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Al-Zoubi RM, Abu-Hijleh H, Zarour A, Zakaria ZZ, Yassin A, Al-Ansari AA, Al-Asmakh M, Bawadi H. Zebrafish Model in Illuminating the Complexities of Post-Traumatic Stress Disorders: A Unique Research Tool. Int J Mol Sci 2024; 25:4895. [PMID: 38732113 PMCID: PMC11084870 DOI: 10.3390/ijms25094895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 02/13/2024] [Accepted: 02/16/2024] [Indexed: 05/13/2024] Open
Abstract
Post-traumatic stress disorder (PTSD) is a debilitating psychological condition that may develop in certain individuals following exposure to life-threatening or traumatic events. Distressing symptoms, including flashbacks, are characterized by disrupted stress responses, fear, anxiety, avoidance tendencies, and disturbances in sleep patterns. The enduring effects of PTSD can profoundly impact personal and familial relationships, as well as social, medical, and financial stability. The prevalence of PTSD varies among different populations and is influenced by the nature of the traumatic event. Recently, zebrafish have emerged as a valuable model organism in studying various conditions and disorders. Zebrafish display robust behavioral patterns that can be effectively quantified using advanced video-tracking tools. Due to their relatively simple nervous system compared to humans, zebrafish are particularly well suited for behavioral investigations. These unique characteristics make zebrafish an appealing model for exploring the underlying molecular and genetic mechanisms that govern behavior, thus offering a powerful comparative platform for gaining deeper insights into PTSD. This review article aims to provide updates on the pathophysiology of PTSD and the genetic responses associated with psychological stress. Additionally, it highlights the significance of zebrafish behavior as a valuable tool for comprehending PTSD better. By leveraging zebrafish as a model organism, researchers can potentially uncover novel therapeutic interventions for the treatment of PTSD and contribute to a more comprehensive understanding of this complex condition.
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Affiliation(s)
- Raed M. Al-Zoubi
- Department of Chemistry, Jordan University of Science and Technology, P.O. Box 3030, Irbid 22110, Jordan;
- Surgical Research Section, Department of Surgery, Hamad Medical Corporation, Doha P.O. Box 3050, Qatar; (A.Y.); (A.A.A.-A.)
- Department of Biomedical Sciences, QU-Health, College of Health Sciences, Qatar University, Doha 2713, Qatar
| | - Haya Abu-Hijleh
- Department of Human Nutrition, QU-Health, College of Health Sciences, Qatar University, Doha 2713, Qatar; (H.A.-H.); (M.A.-A.)
| | - Ahmad Zarour
- Department of Surgery, Acute Care Surgery, Hamad Medical Corporation, Doha P.O. Box 3050, Qatar;
| | - Zain Z. Zakaria
- Vice President for Medical and Health Sciences Office, QU-Health, Qatar University, Doha 2713, Qatar;
| | - Aksam Yassin
- Surgical Research Section, Department of Surgery, Hamad Medical Corporation, Doha P.O. Box 3050, Qatar; (A.Y.); (A.A.A.-A.)
- Center of Medicine and Health Sciences, Dresden International University, 01069 Dresden, Germany
| | - Abdulla A. Al-Ansari
- Surgical Research Section, Department of Surgery, Hamad Medical Corporation, Doha P.O. Box 3050, Qatar; (A.Y.); (A.A.A.-A.)
| | - Maha Al-Asmakh
- Department of Human Nutrition, QU-Health, College of Health Sciences, Qatar University, Doha 2713, Qatar; (H.A.-H.); (M.A.-A.)
- Biomedical Research Center, Qatar University, Doha P.O. Box 2713, Qatar
| | - Hiba Bawadi
- Department of Human Nutrition, QU-Health, College of Health Sciences, Qatar University, Doha 2713, Qatar; (H.A.-H.); (M.A.-A.)
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2
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Fujii K, Yamakawa K, Takeda Y, Okuda N, Takasu A, Ono F. Understanding the pathophysiology of acute critical illness: translational lessons from zebrafish models. Intensive Care Med Exp 2024; 12:8. [PMID: 38291192 PMCID: PMC10828313 DOI: 10.1186/s40635-024-00595-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 01/10/2024] [Indexed: 02/01/2024] Open
Abstract
The models used to investigate the pathophysiological mechanisms of acute critical illness are not limited to mammalian species. The zebrafish (Danio rerio) is a popular model organism for studying diseases due to its transparency and rapid development. The genes and signaling pathways involved in acute critical illness appear highly conserved among zebrafish and humans. Forward genetics such as random mutagenesis by a chemical mutagen or reverse genetics methods represented by CRISPR/Cas9 allowed researchers to reveal multiple novel aspects of pathological processes in areas including infection, immunity, and regeneration. As a model of sepsis, transgenic zebrafish allowed the visualization of lipopolysaccharide (LPS)-induced vascular leakage in vivo and the demonstration of changes in the expression of cellular junction proteins. Other transgenic zebrafish visualizing the extravascular migration of neutrophils and macrophages have demonstrated a decrease in neutrophil numbers and an increased expression of an inflammatory gene, which replicates a phenomenon observed in humans in clinically encountered sepsis. The regenerative potential and the visibility of zebrafish organs also enabled clarification of important mechanisms in wound healing, angiogenesis, and neurogenesis. After spinal cord injury (SCI), a marker gene expressed in glial bridging was discovered. Furthermore, localized epithelial-to-mesenchymal transition (EMT) and molecular mechanisms leading to spinal cord repair were revealed. These translational studies using zebrafish show the potential of the model system for the treatment of acute critical illnesses such as sepsis, organ failure, and trauma.
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Affiliation(s)
- Kensuke Fujii
- Department of Emergency and Critical Care Medicine, Osaka Medical and Pharmaceutical University, 2-7 Daigakumachi, Takatsuki, Osaka, 569-8686, Japan
| | - Kazuma Yamakawa
- Department of Emergency and Critical Care Medicine, Osaka Medical and Pharmaceutical University, 2-7 Daigakumachi, Takatsuki, Osaka, 569-8686, Japan.
| | - Yuriko Takeda
- Department of Emergency and Critical Care Medicine, Osaka Medical and Pharmaceutical University, 2-7 Daigakumachi, Takatsuki, Osaka, 569-8686, Japan
| | - Natsuko Okuda
- Department of Physiology, Osaka Medical and Pharmaceutical University, 2-7 Daigakumachi, Takatsuki, Osaka, 569-8686, Japan
| | - Akira Takasu
- Department of Emergency and Critical Care Medicine, Osaka Medical and Pharmaceutical University, 2-7 Daigakumachi, Takatsuki, Osaka, 569-8686, Japan
| | - Fumihito Ono
- Department of Physiology, Osaka Medical and Pharmaceutical University, 2-7 Daigakumachi, Takatsuki, Osaka, 569-8686, Japan
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3
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Rosello M, Serafini M, Concordet JP, Del Bene F. Precise mutagenesis in zebrafish using cytosine base editors. Nat Protoc 2023; 18:2794-2813. [PMID: 37495752 DOI: 10.1038/s41596-023-00854-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 05/11/2023] [Indexed: 07/28/2023]
Abstract
Base editing is a powerful CRISPR-based technology for introducing precise substitutions into the genome. This technology greatly advances mutagenesis possibilities in vivo, particularly in zebrafish, for which the generation of precise point mutations is still challenging. Zebrafish have emerged as an important model for genetic studies and in vivo disease modeling. With the development of different base editor variants that recognize protospacer-adjacent motifs (PAMs) other than the classical 5'-NGG-3' PAM, it is now possible to design and test several guide RNAs to find the most efficient way to precisely introduce the desired substitution. Here, we describe the experimental design strategies and protocols for cytosine base editing in zebrafish, from guide RNA design and selection of base editor variants to generation of the zebrafish mutant line carrying the substitution of interest. By using co-selection by introducing a loss-of-function mutation in genes necessary for the formation of pigments, injected embryos with highly efficient base editing can be directly analyzed to determine the phenotypic impact of the targeted substitution. The generation of mutant embryos after base editor injections in zebrafish can be completed within 2 weeks.
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Affiliation(s)
- Marion Rosello
- Sorbonne Université, INSERM U968, CNRS UMR 7210, Institut de la Vision, Paris, France.
| | - Malo Serafini
- Sorbonne Université, INSERM U968, CNRS UMR 7210, Institut de la Vision, Paris, France
| | - Jean-Paul Concordet
- Museúm National d'Histoire Naturelle, INSERM U1154, CNRS UMR 7196, Paris, France
| | - Filippo Del Bene
- Sorbonne Université, INSERM U968, CNRS UMR 7210, Institut de la Vision, Paris, France.
