1
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Mackay TFC, Anholt RRH. Pleiotropy, epistasis and the genetic architecture of quantitative traits. Nat Rev Genet 2024; 25:639-657. [PMID: 38565962 PMCID: PMC11330371 DOI: 10.1038/s41576-024-00711-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2024] [Indexed: 04/04/2024]
Abstract
Pleiotropy (whereby one genetic polymorphism affects multiple traits) and epistasis (whereby non-linear interactions between genetic polymorphisms affect the same trait) are fundamental aspects of the genetic architecture of quantitative traits. Recent advances in the ability to characterize the effects of polymorphic variants on molecular and organismal phenotypes in human and model organism populations have revealed the prevalence of pleiotropy and unexpected shared molecular genetic bases among quantitative traits, including diseases. By contrast, epistasis is common between polymorphic loci associated with quantitative traits in model organisms, such that alleles at one locus have different effects in different genetic backgrounds, but is rarely observed for human quantitative traits and common diseases. Here, we review the concepts and recent inferences about pleiotropy and epistasis, and discuss factors that contribute to similarities and differences between the genetic architecture of quantitative traits in model organisms and humans.
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Affiliation(s)
- Trudy F C Mackay
- Center for Human Genetics, Clemson University, Greenwood, SC, USA.
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA.
| | - Robert R H Anholt
- Center for Human Genetics, Clemson University, Greenwood, SC, USA.
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA.
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2
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Nakagawa Y, Kaneko T. Improvement of survivability and developmental ability in vitrified rat oocytes. Cryobiology 2024; 115:104882. [PMID: 38452847 DOI: 10.1016/j.cryobiol.2024.104882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 03/04/2024] [Accepted: 03/04/2024] [Indexed: 03/09/2024]
Abstract
Oocyte cryopreservation is useful for human fertility treatment and strain preservation in both experimental and domestic animals. However, the embryonic development of vitrified rat oocytes was lower than that of vitrified embryos. To increase the viability of vitrified oocytes, intracellular ice formation during cooling and warming must be prevented. Rapid warming is important to prevent ice formation. Furthermore, suppressing the spontaneous activation of oocytes is also important because vitrification promotes the spontaneous activation of rat oocytes, and thus compromise developmental competence of the gametes. MG132, a proteasome inhibitor, suppresses the spontaneous activation of rat oocytes. Here, we examined the effects of rapid warming and MG132 treatment on the survival and embryonic development of vitrified rat oocytes. The warming rate was adjusted by changing the vitrification solution volume and warming solution temperature. The survival rate of oocytes vitrified in 10 μL solution and warmed at 50 °C (94%) was significantly higher than that of oocytes vitrified in 100 μL and 10 μL solution and warmed at 37 °C (49% and 81%, respectively). Furthermore, the rate of embryonic development of vitrified oocytes treated with MG132 during vitrification, warming, and intracytoplasmic sperm injection (ICSI) (44%) was significantly higher than that of untreated gametes (10%). Offspring were obtained after transferring embryos derived from MG132-treated vitrified oocytes (14%). Altogether, the survivability of vitrified rat oocytes increased by rapid warming, and MG132 improved embryonic development after ICSI.
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Affiliation(s)
- Yuki Nakagawa
- Department of Chemistry and Biological Sciences, Faculty of Science and Engineering, Iwate University, Iwate, 020-8551, Japan
| | - Takehito Kaneko
- Department of Chemistry and Biological Sciences, Faculty of Science and Engineering, Iwate University, Iwate, 020-8551, Japan; Division of Fundamental and Applied Sciences, Graduate School of Science and Engineering, Iwate University, Iwate, 020-8551, Japan.
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3
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Soufizadeh P, Mansouri V, Ahmadbeigi N. A review of animal models utilized in preclinical studies of approved gene therapy products: trends and insights. Lab Anim Res 2024; 40:17. [PMID: 38649954 PMCID: PMC11034049 DOI: 10.1186/s42826-024-00195-6] [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: 11/09/2023] [Revised: 02/18/2024] [Accepted: 02/23/2024] [Indexed: 04/25/2024] Open
Abstract
Scientific progress heavily relies on rigorous research, adherence to scientific standards, and transparent reporting. Animal models play a crucial role in advancing biomedical research, especially in the field of gene therapy. Animal models are vital tools in preclinical research, allowing scientists to predict outcomes and understand complex biological processes. The selection of appropriate animal models is critical, considering factors such as physiological and pathophysiological similarities, availability, and ethical considerations. Animal models continue to be indispensable tools in preclinical gene therapy research. Advancements in genetic engineering and model selection have improved the fidelity and relevance of these models. As gene therapy research progresses, careful consideration of animal models and transparent reporting will contribute to the development of effective therapies for various genetic disorders and diseases. This comprehensive review explores the use of animal models in preclinical gene therapy studies for approved products up to September 2023. The study encompasses 47 approved gene therapy products, with a focus on preclinical trials. This comprehensive analysis serves as a valuable reference for researchers in the gene therapy field, aiding in the selection of suitable animal models for their preclinical investigations.
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Affiliation(s)
- Parham Soufizadeh
- Gene Therapy Research Center, Digestive Diseases Research Institute, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
- Biomedical Research Institute, University of Tehran, Tehran, Iran
| | - Vahid Mansouri
- Gene Therapy Research Center, Digestive Diseases Research Institute, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Naser Ahmadbeigi
- Gene Therapy Research Center, Digestive Diseases Research Institute, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran.
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4
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Ma X, Xing Y, Zhai R, Du Y, Yan H. Development and advancements in rodent MRI-based brain atlases. Heliyon 2024; 10:e27421. [PMID: 38510053 PMCID: PMC10950579 DOI: 10.1016/j.heliyon.2024.e27421] [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: 01/25/2023] [Revised: 02/15/2024] [Accepted: 02/28/2024] [Indexed: 03/22/2024] Open
Abstract
Rodents, particularly mice and rats, are extensively utilized in fundamental neuroscience research. Brain atlases have played a pivotal role in this field, evolving from traditional printed histology atlases to digital atlases incorporating diverse imaging datasets. Magnetic resonance imaging (MRI)-based brain atlases, also known as brain maps, have been employed in specific studies. However, the existence of numerous versions of MRI-based brain atlases has impeded their standardized application and widespread use, despite the consensus within the academic community regarding their significance in mice and rats. Furthermore, there is a dearth of comprehensive and systematic reviews on MRI-based brain atlases for rodents. This review aims to bridge this gap by providing a comprehensive overview of the advancements in MRI-based brain atlases for rodents, with a specific focus on mice and rats. It seeks to explore the advantages and disadvantages of histologically printed brain atlases in comparison to MRI brain atlases, delineate the standardized methods for creating MRI brain atlases, and summarize their primary applications in neuroscience research. Additionally, this review aims to assist researchers in selecting appropriate versions of MRI brain atlases for their studies or refining existing MRI brain atlas resources, thereby facilitating the development and widespread adoption of standardized MRI-based brain atlases in rodents.
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Affiliation(s)
- Xiaoyi Ma
- Department of Geriatrics, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Yao Xing
- School of Information Science and Technology, Fudan University, Shanghai, 200433, China
- Wuhan United Imaging Life Science Instrument Co., Ltd., Wuhan, 430071, China
| | - Renkuan Zhai
- Wuhan United Imaging Life Science Instrument Co., Ltd., Wuhan, 430071, China
| | - Yingying Du
- Wuhan United Imaging Life Science Instrument Co., Ltd., Wuhan, 430071, China
| | - Huanhuan Yan
- Shenzhen United Imaging Research Institute of Innovative Medical Equipment, Shenzhen, 518048, China
- Paul C. Lauterbur Research Center for Biomedical Imaging, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
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5
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Laulederkind SJF, Hayman GT, Wang SJ, Kaldunski ML, Vedi M, Demos WM, Tutaj M, Smith JR, Lamers L, Gibson AC, Thorat K, Thota J, Tutaj MA, De Pons JL, Dwinell MR, Kwitek AE. The Rat Genome Database: Genetic, Genomic, and Phenotypic Data Across Multiple Species. Curr Protoc 2023; 3:e804. [PMID: 37347557 PMCID: PMC10335880 DOI: 10.1002/cpz1.804] [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: 06/24/2023]
Abstract
The laboratory rat, Rattus norvegicus, is an important model of human health and disease, and experimental findings in the rat have relevance to human physiology and disease. The Rat Genome Database (RGD, https://rgd.mcw.edu) is a model organism database that provides access to a wide variety of curated rat data including disease associations, phenotypes, pathways, molecular functions, biological processes, cellular components, and chemical interactions for genes, quantitative trait loci, and strains. We present an overview of the database followed by specific examples that can be used to gain experience in employing RGD to explore the wealth of functional data available for the rat and other species. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Navigating the Rat Genome Database (RGD) home page Basic Protocol 2: Using the RGD search functions Basic Protocol 3: Searching for quantitative trait loci Basic Protocol 4: Using the RGD genome browser (JBrowse) to find phenotypic annotations Basic Protocol 5: Using OntoMate to find gene-disease data Basic Protocol 6: Using MOET to find gene-ontology enrichment Basic Protocol 7: Using OLGA to generate gene lists for analysis Basic Protocol 8: Using the GA tool to analyze ontology annotations for genes Basic Protocol 9: Using the RGD InterViewer tool to find protein interaction data Basic Protocol 10: Using the RGD Variant Visualizer tool to find genetic variant data Basic Protocol 11: Using the RGD Disease Portals to find disease, phenotype, and other information Basic Protocol 12: Using the RGD Phenotypes & Models Portal to find qualitative and quantitative phenotype data and other rat strain-related information Basic Protocol 13: Using the RGD Pathway Portal to find disease and phenotype data via molecular pathways.
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Affiliation(s)
| | - G. Thomas Hayman
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Shur-Jen Wang
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Mary L. Kaldunski
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Mahima Vedi
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Wendy M. Demos
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Monika Tutaj
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Jennifer R. Smith
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Logan Lamers
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Adam C. Gibson
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Ketaki Thorat
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Jyothi Thota
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Marek A. Tutaj
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Jeffrey L. De Pons
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Melinda R. Dwinell
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Anne E. Kwitek
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin
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Wake Y, Endo M, Tsunoda S, Tawara H, Abe H, Nakagawa Y, Kaneko T. Successful induction of pseudopregnancy using sonic vibration in mice. Sci Rep 2023; 13:3604. [PMID: 36869082 PMCID: PMC9984469 DOI: 10.1038/s41598-023-30774-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 02/28/2023] [Indexed: 03/05/2023] Open
Abstract
Embryo transfer (ET) is an essential reproductive technology for the production of new animal strains and maintenance of genetic resources. We developed a method, named Easy-ET, to induce pseudopregnancy in female rats by artificial stimulation using sonic vibration instead of mating with vasectomized males. This study examined the application of this method for the induction of pseudopregnancy in mice. Offspring were obtained from two-cell embryos transferred into females with pseudopregnancy induced using sonic vibration in proestrus on the day before embryo transfer. Furthermore, high developmental rates of offspring were observed when pronuclear and two-cell embryos were transferred to females in estrus that were stimulated on the day of embryo transfer. Genome-edited mice were also obtained using frozen-warmed pronuclear embryos with clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated system (Cas) nucleases introduced using the technique for animal knockout system by electroporation (TAKE) method, which were transferred to females with pseudopregnancy induced on the day of embryo transfer. This study demonstrated that induction of pseudopregnancy by sonic vibration was also possible in mice.
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Affiliation(s)
- Yui Wake
- Division of Science and Engineering, Graduate School of Arts and Science, Iwate University, Iwate, 020-8551, Japan
| | - Marina Endo
- Division of Science and Engineering, Graduate School of Arts and Science, Iwate University, Iwate, 020-8551, Japan
| | | | | | - Hisayuki Abe
- Institute for Animal Reproduction, Ibaraki, 300-0134, Japan
| | - Yuki Nakagawa
- Department of Chemistry and Biological Sciences, Faculty of Science and Engineering, Iwate University, Iwate, 020-8551, Japan
| | - Takehito Kaneko
- Division of Science and Engineering, Graduate School of Arts and Science, Iwate University, Iwate, 020-8551, Japan.
- Department of Chemistry and Biological Sciences, Faculty of Science and Engineering, Iwate University, Iwate, 020-8551, Japan.
