital Edouard Herriot, Hospices Civils de Lyon, Lyon, France
- Pathophysiology of Injury-Induced Immunosuppression (PI3), EA 7426 Hospices Civils de Lyon, bioMérieux, Université Claude Bernard Lyon 1, Hôpital Edouard Herriot, Lyon, France
| | - Guy Boivin
- Research Center in Infectious Diseases of the CHU de Quebec and Laval University, Quebec City, QC, Canada
| | - Manuel Rosa-Calatrava
- Virologie et Pathologie Humaine—VirPath Team, Centre International de Recherche en Infectiologie, INSERM U1111, CNRS UMR5308, ENS Lyon, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
- VirNext, Faculté de Médecine RTH Laennec, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
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Landis JB, Soltis DE, Soltis PS. Comparative transcriptomic analysis of the evolution and development of flower size in Saltugilia (Polemoniaceae). BMC Genomics 2017; 18:475. [PMID: 28645249 PMCID: PMC5481933 DOI: 10.1186/s12864-017-3868-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 06/16/2017] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Flower size varies dramatically across angiosperms, representing innovations over the course of >130 million years of evolution and contributing substantially to relationships with pollinators. However, the genetic underpinning of flower size is not well understood. Saltugilia (Polemoniaceae) provides an excellent non-model system for extending the genetic study of flower size to interspecific differences that coincide with variation in pollinators. RESULTS Using targeted gene capture methods, we infer phylogenetic relationships among all members of Saltugilia to provide a framework for investigating the genetic control of flower size differences via RNA-Seq de novo assembly. Nuclear concatenation and species tree inference methods provide congruent topologies. The inferred evolutionary trajectory of flower size is from small flowers to larger flowers. We identified 4 to 10,368 transcripts that are differentially expressed during flower development, with many unigenes associated with cell wall modification and components of the auxin and gibberellin pathways. CONCLUSIONS Saltugilia is an excellent model for investigating covarying floral and pollinator evolution. Four candidate genes from model systems (BIG BROTHER, BIG PETAL, GASA, and LONGIFOLIA) show differential expression during development of flowers in Saltugilia, and four other genes (FLOWERING-PROMOTING FACTOR 1, PECTINESTERASE, POLYGALACTURONASE, and SUCROSE SYNTHASE) fit into hypothesized organ size pathways. Together, these gene sets provide a strong foundation for future functional studies to determine their roles in specifying interspecific differences in flower size.
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Affiliation(s)
- Jacob B. Landis
- Department of Biology, University of Florida, Gainesville, FL 32611 USA
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611 USA
- Department of Botany and Plant Sciences, University of California Riverside, 4412 Boyce Hall, 3401 Watkins Drive, Riverside, CA 92521 USA
| | - Douglas E. Soltis
- Department of Biology, University of Florida, Gainesville, FL 32611 USA
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611 USA
- Genetics Institute, University of Florida, Gainesville, FL 32610 USA
| | - Pamela S. Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611 USA
- Genetics Institute, University of Florida, Gainesville, FL 32610 USA
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Rey B, Dégletagne C, Duchamp C. Transcriptomic data analysis and differential gene expression of antioxidant pathways in king penguin juveniles ( Aptenodytes patagonicus) before and after acclimatization to marine life. Data Brief 2016; 9:549-555. [PMID: 27752524 PMCID: PMC5061121 DOI: 10.1016/j.dib.2016.09.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 09/07/2016] [Accepted: 09/14/2016] [Indexed: 12/23/2022] Open
Abstract
In this article, we present differentially expressed gene profiles in the pectoralis muscle of wild juvenile king penguins that were either naturally acclimated to cold marine environment or experimentally immersed in cold water as compared with penguin juveniles that never experienced cold water immersion. Transcriptomic data were obtained by hybridizing penguins total cDNA on Affymetrix GeneChip Chicken Genome arrays and analyzed using maxRS algorithm, “Transcriptome analysis in non-model species: a new method for the analysis of heterologous hybridization on microarrays” (Dégletagne et al., 2010) [1]. We focused on genes involved in multiple antioxidant pathways. For better clarity, these differentially expressed genes were clustered into six functional groups according to their role in controlling redox homeostasis. The data are related to a comprehensive research study on the ontogeny of antioxidant functions in king penguins, “Hormetic response triggers multifaceted anti-oxidant strategies in immature king penguins (Aptenodytes patagonicus)” (Rey et al., 2016) [2]. The raw microarray dataset supporting the present analyses has been deposited at the Gene Expression Omnibus (GEO) repository under accessions GEO: GSE17725 and GEO: GSE82344.