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4
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White RM, Patton EE. Adult zebrafish as advanced models of human disease. Dis Model Mech 2023; 16:dmm050351. [PMID: 37522272 PMCID: PMC10655866 DOI: 10.1242/dmm.050351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/01/2023] Open
Abstract
Modelling adult diseases to understand their aetiology and progression, and to develop new therapies, is a major challenge for medical biology. We are excited by new efforts in the zebrafish community to develop models of adult diseases that range from cancer to heart, infectious and age-related diseases, and those that relate to toxicology and complex social behaviours. Here, we discuss some of the advances in the field of zebrafish models of adult disease, and where we see opportunities and challenges ahead.
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Affiliation(s)
- Richard M. White
- Ludwig Cancer Institute, Nuffield Department of Medicine, Old Road Campus Research Building, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - E. Elizabeth Patton
- MRC Human Genetics Unit, CRUK Scotland Centre and Edinburgh Cancer Research, Institute of Genetics and Cancer, The University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh EH42XU, UK
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5
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Diogo P, Martins G, Simão M, Marreiros A, Eufrásio AC, Cabrita E, Gavaia PJ. Type I Diabetes in Zebrafish Reduces Sperm Quality and Increases Insulin and Glucose Transporter Transcripts. Int J Mol Sci 2023; 24:ijms24087035. [PMID: 37108202 PMCID: PMC10138585 DOI: 10.3390/ijms24087035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/03/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
Type I diabetes is a prominent human pathology with increasing incidence in the population; however, its cause is still unknown. This disease promotes detrimental effects on reproduction, such as lower sperm motility and DNA integrity. Hence, the investigation of the underlying mechanisms of this metabolic disturbance in reproduction and its transgenerational consequences is of the utmost importance. The zebrafish is a useful model for this research considering its high homology with human genes as well as its fast generation and regeneration abilities. Therefore, we aimed to investigate sperm quality and genes relevant to diabetes in the spermatozoa of Tg(ins:nfsb-mCherry) zebrafish, a model for type I diabetes. Diabetic Tg(ins:nfsb-mCherry) males showed significantly higher expression of transcripts for insulin a (insa) and glucose transporter (slc2a2) compared to controls. Sperm obtained from the same treatment group showed significantly lower sperm motility, plasma membrane viability, and DNA integrity compared to that from the control group. Upon sperm cryopreservation, sperm freezability was reduced, which could be a consequence of poor initial sperm quality. Altogether, the data showed similar detrimental effects related to type I diabetes in zebrafish spermatozoa at the cellular and molecular levels. Therefore, our study validates the zebrafish model for type I diabetes research in germ cells.
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Affiliation(s)
- Patrícia Diogo
- Faculty of Sciences and Technology (FCT), University of Algarve, 8005-139 Faro, Portugal
- Centre of Marine Sciences (CCMAR), University of Algarve, 8005-139 Faro, Portugal
- Necton-Companhia Portuguesa de Culturas Marinhas S.A, Belamandil s/n, 8700-152 Olhão, Portugal
| | - Gil Martins
- Faculty of Sciences and Technology (FCT), University of Algarve, 8005-139 Faro, Portugal
- Centre of Marine Sciences (CCMAR), University of Algarve, 8005-139 Faro, Portugal
- Faculty of Medicine and Biomedical Sciences (FMCB), University of Algarve, 8005-139 Faro, Portugal
| | - Márcio Simão
- Centre of Marine Sciences (CCMAR), University of Algarve, 8005-139 Faro, Portugal
- Faculty of Medicine and Biomedical Sciences (FMCB), University of Algarve, 8005-139 Faro, Portugal
| | - Ana Marreiros
- Faculty of Medicine and Biomedical Sciences (FMCB), University of Algarve, 8005-139 Faro, Portugal
- Algarve Biomedical Center (ABC), University of Algarve, 8005-139 Faro, Portugal
| | - Ana Catarina Eufrásio
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, 4200-135 Porto, Portugal
- Instituto de Biologia Molecular e Celular (IBMC), 4200-135 Porto, Portugal
| | - Elsa Cabrita
- Faculty of Sciences and Technology (FCT), University of Algarve, 8005-139 Faro, Portugal
- Centre of Marine Sciences (CCMAR), University of Algarve, 8005-139 Faro, Portugal
| | - Paulo Jorge Gavaia
- Centre of Marine Sciences (CCMAR), University of Algarve, 8005-139 Faro, Portugal
- Faculty of Medicine and Biomedical Sciences (FMCB), University of Algarve, 8005-139 Faro, Portugal
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6
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Porto VA, da Rocha Júnior ER, Ursulino JS, Porto RS, da Silva M, de Jesus LWO, Oliveira JMD, Crispim AC, Santos JCC, Aquino TMD. NMR-based metabolomics applied to ecotoxicology with zebrafish (Danio rerio) as a prominent model for metabolic profiling and biomarker discovery: Overviewing the most recent approaches. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 868:161737. [PMID: 36693575 DOI: 10.1016/j.scitotenv.2023.161737] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/28/2022] [Accepted: 01/17/2023] [Indexed: 06/17/2023]
Abstract
Metabolomics is an innovative approach used in the medical, toxicological, and biological sciences. As an interdisciplinary topic, metabolomics and its relation with the environment and toxicological research are extensive. The use of substances, such as drugs and pesticides, contributes to the continuous releasing of xenobiotics into the environment, harming organisms and their habitats. In this context, fish are important bioindicators of the environmental condition and have often been used as model species. Among them, zebrafish (Danio rerio) presents itself as a versatile and straightforward option due to its unique attributes for research. Zebrafish proves to be a valuable model for toxicity assays and also for metabolomics profiling by analytical tools. Thus, NMR-based metabolomics associated with statistical analysis can reasonably assist researchers in critical factors related to discovering and validating biomarkers through accurate diagnosis. Therefore, this review aimed to report the studies that applied zebrafish as a model for (eco)toxicological assays and essentially utilized NMR-based metabolomics analysis to assess the biochemical profile and thus suggest the potential biological marker.
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Affiliation(s)
- Viviane Amaral Porto
- Research Group on Therapeutic Strategies, Institute of Chemistry and Biotechnology, Federal University of Alagoas, Maceió, AL, Brazil.
| | | | - Jeferson Santana Ursulino
- Research Group on Therapeutic Strategies, Institute of Chemistry and Biotechnology, Federal University of Alagoas, Maceió, AL, Brazil
| | - Ricardo Silva Porto
- Institute of Chemistry and Biotechnology, Federal University of Alagoas, Maceió, AL, Brazil
| | - Marciliano da Silva
- Laboratory of Applied Animal Morphophysiology, Institute of Biological and Health Sciences, Federal University of Alagoas, Maceió, AL, Brazil
| | - Lázaro Wender Oliveira de Jesus
- Laboratory of Applied Animal Morphophysiology, Institute of Biological and Health Sciences, Federal University of Alagoas, Maceió, AL, Brazil
| | | | - Alessandre Carmo Crispim
- Research Group on Therapeutic Strategies, Institute of Chemistry and Biotechnology, Federal University of Alagoas, Maceió, AL, Brazil
| | | | - Thiago Mendonça de Aquino
- Research Group on Therapeutic Strategies, Institute of Chemistry and Biotechnology, Federal University of Alagoas, Maceió, AL, Brazil
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7
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Maciag M, Plazinski W, Pulawski W, Kolinski M, Jozwiak K, Plazinska A. A comprehensive pharmacological analysis of fenoterol and its derivatives to unravel the role of β 2-adrenergic receptor in zebrafish. Biomed Pharmacother 2023; 160:114355. [PMID: 36739761 DOI: 10.1016/j.biopha.2023.114355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
β-adrenergic receptors (βARs) belong to a key molecular targets that regulate the most important processes occurring in the human organism. Although over the last decades a zebrafish model has been developed as a model complementary to rodents in biomedical research, the role of β2AR in regulation of pathological and toxicological effects remains to elucidate. Therefore, the study aimed to clarify the role of β2AR with a particular emphasis on the distinct role of subtypes A and B of zebrafish β2AR. As model compounds selective β2AR agonists - (R,R)-fenoterol ((R,R)-Fen) and its new derivatives: (R,R)-4'-methoxyfenoterol ((R,R)-MFen) and (R,R)-4'-methoxy-1-naphtylfenoterol ((R,R)-MNFen) - were tested. We described dose-dependent changes observed after fenoterols exposure in terms of general toxicity, cardiotoxicity and neurobehavioural responses. Subsequently, to better characterise the role of β2-adrenergic stimulation in zebrafish, we have performed a series of molecular docking simulations. Our results indicate that (R,R)-Fen displays the highest affinity for subtype A of zebrafish β2AR and β2AAR might be involved in pigment depletion. (R,R)-MFen shows the lowest affinity for zebrafish β2ARs out of the tested fenoterols and this might be associated with its cardiotoxic and anxiogenic effects. (R,R)-MNFen displays the highest affinity for subtype B of zebrafish β2AR and modulation of this receptor might be associated with the development of malformations, increases locomotor activity and induces a negative chronotropic effect. Taken together, the presented data offer insights into the functional responses of the zebrafish β2ARs confirming their intraspecies conservation, and support the translation of the zebrafish model in pharmacological and toxicological research.