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7
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Ramos A, Granzotto N, Kremer R, Boeder AM, de Araújo JFP, Pereira AG, Izídio GS. Hunting for Genes Underlying Emotionality in the Laboratory Rat: Maps, Tools and Traps. Curr Neuropharmacol 2023; 21:1840-1863. [PMID: 36056863 PMCID: PMC10514530 DOI: 10.2174/1570159x20666220901154034] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 06/13/2022] [Accepted: 07/28/2022] [Indexed: 11/22/2022] Open
Abstract
Scientists have systematically investigated the hereditary bases of behaviors since the 19th century, moved by either evolutionary questions or clinically-motivated purposes. The pioneer studies on the genetic selection of laboratory animals had already indicated, one hundred years ago, the immense complexity of analyzing behaviors that were influenced by a large number of small-effect genes and an incalculable amount of environmental factors. Merging Mendelian, quantitative and molecular approaches in the 1990s made it possible to map specific rodent behaviors to known chromosome regions. From that point on, Quantitative Trait Locus (QTL) analyses coupled with behavioral and molecular techniques, which involved in vivo isolation of relevant blocks of genes, opened new avenues for gene mapping and characterization. This review examines the QTL strategy applied to the behavioral study of emotionality, with a focus on the laboratory rat. We discuss the challenges, advances and limitations of the search for Quantitative Trait Genes (QTG) playing a role in regulating emotionality. For the past 25 years, we have marched the long journey from emotionality-related behaviors to genes. In this context, our experiences are used to illustrate why and how one should move forward in the molecular understanding of complex psychiatric illnesses. The promise of exploring genetic links between immunological and emotional responses are also discussed. New strategies based on humans, rodents and other animals (such as zebrafish) are also acknowledged, as they are likely to allow substantial progress to be made in the near future.
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Affiliation(s)
- André Ramos
- Behavior Genetics Laboratory, Department of Cell Biology, Embryology and Genetics, Center of Biological Sciences, Federal University of Santa Catarina, Florianopolis, Brazil
| | - Natalli Granzotto
- Behavior Genetics Laboratory, Department of Cell Biology, Embryology and Genetics, Center of Biological Sciences, Federal University of Santa Catarina, Florianopolis, Brazil
- Graduate Program of Pharmacology, Center of Biological Sciences, Federal University of Santa Catarina, Florianopolis, Brazil
| | - Rafael Kremer
- Behavior Genetics Laboratory, Department of Cell Biology, Embryology and Genetics, Center of Biological Sciences, Federal University of Santa Catarina, Florianopolis, Brazil
- Graduate Program of Developmental and Cellular Biology, Center of Biological Sciences, Federal University of Santa Catarina, Florianopolis, Brazil
| | - Ariela Maína Boeder
- Behavior Genetics Laboratory, Department of Cell Biology, Embryology and Genetics, Center of Biological Sciences, Federal University of Santa Catarina, Florianopolis, Brazil
- Graduate Program of Pharmacology, Center of Biological Sciences, Federal University of Santa Catarina, Florianopolis, Brazil
| | - Julia Fernandez Puñal de Araújo
- Behavior Genetics Laboratory, Department of Cell Biology, Embryology and Genetics, Center of Biological Sciences, Federal University of Santa Catarina, Florianopolis, Brazil
- Graduate Program of Developmental and Cellular Biology, Center of Biological Sciences, Federal University of Santa Catarina, Florianopolis, Brazil
| | - Aline Guimarães Pereira
- Behavior Genetics Laboratory, Department of Cell Biology, Embryology and Genetics, Center of Biological Sciences, Federal University of Santa Catarina, Florianopolis, Brazil
- Graduate Program of Developmental and Cellular Biology, Center of Biological Sciences, Federal University of Santa Catarina, Florianopolis, Brazil
| | - Geison Souza Izídio
- Behavior Genetics Laboratory, Department of Cell Biology, Embryology and Genetics, Center of Biological Sciences, Federal University of Santa Catarina, Florianopolis, Brazil
- Graduate Program of Pharmacology, Center of Biological Sciences, Federal University of Santa Catarina, Florianopolis, Brazil
- Graduate Program of Developmental and Cellular Biology, Center of Biological Sciences, Federal University of Santa Catarina, Florianopolis, Brazil
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8
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Shivambu N, Shivambu TC, Downs CT, Willows‐Munro S. Genetic diversity of rodent species sold in South African pet shops. Afr J Ecol 2022. [DOI: 10.1111/aje.13085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ndivhuwo Shivambu
- Centre for Excellence in Invasion Biology, and Centre for Functional Biodiversity, School of Life Sciences University of KwaZulu‐Natal Pietermaritzburg South Africa
| | - Tinyiko C. Shivambu
- Centre for Excellence in Invasion Biology, and Centre for Functional Biodiversity, School of Life Sciences University of KwaZulu‐Natal Pietermaritzburg South Africa
| | - Colleen T. Downs
- Centre for Excellence in Invasion Biology, and Centre for Functional Biodiversity, School of Life Sciences University of KwaZulu‐Natal Pietermaritzburg South Africa
| | - Sandi Willows‐Munro
- Centre for Excellence in Invasion Biology, and Centre for Functional Biodiversity, School of Life Sciences University of KwaZulu‐Natal Pietermaritzburg South Africa
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Yip JLK, Balasuriya GK, Spencer SJ, Hill-Yardin EL. Examining enteric nervous system function in rat and mouse: an interspecies comparison of colonic motility. Am J Physiol Gastrointest Liver Physiol 2022; 323:G477-G487. [PMID: 36126271 DOI: 10.1152/ajpgi.00175.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Gastrointestinal motility is crucial to gut health and has been associated with different disorders such as inflammatory bowel diseases and postoperative ileus. Despite rat and mouse being the two animal models most widely used in gastrointestinal research, minimal studies in rats have investigated gastrointestinal motility. Therefore, our study provides a comparison of colonic motility in the mouse and rat to clarify species differences and assess the relative effectiveness of each animal model for colonic motility research. We describe the protocol modifications and optimization undertaken to enable video imaging of colonic motility in the rat. Apart from the broad difference in terms of gastrointestinal diameter and length, we identified differences in the fundamental histology of the proximal colon such that the rat had larger villus height-to-width and villus height-to-crypt depth ratios compared with mouse. Since gut motility is tightly regulated by the enteric nervous system (ENS), we investigated how colonic contractile activity within each rodent species responds to modulation of the ENS inhibitory neuronal network. Here we used Nω-nitro-l-arginine (l-NNA), an inhibitor of nitric oxide synthase (NOS) to assess proximal colon responses to the stimulatory effect of blocking the major inhibitory neurotransmitter, nitric oxide (NO). In rats, the frequency of proximal colonic contractions increased in the presence of l-NNA (vs. control levels) to a greater extent than in mice. This is despite a similar number of NOS-expressing neurons in the myenteric plexus across species. Given this increase in colonic contraction frequency, the rat represents another relevant animal model for investigating how gastrointestinal motility is regulated by the inhibitory neuronal network of the ENS.NEW & NOTEWORTHY Mice and rats are widely used in gastrointestinal research but have fundamental differences that make them important as different models for different questions. We found that mice have a higher villi length-to-width and villi length-to-crypt depth ratio than rat in proximal colon. Using the ex vivo video imaging technique, we observed that rat colon has more prominent response to blockade of major inhibitory neurotransmitter (nitric oxide) in myenteric plexus than mouse colon.
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Affiliation(s)
- Jackson L K Yip
- School of Health and Biomedical Sciences, RMIT University, Bundoora, Victoria, Australia
| | - Gayathri K Balasuriya
- Department of Physiology and Cell Biology, Kobe University School of Medicine, Kobe, Japan
| | - Sarah J Spencer
- School of Health and Biomedical Sciences, RMIT University, Bundoora, Victoria, Australia.,ARC Centre of Excellence for Nanoscale Biophotonics, RMIT University, Melbourne, Victoria, Australia
| | - Elisa L Hill-Yardin
- School of Health and Biomedical Sciences, RMIT University, Bundoora, Victoria, Australia
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Munro D, Wang T, Chitre AS, Polesskaya O, Ehsan N, Gao J, Gusev A, Woods LS, Saba L, Chen H, Palmer A, Mohammadi P. The regulatory landscape of multiple brain regions in outbred heterogeneous stock rats. Nucleic Acids Res 2022; 50:10882-10895. [PMID: 36263809 PMCID: PMC9638908 DOI: 10.1093/nar/gkac912] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 08/17/2022] [Accepted: 10/05/2022] [Indexed: 11/14/2022] Open
Abstract
Heterogeneous Stock (HS) rats are a genetically diverse outbred rat population that is widely used for studying genetics of behavioral and physiological traits. Mapping Quantitative Trait Loci (QTL) associated with transcriptional changes would help to identify mechanisms underlying these traits. We generated genotype and transcriptome data for five brain regions from 88 HS rats. We identified 21 392 cis-QTLs associated with expression and splicing changes across all five brain regions and validated their effects using allele specific expression data. We identified 80 cases where eQTLs were colocalized with genome-wide association study (GWAS) results from nine physiological traits. Comparing our dataset to human data from the Genotype-Tissue Expression (GTEx) project, we found that the HS rat data yields twice as many significant eQTLs as a similarly sized human dataset. We also identified a modest but highly significant correlation between genetic regulatory variation among orthologous genes. Surprisingly, we found less genetic variation in gene regulation in HS rats relative to humans, though we still found eQTLs for the orthologs of many human genes for which eQTLs had not been found. These data are available from the RatGTEx data portal (RatGTEx.org) and will enable new discoveries of the genetic influences of complex traits.
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Affiliation(s)
- Daniel Munro
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA,Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, USA
| | - Tengfei Wang
- Department of Pharmacology, Addiction Science and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Apurva S Chitre
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Oksana Polesskaya
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Nava Ehsan
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, USA
| | - Jianjun Gao
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Alexander Gusev
- Division of Population Sciences, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Leah C Solberg Woods
- Section of Molecular Medicine, Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Laura M Saba
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Hao Chen
- Department of Pharmacology, Addiction Science and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Abraham A Palmer
- Correspondence may also be addressed to Abraham A. Palmer. Tel: +1 858 534 2093;
| | - Pejman Mohammadi
- To whom correspondence should be addressed. Tel: +1 858 784 8746;
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11
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Takeo T, Nakao S, Mikoda N, Yamaga K, Maeda R, Tsuchiyama S, Nakatsukasa E, Nakagata N. Optimized protocols for sperm cryopreservation and in vitro fertilization in the rat. Lab Anim (NY) 2022; 51:256-274. [DOI: 10.1038/s41684-022-01053-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 08/15/2022] [Indexed: 11/05/2022]
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12
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Wirth F, Staudt KJ, Araújo BV, Ishida K. Experimental models for pharmacokinetic and pharmacodynamic studies of antifungals used in cryptococcosis treatment. Future Microbiol 2022; 17:969-982. [PMID: 35694892 DOI: 10.2217/fmb-2021-0291] [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: 11/21/2022] Open
Abstract
Studies on cryptococcosis in the mammal animal model have demonstrated the occurrence of central nervous system infection and similarities in fungal pathogenicity with clinical and immunological features of the human infection. Although there is still a lack of studies involving pharmacokinetics (PK) and pharmacodynamics (PD) in animal models of cryptococcosis in the literature, these experimental models are useful for understanding this mycosis and antifungal effectiveness in improving the therapeutic schemes. The scope of this review is to describe and discuss the main mammal animal models for PK and PD studies of antifungals used in cryptococcosis treatment. Alternative models and computational methods are also addressed. All approaches for PK/PD studies are relevant to investigating drug-infection interaction and improving cryptococcosis therapy.
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Affiliation(s)
- Fernanda Wirth
- Laboratory of Antifungal Chemotherapy, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, 05508-000, Brazil
| | - Keli J Staudt
- Faculty of Pharmacy, Pharmaceutical Sciences Post-Graduation Program, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, 90610-000, Brazil
| | - Bibiana V Araújo
- Faculty of Pharmacy, Pharmaceutical Sciences Post-Graduation Program, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, 90610-000, Brazil
| | - Kelly Ishida
- Laboratory of Antifungal Chemotherapy, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, 05508-000, Brazil
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Oikawa M, Kobayashi H, Sanbo M, Mizuno N, Iwatsuki K, Takashima T, Yamauchi K, Yoshida F, Yamamoto T, Shinohara T, Nakauchi H, Kurimoto K, Hirabayashi M, Kobayashi T. Functional primordial germ cell-like cells from pluripotent stem cells in rats. Science 2022; 376:176-179. [PMID: 35389778 DOI: 10.1126/science.abl4412] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The in vitro generation of germ cells from pluripotent stem cells (PSCs) can have a substantial effect on future reproductive medicine and animal breeding. A decade ago, in vitro gametogenesis was established in the mouse. However, induction of primordial germ cell-like cells (PGCLCs) to produce gametes has not been achieved in any other species. Here, we demonstrate the induction of functional PGCLCs from rat PSCs. We show that epiblast-like cells in floating aggregates form rat PGCLCs. The gonadal somatic cells support maturation and epigenetic reprogramming of the PGCLCs. When rat PGCLCs are transplanted into the seminiferous tubules of germline-less rats, functional spermatids-that is, those capable of siring viable offspring-are generated. Insights from our rat model will elucidate conserved and divergent mechanisms essential for the broad applicability of in vitro gametogenesis.