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Affiliation(s)
- Benjamin Rey
- Université de Lyon, F-69000, Lyon, Université Lyon 1, CNRS - Laboratoire de Biométrie et Biologie Evolutive, F-69622 Villeurbanne Cedex, France
| | - Cyril Dégletagne
- Université de Lyon, F-69000, Lyon, Université Lyon 1, CNRS - Laboratoire d׳Ecologie des Hydrosystèmes Naturels et Anthropisés, F-69622 Villeurbanne Cedex, France
| | - Claude Duchamp
- Université de Lyon, F-69000, Lyon, Université Lyon 1, CNRS - Laboratoire d׳Ecologie des Hydrosystèmes Naturels et Anthropisés, F-69622 Villeurbanne Cedex, France
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Rey B, Dégletagne C, Bodennec J, Monternier PA, Mortz M, Roussel D, Romestaing C, Rouanet JL, Tornos J, Duchamp C. Hormetic response triggers multifaceted anti-oxidant strategies in immature king penguins (Aptenodytes patagonicus). Free Radic Biol Med 2016; 97:577-587. [PMID: 27449544 DOI: 10.1016/j.freeradbiomed.2016.07.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 06/10/2016] [Accepted: 07/18/2016] [Indexed: 12/11/2022]
Abstract
Repeated deep dives are highly pro-oxidative events for air-breathing aquatic foragers such as penguins. At fledging, the transition from a strictly terrestrial to a marine lifestyle may therefore trigger a complex set of anti-oxidant responses to prevent chronic oxidative stress in immature penguins but these processes are still undefined. By combining in vivo and in vitro approaches with transcriptome analysis, we investigated the adaptive responses of sea-acclimatized (SA) immature king penguins (Aptenodytes patagonicus) compared with pre-fledging never-immersed (NI) birds. In vivo, experimental immersion into cold water stimulated a higher thermogenic response in SA penguins than in NI birds, but both groups exhibited hypothermia, a condition favouring oxidative stress. In vitro, the pectoralis muscles of SA birds displayed increased oxidative capacity and mitochondrial protein abundance but unchanged reactive oxygen species (ROS) generation per g tissue because ROS production per mitochondria was reduced. The genes encoding oxidant-generating proteins were down-regulated in SA birds while mRNA abundance and activity of the main antioxidant enzymes were up-regulated. Genes encoding proteins involved in repair mechanisms of oxidized DNA or proteins and in degradation processes were also up-regulated in SA birds. Sea life also increased the degree of fatty acid unsaturation in muscle mitochondrial membranes resulting in higher intrinsic susceptibility to ROS. Oxidative damages to protein or DNA were reduced in SA birds. Repeated experimental immersions of NI penguins in cold-water partially mimicked the effects of acclimatization to marine life, modified the expression of fewer genes related to oxidative stress but in a similar way as in SA birds and increased oxidative damages to DNA. It is concluded that the multifaceted plasticity observed after marine life may be crucial to maintain redox homeostasis in active tissues subjected to high pro-oxidative pressure in diving birds. Initial immersions in cold-water may initiate an hormetic response triggering essential changes in the adaptive antioxidant response to marine life.
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Affiliation(s)
- Benjamin Rey
- Université de Lyon, Université Lyon 1, CNRS - Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France; Brain Function Research Group, School of Physiology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Cyril Dégletagne
- Université de Lyon; Université Lyon 1, CNRS - Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés, Villeurbanne Cedex, France.
| | - Jacques Bodennec
- Université de Lyon, Université Lyon 1, CNRS - Neuroscience Research Centre, Villeurbanne, France.
| | - Pierre-Axel Monternier
- Université de Lyon; Université Lyon 1, CNRS - Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés, Villeurbanne Cedex, France.
| | - Mathieu Mortz
- Université de Lyon; Université Lyon 1, CNRS - Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés, Villeurbanne Cedex, France.
| | - Damien Roussel
- Université de Lyon; Université Lyon 1, CNRS - Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés, Villeurbanne Cedex, France.
| | - Caroline Romestaing
- Université de Lyon; Université Lyon 1, CNRS - Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés, Villeurbanne Cedex, France.
| | - Jean-Louis Rouanet
- Université de Lyon; Université Lyon 1, CNRS - Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés, Villeurbanne Cedex, France.
| | - Jeremy Tornos
- Université de Lyon; Université Lyon 1, CNRS - Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés, Villeurbanne Cedex, France.
| | - Claude Duchamp
- Université de Lyon; Université Lyon 1, CNRS - Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés, Villeurbanne Cedex, France.