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Affiliation(s)
- Monika Maciag
- Department of Biopharmacy, Medical University of Lublin, 4a Chodzki Street, 20-093 Lublin, Poland; Independent Laboratory of Behavioral Studies, Medical University of Lublin, 4a Chodzki Street, 20-093 Lublin, Poland.
| | - Wojciech Plazinski
- Department of Biopharmacy, Medical University of Lublin, 4a Chodzki Street, 20-093 Lublin, Poland; Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 8 Niezapominajek Street, 30-239 Cracow, Poland
| | - Wojciech Pulawski
- Bioinformatics Laboratory, Mossakowski Medical Research Centre, Polish Academy of Sciences, e Pawinskiego Street, 02-106 Warsaw, Poland
| | - Michal Kolinski
- Bioinformatics Laboratory, Mossakowski Medical Research Centre, Polish Academy of Sciences, e Pawinskiego Street, 02-106 Warsaw, Poland
| | - Krzysztof Jozwiak
- Department of Biopharmacy, Medical University of Lublin, 4a Chodzki Street, 20-093 Lublin, Poland
| | - Anita Plazinska
- Department of Biopharmacy, Medical University of Lublin, 4a Chodzki Street, 20-093 Lublin, Poland.
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8
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Petry F, Oltramari AR, Kuhn KZ, Schneider SE, Mazon SC, Garbinato CLL, Aguiar GPS, Kreutz LC, Oliveira JV, Siebel AM, Müller LG. Fluoxetine and Curcumin Prevent the Alterations in Locomotor and Exploratory Activities and Social Interaction Elicited by Immunoinflammatory Activation in Zebrafish: Involvement of BDNF and Proinflammatory Cytokines. ACS Chem Neurosci 2023; 14:389-399. [PMID: 36634245 DOI: 10.1021/acschemneuro.2c00475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The increase in proinflammatory cytokine expression causes behavioral changes consistent with sickness behavior, and this led to the suggestion that depression might be a psychoneuroimmunological phenomenon. Here, we evaluated the effects of the pretreatment with fluoxetine (10 mg/kg, i.p.) and curcumin (0.5 mg/kg, i.p.) on the immune response elicited by the inoculation of an Aeromonas hydrophila bacterin in zebrafish. Non-pretreated but A. hydrophila-inoculated and sham-inoculated groups of fish served as controls. The social preference, locomotor, exploratory activities, and cerebral expression of il1b, il6, tnfa, and bdnf mRNA were compared among the groups. Behavioral changes characteristic of sickness behavior and a significant increase in the expression of il1b and il6 cytokines were found in fish from the immunostimulated group. The behavioral alterations caused by the inflammatory process were different between males and females, which was coincident with the increased expression of cerebral BDNF. Fluoxetine and curcumin prevented the sickness behavior induced by A. hydrophila and the increased expression of proinflammatory cytokines. Our results point to the potential of zebrafish as a translational model in studies related to neuroinflammation and demonstrate for the first time the effects of fluoxetine and curcumin on zebrafish sickness behavior.
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Affiliation(s)
- Fernanda Petry
- Graduate Program in Environmental Sciences, Community University of Chapecó Region (Unochapecó), Servidão Anjo da Guarda, 295 D, Chapecó, Santa Catarina89809-900, Brazil
| | - Amanda R Oltramari
- School of Agriculture and Environment, Community University of Chapecó Region (Unochapecó), Servidão Anjo da Guarda, 295 D, Chapecó, Santa Catarina89809-900, Brazil
| | - Ketelin Z Kuhn
- School of Health Sciences, Community University of Chapecó Region (Unochapecó), Servidão Anjo da Guarda, 295 D, Chapecó, Santa Catarina89809-900, Brazil
| | - Sabrina E Schneider
- School of Agriculture and Environment, Community University of Chapecó Region (Unochapecó), Servidão Anjo da Guarda, 295 D, Chapecó, Santa Catarina89809-900, Brazil
| | - Samara C Mazon
- Graduate Program in Environmental Sciences, Community University of Chapecó Region (Unochapecó), Servidão Anjo da Guarda, 295 D, Chapecó, Santa Catarina89809-900, Brazil
| | - Cristiane L L Garbinato
- Graduate Program in Environmental Sciences, Community University of Chapecó Region (Unochapecó), Servidão Anjo da Guarda, 295 D, Chapecó, Santa Catarina89809-900, Brazil
| | - Gean P S Aguiar
- Graduate Program in Environmental Sciences, Community University of Chapecó Region (Unochapecó), Servidão Anjo da Guarda, 295 D, Chapecó, Santa Catarina89809-900, Brazil
| | - Luiz C Kreutz
- Laboratory of Advanced Microbiology and Immunology, Graduate Program in Bioexperimentation, University of Passo Fundo (UPF), BR 285, São José, Passo Fundo, Rio Grande do Sul99052-900, Brazil
| | - J Vladimir Oliveira
- Department of Chemical and Food Engineering, Federal University of Santa Catarina (UFSC), R. Eng. Agronômico Andrei Cristian Ferreira, Trindade, Florianópolis, Santa Catarina88040-900, Brazil
| | - Anna M Siebel
- Institute of Biological Sciences, Federal University of Rio Grande, Av. Itália, Km 8, Rio Grande, Rio Grande do Sul96203-900, Brazil
| | - Liz G Müller
- Graduate Program in Environmental Sciences, Community University of Chapecó Region (Unochapecó), Servidão Anjo da Guarda, 295 D, Chapecó, Santa Catarina89809-900, Brazil.,School of Health Sciences, Community University of Chapecó Region (Unochapecó), Servidão Anjo da Guarda, 295 D, Chapecó, Santa Catarina89809-900, Brazil
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9
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Baranasic D, Hörtenhuber M, Balwierz PJ, Zehnder T, Mukarram AK, Nepal C, Várnai C, Hadzhiev Y, Jimenez-Gonzalez A, Li N, Wragg J, D'Orazio FM, Relic D, Pachkov M, Díaz N, Hernández-Rodríguez B, Chen Z, Stoiber M, Dong M, Stevens I, Ross SE, Eagle A, Martin R, Obasaju O, Rastegar S, McGarvey AC, Kopp W, Chambers E, Wang D, Kim HR, Acemel RD, Naranjo S, Łapiński M, Chong V, Mathavan S, Peers B, Sauka-Spengler T, Vingron M, Carninci P, Ohler U, Lacadie SA, Burgess SM, Winata C, van Eeden F, Vaquerizas JM, Gómez-Skarmeta JL, Onichtchouk D, Brown BJ, Bogdanovic O, van Nimwegen E, Westerfield M, Wardle FC, Daub CO, Lenhard B, Müller F. Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements. Nat Genet 2022; 54:1037-1050. [PMID: 35789323 PMCID: PMC9279159 DOI: 10.1038/s41588-022-01089-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 05/03/2022] [Indexed: 12/12/2022]
Abstract
Zebrafish, a popular organism for studying embryonic development and for modeling human diseases, has so far lacked a systematic functional annotation program akin to those in other animal models. To address this, we formed the international DANIO-CODE consortium and created a central repository to store and process zebrafish developmental functional genomic data. Our data coordination center ( https://danio-code.zfin.org ) combines a total of 1,802 sets of unpublished and re-analyzed published genomic data, which we used to improve existing annotations and show its utility in experimental design. We identified over 140,000 cis-regulatory elements throughout development, including classes with distinct features dependent on their activity in time and space. We delineated the distinct distance topology and chromatin features between regulatory elements active during zygotic genome activation and those active during organogenesis. Finally, we matched regulatory elements and epigenomic landscapes between zebrafish and mouse and predicted functional relationships between them beyond sequence similarity, thus extending the utility of zebrafish developmental genomics to mammals.