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Affiliation(s)
- Mami Oikawa
- Division of Mammalian Embryology, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 108-8639, Japan.,Center for Genetic Analysis of Behavior, National Institute for Physiological Sciences, Okazaki, Aichi 444-8787, Japan
| | - Hisato Kobayashi
- Department of Embryology, Nara Medical University, Kashihara, Nara 634-0813, Japan
| | - Makoto Sanbo
- Center for Genetic Analysis of Behavior, National Institute for Physiological Sciences, Okazaki, Aichi 444-8787, Japan
| | - Naoaki Mizuno
- Division of Stem Cell Therapy, Distinguished Professor Unit, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
| | - Kenyu Iwatsuki
- Division of Mammalian Embryology, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 108-8639, Japan.,Graduate School of Medicine, Science and Technology, Shinshu University, Ueda, Nagano 386-8567, Japan
| | - Tomoya Takashima
- Department of Embryology, Nara Medical University, Kashihara, Nara 634-0813, Japan.,Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Tokyo 156-8502, Japan
| | - Keiko Yamauchi
- Center for Genetic Analysis of Behavior, National Institute for Physiological Sciences, Okazaki, Aichi 444-8787, Japan
| | - Fumika Yoshida
- Center for Genetic Analysis of Behavior, National Institute for Physiological Sciences, Okazaki, Aichi 444-8787, Japan
| | - Takuya Yamamoto
- Center for iPS Cell Research and Application, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan.,Institute for the Advanced Study of Human Biology, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan.,Medical-risk Avoidance Based on iPS Cells Team, RIKEN Center for Advanced Intelligence Project, Sakyo-ku, Kyoto 606-8507, Japan
| | - Takashi Shinohara
- Department of Molecular Genetics, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hiromitsu Nakauchi
- Division of Stem Cell Therapy, Distinguished Professor Unit, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 108-8639, Japan.,Institute for Stem Cell Biology and Regenerative Medicine, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kazuki Kurimoto
- Department of Embryology, Nara Medical University, Kashihara, Nara 634-0813, Japan
| | - Masumi Hirabayashi
- Center for Genetic Analysis of Behavior, National Institute for Physiological Sciences, Okazaki, Aichi 444-8787, Japan.,The Graduate University of Advanced Studies, Okazaki, Aichi 444-8787, Japan
| | - Toshihiro Kobayashi
- Division of Mammalian Embryology, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 108-8639, Japan.,Center for Genetic Analysis of Behavior, National Institute for Physiological Sciences, Okazaki, Aichi 444-8787, Japan
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14
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Senko AN, Overall RW, Silhavy J, Mlejnek P, Malínská H, Hüttl M, Marková I, Fabel KS, Lu L, Stuchlik A, Williams RW, Pravenec M, Kempermann G. Systems genetics in the rat HXB/BXH family identifies Tti2 as a pleiotropic quantitative trait gene for adult hippocampal neurogenesis and serum glucose. PLoS Genet 2022; 18:e1009638. [PMID: 35377872 PMCID: PMC9060359 DOI: 10.1371/journal.pgen.1009638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 05/02/2022] [Accepted: 03/07/2022] [Indexed: 11/19/2022] Open
Abstract
Neurogenesis in the adult hippocampus contributes to learning and memory in the healthy brain but is dysregulated in metabolic and neurodegenerative diseases. The molecular relationships between neural stem cell activity, adult neurogenesis, and global metabolism are largely unknown. Here we applied unbiased systems genetics methods to quantify genetic covariation among adult neurogenesis and metabolic phenotypes in peripheral tissues of a genetically diverse family of rat strains, derived from a cross between the spontaneously hypertensive (SHR/OlaIpcv) strain and Brown Norway (BN-Lx/Cub). The HXB/BXH family is a very well established model to dissect genetic variants that modulate metabolic and cardiovascular diseases and we have accumulated deep phenome and transcriptome data in a FAIR-compliant resource for systematic and integrative analyses. Here we measured rates of precursor cell proliferation, survival of new neurons, and gene expression in the hippocampus of the entire HXB/BXH family, including both parents. These data were combined with published metabolic phenotypes to detect a neurometabolic quantitative trait locus (QTL) for serum glucose and neuronal survival on Chromosome 16: 62.1-66.3 Mb. We subsequently fine-mapped the key phenotype to a locus that includes the Telo2-interacting protein 2 gene (Tti2)-a chaperone that modulates the activity and stability of PIKK kinases. To verify the hypothesis that differences in neurogenesis and glucose levels are caused by a polymorphism in Tti2, we generated a targeted frameshift mutation on the SHR/OlaIpcv background. Heterozygous SHR-Tti2+/- mutants had lower rates of hippocampal neurogenesis and hallmarks of dysglycemia compared to wild-type littermates. Our findings highlight Tti2 as a causal genetic link between glucose metabolism and structural brain plasticity. In humans, more than 800 genomic variants are linked to TTI2 expression, seven of which have associations to protein and blood stem cell factor concentrations, blood pressure and frontotemporal dementia.
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Affiliation(s)
- Anna N. Senko
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Germany
- CRTD–Center for Regenerative Therapies Dresden, Technische Universität Dresden, Germany
| | - Rupert W. Overall
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Germany
- CRTD–Center for Regenerative Therapies Dresden, Technische Universität Dresden, Germany
| | - Jan Silhavy
- Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Petr Mlejnek
- Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Hana Malínská
- Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Martina Hüttl
- Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Irena Marková
- Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Klaus S. Fabel
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Germany
- CRTD–Center for Regenerative Therapies Dresden, Technische Universität Dresden, Germany
| | - Lu Lu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Ales Stuchlik
- Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Robert W. Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Michal Pravenec
- Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Gerd Kempermann
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Germany
- CRTD–Center for Regenerative Therapies Dresden, Technische Universität Dresden, Germany
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15
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Nakagawa Y, Kaneko T. Treatment with MG132 prevents spontaneous activation of rat oocyte in culture and promotes embryonic development after intracytoplasmic sperm injection. Sci Rep 2022; 12:2706. [PMID: 35177721 PMCID: PMC8854420 DOI: 10.1038/s41598-022-06714-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 02/04/2022] [Indexed: 11/17/2022] Open
Abstract
Intracytoplasmic sperm injection (ICSI) is an effective reproductive technique for obtaining rat offspring using preserved sperm with low or no motility. However, rat oocytes undergo spontaneous activation immediately after retrieval from the oviduct and poorly develop after ICSI unless it is performed quickly. Here, we evaluated whether treatment with MG132, the proteasome inhibitor, suppresses the spontaneous activation of oocytes before and during ICSI. After retrieval from the oviducts, the rate of development into morula and blastocyst from the oocytes cultured in vitro for 1 h prior to ICSI significantly decreased compared with that from the control oocytes subject to ICSI without culture (7% versus 36%). However, a higher proportion of oocytes treated with MG132 for 0, 1, and 3 h before and during ICSI developed into morulae and blastocysts (70%, 60%, and 52%, respectively). Offspring were obtained from oocytes treated with MG132 for 0 and 1 h before and during ICSI (percentage: 31%). Altogether, MG132 could suppress the spontaneous activation of rat oocytes and increase embryonic development after ICSI.
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Affiliation(s)
- Yuki Nakagawa
- Department of Chemistry and Biological Sciences, Faculty of Science and Engineering, Iwate University, Morioka, Iwate, 020-8551, Japan
| | - Takehito Kaneko
- Department of Chemistry and Biological Sciences, Faculty of Science and Engineering, Iwate University, Morioka, Iwate, 020-8551, Japan.
- Division of Fundamental and Applied Sciences, Graduate School of Science and Engineering, Iwate University, Morioka, Iwate, 020-8551, Japan.
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16
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Successful pseudopregnancy of rats by short period artificial stimulation using sonic vibration. Sci Rep 2022; 12:1187. [PMID: 35075219 PMCID: PMC8786822 DOI: 10.1038/s41598-022-05293-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 01/04/2022] [Indexed: 11/09/2022] Open
Abstract
Psuedopregnancy for embryo transfer (ET) is usually induced in rats by mating with vasectomized males. Previously, we successfully induced pseudopregnancy using sonic vibration instead (Easy-ET method). The transferred embryos developed normally. Conventionally, stimulation is performed 7 × 30 s with 5 min intervals at the day before ET. However, this protocol is time-consuming because it imitates natural mating behavior. Here, we investigated pseudopregnancy induction with shorter stimulation times. Stimulation was performed 2 × 30 s, with 30 s intervals at the proestrus stage at the day before ET. Of the transferred pronuclear or two-cell embryos, 43% or 62% developed normally, respectively. Furthermore, 67% or 68% of transferred pronuclear or two-cell embryos in rats at estrus stage stimulated on the day of ET developed normally, respectively. Pseudopregnancy was successfully induced with shorter stimulation. Furthermore, this protocol may be used to perform a single-day stimulation and ET operation at the estrus stage.
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17
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Dahale S, Ruiz-Orera J, Silhavy J, Hübner N, van Heesch S, Pravenec M, Atanur SS. Cap analysis of gene expression reveals alternative promoter usage in a rat model of hypertension. Life Sci Alliance 2022; 5:5/4/e202101234. [PMID: 34996843 PMCID: PMC8742872 DOI: 10.26508/lsa.202101234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 12/26/2021] [Accepted: 12/28/2021] [Indexed: 11/24/2022] Open
Abstract
The role of alternative promoter usage in tissue-specific gene expression has been well established; however, its role in complex diseases is poorly understood. We performed cap analysis of gene expression (CAGE) sequencing from the left ventricle of a rat model of hypertension, the spontaneously hypertensive rat (SHR), and a normotensive strain, Brown Norway to understand the role of alternative promoter usage in complex disease. We identified 26,560 CAGE-defined transcription start sites in the rat left ventricle, including 1,970 novel cardiac transcription start sites. We identified 28 genes with alternative promoter usage between SHR and Brown Norway, which could lead to protein isoforms differing at the amino terminus between two strains and 475 promoter switching events altering the length of the 5' UTR. We found that the shift in Insr promoter usage was significantly associated with insulin levels and blood pressure within a panel of HXB/BXH recombinant inbred rat strains, suggesting that hyperinsulinemia due to insulin resistance might lead to hypertension in SHR. Our study provides a preliminary evidence of alternative promoter usage in complex diseases.
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Affiliation(s)
- Sonal Dahale
- Department of Metabolism, Digestion, and Reproduction, Faculty of Medicine, Imperial College London, London, UK.,Department of Microbial Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Jorge Ruiz-Orera
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Jan Silhavy
- Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Norbert Hübner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.,Charité -Universitätsmedizin, Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany
| | | | - Michal Pravenec
- Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Santosh S Atanur
- Department of Metabolism, Digestion, and Reproduction, Faculty of Medicine, Imperial College London, London, UK .,The National Institute for Health Research, Imperial Biomedical Research Centre, ITMAT Data Science Group, Imperial College London, London, UK
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18
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Kaldunski ML, Smith JR, Hayman GT, Brodie K, De Pons JL, Demos WM, Gibson AC, Hill ML, Hoffman MJ, Lamers L, Laulederkind SJF, Nalabolu HS, Thorat K, Thota J, Tutaj M, Tutaj MA, Vedi M, Wang SJ, Zacher S, Dwinell MR, Kwitek AE. The Rat Genome Database (RGD) facilitates genomic and phenotypic data integration across multiple species for biomedical research. Mamm Genome 2021; 33:66-80. [PMID: 34741192 PMCID: PMC8570235 DOI: 10.1007/s00335-021-09932-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 10/21/2021] [Indexed: 01/21/2023]
Abstract
Model organism research is essential for discovering the mechanisms of human diseases by defining biologically meaningful gene to disease relationships. The Rat Genome Database (RGD, ( https://rgd.mcw.edu )) is a cross-species knowledgebase and the premier online resource for rat genetic and physiologic data. This rich resource is enhanced by the inclusion and integration of comparative data for human and mouse, as well as other human disease models including chinchilla, dog, bonobo, pig, 13-lined ground squirrel, green monkey, and naked mole-rat. Functional information has been added to records via the assignment of annotations based on sequence similarity to human, rat, and mouse genes. RGD has also imported well-supported cross-species data from external resources. To enable use of these data, RGD has developed a robust infrastructure of standardized ontologies, data formats, and disease- and species-centric portals, complemented with a suite of innovative tools for discovery and analysis. Using examples of single-gene and polygenic human diseases, we illustrate how data from multiple species can help to identify or confirm a gene as involved in a disease and to identify model organisms that can be studied to understand the pathophysiology of a gene or pathway. The ultimate aim of this report is to demonstrate the utility of RGD not only as the core resource for the rat research community but also as a source of bioinformatic tools to support a wider audience, empowering the search for appropriate models for human afflictions.