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Iacobas DA. The Genomic Fabric Perspective on the Transcriptome Between Universal Quantifiers and Personalized Genomic Medicine. ACTA ACUST UNITED AC 2016. [DOI: 10.1007/s13752-016-0245-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Alterations of circulating lymphoid committed progenitor cellular metabolism after allogeneic stem cell transplantation in humans. Exp Hematol 2016; 44:811-816.e3. [PMID: 27321893 DOI: 10.1016/j.exphem.2016.05.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 05/13/2016] [Accepted: 05/17/2016] [Indexed: 02/01/2023]
Abstract
Lymphoid-committed CD34(+)lin(-)CD10(+)CD24(-) progenitors undergo a rebound at month 3 after allogeneic hematopoietic stem cell transplantation (allo-HSCT) in the absence of acute graft-versus-host disease (aGVHD). Here, we analyzed transcriptional programs of cell-sorted circulating lymphoid-committed progenitors and CD34(+)Lin(-)CD10(-) nonlymphoid progenitors in 11 allo-HSCT patients who had (n = 5) or had not (n = 6) developed grade 2 or 3 aGVHD and in 7 age-matched healthy donors. Major upregulated pathways include protein synthesis, energy production, cell cycle regulation, and cytoskeleton organization. Notably, genes from protein biogenesis, translation machinery, and cell cycle (CDK6) were overexpressed in progenitors from patients in the absence of aGVHD compared with healthy donors and patients affected by aGVHD. Expression of many genes from the mitochondrial oxidative phosphorylation metabolic pathway leading to ATP production were more specifically increased in lymphoid-committed progenitors in the absence of aGVHD. This was also the case for genes involved in cell mobilization such as those regulating Rho GTPase activity. In all, we found that circulating lymphoid-committed progenitors undergo profound changes in metabolism, favoring cell proliferation, energy production, and cell mobilization after allo-HSCT in humans. These mechanisms are abolished in the case of aGVHD or its treatment, indicating a persistent cell-intrinsic defect after exit from the bone marrow.
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Rey B, Pélisson PF, Bel-Venner MC, Voituron Y, Venner S. Revisiting the link between breeding effort and oxidative balance through field evaluation of two sympatric sibling insect species. Evolution 2015; 69:815-22. [DOI: 10.1111/evo.12586] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 12/05/2014] [Indexed: 01/14/2023]
Affiliation(s)
- Benjamin Rey
- Laboratoire de Biométrie et Biologie Evolutive, CNRS, UMR; Université Lyon 1, Université de Lyon; Villeurbanne France
- Wildlife Conservation Physiology, Brain Function Research Group, School of Physiology, Faculty of Health Sciences; University of the Witwatersrand; Johannesburg South Africa
| | - Pierre-François Pélisson
- Laboratoire de Biométrie et Biologie Evolutive, CNRS, UMR; Université Lyon 1, Université de Lyon; Villeurbanne France
| | - Marie-Claude Bel-Venner
- Laboratoire de Biométrie et Biologie Evolutive, CNRS, UMR; Université Lyon 1, Université de Lyon; Villeurbanne France
| | - Yann Voituron
- Laboratoire d’Ecologie des Hydrosystèmes Naturels et Anthropisés, CNRS, UMR; Université Lyon 1, Université de Lyon; Villeurbanne France
| | - Samuel Venner
- Laboratoire de Biométrie et Biologie Evolutive, CNRS, UMR; Université Lyon 1, Université de Lyon; Villeurbanne France
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Biggar KK, Storey KB. New Approaches to Comparative and Animal Stress Biology Research in the Post-genomic Era: A Contextual Overview. Comput Struct Biotechnol J 2014; 11:138-46. [PMID: 25408848 PMCID: PMC4232569 DOI: 10.1016/j.csbj.2014.09.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 09/07/2014] [Accepted: 09/11/2014] [Indexed: 02/06/2023] Open
Abstract
Although much is known about the physiological responses of many environmental stresses in tolerant animals, studies evaluating the regulation of stress-induced mechanisms that regulate the transitions to and from this state are beginning to explore new and fascinating areas of molecular research. Current findings have developed a general, but refined, view of the important molecular pathways contributing to stress-survival. However, studies utilizing newly developed technologies that broadly focus on genomic and proteomic screening are beginning to identify many new targets for future study. This minireview will provide a contextual overview on the use of DNA/RNA sequencing, microRNA annotation and prediction software, protein structure and function prediction tools, as well as methods of high-throughput protein expression analysis. We will also use select examples to highlight the existing use of these technologies in stress biology research. Such tools can be used in comparative stress biology in the characterization of animal responses to environmental challenges. Although there are many areas of study left to be explored, research in comparative stress biology will always be continuing as new technologies allow the further analysis of cell function, and new paradigms in gene regulation and regulatory molecules (such as microRNAs) are continuing to be discovered. Building upon the findings of past research, while utilizing new technologies in the appropriate manner, future studies can be carried out in new and exciting areas still unexplored. Proper use of rapidly developing technologies will help to create a complete understanding of the animal stress response and survival mechanisms utilized by many diverse organisms.