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Affiliation(s)
- Damir Baranasic
- MRC London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, UK
| | - Matthias Hörtenhuber
- Department of Biosciences and Nutrition, Karolinska Institutet, NEO, Huddinge, Sweden
| | - Piotr J Balwierz
- MRC London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, UK
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Tobias Zehnder
- MRC London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, UK
- Max Planck Institute for Molecular Genetics, Department of Computational Molecular Biology, Berlin, Germany
| | - Abdul Kadir Mukarram
- Department of Biosciences and Nutrition, Karolinska Institutet, NEO, Huddinge, Sweden
| | - Chirag Nepal
- Biotech Research and Innovation Centre (BRIC), Department of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Csilla Várnai
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- Centre for Computational Biology, University of Birmingham, Birmingham, UK
| | - Yavor Hadzhiev
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Ada Jimenez-Gonzalez
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Nan Li
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Joseph Wragg
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Fabio M D'Orazio
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Dorde Relic
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Mikhail Pachkov
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Noelia Díaz
- Max Planck Institute for Molecular Biomedicine, Muenster, Germany
- Institute of Marine Sciences, Barcelona, Spain
| | | | - Zelin Chen
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Marcus Stoiber
- Environmental Genomics & Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Michaël Dong
- Department of Biosciences and Nutrition, Karolinska Institutet, NEO, Huddinge, Sweden
| | - Irene Stevens
- Department of Biosciences and Nutrition, Karolinska Institutet, NEO, Huddinge, Sweden
| | - Samuel E Ross
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Anne Eagle
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | - Ryan Martin
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | - Oluwapelumi Obasaju
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Sepand Rastegar
- Institute of Biological and Chemical Systems - Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Alison C McGarvey
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Wolfgang Kopp
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Emily Chambers
- Sheffield Bioinformatics Core, Sheffield Institute of Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Dennis Wang
- Sheffield Bioinformatics Core, Sheffield Institute of Translational Neuroscience, University of Sheffield, Sheffield, UK
- Singapore Institute for Clinical Sciences, Singapore, Singapore
| | - Hyejeong R Kim
- Bateson Centre/Biomedical Science, University of Sheffield, Sheffield, UK
| | - Rafael D Acemel
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
- Epigenetics and Sex Development Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Silvia Naranjo
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - Maciej Łapiński
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Vanessa Chong
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | | | - Bernard Peers
- Laboratory of Zebrafish Development and Disease Models (ZDDM), GIGA-R, SART TILMAN, University of Liège, Liège, Belgium
| | - Tatjana Sauka-Spengler
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Martin Vingron
- Max Planck Institute for Molecular Genetics, Department of Computational Molecular Biology, Berlin, Germany
| | - Piero Carninci
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Fondazione Human Technopole, Milano, Italy
| | - Uwe Ohler
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
- Institute of Biology, Humboldt University, Berlin, Germany
| | - Scott Allen Lacadie
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Shawn M Burgess
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
| | - Cecilia Winata
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Freek van Eeden
- Bateson Centre/Biomedical Science, University of Sheffield, Sheffield, UK
| | - Juan M Vaquerizas
- MRC London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, UK
- Max Planck Institute for Molecular Biomedicine, Muenster, Germany
| | - José Luis Gómez-Skarmeta
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - Daria Onichtchouk
- Department of Developmental Biology, Signalling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Ben James Brown
- Environmental Genomics & Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ozren Bogdanovic
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Erik van Nimwegen
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland
| | | | - Fiona C Wardle
- Randall Centre for Cell & Molecular Biophysics, Guy's Campus, King's College London, London, UK
| | - Carsten O Daub
- Department of Biosciences and Nutrition, Karolinska Institutet, NEO, Huddinge, Sweden.
- Science for Life Laboratory, Solna, Sweden.
| | - Boris Lenhard
- MRC London Institute of Medical Sciences, London, UK.
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, UK.
| | - Ferenc Müller
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.
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10
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Gazzi T, Brennecke B, Atz K, Korn C, Sykes D, Forn-Cuni G, Pfaff P, Sarott RC, Westphal MV, Mostinski Y, Mach L, Wasinska-Kalwa M, Weise M, Hoare BL, Miljuš T, Mexi M, Roth N, Koers EJ, Guba W, Alker A, Rufer AC, Kusznir EA, Huber S, Raposo C, Zirwes EA, Osterwald A, Pavlovic A, Moes S, Beck J, Nettekoven M, Benito-Cuesta I, Grande T, Drawnel F, Widmer G, Holzer D, van der Wel T, Mandhair H, Honer M, Fingerle J, Scheffel J, Broichhagen J, Gawrisch K, Romero J, Hillard CJ, Varga ZV, van der Stelt M, Pacher P, Gertsch J, Ullmer C, McCormick PJ, Oddi S, Spaink HP, Maccarrone M, Veprintsev DB, Carreira EM, Grether U, Nazaré M. Detection of cannabinoid receptor type 2 in native cells and zebrafish with a highly potent, cell-permeable fluorescent probe. Chem Sci 2022; 13:5539-5545. [PMID: 35694350 PMCID: PMC9116301 DOI: 10.1039/d1sc06659e] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/22/2022] [Indexed: 12/16/2022] Open
Abstract
Despite its essential role in the (patho)physiology of several diseases, CB2R tissue expression profiles and signaling mechanisms are not yet fully understood. We report the development of a highly potent, fluorescent CB2R agonist probe employing structure-based reverse design. It commences with a highly potent, preclinically validated ligand, which is conjugated to a silicon-rhodamine fluorophore, enabling cell permeability. The probe is the first to preserve interspecies affinity and selectivity for both mouse and human CB2R. Extensive cross-validation (FACS, TR-FRET and confocal microscopy) set the stage for CB2R detection in endogenously expressing living cells along with zebrafish larvae. Together, these findings will benefit clinical translatability of CB2R based drugs. Detection and visualization of the cannabinoid receptor type 2 by a cell-permeable high affinity fluorescent probe platform enables tracing receptor trafficking in live cells and in zebrafish.![]()
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Affiliation(s)
- Thais Gazzi
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Campus Berlin-Buch 13125 Berlin Germany
| | - Benjamin Brennecke
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Campus Berlin-Buch 13125 Berlin Germany
| | - Kenneth Atz
- Roche Pharma Research & Early Development, Roche Innovation Center Basel F. Hoffmann-La Roche Ltd. 4070 Basel Switzerland
| | - Claudia Korn
- Roche Pharma Research & Early Development, Roche Innovation Center Basel F. Hoffmann-La Roche Ltd. 4070 Basel Switzerland
| | - David Sykes
- Faculty of Medicine & Health Sciences, University of Nottingham Nottingham NG7 2UH England UK.,United Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham Midlands England UK
| | | | - Patrick Pfaff
- Laboratorium für Organische Chemie, Eidgenössische Technische Hochschule Zürich Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| | - Roman C Sarott
- Laboratorium für Organische Chemie, Eidgenössische Technische Hochschule Zürich Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| | - Matthias V Westphal
- Laboratorium für Organische Chemie, Eidgenössische Technische Hochschule Zürich Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| | - Yelena Mostinski
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Campus Berlin-Buch 13125 Berlin Germany
| | - Leonard Mach
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Campus Berlin-Buch 13125 Berlin Germany
| | - Malgorzata Wasinska-Kalwa
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Campus Berlin-Buch 13125 Berlin Germany
| | - Marie Weise
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Campus Berlin-Buch 13125 Berlin Germany
| | - Bradley L Hoare
- Faculty of Medicine & Health Sciences, University of Nottingham Nottingham NG7 2UH England UK.,United Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham Midlands England UK
| | - Tamara Miljuš
- Faculty of Medicine & Health Sciences, University of Nottingham Nottingham NG7 2UH England UK.,United Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham Midlands England UK
| | - Maira Mexi
- Faculty of Medicine & Health Sciences, University of Nottingham Nottingham NG7 2UH England UK.,United Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham Midlands England UK
| | - Nicolas Roth
- William Harvey Research Institute, Barts and the London School of Medicine, Queen Mary University of London London EC1M 6BQ England UK
| | - Eline J Koers
- Faculty of Medicine & Health Sciences, University of Nottingham Nottingham NG7 2UH England UK.,United Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham Midlands England UK
| | - Wolfgang Guba
- Roche Pharma Research & Early Development, Roche Innovation Center Basel F. Hoffmann-La Roche Ltd. 4070 Basel Switzerland
| | - André Alker
- Roche Pharma Research & Early Development, Roche Innovation Center Basel F. Hoffmann-La Roche Ltd. 4070 Basel Switzerland
| | - Arne C Rufer
- Roche Pharma Research & Early Development, Roche Innovation Center Basel F. Hoffmann-La Roche Ltd. 4070 Basel Switzerland
| | - Eric A Kusznir