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Affiliation(s)
- M L Kaldunski
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - J R Smith
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - G T Hayman
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - K Brodie
- Clinical and Translational Science Institute, Medical College of Wisconsin, Milwaukee, WI, USA
| | - J L De Pons
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - W M Demos
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - A C Gibson
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - M L Hill
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - M J Hoffman
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - L Lamers
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - S J F Laulederkind
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - H S Nalabolu
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - K Thorat
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - J Thota
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - M Tutaj
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - M A Tutaj
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - M Vedi
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - S J Wang
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - S Zacher
- Information Services, Medical College of Wisconsin, Milwaukee, WI, USA
| | - M R Dwinell
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - A E Kwitek
- Department of Biomedical Engineering, The Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA.
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA.
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19
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Ongidi IH, Abdulsalaam FY, Amuti TM, Kaisha WO, Awori KO, Pulei AN. Microscopic features of the rat adrenal gland associated with chronic codeine phosphate administration. Anat Cell Biol 2021; 54:241-248. [PMID: 33850059 PMCID: PMC8225479 DOI: 10.5115/acb.20.230] [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: 08/28/2020] [Revised: 01/26/2021] [Accepted: 02/24/2021] [Indexed: 11/27/2022] Open
Abstract
Codeine is an opioid analgesic and antitussive that has been widely abused. Some adverse effects noted with its abuse include adrenocortical insufficiency and activation of the hypothalamic-pituitary-adrenal axis. The structural basis for these dysfunctions is not clearly understood. Twenty-five adult male rats were used for the study. They were divided into intervention and control groups that were administered 40 mg/kg of codeine phosphate and normal saline respectively by gavage daily for 50 days. Subsequently, both groups were given normal saline for a further fourteen days to note recovery changes. At day 0, 50 and 64, rats were randomly selected from both groups, euthanized and adrenal glands harvested for histological processing and analysis. At day 50 of codeine administration, the adrenal glands demonstrated an increase in zona fasciculata thickness but a decrease in zona reticularis thickness. Lower values were noted in the volume density of zona reticularis and cells count of the medulla in the experimental compared to the control groups (P-value<0.05). The experimental group also showed an increase in vascularization and connective tissue in the glands. After 14 days of recovery, most of the changes observed in experimental animals were reversed and the adrenal glands in both groups had similar features. A decrease in cell count of the adrenal medulla was however observed (P-value<0.05). In conclusion administration of codeine phosphate causes discernible changes in the microscopic structure of the adrenal gland, most of which appear to be reversed after two weeks recovery period.
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Affiliation(s)
- Ibsen Henric Ongidi
- Department of Human Anatomy, School of Medicine, University of Nairobi, Nairobi, Kenya
| | | | - Thomas Mombo Amuti
- Department of Human Anatomy, School of Medicine, University of Nairobi, Nairobi, Kenya
| | - Wycliffe O Kaisha
- Department of Human Anatomy, School of Medicine, University of Nairobi, Nairobi, Kenya
| | - Kirsteen O Awori
- Department of Human Anatomy, School of Medicine, University of Nairobi, Nairobi, Kenya
| | - Anne Naipanoi Pulei
- Department of Human Anatomy, School of Medicine, University of Nairobi, Nairobi, Kenya
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20
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Szpirer C. Rat Models of Human Diseases and Related Phenotypes: A Novel Inventory of Causative Genes. Mamm Genome 2021; 33:88-90. [PMID: 34184128 DOI: 10.1007/s00335-021-09876-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 05/11/2021] [Indexed: 10/21/2022]
Abstract
The laboratory rat (Rattus norvegicus) has been used for a long time as the model of choice in several biomedical disciplines. In 2020, I made an inventory of rat genes that had been identified as underlying diseases or playing a key role in critical biological processes that are altered in diseases. Over 350 genes could be found, a significant number of which have similar effects in rat and humans (Szpirer in J Biomed Sci 27:84-155, 2020). However, a few rat disease genes were unintentionally overlooked; in addition, since this review was published, numerous rat genes were inactivated by targeted mutations, revealing their potential role in diseases. It thus seems appropriate to update these data, which is the aim of this paper.
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Affiliation(s)
- Claude Szpirer
- Université Libre de Bruxelles, B-6041, Gosselies, Belgium. .,, Avenue Jassogne, 27, B-1410, Waterloo, Belgium.
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21
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Hume DA, Caruso M, Keshvari S, Patkar OL, Sehgal A, Bush SJ, Summers KM, Pridans C, Irvine KM. The Mononuclear Phagocyte System of the Rat. THE JOURNAL OF IMMUNOLOGY 2021; 206:2251-2263. [PMID: 33965905 DOI: 10.4049/jimmunol.2100136] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 03/01/2021] [Indexed: 12/14/2022]
Abstract
The laboratory rat continues to be the model of choice for many studies of physiology, behavior, and complex human diseases. Cells of the mononuclear phagocyte system (MPS; monocytes, macrophages, and dendritic cells) are abundant residents in every tissue in the body and regulate postnatal development, homeostasis, and innate and acquired immunity. Recruitment and proliferation of MPS cells is an essential component of both initiation and resolution of inflammation. The large majority of current knowledge of MPS biology is derived from studies of inbred mice, but advances in technology and resources have eliminated many of the advantages of the mouse as a model. In this article, we review the tools available and the current state of knowledge of development, homeostasis, regulation, and diversity within the MPS of the rat.
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Affiliation(s)
- David A Hume
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia
| | - Melanie Caruso
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia
| | - Sahar Keshvari
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia
| | - Omkar L Patkar
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia
| | - Anuj Sehgal
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia
| | - Stephen J Bush
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Kim M Summers
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia
| | - Clare Pridans
- Centre for Inflammation Research, University of Edinburgh, Edinburgh, United Kingdom.,Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Katharine M Irvine
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia
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22
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Hasanpour M, Mitricheva E, Logothetis N, Noori HR. Intensive longitudinal characterization of multidimensional biobehavioral dynamics in laboratory rats. Cell Rep 2021; 35:108987. [PMID: 33852865 DOI: 10.1016/j.celrep.2021.108987] [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: 10/15/2020] [Revised: 01/04/2021] [Accepted: 03/23/2021] [Indexed: 11/26/2022] Open
Abstract
Rats have been used as animal models for human diseases for more than a century, yet a systematic understanding of basal biobehavioral phenotypes of laboratory rats is still missing. In this study, we utilize wireless tracking technology and videography, collect and analyze more than 130 billion data points to fill this gap, and characterize the evolution of behavior and physiology of group-housed male and female rats (n = 114) of the most commonly used strains (Lister Hooded, Long-Evans, Sprague-Dawley, and Wistar) throughout their development. The resulting intensive longitudinal data suggest the existence of strain and sex differences and bi-stable developmental states. Under standard laboratory 12-h light/12-h dark conditions, our study found the presence of multiple oscillations such as circatidal-like rhythms in locomotor activity. The overall findings further suggest that frequent movement along cage walls or thigmotaxic activity may be a physical feature of motion in constrained spaces, critically affecting the interpretation of basal behavior of rats in cages.
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Affiliation(s)
- Mehrdad Hasanpour
- Department of Physiology of Cognitive Processes, Max Planck Institute for Biological Cybernetics, Tübingen, Germany
| | - Ekaterina Mitricheva
- Department of Physiology of Cognitive Processes, Max Planck Institute for Biological Cybernetics, Tübingen, Germany; International Center for Primate Brain Research, Center for Excellence in Brain Science and Intelligence Technology (CEBSIT)/Institute of Neuroscience (ION), Chinese Academy of Sciences, Shanghai, China
| | - Nikos Logothetis
- Department of Physiology of Cognitive Processes, Max Planck Institute for Biological Cybernetics, Tübingen, Germany; International Center for Primate Brain Research, Center for Excellence in Brain Science and Intelligence Technology (CEBSIT)/Institute of Neuroscience (ION), Chinese Academy of Sciences, Shanghai, China; Imaging Science and Biomedical Engineering, University of Manchester, Manchester, UK
| | - Hamid R Noori
- Department of Physiology of Cognitive Processes, Max Planck Institute for Biological Cybernetics, Tübingen, Germany; International Center for Primate Brain Research, Center for Excellence in Brain Science and Intelligence Technology (CEBSIT)/Institute of Neuroscience (ION), Chinese Academy of Sciences, Shanghai, China; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
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23
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Blastocyst complementation using Prdm14-deficient rats enables efficient germline transmission and generation of functional mouse spermatids in rats. Nat Commun 2021; 12:1328. [PMID: 33637711 PMCID: PMC7910474 DOI: 10.1038/s41467-021-21557-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 01/29/2021] [Indexed: 02/06/2023] Open
Abstract
Murine animal models from genetically modified pluripotent stem cells (PSCs) are essential for functional genomics and biomedical research, which require germline transmission for the establishment of colonies. However, the quality of PSCs, and donor-host cell competition in chimeras often present strong barriers for germline transmission. Here, we report efficient germline transmission of recalcitrant PSCs via blastocyst complementation, a method to compensate for missing tissues or organs in genetically modified animals via blastocyst injection of PSCs. We show that blastocysts from germline-deficient Prdm14 knockout rats provide a niche for the development of gametes originating entirely from the donor PSCs without any detriment to somatic development. We demonstrate the potential of this approach by creating PSC-derived Pax2/Pax8 double mutant anephric rats, and rescuing germline transmission of a PSC carrying a mouse artificial chromosome. Furthermore, we generate mouse PSC-derived functional spermatids in rats, which provides a proof-of-principle for the generation of xenogenic gametes in vivo. We believe this approach will become a useful system for generating PSC-derived germ cells in the future.
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Lee JM, Kim U, Yang H, Ryu B, Kim J, Sakuma T, Yamamoto T, Park JH. TALEN-mediated generation of Nkx3.1 knockout rat model. Prostate 2021; 81:182-193. [PMID: 33368416 DOI: 10.1002/pros.24095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 11/16/2020] [Accepted: 11/21/2020] [Indexed: 11/05/2022]
Abstract
BACKGROUND Recent developments in gene editing, using transcriptional activator-like effector nucleases (TALENs), have greatly helped the generation of genetically engineered animal models. The NK3 homeobox 1 (NKX3.1) protein plays important roles in prostate development and protein production, and functions as a tumor suppressor. Recently, NKX3.1 was shown to be associated with breast cancer in humans. METHODS Our aim was to create a new rat model to elucidate the functions of NKX3.1. To that end, we generated Nkx3.1 knockout rats using TALENs and analyzed their phenotype. TALEN-mediated Nkx3.1 knockout was confirmed by T7 endonuclease I (T7E1) assay and DNA sequencing. Prostate weight and fertility were evaluated in the knockout rats, besides determining the proportion of epithelial cells and messenger RNA (mRNA) expression of genes associated with carcinogenesis. Breast tumors were examined by histopathology. RESULTS Results suggested Nkx3.1 knockout rats have reduced fertility, decreased prostate weights, and increased epithelial cell layers. The mRNA expression of genes related to prostate carcinogenesis, namely Ar, Akt, and Pi3k, also increased. Moreover, the Nkx3.1 knockout rats often developed malignant breast tumors. CONCLUSIONS We, therefore, successfully created the first Nkx3.1 knockout rat model, using TALEN-mediated gene targeting, and used it to identify defects associated with Nkx3.1 deficiency, not previously observed in mice. Loss of Nkx3.1 in rats led to lower reproductive capacity, and decreased prostate weights, apart from the risk of developing breast cancer. We, thus, proposed Nkx3.1 knockout rats as reliable models for studying the role of NKX3.1 in decreased prostate weights, fertility, and breast cancer, as well as in prostate cancer.