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Affiliation(s)
| | - Kenneth B. Storey
- Institute of Biochemistry, Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada
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Jayapal KP, Goudar CT. Transcriptomics as a tool for assessing the scalability of mammalian cell perfusion systems. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2013; 139:227-43. [PMID: 23949697 DOI: 10.1007/10_2013_239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
DNA microarray-based transcriptomics have been used to determine the time course of laboratory and manufacturing-scale perfusion bioreactors in an attempt to characterize cell physiological state at these two bioreactor scales. Given the limited availability of genomic data for baby hamster kidney (BHK) cells, a Chinese hamster ovary (CHO)-based microarray was used following a feasibility assessment of cross-species hybridization. A heat shock experiment was performed using both BHK and CHO cells and resulting DNA microarray data were analyzed using a filtering criteria of perfect match (PM)/single base mismatch (MM) > 1.5 and PM-MM > 50 to exclude probes with low specificity or sensitivity for cross-species hybridizations. For BHK cells, 8910 probe sets (39 %) passed the cutoff criteria, whereas 12,961 probe sets (56 %) passed the cutoff criteria for CHO cells. Yet, the data from BHK cells allowed distinct clustering of heat shock and control samples as well as identification of biologically relevant genes as being differentially expressed, indicating the utility of cross-species hybridization. Subsequently, DNA microarray analysis was performed on time course samples from laboratory- and manufacturing-scale perfusion bioreactors that were operated under the same conditions. A majority of the variability (37 %) was associated with the first principal component (PC-1). Although PC-1 changed monotonically with culture duration, the trends were very similar in both the laboratory and manufacturing-scale bioreactors. Therefore, despite time-related changes to the cell physiological state, transcriptomic fingerprints were similar across the two bioreactor scales at any given instance in culture. Multiple genes were identified with time-course expression profiles that were very highly correlated (> 0.9) with bioprocess variables of interest. Although the current incomplete annotation limits the biological interpretation of these observations, their full potential may be realized in due course when richer genomic data become available. By taking a pragmatic approach of transcriptome fingerprinting, we have demonstrated the utility of systems biology to support the comparability of laboratory and manufacturing-scale perfusion systems. Scale-down model qualification is the first step in process characterization and hence is an integral component of robust regulatory filings. Augmenting the current paradigm, which relies primarily on cell culture and product quality information, with gene expression data can help make a substantially stronger case for similarity. With continued advances in systems biology approaches, we expect them to be seamlessly integrated into bioprocess development, which can translate into more robust and high yielding processes that can ultimately reduce cost of care for patients.
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Affiliation(s)
- Karthik P Jayapal
- Cell Culture Development, Global Biological Development Bayer HealthCare, 800 Dwight Way, Berkeley, CA, 94710, USA
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Aranda M, DeSalvo MK, Bayer T, Medina M, Voolstra CR. Evolutionary insights into scleractinian corals using comparative genomic hybridizations. BMC Genomics 2012; 13:501. [PMID: 22994626 PMCID: PMC3469353 DOI: 10.1186/1471-2164-13-501] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Accepted: 09/11/2012] [Indexed: 12/04/2022] Open
Abstract
Background Coral reefs belong to the most ecologically and economically important ecosystems on our planet. Yet, they are under steady decline worldwide due to rising sea surface temperatures, disease, and pollution. Understanding the molecular impact of these stressors on different coral species is imperative in order to predict how coral populations will respond to this continued disturbance. The use of molecular tools such as microarrays has provided deep insight into the molecular stress response of corals. Here, we have performed comparative genomic hybridizations (CGH) with different coral species to an Acropora palmata microarray platform containing 13,546 cDNA clones in order to identify potentially rapidly evolving genes and to determine the suitability of existing microarray platforms for use in gene expression studies (via heterologous hybridization). Results Our results showed that the current microarray platform for A. palmata is able to provide biological relevant information for a wide variety of coral species covering both the complex clade as well the robust clade. Analysis of the fraction of highly diverged genes showed a significantly higher amount of genes without annotation corroborating previous findings that point towards a higher rate of divergence for taxonomically restricted genes. Among the genes with annotation, we found many mitochondrial genes to be highly diverged in M. faveolata when compared to A. palmata, while the majority of nuclear encoded genes maintained an average divergence rate. Conclusions The use of present microarray platforms for transcriptional analyses in different coral species will greatly enhance the understanding of the molecular basis of stress and health and highlight evolutionary differences between scleractinian coral species. On a genomic basis, we show that cDNA arrays can be used to identify patterns of divergence. Mitochondrion-encoded genes seem to have diverged faster than nuclear encoded genes in robust corals. Accordingly, this needs to be taken into account when using mitochondrial markers for scleractinian phylogenies.