- Roche Pharma Research & Early Development, Roche Innovation Center Basel F. Hoffmann-La Roche Ltd. 4070 Basel Switzerland
| | - Sylwia Huber
- Roche Pharma Research & Early Development, Roche Innovation Center Basel F. Hoffmann-La Roche Ltd. 4070 Basel Switzerland
| | - Catarina Raposo
- Roche Pharma Research & Early Development, Roche Innovation Center Basel F. Hoffmann-La Roche Ltd. 4070 Basel Switzerland
| | - Elisabeth A Zirwes
- Roche Pharma Research & Early Development, Roche Innovation Center Basel F. Hoffmann-La Roche Ltd. 4070 Basel Switzerland
| | - Anja Osterwald
- Roche Pharma Research & Early Development, Roche Innovation Center Basel F. Hoffmann-La Roche Ltd. 4070 Basel Switzerland
| | - Anto Pavlovic
- Roche Pharma Research & Early Development, Roche Innovation Center Basel F. Hoffmann-La Roche Ltd. 4070 Basel Switzerland
| | - Svenja Moes
- Roche Pharma Research & Early Development, Roche Innovation Center Basel F. Hoffmann-La Roche Ltd. 4070 Basel Switzerland
| | - Jennifer Beck
- Roche Pharma Research & Early Development, Roche Innovation Center Basel F. Hoffmann-La Roche Ltd. 4070 Basel Switzerland
| | - Matthias Nettekoven
- Roche Pharma Research & Early Development, Roche Innovation Center Basel F. Hoffmann-La Roche Ltd. 4070 Basel Switzerland
| | - Irene Benito-Cuesta
- Faculty of Experimental Sciences, Universidad Francisco de Vitoria Pozuelo de Alarcón 28223 Madrid Spain
| | - Teresa Grande
- Faculty of Experimental Sciences, Universidad Francisco de Vitoria Pozuelo de Alarcón 28223 Madrid Spain
| | - Faye Drawnel
- Roche Pharma Research & Early Development, Roche Innovation Center Basel F. Hoffmann-La Roche Ltd. 4070 Basel Switzerland
| | - Gabriella Widmer
- Roche Pharma Research & Early Development, Roche Innovation Center Basel F. Hoffmann-La Roche Ltd. 4070 Basel Switzerland
| | - Daniela Holzer
- Roche Pharma Research & Early Development, Roche Innovation Center Basel F. Hoffmann-La Roche Ltd. 4070 Basel Switzerland
| | - Tom van der Wel
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University 2333 CC Leiden the Netherlands
| | - Harpreet Mandhair
- Institute of Biochemistry and Molecular Medicine, University of Bern 3012 Bern Switzerland
| | - Michael Honer
- Roche Pharma Research & Early Development, Roche Innovation Center Basel F. Hoffmann-La Roche Ltd. 4070 Basel Switzerland
| | - Jürgen Fingerle
- Roche Pharma Research & Early Development, Roche Innovation Center Basel F. Hoffmann-La Roche Ltd. 4070 Basel Switzerland
| | - Jörg Scheffel
- Dermatological Allergology, Allergie-Centrum-Charité, Department of Dermatology and Allergy, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin Berlin Germany.,Allergology, Fraunhofer Institute for Translational Medicine and Pharmacology ITMP Berlin Germany
| | - Johannes Broichhagen
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Campus Berlin-Buch 13125 Berlin Germany
| | - Klaus Gawrisch
- National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health Rockville MD 20852 USA
| | - Julián Romero
- Faculty of Experimental Sciences, Universidad Francisco de Vitoria Pozuelo de Alarcón 28223 Madrid Spain
| | - Cecilia J Hillard
- Department of Pharmacology and Toxicology, Neuroscience Research Center, Medical College of Wisconsin Milwaukee WI 53226 USA
| | - Zoltan V Varga
- National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health Rockville MD 20852 USA.,HCEMM-SU Cardiometabolic Immunology Research Group, Department of Pharmacology and Pharmacotherapy, Semmelweis University 1085 Budapest Hungary
| | - Mario van der Stelt
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University 2333 CC Leiden the Netherlands
| | - Pal Pacher
- National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health Rockville MD 20852 USA
| | - Jürg Gertsch
- Institute of Biochemistry and Molecular Medicine, University of Bern 3012 Bern Switzerland
| | - Christoph Ullmer
- Roche Pharma Research & Early Development, Roche Innovation Center Basel F. Hoffmann-La Roche Ltd. 4070 Basel Switzerland
| | - Peter J McCormick
- William Harvey Research Institute, Barts and the London School of Medicine, Queen Mary University of London London EC1M 6BQ England UK
| | - Sergio Oddi
- Faculty of Veterinary Medicine, University of Teramo 64100 Teramo European Italy.,European Center for Brain Research (CERC), Santa Lucia Foundation 00179 Rome Italy
| | - Herman P Spaink
- Leiden University Einsteinweg 55 2333 CC Leiden the Netherlands
| | - Mauro Maccarrone
- European Center for Brain Research (CERC), Santa Lucia Foundation 00179 Rome Italy.,Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila 67100 L'Aquila Italy
| | - Dmitry B Veprintsev
- Faculty of Medicine & Health Sciences, University of Nottingham Nottingham NG7 2UH England UK.,United Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham Midlands England UK
| | - Erick M Carreira
- Laboratorium für Organische Chemie, Eidgenössische Technische Hochschule Zürich Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| | - Uwe Grether
- Roche Pharma Research & Early Development, Roche Innovation Center Basel F. Hoffmann-La Roche Ltd. 4070 Basel Switzerland
| | - Marc Nazaré
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Campus Berlin-Buch 13125 Berlin Germany
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11
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Type 2 Diabetes Induced by Changes in Proteomic Profiling of Zebrafish Chronically Exposed to a Mixture of Organochlorine Pesticides at Low Concentrations. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19094991. [PMID: 35564385 PMCID: PMC9100612 DOI: 10.3390/ijerph19094991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/07/2022] [Accepted: 04/15/2022] [Indexed: 02/04/2023]
Abstract
Effect of organochlorine pesticides (OCPs) mixtures on development of type 2 diabetes mellitus (T2DM) and the underlying mechanism, especially at protein levels, are largely unknown. We exposed a mixture of five OCPs to zebrafish at concentrations of 0, 0.05, 0.25, 2.5, and 25 μg/L for 12 weeks. Differentially expressed proteins (DEPs) were quantitatively identified in female zebrafish livers, and its functional study was conducted. The significantly high glucose and low insulin levels were observed only at 0.05 μg/L, linking to the different pattern of DEPs than other concentrations. A total of 1082 proteins was quantified, of which 321 proteins formed 6 clusters in protein dynamics analysis. The enriched pathways in cluster 3 showing distinct pattern of DEPs could explain the nonlinear response at 0.05 μg/L, indicating that OCP mixtures adversely affected proteins associated with mitochondrial function and energy metabolism. We proposed a feasible mechanism that decrease in expression of aldehyde dehydrogenase led to abnormal accumulation of aldehydes, reducing expression of glyceraldehyde 3-phosphate dehydrogenase, and resulting in disruption of glucose homeostasis. Our findings help to better understand the causality of T2DM by exposure to OCP mixtures and to identify biomarkers in the protein expression level.
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12
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Australindolones, New Aminopyrimidine Substituted Indolone Alkaloids from an Antarctic Tunicate Synoicum sp. Mar Drugs 2022; 20:md20030196. [PMID: 35323495 PMCID: PMC8949045 DOI: 10.3390/md20030196] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/01/2022] [Accepted: 03/06/2022] [Indexed: 02/01/2023] Open
Abstract
Five new alkaloids have been isolated from the lipophilic extract of the Antarctic tunicate Synoicum sp. Deep-sea specimens of Synoicum sp. were collected during a 2011 cruise of the R/V Nathanial B. Palmer to the southern Scotia Arc, Antarctica. Crude extracts from the invertebrates obtained during the cruise were screened in a zebrafish-based phenotypic assay. The Synoicum sp. extract induced embryonic dysmorphology characterized by axis truncation, leading to the isolation of aminopyrimidine substituted indolone (1–4) and indole (5–12) alkaloids. While the primary bioactivity tracked with previously reported meridianins A–G (5–11), further investigation resulted in the isolation and characterization of australindolones A–D (1–4) and the previously unreported meridianin H (12).
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13
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Dubey S, Diep DB, Evensen Ø, Munang’andu HM. Garvicin KS, a Broad-Spectrum Bacteriocin Protects Zebrafish Larvae against Lactococcus garvieae Infection. Int J Mol Sci 2022; 23:ijms23052833. [PMID: 35269976 PMCID: PMC8910950 DOI: 10.3390/ijms23052833] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 02/28/2022] [Accepted: 03/01/2022] [Indexed: 12/19/2022] Open
Abstract
Bacteriocins are emerging as a viable alternative to antibiotics due to their ability to inhibit growth or kill antibiotic resistant pathogens. Herein, we evaluated the ability of the bacteriocin Garvicin KS (GarKS) produced by Lactococcus garvieae KS1546 isolated from cow milk to inhibit the growth of fish and foodborne bacterial pathogens. We found that GarKS inhibited the growth of five fish L. garvieae strains isolated from infected trout and eels. Among fish pathogens, GarKS inhibited the growth of Streptococcus agalactiae serotypes Ia and Ib, and Aeromonas hydrophila but did not inhibit the growth of Edwardsiella tarda. In addition, it inhibited the growth of A. salmonicida strain 6421 but not A. salmonicida strain 6422 and Yersinia ruckeri. There was no inhibition of three foodborne bacterial species, namely Salmonella enterica, Klebsiella pneumoniae, and Escherichia coli. In vitro cytotoxicity tests using different GarKS concentrations showed that the highest concentration of 33 µg/mL exhibited low cytotoxicity, while concentrations ≤3.3 µg/mL had no cytotoxicity on CHSE-214 and RTG-2 cells. In vivo tests showed that zebrafish larvae treated with 33 µg/mL and 3.3 µg/mL GarKS prior to challenge had 53% and 48% survival, respectively, while concentrations ≤0.33 µg/mL were nonprotective. Altogether, these data show that GarKS has a broad inhibitory spectrum against Gram positive and negative bacteria and that it has potential applications as a therapeutic agent for a wide range of bacterial pathogens. Thus, future studies should include clinical trials to test the efficacy of GarKS against various bacterial pathogens in farmed fish.