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Affiliation(s)
- Ji Min Lee
- Department of Laboratory Animal Medicine, Research Institute for Veterinary Science, BK21 PLUS Program for Creative Veterinary Science Research, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Ukjin Kim
- Department of Laboratory Animal Medicine, Research Institute for Veterinary Science, BK21 PLUS Program for Creative Veterinary Science Research, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Hyokyung Yang
- Department of Laboratory Animal Medicine, Research Institute for Veterinary Science, BK21 PLUS Program for Creative Veterinary Science Research, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Bokyeong Ryu
- Department of Laboratory Animal Medicine, Research Institute for Veterinary Science, BK21 PLUS Program for Creative Veterinary Science Research, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Jin Kim
- Department of Laboratory Animal Medicine, Research Institute for Veterinary Science, BK21 PLUS Program for Creative Veterinary Science Research, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Tetsushi Sakuma
- Division of Integrated Sciences for Life, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Takashi Yamamoto
- Division of Integrated Sciences for Life, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Jae-Hak Park
- Department of Laboratory Animal Medicine, Research Institute for Veterinary Science, BK21 PLUS Program for Creative Veterinary Science Research, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
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25
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Pridans C, Irvine KM, Davis GM, Lefevre L, Bush SJ, Hume DA. Transcriptomic Analysis of Rat Macrophages. Front Immunol 2021; 11:594594. [PMID: 33633725 PMCID: PMC7902030 DOI: 10.3389/fimmu.2020.594594] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 12/17/2020] [Indexed: 12/13/2022] Open
Abstract
The laboratory rat is widely used as a model for human diseases. Many of these diseases involve monocytes and tissue macrophages in different states of activation. Whilst methods for in vitro differentiation of mouse macrophages from embryonic stem cells (ESC) and bone marrow (BM) are well established, these are lacking for the rat. The gene expression profiles of rat macrophages have also not been characterised to the same extent as mouse. We have established the methodology for production of rat ESC-derived macrophages and compared their gene expression profiles to macrophages obtained from the lung and peritoneal cavity and those differentiated from BM and blood monocytes. We determined the gene signature of Kupffer cells in the liver using rats deficient in macrophage colony stimulating factor receptor (CSF1R). We also examined the response of BM-derived macrophages to lipopolysaccharide (LPS). The results indicate that many, but not all, tissue-specific adaptations observed in mice are conserved in the rat. Importantly, we show that unlike mice, rat macrophages express the CSF1R ligand, colony stimulating factor 1 (CSF1).
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Affiliation(s)
- Clare Pridans
- Centre for Inflammation Research, University of Edinburgh Centre for Inflammation Research, Edinburgh, United Kingdom
- Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh, United Kingdom
| | - Katharine M. Irvine
- Mater Research Institute Mater Research Institute – University of Queensland, Brisbane, QLD, Australia
| | - Gemma M. Davis
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Lucas Lefevre
- UK Dementia Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Stephen J. Bush
- Nuffield Department of Clinical Medicine, University of Oxford, Headington, United Kingdom
| | - David A. Hume
- Mater Research Institute Mater Research Institute – University of Queensland, Brisbane, QLD, Australia
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26
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Cheng Y, Sun D, Zhu B, Zhou W, Lv C, Kou F, Wei H. Integrative Metabolic and Proteomic Profiling of the Brainstem in Spontaneously Hypertensive Rats. J Proteome Res 2020; 19:4114-4124. [DOI: 10.1021/acs.jproteome.0c00585] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Yu Cheng
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Dongmei Sun
- School of Acupuncture-Moxibustion and Tuina, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Bangjie Zhu
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wenbin Zhou
- Shanghai Zhulian Intelligent Technology Ltd. Co., Shanghai 201323, China
| | - Chunming Lv
- Shanghai Zhulian Intelligent Technology Ltd. Co., Shanghai 201323, China
| | - Fang Kou
- Institute of Interdisciplinary Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Hai Wei
- Institute of Interdisciplinary Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
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27
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Szpirer C. Rat models of human diseases and related phenotypes: a systematic inventory of the causative genes. J Biomed Sci 2020; 27:84. [PMID: 32741357 PMCID: PMC7395987 DOI: 10.1186/s12929-020-00673-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 07/09/2020] [Indexed: 12/13/2022] Open
Abstract
The laboratory rat has been used for a long time as the model of choice in several biomedical disciplines. Numerous inbred strains have been isolated, displaying a wide range of phenotypes and providing many models of human traits and diseases. Rat genome mapping and genomics was considerably developed in the last decades. The availability of these resources has stimulated numerous studies aimed at discovering causal disease genes by positional identification. Numerous rat genes have now been identified that underlie monogenic or complex diseases and remarkably, these results have been translated to the human in a significant proportion of cases, leading to the identification of novel human disease susceptibility genes, helping in studying the mechanisms underlying the pathological abnormalities and also suggesting new therapeutic approaches. In addition, reverse genetic tools have been developed. Several genome-editing methods were introduced to generate targeted mutations in genes the function of which could be clarified in this manner [generally these are knockout mutations]. Furthermore, even when the human gene causing a disease had been identified without resorting to a rat model, mutated rat strains (in particular KO strains) were created to analyze the gene function and the disease pathogenesis. Today, over 350 rat genes have been identified as underlying diseases or playing a key role in critical biological processes that are altered in diseases, thereby providing a rich resource of disease models. This article is an update of the progress made in this research and provides the reader with an inventory of these disease genes, a significant number of which have similar effects in rat and humans.
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Affiliation(s)
- Claude Szpirer
- Université Libre de Bruxelles, B-6041, Gosselies, Belgium.
- , Waterloo, Belgium.
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28
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Icick R, Forget B, Cloëz-Tayarani I, Pons S, Maskos U, Besson M. Genetic susceptibility to nicotine addiction: Advances and shortcomings in our understanding of the CHRNA5/A3/B4 gene cluster contribution. Neuropharmacology 2020; 177:108234. [PMID: 32738310 DOI: 10.1016/j.neuropharm.2020.108234] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 06/28/2020] [Accepted: 07/07/2020] [Indexed: 12/12/2022]
Abstract
Over the last decade, robust human genetic findings have been instrumental in elucidating the heritable basis of nicotine addiction (NA). They highlight coding and synonymous polymorphisms in a cluster on chromosome 15, encompassing the CHRNA5, CHRNA3 and CHRNB4 genes, coding for three subunits of the nicotinic acetylcholine receptor (nAChR). They have inspired an important number of preclinical studies, and will hopefully lead to the definition of novel drug targets for treating NA. Here, we review these candidate gene and genome-wide association studies (GWAS) and their direct implication in human brain function and NA-related phenotypes. We continue with a description of preclinical work in transgenic rodents that has led to a mechanistic understanding of several of the genetic hits. We also highlight important issues with regards to CHRNA3 and CHRNB4 where we are still lacking a dissection of their role in NA, including even in preclinical models. We further emphasize the use of human induced pluripotent stem cell-derived models for the analysis of synonymous and intronic variants on a human genomic background. Finally, we indicate potential avenues to further our understanding of the role of this human genetic variation. This article is part of the special issue on 'Contemporary Advances in Nicotine Neuropharmacology'.
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Affiliation(s)
- Romain Icick
- Neurobiologie Intégrative des Systèmes Cholinergiques, CNRS UMR3571, Institut Pasteur, 25 Rue du Dr Roux, 75724, Paris Cedex 15, France; Département de Psychiatrie et de Médecine Addictologique, Groupe Hospitalier Saint-Louis, Lariboisière, Fernand Widal, Assistance-Publique Hôpitaux de Paris, Paris, F-75010, France; INSERM UMR-S1144, Paris, F-75006, France; FHU "NOR-SUD", Assistance-Publique Hôpitaux de Paris, Paris, F-75001, France
| | - Benoît Forget
- Neurobiologie Intégrative des Systèmes Cholinergiques, CNRS UMR3571, Institut Pasteur, 25 Rue du Dr Roux, 75724, Paris Cedex 15, France; Génétique Humaine et Fonctions Cognitives, CNRS UMR3571, Institut Pasteur, 25 Rue du Dr Roux, 75724, Paris Cedex 15, France
| | - Isabelle Cloëz-Tayarani
- Neurobiologie Intégrative des Systèmes Cholinergiques, CNRS UMR3571, Institut Pasteur, 25 Rue du Dr Roux, 75724, Paris Cedex 15, France; FHU "NOR-SUD", Assistance-Publique Hôpitaux de Paris, Paris, F-75001, France
| | - Stéphanie Pons
- Neurobiologie Intégrative des Systèmes Cholinergiques, CNRS UMR3571, Institut Pasteur, 25 Rue du Dr Roux, 75724, Paris Cedex 15, France; FHU "NOR-SUD", Assistance-Publique Hôpitaux de Paris, Paris, F-75001, France
| | - Uwe Maskos
- Neurobiologie Intégrative des Systèmes Cholinergiques, CNRS UMR3571, Institut Pasteur, 25 Rue du Dr Roux, 75724, Paris Cedex 15, France; FHU "NOR-SUD", Assistance-Publique Hôpitaux de Paris, Paris, F-75001, France
| | - Morgane Besson
- Neurobiologie Intégrative des Systèmes Cholinergiques, CNRS UMR3571, Institut Pasteur, 25 Rue du Dr Roux, 75724, Paris Cedex 15, France; FHU "NOR-SUD", Assistance-Publique Hôpitaux de Paris, Paris, F-75001, France.
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29
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Pignolo RJ, Passos JF, Khosla S, Tchkonia T, Kirkland JL. Reducing Senescent Cell Burden in Aging and Disease. Trends Mol Med 2020; 26:630-638. [PMID: 32589933 DOI: 10.1016/j.molmed.2020.03.005] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 02/27/2020] [Accepted: 03/19/2020] [Indexed: 12/20/2022]
Abstract
Cellular senescence is a primary aging process and tumor suppressive mechanism characterized by irreversible growth arrest, apoptosis resistance, production of a senescence-associated secretory phenotype (SASP), mitochondrial dysfunction, and alterations in DNA and chromatin. In preclinical aging models, accumulation of senescent cells is associated with multiple chronic diseases and disorders, geriatric syndromes, multimorbidity, and accelerated aging phenotypes. In animals, genetic and pharmacologic reduction of senescent cell burden results in the prevention, delay, and/or alleviation of a variety of aging-related diseases and sequelae. Early clinical trials have thus far focused on safety and target engagement of senolytic agents that clear senescent cells. We hypothesize that these pharmacologic interventions may have transformative effects on geriatric medicine.
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Affiliation(s)
- Robert J Pignolo
- Mayo Clinic Departments of Medicine, Physiology and Biomedical Engineering, and the Kogod Center on Aging, Rochester, MN, USA.
| | - João F Passos
- Mayo Clinic Departments of Medicine, Physiology and Biomedical Engineering, and the Kogod Center on Aging, Rochester, MN, USA
| | - Sundeep Khosla
- Mayo Clinic Departments of Medicine, Physiology and Biomedical Engineering, and the Kogod Center on Aging, Rochester, MN, USA
| | - Tamara Tchkonia
- Mayo Clinic Departments of Medicine, Physiology and Biomedical Engineering, and the Kogod Center on Aging, Rochester, MN, USA
| | - James L Kirkland
- Mayo Clinic Departments of Medicine, Physiology and Biomedical Engineering, and the Kogod Center on Aging, Rochester, MN, USA
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30
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Kobayashi T, Kobayashi H, Goto T, Takashima T, Oikawa M, Ikeda H, Terada R, Yoshida F, Sanbo M, Nakauchi H, Kurimoto K, Hirabayashi M. Germline development in rat revealed by visualization and deletion of Prdm14. Development 2020; 147:dev.183798. [PMID: 32001439 DOI: 10.1242/dev.183798] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 01/15/2020] [Indexed: 12/22/2022]
Abstract
Primordial germ cells (PGCs), the founder cells of the germline, are specified in pre-gastrulating embryos in mammals, and subsequently migrate towards gonads to mature into functional gametes. Here, we investigated PGC development in rats, by genetically modifying Prdm14, a unique marker and an essential PGC transcriptional regulator. We trace PGC development in rats, for the first time, from specification until the sex determination stage in fetal gonads using Prdm14 H2BVenus knock-in rats. We uncover that the crucial role of Prdm14 in PGC specification is conserved between rat and mice, by analyzing Prdm14-deficient rat embryos. Notably, loss of Prdm14 completely abrogates the PGC program, as demonstrated by failure of the maintenance and/or activation of germ cell markers and pluripotency genes. Finally, we profile the transcriptome of the post-implantation epiblast and all PGC stages in rat to reveal enrichment of distinct gene sets at each transition point, thereby providing an accurate transcriptional timeline for rat PGC development. Thus, the novel genetically modified rats and data sets obtained in this study will advance our knowledge on conserved versus species-specific features for germline development in mammals.