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Affiliation(s)
- Manuel Aranda
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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Teulier L, Dégletagne C, Rey B, Tornos J, Keime C, de Dinechin M, Raccurt M, Rouanet JL, Roussel D, Duchamp C. Selective upregulation of lipid metabolism in skeletal muscle of foraging juvenile king penguins: an integrative study. Proc Biol Sci 2012; 279:2464-72. [PMID: 22357259 DOI: 10.1098/rspb.2011.2664] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The passage from shore to marine life of juvenile penguins represents a major energetic challenge to fuel intense and prolonged demands for thermoregulation and locomotion. Some functional changes developed at this crucial step were investigated by comparing pre-fledging king penguins with sea-acclimatized (SA) juveniles (Aptenodytes patagonicus). Transcriptomic analysis of pectoralis muscle biopsies revealed that most genes encoding proteins involved in lipid transport or catabolism were upregulated, while genes involved in carbohydrate metabolism were mostly downregulated in SA birds. Determination of muscle enzymatic activities showed no changes in enzymes involved in the glycolytic pathway, but increased 3-hydroxyacyl-CoA dehydrogenase, an enzyme of the β-oxidation pathway. The respiratory rates of isolated muscle mitochondria were much higher with a substrate arising from lipid metabolism (palmitoyl-L-carnitine) in SA juveniles than in terrestrial controls, while no difference emerged with a substrate arising from carbohydrate metabolism (pyruvate). In vivo, perfusion of a lipid emulsion induced a fourfold larger thermogenic effect in SA than in control juveniles. The present integrative study shows that fuel selection towards lipid oxidation characterizes penguin acclimatization to marine life. Such acclimatization may involve thyroid hormones through their nuclear beta receptor and nuclear coactivators.
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Affiliation(s)
- Loic Teulier
- Université de Lyon, UMR5023 Ecologie des Hydrosystèmes Naturels et Anthropisés, Université Lyon 1, ENTPE, CNRS, 6 rue Raphaël Dubois, 69622 Villeurbanne, France
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Iacobas S, Thomas NM, Iacobas DA. Plasticity of the myelination genomic fabric. Mol Genet Genomics 2012; 287:237-46. [PMID: 22246408 DOI: 10.1007/s00438-012-0673-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Accepted: 01/03/2012] [Indexed: 01/11/2023]
Abstract
This study aimed to quantify the influence of the astrocyte proximity on myelination genomic fabric (MYE) of oligodendrocytes, defined as the most interconnected and stably expressed gene web responsible for myelination. Such quantitation is important to evaluate whether astrocyte signaling may contribute to demyelination when impaired and remyelination when properly restored. For this, we compared changes in the gene expression profiles of immortalized precursor oligodendrocytes (Oli-neu), stimulated to differentiate by the proximity of nontouching astrocytes or treatment with db-cAMP. In a previous paper, we reported that the astrocyte proximity upregulated or turned-on a large number of myelination genes and substantially enriched the Ca(2+)-signaling and cytokine receptor regulatory networks of MYE in Oli-neu cells. Here, we introduce the "transcriptomic distance" to evaluate fabric remodeling and "pair-wise relevance" to identify the most influential gene pairs. Together with the prominence gene analysis used to select and rank the fabric genes, these novel analytical tools provide a comprehensively quantitative view of the physio/pathological transformations of the transcriptomic programs of myelinating cells. Applied to our data, the analyses revealed not only that the astrocyte neighborhood is a substantially more powerful regulator of myelination than the differentiating treatment but also the molecular mechanisms of the two differentiating paradigms are different. By inducing a profound remodeling of MYE and regulatory transcriptomic networks, the astrocyte-oligodendrocyte intercommunication may be considered as a major player in both pathophysiology and therapy of neurodegenerative diseases related to myelination.