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Affiliation(s)
- Saurabh Dubey
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, P.O. Box 5003, 1433 Ås, Norway; (S.D.); (Ø.E.)
- Department of Production Medicine, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, P.O. Box 5003, 1433 Ås, Norway
| | - Dzung B. Diep
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1433 Ås, Norway;
| | - Øystein Evensen
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, P.O. Box 5003, 1433 Ås, Norway; (S.D.); (Ø.E.)
| | - Hetron M. Munang’andu
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, P.O. Box 5003, 1433 Ås, Norway; (S.D.); (Ø.E.)
- Department of Production Medicine, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, P.O. Box 5003, 1433 Ås, Norway
- Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway
- Correspondence: ; Tel.: +47-98-86-86-83
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14
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Lee JG, Lee S, Jeon J, Kong HG, Cho HJ, Kim JH, Kim SY, Oh MJ, Lee D, Seo N, Park KH, Yu K, An HJ, Ryu CM, Lee JS. Host tp53 mutation induces gut dysbiosis eliciting inflammation through disturbed sialic acid metabolism. MICROBIOME 2022; 10:3. [PMID: 34991725 PMCID: PMC8733924 DOI: 10.1186/s40168-021-01191-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 11/07/2021] [Indexed: 05/02/2023]
Abstract
BACKGROUND Host tp53 mutations are frequently found during the early stages of colitis-associated colorectal cancer (CAC), but whether such mutations induce gut microbiota dysbiosis and chronic intestinal inflammation that contributes to the development of CAC, remains unknown. RESULTS We found that zebrafish tp53 mutant larvae exhibited elevated intestinal inflammation, by monitoring the NFκB activity in the mid-distal intestines of zebrafish larvae using an NFκB:EGFP transgenic reporter line in vivo as well as neutrophil infiltration into the intestine. This inflammation was due to dysbiotic gut microbiota with reduced diversity, revealed using both 16S rRNA amplicon sequencing and a germfree larva model. In this dysbiosis, Aeromonas spp. were aberrantly enriched as major pathobionts and exhibited the capacity for aggressive colonization in tp53 mutants. Importantly, the ex-germfree experiments supported the causality of the host tp53 mutation for inducing the inflammation. Transcriptome and high-performance liquid chromatography analyses of the host gastrointestinal tracts identified dysregulated sialic acid (SA) metabolism concomitant with increased host Neu5Gc levels as the key determinant of aberrant inflammation, which was reversed by the sialidase inhibitors oseltamivir and Philippin A. CONCLUSIONS These results demonstrate a crucial role for host tp53 in maintaining symbiosis and immune homeostasis via SA metabolism. Disturbed SA metabolism via a tp53 mutation may be exploited by specific elements of the gut microbiome, eliciting both dysbiosis and inflammation. Manipulating sialometabolism may therefore provide an efficacious therapeutic strategy for tp53 mutation-induced dysbiosis, inflammation, and ultimately, related cancers. Video Abstract.
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Affiliation(s)
- Jae-Geun Lee
- Disease Target Structure Research Center, KRIBB, Daejeon, 34141, Republic of Korea
- KRIBB School, University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea
| | - Soohyun Lee
- Infectious Disease Research Center, KRIBB, Daejeon, 34141, Republic of Korea
| | - Juhee Jeon
- Disease Target Structure Research Center, KRIBB, Daejeon, 34141, Republic of Korea
- Stembio. Ltd, Entrepreneur 306, Soonchunhyang-ro 22, Sinchang-myeon, Asan-si, Chungcheongnam-do, 31538, Republic of Korea
| | - Hyun Gi Kong
- Infectious Disease Research Center, KRIBB, Daejeon, 34141, Republic of Korea
- Crop Protection Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do, 54875, Republic of Korea
| | - Hyun-Ju Cho
- Disease Target Structure Research Center, KRIBB, Daejeon, 34141, Republic of Korea
- Dementia DTC R&D Convergence Program, KIST, Hwarang-ro 14 gil 5, Seongbuk-gu, Seoul, 02792, Republic of Korea
| | - Jong-Hwan Kim
- Korean Bioinformation Center, KRIBB, Daejeon, 34141, Republic of Korea
| | - Seon-Young Kim
- KRIBB School, University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea
- Korean Bioinformation Center, KRIBB, Daejeon, 34141, Republic of Korea
| | - Myung Jin Oh
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Daum Lee
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Nari Seo
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Ki Hun Park
- Division of Applied Life Science (BK21 plus), IALS, Gyeongsang National University, Jinju-si, Gyeongsangnam-do, 52828, Republic of Korea
| | - Kweon Yu
- Disease Target Structure Research Center, KRIBB, Daejeon, 34141, Republic of Korea
- KRIBB School, University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea
- Dementia DTC R&D Convergence Program, KIST, Hwarang-ro 14 gil 5, Seongbuk-gu, Seoul, 02792, Republic of Korea
| | - Hyun Joo An
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Choong-Min Ryu
- KRIBB School, University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea.
- Infectious Disease Research Center, KRIBB, Daejeon, 34141, Republic of Korea.
| | - Jeong-Soo Lee
- Disease Target Structure Research Center, KRIBB, Daejeon, 34141, Republic of Korea.
- KRIBB School, University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea.
- Dementia DTC R&D Convergence Program, KIST, Hwarang-ro 14 gil 5, Seongbuk-gu, Seoul, 02792, Republic of Korea.
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15
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Braems E, Tziortzouda P, Van Den Bosch L. Exploring the alternative: Fish, flies and worms as preclinical models for ALS. Neurosci Lett 2021; 759:136041. [PMID: 34118308 DOI: 10.1016/j.neulet.2021.136041] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 04/15/2021] [Accepted: 06/01/2021] [Indexed: 12/22/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is an incurable neurodegenerative disorder characterized by the loss of upper and lower motor neurons. In general, patients succumb to respiratory insufficiency due to respiratory muscle weakness. Despite many promising therapeutic strategies primarily identified in rodent models, patient trials remain rather unsuccessful. There is a clear need for alternative approaches, which could provide directions towards the justified use of rodents and which increase the likelihood to identify new promising clinical candidates. In the last decades, the use of fast genetic approaches and the development of high-throughput screening platforms in the nematode Caenorhabditis elegans, in the fruit fly (Drosophila melanogaster) and in zebrafish (Danio rerio) have contributed to new insights into ALS pathomechanisms, disease modifiers and therapeutic targets. In this mini-review, we provide an overview of these alternative small animal studies, modeling the most common ALS genes and discuss the most recent preclinical discoveries. We conclude that small animal models will not replace rodent models, yet they clearly represent an important asset for preclinical studies.
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Affiliation(s)
- Elke Braems
- KU Leuven - University of Leuven, Department of Neurosciences, Experimental Neurology, and Leuven Brain Institute (LBI), Leuven, Belgium; VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, Leuven, Belgium
| | - Paraskevi Tziortzouda
- KU Leuven - University of Leuven, Department of Neurosciences, Experimental Neurology, and Leuven Brain Institute (LBI), Leuven, Belgium; VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, Leuven, Belgium
| | - Ludo Van Den Bosch
- KU Leuven - University of Leuven, Department of Neurosciences, Experimental Neurology, and Leuven Brain Institute (LBI), Leuven, Belgium; VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, Leuven, Belgium.
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16
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Figiel DM, Elsayed R, Nelson AC. Investigating the molecular guts of endoderm formation using zebrafish. Brief Funct Genomics 2021:elab013. [PMID: 33754635 DOI: 10.1093/bfgp/elab013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 01/27/2021] [Accepted: 02/19/2021] [Indexed: 02/07/2023] Open
Abstract
The vertebrate endoderm makes major contributions to the respiratory and gastrointestinal tracts and all associated organs. Zebrafish and humans share a high degree of genetic homology and strikingly similar endodermal organ systems. Combined with a multitude of experimental advantages, zebrafish are an attractive model organism to study endoderm development and disease. Recent functional genomics studies have shed considerable light on the gene regulatory programs governing early zebrafish endoderm development, while advances in biological and technological approaches stand to further revolutionize our ability to investigate endoderm formation, function and disease. Here, we discuss the present understanding of endoderm specification in zebrafish compared to other vertebrates, how current and emerging methods will allow refined and enhanced analysis of endoderm formation, and how integration with human data will allow modeling of the link between non-coding sequence variants and human disease.