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Affiliation(s)
- Toshihiro Kobayashi
- Section of Mammalian Transgenesis, Center for Genetic Analysis of Behavior, National Institute for Physiological Sciences, Okazaki, 444-8787 Aichi, Japan.,Department of Physiological Sciences, The Graduate University of Advanced Studies, Okazaki, 444-8787 Aichi, Japan
| | - Hisato Kobayashi
- Department of Embryology, Nara Medical University, Kashihara, 634-0813 Nara, Japan
| | - Teppei Goto
- Section of Mammalian Transgenesis, Center for Genetic Analysis of Behavior, National Institute for Physiological Sciences, Okazaki, 444-8787 Aichi, Japan
| | - Tomoya Takashima
- Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, 156-8502 Tokyo, Japan
| | - Mami Oikawa
- Section of Mammalian Transgenesis, Center for Genetic Analysis of Behavior, National Institute for Physiological Sciences, Okazaki, 444-8787 Aichi, Japan
| | - Hiroki Ikeda
- Department of Embryology, Nara Medical University, Kashihara, 634-0813 Nara, Japan
| | - Reiko Terada
- Section of Mammalian Transgenesis, Center for Genetic Analysis of Behavior, National Institute for Physiological Sciences, Okazaki, 444-8787 Aichi, Japan
| | - Fumika Yoshida
- Section of Mammalian Transgenesis, Center for Genetic Analysis of Behavior, National Institute for Physiological Sciences, Okazaki, 444-8787 Aichi, Japan
| | - Makoto Sanbo
- Section of Mammalian Transgenesis, Center for Genetic Analysis of Behavior, National Institute for Physiological Sciences, Okazaki, 444-8787 Aichi, Japan
| | - Hiromitsu Nakauchi
- Division of Stem Cell Therapy, Institute of Medical Science, The University of Tokyo, Minato-ku, 108-8639 Tokyo, Japan.,Institute for Stem Cell Biology and Regenerative Medicine, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kazuki Kurimoto
- Department of Embryology, Nara Medical University, Kashihara, 634-0813 Nara, Japan
| | - Masumi Hirabayashi
- Section of Mammalian Transgenesis, Center for Genetic Analysis of Behavior, National Institute for Physiological Sciences, Okazaki, 444-8787 Aichi, Japan .,Department of Physiological Sciences, The Graduate University of Advanced Studies, Okazaki, 444-8787 Aichi, Japan
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31
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Abidi A, Laurent T, Bériou G, Bouchet-Delbos L, Fourgeux C, Louvet C, Triki-Marrakchi R, Poschmann J, Josien R, Martin J. Characterization of Rat ILCs Reveals ILC2 as the Dominant Intestinal Subset. Front Immunol 2020; 11:255. [PMID: 32140157 PMCID: PMC7043102 DOI: 10.3389/fimmu.2020.00255] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 01/30/2020] [Indexed: 12/17/2022] Open
Abstract
Innate lymphoid cells (ILCs) are tissue-resident lymphocytes that lack antigen-specific receptors and exhibit innate effector functions such as cytokine production that play an important role in immediate responses to pathogens especially at mucosal sites. Mouse and human ILC subsets have been extensively characterized in various tissues and in blood. In this study, we present the first characterization of ILCs and ILC subsets in rat gut and secondary lymphoid organs using flow cytometry and single cell RNA sequencing. Our results show that phenotype and function of rat ILC subsets are conserved as compared to human and mouse ILCs. However, and in contrast to human and mouse, our study unexpectedly revealed that ILC2 and not ILC3 was the dominant ILC subset in the rat intestinal lamina propria. ILC2 predominance in the gut was independent of rat strain, sex or housing facility. In contrast, ILC3 was the predominant ILC subset in mesenteric lymph nodes and Peyer patches. In conclusion, our study demonstrates that in spite of highly conserved phenotype and function between mice, rat and humans, the distribution of ILC subsets in the intestinal mucosa is dependent on the species likely in response to both genetic and environmental factors.
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Affiliation(s)
- Ahmed Abidi
- Université de Nantes, Inserm, CHU Nantes, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes, France.,Université de Tunis El Manar, Laboratoire de Génétique, Immunologie et Pathologies Humaines, Faculté des Sciences de Tunis, Tunis, Tunisia
| | - Thomas Laurent
- Université de Nantes, Inserm, CHU Nantes, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes, France
| | - Gaëlle Bériou
- Université de Nantes, Inserm, CHU Nantes, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes, France
| | - Laurence Bouchet-Delbos
- Université de Nantes, Inserm, CHU Nantes, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes, France
| | - Cynthia Fourgeux
- Université de Nantes, Inserm, CHU Nantes, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes, France
| | - Cédric Louvet
- Université de Nantes, Inserm, CHU Nantes, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes, France
| | - Raja Triki-Marrakchi
- Université de Tunis El Manar, Laboratoire de Génétique, Immunologie et Pathologies Humaines, Faculté des Sciences de Tunis, Tunis, Tunisia
| | - Jeremie Poschmann
- Université de Nantes, Inserm, CHU Nantes, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes, France
| | - Régis Josien
- Université de Nantes, Inserm, CHU Nantes, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes, France.,CHU Nantes, Laboratoire d'Immunologie, Nantes, France
| | - Jérôme Martin
- Université de Nantes, Inserm, CHU Nantes, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes, France.,CHU Nantes, Laboratoire d'Immunologie, Nantes, France
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32
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Kaneko T, Endo M, Tsunoda S, Nakagawa Y, Abe H. Simple induction of pseudopregnancy by artificial stimulation using a sonic vibration in rats. Sci Rep 2020; 10:2729. [PMID: 32066799 PMCID: PMC7026161 DOI: 10.1038/s41598-020-59611-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 01/30/2020] [Indexed: 11/26/2022] Open
Abstract
Embryo transfer has been used as one of the essential reproductive technologies for production of new strains and maintenance of genetic resources in animals. Mating with vasectomised male rats is a requirement for inducing pseudopregnancy in female rats selected for embryo transfer. Although this procedure has been used routinely, large breeding space and high expenditure are required to maintain a sufficient number of females and vasectomised males. This study was performed to induce pseudopregnancy in females by artificial stimulation using sonic vibration instead of vasectomised males. The females continued to be in the dioestrus stage for at least 14 days after artificial stimulation was performed. Of fresh 2-cell embryos that transferred into the oviducts of females after artificial stimulation, 56% was implanted and 50% was developed to offspring. Approximately 46% of the frozen 2-cell embryos were implanted and 24% developed into offspring. Furthermore, 66% of the fresh pronuclear embryos were implanted and 60% developed into offspring. This study successfully induced pseudopregnancy in rat females by artificial stimulation using a sonic vibration. This method, ‘Easy-ET’, was useful for efficient production and maintenance of rat strains.
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Affiliation(s)
- Takehito Kaneko
- Division of Science and Engineering Graduate School of Arts and Science, Iwate University, Iwate, 020-8551, Japan. .,Department of Chemistry and Biological Sciences, Faculty of Science and Engineering, Iwate University, Iwate, 020-8551, Japan.
| | - Marina Endo
- Division of Science and Engineering Graduate School of Arts and Science, Iwate University, Iwate, 020-8551, Japan
| | | | - Yuki Nakagawa
- Department of Chemistry and Biological Sciences, Faculty of Science and Engineering, Iwate University, Iwate, 020-8551, Japan
| | - Hisayuki Abe
- Institute for Animal Reproduction, Ibaraki, 300-0134, Japan
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33
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Kaneko T, Nakagawa Y. Genome editing of rodents by electroporation of CRISPR/Cas9 into frozen-warmed pronuclear-stage embryos. Cryobiology 2020; 92:231-234. [PMID: 31987837 DOI: 10.1016/j.cryobiol.2020.01.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 01/21/2020] [Accepted: 01/21/2020] [Indexed: 01/18/2023]
Abstract
Genome edited animals can now be easily produced using the clustered regularly interspaced short palindromic repeat (CRISPR) and CRISPR-associated protein 9 (Cas9) system. Traditionally, these animals have been produced by the introduction of endonucleases into pronuclear-stage embryos. Recently, a novel electroporation method, the "Technique for Animal Knockout system by Electroporation (TAKE)," has been established as a simple and highly efficient tool to introduce endonucleases into embryos instead of methods such as microinjection. Use of frozen-warmed pronuclear-stage embryos in this method has further contributed to efficient production of genome edited animals. However, early developmental stage embryos, including pronuclear-stage embryos, especially those of rats, sometimes show low resistance to physical damage by vitrification and introduction of endonucleases during microinjection. In this study, we propose an ethanol-free, slow-freezing method to reduce physical damage to pronuclear-stage embryos followed by the TAKE method. All mouse and rat frozen embryos were survived after electroporation, and 18% and 100% of offspring were edited target gene, respectively. The resulting protocol is an efficient method for producing genome edited animals.
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Affiliation(s)
- Takehito Kaneko
- Department of Chemistry and Biological Sciences, Faculty of Science and Engineering, Iwate University, Iwate, 020-8551, Japan; Division of Fundamental and Applied Sciences, Graduate School of Science and Engineering, Iwate University, Iwate, 020-8551, Japan.
| | - Yuki Nakagawa
- Department of Chemistry and Biological Sciences, Faculty of Science and Engineering, Iwate University, Iwate, 020-8551, Japan
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34
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Noshahr ZS, Salmani H, Khajavi Rad A, Sahebkar A. Animal Models of Diabetes-Associated Renal Injury. J Diabetes Res 2020; 2020:9416419. [PMID: 32566684 PMCID: PMC7256713 DOI: 10.1155/2020/9416419] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 04/28/2020] [Indexed: 12/29/2022] Open
Abstract
Diabetic nephropathy (DN) is the main factor leading to end-stage renal disease (ESRD) and subsequent morbidity and mortality. Importantly, the prevalence of DN is continuously increasing in developed countries. Many rodent models of type 1 and type 2 diabetes have been established to elucidate the pathogenesis of diabetes and examine novel therapies against DN. These models are developed by chemical, surgical, genetic, drug, and diet/nutrition interventions or combination of two or more methods. The main characteristics of DN including a decrease in renal function, albuminuria and mesangiolysis, mesangial expansion, and nodular glomerulosclerosis should be exhibited by an animal model of DN. However, a rodent model possessing all of the abovementioned features of human DN has not yet been developed. Furthermore, mice of different genetic backgrounds and strains show different levels of susceptibility to DN with respect to albuminuria and development of glomerular and tubulointerstitial lesions. Therefore, the type of diabetes, development of nephropathy, duration of the study, cost of maintaining and breeding, and animals' mortality rate are important factors that might be affected by the type of DN model. In this review, we discuss the pros and cons of different rodent models of diabetes that are being used to study DN.
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Affiliation(s)
- Zahra Samadi Noshahr
- Department of Physiology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hossein Salmani
- Department of Physiology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Abolfazl Khajavi Rad
- Department of Physiology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Neurogenic Inflammation Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amirhossein Sahebkar
- Halal Research Center of IRI, FDA, Tehran, Iran
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
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Abstract
Mice (Mus musculus) and rats (Rattus norvegicus) have long served as model systems for biomedical research. However, they are also excellent models for studying the evolution of populations, subspecies, and species. Within the past million years, they have spread in various waves across large parts of the globe, with the most recent spread in the wake of human civilization. They have developed into commensal species, but have also been able to colonize extreme environments on islands free of human civilization. Given that ample genomic and genetic resources are available for these species, they have thus also become ideal mammalian systems for evolutionary studies on adaptation and speciation, particularly in the combination with the rapid developments in population genomics. The chapter provides an overview of the systems and their history, as well as of available resources.
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Affiliation(s)
- Kristian K Ullrich
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany.
| | - Diethard Tautz
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
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Lerman LO, Kurtz TW, Touyz RM, Ellison DH, Chade AR, Crowley SD, Mattson DL, Mullins JJ, Osborn J, Eirin A, Reckelhoff JF, Iadecola C, Coffman TM. Animal Models of Hypertension: A Scientific Statement From the American Heart Association. Hypertension 2019; 73:e87-e120. [PMID: 30866654 DOI: 10.1161/hyp.0000000000000090] [Citation(s) in RCA: 171] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Hypertension is the most common chronic disease in the world, yet the precise cause of elevated blood pressure often cannot be determined. Animal models have been useful for unraveling the pathogenesis of hypertension and for testing novel therapeutic strategies. The utility of animal models for improving the understanding of the pathogenesis, prevention, and treatment of hypertension and its comorbidities depends on their validity for representing human forms of hypertension, including responses to therapy, and on the quality of studies in those models (such as reproducibility and experimental design). Important unmet needs in this field include the development of models that mimic the discrete hypertensive syndromes that now populate the clinic, resolution of ongoing controversies in the pathogenesis of hypertension, and the development of new avenues for preventing and treating hypertension and its complications. Animal models may indeed be useful for addressing these unmet needs.