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Affiliation(s)
- Sanda Iacobas
- D.P. Purpura Department of Neuroscience, Kennedy Center, Albert Einstein College of Medicine of Yeshiva University, Room 713, 1300 Morris Park Avenue, Bronx-New York, NY, 10461, USA
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Darby BJ, Jones KL, Wheeler D, Herman MA. Normalization and centering of array-based heterologous genome hybridization based on divergent control probes. BMC Bioinformatics 2011; 12:183. [PMID: 21600029 PMCID: PMC3125262 DOI: 10.1186/1471-2105-12-183] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2010] [Accepted: 05/21/2011] [Indexed: 11/21/2022] Open
Abstract
Background Hybridization of heterologous (non-specific) nucleic acids onto arrays designed for model-organisms has been proposed as a viable genomic resource for estimating sequence variation and gene expression in non-model organisms. However, conventional methods of normalization that assume equivalent distributions (such as quantile normalization) are inappropriate when applied to non-specific (heterologous) hybridization. We propose an algorithm for normalizing and centering intensity data from heterologous hybridization that makes no prior assumptions of distribution, reduces the false appearance of homology, and provides a way for researchers to confirm whether heterologous hybridization is suitable. Results Data are normalized by adjusting for Gibbs free energy binding, and centered by adjusting for the median of a common set of control probes assumed to be equivalently dissimilar for all species. This procedure was compared to existing approaches and found to be as successful as Loess normalization at detecting sequence variations (deletions) and even more successful than quantile normalization at reducing the accumulation of false positive probe matches between two related nematode species, Caenorhabditis elegans and C. briggsae. Despite the improvements, we still found that probe fluorescence intensity was too poorly correlated with sequence similarity to result in reliable detection of matching probe sequence. Conclusions Cross-species hybridizations can be a way to adapt genome-enabled tools for closely related non-model organisms, but data must be appropriately normalized and centered in a way that accommodates hybridization of nucleic acids with diverged sequence. For short, 25-mer probes, hybridization intensity alone may be insufficiently correlated with sequence similarity to allow reliable inference of homology at the probe level.
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Affiliation(s)
- Brian J Darby
- Ecological Genomics Institute, Division of Biology, Kansas State University, Manhattan, KS 66506, USA
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Ogura A, Yoshida MA, Fukuzaki M, Sese J. In vitro homology search array comprehensively reveals highly conserved genes and their functional characteristics in non-sequenced species. BMC Genomics 2010; 11 Suppl 4:S9. [PMID: 21143818 PMCID: PMC3005928 DOI: 10.1186/1471-2164-11-s4-s9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND With the increase in genomic and transcriptomic data produced by the recent advancements in next generation sequencers and microarrays, it is now easier than ever to conduct large-scale comparative genomic studies for familiar species. However, there are more than ten million species on earth, and the study of all remaining species is not realistic in terms of cost and time. There have been a number of attempts at using microarrays for cross-species hybridization; however, those approaches only utilized the same probes for each species or different probes designed from orthologous genes. To establish easier and cheaper methods for the large-scale comparative genomic study of non-sequenced species, we developed an in vitro homology search array with the aid of a bioinformatic approach to probe design. RESULTS To perform large-scale genomic comparisons of non-sequenced species, we chose squid, one of the most intelligent species among Protostomes, for comparison with human genes. We designed a microarray using human single copy genes and conducted microarray experiments with mRNAs extracted from the squid. Multi-copy genes could not be detected using the microarray in this study because their sequence similarity caused cross-hybridization. A search for squid homologous genes among human genes revealed that 68% of the human probes tested showed the expression of squid homolog genes and 95 genes were confirmed to be expressed highly in squid. Functional classification analysis showed that these highly expressed genes comprise DNA binding proteins, which are under pressure of DNA level mutation and, consequently, show high similarity at the nucleotide level. CONCLUSIONS Our array could detect homologous genes in squids and humans in spite of the distant phylogenic relationships between the species. This experimental method will be useful for identifying homologs in non-sequenced species, for the development of genetic resources and for the collection of information on biodiversity, particularly when using the genome of sibling or closely related species.
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Affiliation(s)
- Atsushi Ogura
- Ochadai Academic Production, Ochanomizu University, Bunkyo, Tokyo, Japan.
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