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Affiliation(s)
- Daniela M Figiel
- Medical Research Council Doctoral Training Partnership in Interdisciplinary Biomedical Research at Warwick Medical School
| | - Randa Elsayed
- Medical Research Council Doctoral Training Partnership in Interdisciplinary Biomedical Research at Warwick Medical School
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17
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Housing, Husbandry and Welfare of a "Classic" Fish Model, the Paradise Fish ( Macropodus opercularis). Animals (Basel) 2021; 11:ani11030786. [PMID: 33799915 PMCID: PMC8000575 DOI: 10.3390/ani11030786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 03/03/2021] [Accepted: 03/07/2021] [Indexed: 11/17/2022] Open
Abstract
Simple Summary Paradise fish (Macropodus opercularis) has been a favored subject of behavioral research during the last decades of the 20th century. Lately, however, with a massively expanding genetic toolkit and a well annotated, fully sequenced genome, zebrafish (Danio rerio) became a central model of recent behavioral research. But, as the zebrafish behavioral repertoire is less complex than that of the paradise fish, the focus on zebrafish is a compromise. With the advent of novel methodologies, we think it is time to bring back paradise fish and develop it into a modern model of behavioral and evolutionary developmental biology (evo-devo) studies. The first step is to define the housing and husbandry conditions that can make a paradise fish a relevant and trustworthy model. Here, we define the relevant welfare parameters for keeping a healthy population of paradise fish and provide a detailed description of our recent experience in raising and successfully breeding this species under laboratory conditions. Abstract Thanks to its small size, external fertilization and fecundity, over the past four decades, zebrafish (Danio rerio) has become the dominant fish model species in biological and biomedical research. Multiple lines of evidence, however, suggest that the reliance on only a handful of genetic model organisms is problematic, as their unique evolutionary histories makes them less than ideal to study biological questions unrelated to their historically contingent adaptations. Therefore, a need has emerged to develop novel model species, better suited for studying particular problems. The paradise fish (Macropodus opercularis) has a much more complex behavioral repertoire than zebrafish and has been a favored model animal in ethological research during the last decades of the previous century. We believe that with currently available, easily adaptable genetic toolkits, this species could be easily developed into a popular model of behavioral genetics. Despite its earlier popularity, however, the description of a detailed housing and husbandry protocol for this species is still missing from scientific literature. We present here a detailed description of how to raise and breed paradise fish successfully under laboratory conditions, and also discuss some of the challenges we faced while creating a stable breeding population for this species in our facility.
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18
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Rosello M, Vougny J, Czarny F, Mione MC, Concordet JP, Albadri S, Del Bene F. Precise base editing for the in vivo study of developmental signaling and human pathologies in zebrafish. eLife 2021; 10:65552. [PMID: 33576334 PMCID: PMC7932688 DOI: 10.7554/elife.65552] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/10/2021] [Indexed: 02/07/2023] Open
Abstract
While zebrafish is emerging as a new model system to study human diseases, an efficient methodology to generate precise point mutations at high efficiency is still lacking. Here we show that base editors can generate C-to-T point mutations with high efficiencies without other unwanted on-target mutations. In addition, we established a new editor variant recognizing an NAA protospacer adjacent motif, expanding the base editing possibilities in zebrafish. Using these approaches, we first generated a base change in the ctnnb1 gene, mimicking oncogenic an mutation of the human gene known to result in constitutive activation of endogenous Wnt signaling. Additionally, we precisely targeted several cancer-associated genes including cbl. With this last target, we created a new zebrafish dwarfism model. Together our findings expand the potential of zebrafish as a model system allowing new approaches for the endogenous modulation of cell signaling pathways and the generation of precise models of human genetic disease-associated mutations.
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Affiliation(s)
- Marion Rosello
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.,Institut Curie, PSL Research University, Inserm U934, CNRS UMR3215, Paris, France
| | - Juliette Vougny
- Institut Curie, PSL Research University, Inserm U934, CNRS UMR3215, Paris, France
| | - François Czarny
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Marina C Mione
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento, Italy
| | - Jean-Paul Concordet
- Muséum National d'Histoire Naturelle, INSERM U1154, CNRS UMR 7196, Paris, France
| | - Shahad Albadri
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Filippo Del Bene
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.,Institut Curie, PSL Research University, Inserm U934, CNRS UMR3215, Paris, France
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19
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Justice MJ. From its roots come branches and growth for Disease Models & Mechanisms. Dis Model Mech 2021; 14:14/1/dmm048915. [PMID: 33735100 PMCID: PMC7859700 DOI: 10.1242/dmm.048915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Monica J Justice
- Program in Genetics and Genome Biology, The Hospital for Sick Children, and Department of Molecular Genetics, The University of Toronto, Toronto, Ontario M5G 0A4, Canada
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20
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Xie Y, Meijer AH, Schaaf MJM. Modeling Inflammation in Zebrafish for the Development of Anti-inflammatory Drugs. Front Cell Dev Biol 2021; 8:620984. [PMID: 33520995 PMCID: PMC7843790 DOI: 10.3389/fcell.2020.620984] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 12/18/2020] [Indexed: 12/16/2022] Open
Abstract
Dysregulation of the inflammatory response in humans can lead to various inflammatory diseases, like asthma and rheumatoid arthritis. The innate branch of the immune system, including macrophage and neutrophil functions, plays a critical role in all inflammatory diseases. This part of the immune system is well-conserved between humans and the zebrafish, which has emerged as a powerful animal model for inflammation, because it offers the possibility to image and study inflammatory responses in vivo at the early life stages. This review focuses on different inflammation models established in zebrafish, and how they are being used for the development of novel anti-inflammatory drugs. The most commonly used model is the tail fin amputation model, in which part of the tail fin of a zebrafish larva is clipped. This model has been used to study fundamental aspects of the inflammatory response, like the role of specific signaling pathways, the migration of leukocytes, and the interaction between different immune cells, and has also been used to screen libraries of natural compounds, approved drugs, and well-characterized pathway inhibitors. In other models the inflammation is induced by chemical treatment, such as lipopolysaccharide (LPS), leukotriene B4 (LTB4), and copper, and some chemical-induced models, such as treatment with trinitrobenzene sulfonic acid (TNBS), specifically model inflammation in the gastro-intestinal tract. Two mutant zebrafish lines, carrying a mutation in the hepatocyte growth factor activator inhibitor 1a gene (hai1a) and the cdp-diacylglycerolinositol 3-phosphatidyltransferase (cdipt) gene, show an inflammatory phenotype, and they provide interesting model systems for studying inflammation. These zebrafish inflammation models are often used to study the anti-inflammatory effects of glucocorticoids, to increase our understanding of the mechanism of action of this class of drugs and to develop novel glucocorticoid drugs. In this review, an overview is provided of the available inflammation models in zebrafish, and how they are used to unravel molecular mechanisms underlying the inflammatory response and to screen for novel anti-inflammatory drugs.
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Affiliation(s)
- Yufei Xie
- Institute of Biology Leiden, Leiden University, Leiden, Netherlands
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21
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Narumi R, Liu S, Ikeda N, Morita O, Tasaki J. Chemical-Induced Cleft Palate Is Caused and Rescued by Pharmacological Modulation of the Canonical Wnt Signaling Pathway in a Zebrafish Model. Front Cell Dev Biol 2020; 8:592967. [PMID: 33381503 PMCID: PMC7767894 DOI: 10.3389/fcell.2020.592967] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 11/02/2020] [Indexed: 11/13/2022] Open
Abstract
Cleft palate is one of the most frequent birth defects worldwide. It causes severe problems regarding eating and speaking and requires long-term treatment. Effective prenatal treatment would contribute to reducing the risk of cleft palate. The canonical Wnt signaling pathway is critically involved in palatogenesis, and genetic or chemical disturbance of this signaling pathway leads to cleft palate. Presently, preventative treatment for cleft palate during prenatal development has limited efficacy, but we expect that zebrafish will provide a useful high-throughput chemical screening model for effective prevention. To achieve this, the zebrafish model should recapitulate cleft palate development and its rescue by chemical modulation of the Wnt pathway. Here, we provide proof of concept for a zebrafish chemical screening model. Zebrafish embryos were treated with 12 chemical reagents known to induce cleft palate in mammals, and all 12 chemicals induced cleft palate characterized by decreased proliferation and increased apoptosis of palatal cells. The cleft phenotype was enhanced by combinatorial treatment with Wnt inhibitor and teratogens. Furthermore, the expression of tcf7 and lef1 as a readout of the pathway was decreased. Conversely, cleft palate was prevented by Wnt agonist and the cellular defects were also prevented. In conclusion, we provide evidence that chemical-induced cleft palate is caused by inhibition of the canonical Wnt pathway. Our results indicate that this zebrafish model is promising for chemical screening for prevention of cleft palate as well as modulation of the Wnt pathway as a therapeutic target.