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37
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Li Y, Meng Q, Yang M, Liu D, Hou X, Tang L, Wang X, Lyu Y, Chen X, Liu K, Yu AM, Zuo Z, Bi H. Current trends in drug metabolism and pharmacokinetics. Acta Pharm Sin B 2019; 9:1113-1144. [PMID: 31867160 PMCID: PMC6900561 DOI: 10.1016/j.apsb.2019.10.001] [Citation(s) in RCA: 128] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 08/23/2019] [Accepted: 09/09/2019] [Indexed: 12/15/2022] Open
Abstract
Pharmacokinetics (PK) is the study of the absorption, distribution, metabolism, and excretion (ADME) processes of a drug. Understanding PK properties is essential for drug development and precision medication. In this review we provided an overview of recent research on PK with focus on the following aspects: (1) an update on drug-metabolizing enzymes and transporters in the determination of PK, as well as advances in xenobiotic receptors and noncoding RNAs (ncRNAs) in the modulation of PK, providing new understanding of the transcriptional and posttranscriptional regulatory mechanisms that result in inter-individual variations in pharmacotherapy; (2) current status and trends in assessing drug-drug interactions, especially interactions between drugs and herbs, between drugs and therapeutic biologics, and microbiota-mediated interactions; (3) advances in understanding the effects of diseases on PK, particularly changes in metabolizing enzymes and transporters with disease progression; (4) trends in mathematical modeling including physiologically-based PK modeling and novel animal models such as CRISPR/Cas9-based animal models for DMPK studies; (5) emerging non-classical xenobiotic metabolic pathways and the involvement of novel metabolic enzymes, especially non-P450s. Existing challenges and perspectives on future directions are discussed, and may stimulate the development of new research models, technologies, and strategies towards the development of better drugs and improved clinical practice.
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Affiliation(s)
- Yuhua Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510275, China
- The First Affiliated Hospital of Nanchang University, Nanchang 330006, China
| | - Qiang Meng
- College of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Mengbi Yang
- School of Pharmacy, the Chinese University of Hong Kong, Hong Kong, China
| | - Dongyang Liu
- Drug Clinical Trial Center, Peking University Third Hospital, Beijing 100191, China
| | - Xiangyu Hou
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Lan Tang
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Xin Wang
- School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Yuanfeng Lyu
- School of Pharmacy, the Chinese University of Hong Kong, Hong Kong, China
| | - Xiaoyan Chen
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Kexin Liu
- College of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Ai-Ming Yu
- UC Davis School of Medicine, Sacramento, CA 95817, USA
| | - Zhong Zuo
- School of Pharmacy, the Chinese University of Hong Kong, Hong Kong, China
| | - Huichang Bi
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510275, China
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38
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Rapid and efficient production of genome-edited animals by electroporation into oocytes injected with frozen or freeze-dried sperm. Cryobiology 2019; 90:71-74. [DOI: 10.1016/j.cryobiol.2019.08.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 08/20/2019] [Accepted: 08/20/2019] [Indexed: 11/22/2022]
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39
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Alfazema N, Barrier M, de Procé SM, Menzies RI, Carter R, Stewart K, Diaz AG, Moyon B, Webster Z, Bellamy CO, Arends MJ, Stimson RH, Morton NM, Aitman TJ, Coan PM. Camk2n1 Is a Negative Regulator of Blood Pressure, Left Ventricular Mass, Insulin Sensitivity, and Promotes Adiposity. Hypertension 2019; 74:687-696. [PMID: 31327268 PMCID: PMC6686962 DOI: 10.1161/hypertensionaha.118.12409] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 12/04/2018] [Accepted: 05/02/2019] [Indexed: 12/13/2022]
Abstract
Metabolic syndrome is a cause of coronary artery disease and type 2 diabetes mellitus. Camk2n1 resides in genomic loci for blood pressure, left ventricle mass, and type 2 diabetes mellitus, and in the spontaneously hypertensive rat model of metabolic syndrome, Camk2n1 expression is cis-regulated in left ventricle and fat and positively correlates with adiposity. Therefore, we knocked out Camk2n1 in spontaneously hypertensive rat to investigate its role in metabolic syndrome. Compared with spontaneously hypertensive rat, Camk2n1-/- rats had reduced cardiorenal CaMKII (Ca2+/calmodulin-dependent kinase II) activity, lower blood pressure, enhanced nitric oxide bioavailability, and reduced left ventricle mass associated with altered hypertrophic networks. Camk2n1 deficiency reduced insulin resistance, visceral fat, and adipogenic capacity through the altered cell cycle and complement pathways, independent of CaMKII. In human visceral fat, CAMK2N1 expression correlated with adiposity and genomic variants that increase CAMK2N1 expression associated with increased risk of coronary artery disease and type 2 diabetes mellitus. Camk2n1 regulates multiple networks that control metabolic syndrome traits and merits further investigation as a therapeutic target in humans.
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Affiliation(s)
- Neza Alfazema
- From the MRC Institute of Genetics and Molecular Medicine, Edinburgh, United Kingdom (N.A., M.B., S.M.d.P., T.J.A., P.M.C.)
| | - Marjorie Barrier
- From the MRC Institute of Genetics and Molecular Medicine, Edinburgh, United Kingdom (N.A., M.B., S.M.d.P., T.J.A., P.M.C.)
| | - Sophie Marion de Procé
- From the MRC Institute of Genetics and Molecular Medicine, Edinburgh, United Kingdom (N.A., M.B., S.M.d.P., T.J.A., P.M.C.)
| | - Robert I. Menzies
- Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, United Kingdom (R.I.M., R.C., K.S., R.H.S., N.M.M.)
| | - Roderick Carter
- Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, United Kingdom (R.I.M., R.C., K.S., R.H.S., N.M.M.)
| | - Kevin Stewart
- Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, United Kingdom (R.I.M., R.C., K.S., R.H.S., N.M.M.)
| | - Ana Garcia Diaz
- MRC London Institute of Medical Sciences, Imperial College London, United Kingdom (A.G.D., B.M., Z.W.)
| | - Ben Moyon
- MRC London Institute of Medical Sciences, Imperial College London, United Kingdom (A.G.D., B.M., Z.W.)
| | - Zoe Webster
- MRC London Institute of Medical Sciences, Imperial College London, United Kingdom (A.G.D., B.M., Z.W.)
| | - Christopher O.C. Bellamy
- Division of Pathology, Centre for Comparative Pathology, Edinburgh CRUK Cancer Centre, United Kingdom (C.O.C.B., M.J.A.)
| | - Mark J. Arends
- Division of Pathology, Centre for Comparative Pathology, Edinburgh CRUK Cancer Centre, United Kingdom (C.O.C.B., M.J.A.)
| | - Roland H. Stimson
- Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, United Kingdom (R.I.M., R.C., K.S., R.H.S., N.M.M.)
| | - Nicholas M. Morton
- Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, United Kingdom (R.I.M., R.C., K.S., R.H.S., N.M.M.)
| | - Timothy J. Aitman
- From the MRC Institute of Genetics and Molecular Medicine, Edinburgh, United Kingdom (N.A., M.B., S.M.d.P., T.J.A., P.M.C.)
| | - Philip M. Coan
- From the MRC Institute of Genetics and Molecular Medicine, Edinburgh, United Kingdom (N.A., M.B., S.M.d.P., T.J.A., P.M.C.)
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40
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Przanowski P, Mondal SS, Cabaj A, Dębski KJ, Wojtas B, Gielniewski B, Kaza B, Kaminska B, Dabrowski M. Open chromatin landscape of rat microglia upon proinvasive or inflammatory polarization. Glia 2019; 67:2312-2328. [PMID: 31339627 DOI: 10.1002/glia.23686] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 06/18/2019] [Accepted: 06/21/2019] [Indexed: 01/02/2023]
Abstract
Microglia are brain-resident, myeloid cells that play important roles in health and brain pathologies. Herein, we report a comprehensive, replicated, false discovery rate-controlled dataset of DNase-hypersensitive (DHS) open chromatin regions for rat microglia. We compared the open chromatin landscapes in untreated primary microglial cultures and cultures stimulated for 6 hr with either glioma-conditioned medium (GCM) or lipopolysaccharide (LPS). Glioma-secreted factors induce proinvasive and immunosuppressive activation of microglia, and these cells then promote tumor growth. The open chromatin landscape of the rat microglia consisted of 126,640 reproducible DHS regions, among which 2,303 and 12,357 showed a significant change in openness following stimulation with GCM or LPS, respectively. Active genes exhibited constitutively open promoters, but there was no direct dependence between the aggregated openness of DHS regions near a gene and its expression. Individual regions mapped to the same gene often presented different patterns of openness changes. GCM-regulated DHS regions were more frequent in areas away from gene bodies, while LPS-regulated regions were more frequent in introns. GCM and LPS differentially affected the openness of regions mapped to immune checkpoint genes. The two treatments differentially affected the aggregated openness of regions mapped to genes in the Toll-like receptor signaling and axon guidance pathways, suggesting that the molecular machinery used by migrating microglia is similar to that of growing axons and that modulation of these pathways is instrumental in the induction of proinvasive polarization of microglia by glioma. Our dataset of open chromatin regions paves the way for studies of gene regulation in rat microglia.
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Affiliation(s)
- Piotr Przanowski
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Shamba S Mondal
- Laboratory of Bioinformatics, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Aleksandra Cabaj
- Laboratory of Bioinformatics, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Konrad J Dębski
- Laboratory of Bioinformatics, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Bartosz Wojtas
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Bartłomiej Gielniewski
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Beata Kaza
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Bozena Kaminska
- Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Michal Dabrowski
- Laboratory of Bioinformatics, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
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41
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A novel approach to differentiate rat embryonic stem cells in vitro reveals a role for RNF12 in activation of X chromosome inactivation. Sci Rep 2019; 9:6068. [PMID: 30988473 PMCID: PMC6465393 DOI: 10.1038/s41598-019-42246-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 03/27/2019] [Indexed: 02/07/2023] Open
Abstract
X chromosome inactivation (XCI) is a mammalian specific, developmentally regulated process relying on several mechanisms including antisense transcription, non-coding RNA-mediated silencing, and recruitment of chromatin remodeling complexes. In vitro modeling of XCI, through differentiation of embryonic stem cells (ESCs), provides a powerful tool to study the dynamics of XCI, overcoming the need for embryos, and facilitating genetic modification of key regulatory players. However, to date, robust initiation of XCI in vitro has been mostly limited to mouse pluripotent stem cells. Here, we adapted existing protocols to establish a novel monolayer differentiation protocol for rat ESCs to study XCI. We show that differentiating rat ESCs properly downregulate pluripotency factor genes, and present female specific Xist RNA accumulation and silencing of X-linked genes. We also demonstrate that RNF12 seems to be an important player in regulation of initiation of XCI in rat, acting as an Xist activator. Our work provides the basis to investigate the mechanisms directing the XCI process in a model organism different from the mouse.
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42
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Wang D, Wang Y, Liu H, Tong C, Ying Q, Sachinidis A, Li L, Peng L. Laminin promotes differentiation of rat embryonic stem cells into cardiomyocytes by activating the integrin/FAK/PI3K p85 pathway. J Cell Mol Med 2019; 23:3629-3640. [PMID: 30907509 PMCID: PMC6484303 DOI: 10.1111/jcmm.14264] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 01/02/2019] [Accepted: 01/10/2019] [Indexed: 12/27/2022] Open
Abstract
The generation of germline competent rat embryonic stem cells (rESCs) allows the study of their lineage commitment. Here, we developed a highly efficient system for rESC-derived cardiomyocytes, and even the formation of three-dimensional (3D)-like cell clusters with cTNT and α-Actinin. We have validated that laminin can interact with membrane integrin to promote the phosphorylation of both phosphatidylinositol 3-kinase (PI3K) p85 and the focal adhesion kinase (FAK). In parallel, GATA4 was up-regulated. Upon inhibiting the integrin, laminin loses the effect on cardiomyocyte differentiation, accompanied with a down-regulation of phosphorylation level of PI3K p85 and FAK. Meanwhile, the expression of Gata4 was inhibited as well. Taken together, laminin is a crucial component in the differentiation of rESCs into cardiomyocytes through increasing their proliferation via interacting with integrin pathway. These results provide new insights into the pathways mediated by extracellular laminin involved in the fate of rESC-derived cardiomyocytes.