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Affiliation(s)
- Rika Narumi
- R&D, Safety Science Research, Kao Corporation, Kawasaki, Japan
| | - Shujie Liu
- R&D, Safety Science Research, Kao Corporation, Ichikai-machi, Japan
| | - Naohiro Ikeda
- R&D, Safety Science Research, Kao Corporation, Kawasaki, Japan
| | - Osamu Morita
- R&D, Safety Science Research, Kao Corporation, Ichikai-machi, Japan
| | - Junichi Tasaki
- R&D, Safety Science Research, Kao Corporation, Kawasaki, Japan
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22
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Muñoz-Sánchez S, van der Vaart M, Meijer AH. Autophagy and Lc3-Associated Phagocytosis in Zebrafish Models of Bacterial Infections. Cells 2020; 9:cells9112372. [PMID: 33138004 PMCID: PMC7694021 DOI: 10.3390/cells9112372] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/24/2020] [Accepted: 10/28/2020] [Indexed: 02/06/2023] Open
Abstract
Modeling human infectious diseases using the early life stages of zebrafish provides unprecedented opportunities for visualizing and studying the interaction between pathogens and phagocytic cells of the innate immune system. Intracellular pathogens use phagocytes or other host cells, like gut epithelial cells, as a replication niche. The intracellular growth of these pathogens can be counteracted by host defense mechanisms that rely on the autophagy machinery. In recent years, zebrafish embryo infection models have provided in vivo evidence for the significance of the autophagic defenses and these models are now being used to explore autophagy as a therapeutic target. In line with studies in mammalian models, research in zebrafish has shown that selective autophagy mediated by ubiquitin receptors, such as p62, is important for host resistance against several bacterial pathogens, including Shigella flexneri, Mycobacterium marinum, and Staphylococcus aureus. Furthermore, an autophagy related process, Lc3-associated phagocytosis (LAP), proved host beneficial in the case of Salmonella Typhimurium infection but host detrimental in the case of S. aureus infection, where LAP delivers the pathogen to a replication niche. These studies provide valuable information for developing novel therapeutic strategies aimed at directing the autophagy machinery towards bacterial degradation.
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23
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Wentzel AS, Petit J, van Veen WG, Fink IR, Scheer MH, Piazzon MC, Forlenza M, Spaink HP, Wiegertjes GF. Transcriptome sequencing supports a conservation of macrophage polarization in fish. Sci Rep 2020; 10:13470. [PMID: 32778701 PMCID: PMC7418020 DOI: 10.1038/s41598-020-70248-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 07/21/2020] [Indexed: 12/12/2022] Open
Abstract
Mammalian macrophages can adopt polarization states that, depending on the exact stimuli present in their extracellular environment, can lead to very different functions. Although these different polarization states have been shown primarily for macrophages of humans and mice, it is likely that polarized macrophages with corresponding phenotypes exist across mammals. Evidence of functional conservation in macrophages from teleost fish suggests that the same, or at least comparable polarization states should also be present in teleosts. However, corresponding transcriptional profiles of marker genes have not been reported thus far. In this study we confirm that macrophages from common carp can polarize into M1- and M2 phenotypes with conserved functions and corresponding transcriptional profiles compared to mammalian macrophages. Carp M1 macrophages show increased production of nitric oxide and a transcriptional profile with increased pro-inflammatory cytokines and mediators, including il6, il12 and saa. Carp M2 macrophages show increased arginase activity and a transcriptional profile with increased anti-inflammatory mediators, including cyr61, timp2b and tgm2b. Our RNA sequencing approach allowed us to list, in an unbiased manner, markers discriminating between M1 and M2 macrophages of teleost fish. We discuss the importance of our findings for the evaluation of immunostimulants for aquaculture and for the identification of gene targets to generate transgenic zebrafish for detailed studies on M1 and M2 macrophages. Above all, we discuss the striking degree of evolutionary conservation of macrophage polarization in a lower vertebrate.
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Affiliation(s)
- Annelieke S Wentzel
- Cell Biology and Immunology Group, Aquaculture and Fisheries Group, Wageningen University and Research, De Elst 1, 6708 WD, Wageningen, The Netherlands
| | - Jules Petit
- Aquaculture and Fisheries Group, Wageningen University and Research, De Elst 1, 6708 WD, Wageningen, The Netherlands
| | - Wouter G van Veen
- Experimental Zoology Group, Wageningen University and Research, De Elst 1, 6708 WD, Wageningen, The Netherlands
| | - Inge Rosenbek Fink
- Cell Biology and Immunology Group, Aquaculture and Fisheries Group, Wageningen University and Research, De Elst 1, 6708 WD, Wageningen, The Netherlands
| | - Marleen H Scheer
- Cell Biology and Immunology Group, Aquaculture and Fisheries Group, Wageningen University and Research, De Elst 1, 6708 WD, Wageningen, The Netherlands
| | - M Carla Piazzon
- Fish Pathology Group, Institute of Aquaculture Torre de La Sal (IATS-CSIC), 12595, Ribera de Cabanes, Castellón, Spain
| | - Maria Forlenza
- Cell Biology and Immunology Group, Aquaculture and Fisheries Group, Wageningen University and Research, De Elst 1, 6708 WD, Wageningen, The Netherlands
| | - Herman P Spaink
- Institute of Biology, Leiden University, Einsteinweg 55, 2332 CC, Leiden, The Netherlands
| | - Geert F Wiegertjes
- Aquaculture and Fisheries Group, Wageningen University and Research, De Elst 1, 6708 WD, Wageningen, The Netherlands.
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24
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Dhar P, Samarasinghe RM, Shigdar S. Antibodies, Nanobodies, or Aptamers-Which Is Best for Deciphering the Proteomes of Non-Model Species? Int J Mol Sci 2020; 21:E2485. [PMID: 32260091 PMCID: PMC7177290 DOI: 10.3390/ijms21072485] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 03/30/2020] [Accepted: 03/30/2020] [Indexed: 12/16/2022] Open
Abstract
This planet is home to countless species, some more well-known than the others. While we have developed many techniques to be able to interrogate some of the "omics", proteomics is becoming recognized as a very important part of the puzzle, given how important the protein is as a functional part of the cell. Within human health, the proteome is fairly well-established, with numerous reagents being available to decipher cellular pathways. Recent research advancements have assisted in characterizing the proteomes of some model (non-human) species, however, in many other species, we are only just touching the surface. This review considers three main reagent classes-antibodies, aptamers, and nanobodies-as a means of continuing to investigate the proteomes of non-model species without the complications of understanding the full protein signature of a species. Considerations of ease of production, potential applications, and the necessity for producing a new reagent depending on homology are presented.
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Affiliation(s)
- Poshmaal Dhar
- School of Medicine, Deakin University, 75 Pigdons Road, Waurn Ponds, Victoria 3216, Australia; (P.D.); (R.M.S.)
- Centre for Molecular and Medical Research, Deakin University, 75 Pigdons Road, Waurn Ponds, Victoria 3216, Australia
| | - Rasika M. Samarasinghe
- School of Medicine, Deakin University, 75 Pigdons Road, Waurn Ponds, Victoria 3216, Australia; (P.D.); (R.M.S.)
- Centre for Molecular and Medical Research, Deakin University, 75 Pigdons Road, Waurn Ponds, Victoria 3216, Australia
| | - Sarah Shigdar
- School of Medicine, Deakin University, 75 Pigdons Road, Waurn Ponds, Victoria 3216, Australia; (P.D.); (R.M.S.)
- Centre for Molecular and Medical Research, Deakin University, 75 Pigdons Road, Waurn Ponds, Victoria 3216, Australia
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25
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Hahn ME, Sadler KC. Casting a wide net: use of diverse model organisms to advance toxicology. Dis Model Mech 2020; 13:dmm043844. [PMID: 32094287 PMCID: PMC7132827 DOI: 10.1242/dmm.043844] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Toxicology - the study of how chemicals interact with biological systems - has clear relevance to human health and disease. Persistent exposure to natural and synthetic chemicals is an unavoidable part of living on our planet; yet, we understand very little about the effects of exposure to the vast majority of chemicals. While epidemiological studies can provide strong statistical inference linking chemical exposure to disease, research in model systems is essential to elucidate the mechanisms of action and to predict outcomes. Most research in toxicology utilizes a handful of mammalian models that represent a few distinct branches of the evolutionary tree. This narrow focus constrains the understanding of chemical-induced disease processes and systems that have evolved in response to exposures. We advocate for casting a wider net in environmental toxicology research to utilize diverse model systems, including zebrafish, and perform more mechanistic studies of cellular responses to chemical exposures to shift the perception of toxicology as an applied science to that of a basic science. This more-inclusive perspective will enrich the field and should remain central to research on chemical-induced disease.
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Affiliation(s)
- Mark E Hahn
- Biology Department, Woods Hole Oceanographic Institution, 45 Water Street, Woods Hole, MA 02543, USA
- Boston University Superfund Research Program, Boston, MA 02118, USA
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