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Affiliation(s)
- Duo Wang
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Department of Pathology and Pathophysiology, Tongji University School of Medicine, Shanghai, China
| | - Yumei Wang
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Department of Pathology and Pathophysiology, Tongji University School of Medicine, Shanghai, China
| | - Huan Liu
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Department of Pathology and Pathophysiology, Tongji University School of Medicine, Shanghai, China
| | - Chang Tong
- Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Qilong Ying
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research at USC, Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Agapios Sachinidis
- Institute of Neurophysiology and Center for Molecular Medicine, University of Cologne, Cologne, Germany
| | - Li Li
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Department of Pathology and Pathophysiology, Tongji University School of Medicine, Shanghai, China
| | - Luying Peng
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Department of Pathology and Pathophysiology, Tongji University School of Medicine, Shanghai, China
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43
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Russell JC, Robins JH, Fewster RM. Phylogeography of Invasive Rats in New Zealand. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00048] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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44
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Tolerance to vitrification of rat embryos at various developmental stages. Cryobiology 2018; 84:1-3. [DOI: 10.1016/j.cryobiol.2018.09.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 09/10/2018] [Accepted: 09/10/2018] [Indexed: 11/23/2022]
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45
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Lee JG, Sung YH, Baek IJ. Generation of genetically-engineered animals using engineered endonucleases. Arch Pharm Res 2018; 41:885-897. [PMID: 29777358 PMCID: PMC6153862 DOI: 10.1007/s12272-018-1037-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Accepted: 05/01/2018] [Indexed: 02/06/2023]
Abstract
The key to successful drug discovery and development is to find the most suitable animal model of human diseases for the preclinical studies. The recent emergence of engineered endonucleases is allowing for efficient and precise genome editing, which can be used to develop potentially useful animal models for human diseases. In particular, zinc finger nucleases, transcription activator-like effector nucleases, and the clustered regularly interspaced short palindromic repeat systems are revolutionizing the generation of diverse genetically-engineered experimental animals including mice, rats, rabbits, dogs, pigs, and even non-human primates that are commonly used for preclinical studies of the drug discovery. Here, we describe recent advances in engineered endonucleases and their application in various laboratory animals. We also discuss the importance of genome editing in animal models for more closely mimicking human diseases.
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Affiliation(s)
- Jong Geol Lee
- ConveRgence mEDIcine research cenTer (CREDIT), Asan Institute for Life Sciences, Asan Medical Center, Seoul, Republic of Korea
- College of Veterinary Medicine, Chungbuk National University, Cheongju, Republic of Korea
| | - Young Hoon Sung
- ConveRgence mEDIcine research cenTer (CREDIT), Asan Institute for Life Sciences, Asan Medical Center, Seoul, Republic of Korea.
- Department of Convergence Medicine, ConveRgence mEDIcine research cenTer (CREDIT), Asan Institute for Life Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea.
| | - In-Jeoung Baek
- ConveRgence mEDIcine research cenTer (CREDIT), Asan Institute for Life Sciences, Asan Medical Center, Seoul, Republic of Korea.
- Department of Convergence Medicine, ConveRgence mEDIcine research cenTer (CREDIT), Asan Institute for Life Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea.
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46
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Izumi R, Kusakabe T, Noguchi M, Iwakura H, Tanaka T, Miyazawa T, Aotani D, Hosoda K, Kangawa K, Nakao K. CRISPR/Cas9-mediated Angptl8 knockout suppresses plasma triglyceride concentrations and adiposity in rats. J Lipid Res 2018; 59:1575-1585. [PMID: 30042156 DOI: 10.1194/jlr.m082099] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 07/22/2018] [Indexed: 12/14/2022] Open
Abstract
Angiopoietin-like protein (ANGPTL)8 is a liver- and adipocyte-derived protein that controls plasma triglyceride (TG) levels. Most animal studies have used mouse models. Here, we generated an Angptl8 KO rat model using a clustered regulatory interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) (CRISPR/Cas9) system to clarify the roles of ANGPTL8 in glucose and lipid metabolism. Compared with WT rats, Angptl8 KO rats had lower body weight and fat content, associated with impaired lipogenesis in adipocytes; no differences existed between the groups in food intake or rectal temperature. Plasma TG levels in both the fasted and refed states were significantly lower in KO than in WT rats, and an oral fat tolerance test showed decreased plasma TG excursion in Angptl8 KO rats. Higher levels of lipase activity in the heart and greater expression of genes related to β-oxidation in heart and skeletal muscle were observed in Angptl8 KO rats. However, there were no significant differences between KO and WT rats in glucose metabolism or the histology of pancreatic β-cells on both standard and high-fat diets. In conclusion, we demonstrated that Angptl8 KO in rats resulted in lower body weight and plasma TG levels without affecting glucose metabolism. ANGPTL8 might be an important therapeutic target for obesity and dyslipidemia.
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Affiliation(s)
- Ryota Izumi
- Medical Innovation Center Kyoto University Graduate School of Medicine, Kyoto, Japan; Department of Diabetes, Endocrinology, and Nutrition, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Toru Kusakabe
- Medical Innovation Center Kyoto University Graduate School of Medicine, Kyoto, Japan; Department of Endocrinology, Metabolism, and Hypertension, Clinical Research Institute, National Hospital Organization Kyoto Medical Center, Kyoto, Japan.
| | - Michio Noguchi
- Medical Innovation Center Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Hiroshi Iwakura
- Medical Innovation Center Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Tomohiro Tanaka
- Medical Innovation Center Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Takashi Miyazawa
- Medical Innovation Center Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Daisuke Aotani
- Medical Innovation Center Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Kiminori Hosoda
- Medical Innovation Center Kyoto University Graduate School of Medicine, Kyoto, Japan; Division of Endocrinology and Metabolism, Department of Lifestyle-Related Diseases, National Cerebral and Cardiovascular Center, Osaka, Japan
| | - Kenji Kangawa
- Medical Innovation Center Kyoto University Graduate School of Medicine, Kyoto, Japan; National Cerebral and Cardiovascular Center Research Institute, Osaka, Japan
| | - Kazuwa Nakao
- Medical Innovation Center Kyoto University Graduate School of Medicine, Kyoto, Japan
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Yang X, Zhou J, He J, Liu J, Wang H, Liu Y, Jiang T, Zhang Q, Fu X, Xu Y. An Immune System-Modified Rat Model for Human Stem Cell Transplantation Research. Stem Cell Reports 2018; 11:514-521. [PMID: 29983387 PMCID: PMC6092637 DOI: 10.1016/j.stemcr.2018.06.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Revised: 06/04/2018] [Accepted: 06/06/2018] [Indexed: 02/04/2023] Open
Abstract
Due to its lack of both innate and acquired immune responses to human cells, the NODSCIDIl2rγ−/− (NSG) mouse model has become an important tool for human stem cell research. When compared with the mouse, the rat is physiologically more similar to humans and offers advantages in preclinical efficacy studies on human stem cells, particularly in evaluating neural, hepatic, and cardiac functions. Therefore, we generated a human SIRPα+Prdkc−/−Il2rγ−/− rat model, denoted NSG-like (NSGL) rat, which expresses human SIRPα and is abolished in the development of B, T, and natural killer cells. When compared with Prdkc−/−Il2rγ−/− (SG) rats, NSGL rats allow more efficient engraftment of human cancer cells and human pluripotent stem cells. In addition, only NSGL rats, but not SG rats, can be engrafted with human hematopoietic stem cells to reconstitute the human immune system. Therefore, NSGL rats represent an improved xenotransplantation model for efficacy studies of human stem cells. Generation of human SIRPα+Prkdc−/−Il2rγ−/− NSG-like (NSGL) rat model NSGL rats lack B, T, and NK cells but express human SIRPα NSGL rats can be efficiently engrafted with human stem cells NSGL rats can be reconstituted by human HSCs to generate a human immune system
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Affiliation(s)
- Xinglong Yang
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Jianlong Zhou
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Jingjin He
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, China; The Eighth Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong 518033, China
| | - Jingfeng Liu
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, China; Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Hui Wang
- The Eighth Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong 518033, China
| | - Yachen Liu
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Tao Jiang
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, China; Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Qianbing Zhang
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Xuemei Fu
- The Eighth Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong 518033, China.
| | - Yang Xu
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, China; The Eighth Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong 518033, China; Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
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48
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Puckett EE, Micci‐Smith O, Munshi‐South J. Genomic analyses identify multiple Asian origins and deeply diverged mitochondrial clades in inbred brown rats ( Rattus norvegicus). Evol Appl 2018; 11:718-726. [PMID: 29875813 PMCID: PMC5979757 DOI: 10.1111/eva.12572] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 10/27/2017] [Indexed: 01/05/2023] Open
Abstract
Over 500 strains of inbred brown rats (Rattus norvegicus) have been developed for use as a biomedical model organism. Most of these inbred lines were derived from the colony established at the Wistar Institute in 1906 or its descendants following worldwide distribution to research and breeding centers. The geographic source of the animals that founded the Wistar colony has been lost to history; thus, we compared 25 inbred rat strains to 326 wild rats from a global diversity dataset at 32 k SNPs, and 47 mitochondrial genomes to identify the source populations. We analyzed nuclear genomic data using principal component analyses and co-ancestry heat maps, and mitogenomes using phylogenetic trees and networks. In the nuclear genome, inbred rats clustered together indicating a single geographic origin for the strains studied and showed admixed ancestral variation with wild rats in eastern Asia and western North America. The Sprague Dawley derived, Wistar derived, and Brown Norway strains each had mitogenomes from different clades which diverged between 13 and 139 kya. Thus, we posit that rats originally collected for captive breeding had high mitochondrial diversity that became fixed through genetic drift and/or artificial selection. Our results show that these important medical models share common genomic ancestry from a few source populations, and opportunities exist to create new strains with diverse genomic backgrounds to provide novel insight into the genomic basis of disease phenotypes.
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Affiliation(s)
- Emily E. Puckett
- Louis Calder Center – Biological Field StationFordham UniversityArmonkNYUSA
| | - Olivia Micci‐Smith
- Louis Calder Center – Biological Field StationFordham UniversityArmonkNYUSA
| | - Jason Munshi‐South
- Louis Calder Center – Biological Field StationFordham UniversityArmonkNYUSA
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49
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Kaneko T. Reproductive technologies for the generation and maintenance of valuable animal strains. J Reprod Dev 2018; 64:209-215. [PMID: 29657233 PMCID: PMC6021608 DOI: 10.1262/jrd.2018-035] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Many types of mutant and genetically engineered strains have been produced in various animal species. Their numbers have dramatically increased in recent years, with new strains being
rapidly produced using genome editing techniques. In the rat, it has been difficult to produce knockout and knock-in strains because the establishment of stem cells has been insufficient.
However, a large number of knockout and knock-in strains can currently be produced using genome editing techniques, including zinc-finger nuclease (ZFN), transcription activator-like
effector nuclease (TALEN), and the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein 9 (Cas9) system. Microinjection technique has also
contributed widely to the production of various kinds of genome edited animal strains. A novel electroporation method, the “Technique for Animal Knockout system by Electroporation (TAKE)”
method, is a simple and highly efficient tool that has accelerated the production of new strains. Gamete preservation is extremely useful for maintaining large numbers of these valuable
strains as genetic resources in the long term. These reproductive technologies, including microinjection, TAKE method, and gamete preservation, strongly support biomedical research and the
bio-resource banking of animal models. In this review, we introduce the latest reproductive technologies used for the production of genetically engineered animals, especially rats, using
genome editing techniques and the efficient maintenance of valuable strains as genetic resources. These technologies can also be applied to other laboratory animals, including mice, and
domestic and wild animal species.
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Affiliation(s)
- Takehito Kaneko
- Division of Science and Engineering, Graduate School of Arts and Science, Iwate University, Iwate 020-8551, Japan.,Department of Chemistry and Biological Sciences, Faculty of Science and Engineering, Iwate University, Iwate 020-8551, Japan.,Soft-Path Science and Engineering Research Center (SPERC), Iwate University, Iwate 020-8551, Japan
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50
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Saba L, Hoffman P, Tabakoff B. Using Baseline Transcriptional Connectomes in Rat to Identify Genetic Pathways Associated with Predisposition to Complex Traits. Methods Mol Biol 2018; 1488:299-317. [PMID: 27933531 DOI: 10.1007/978-1-4939-6427-7_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Although rat is a critical model organism in preclinical medications development, its use in systems genetics studies remains sparse. The PhenoGen database and website contain detailed information on the qualitative and quantitative aspects of the rat brain, liver, heart, and brown adipose transcriptome. This database has been generated using the HXB/BXH recombinant inbred panel and is being expanded to a hybrid rat diversity panel that includes many common inbred strains as well. By using such a panel, the PhenoGen project has created a renewable and cumulative resource for the rat genomics community. The database has been used to reconstruct the brain transcriptome identifying both annotated and unannotated transcribed elements that range in size from 20 nucleotides to over 30,000 nucleotides and elements that have a wide variety of roles in the cell including generation of proteins and regulation of the transcription and translation processes. In all 4 tissues, baseline transcriptional connectomes have been generated to model the relationships among transcripts. These connectomes can be used to identify genetic pathways associated with complex traits and to gain insight into biological function of individual transcripts. The PhenoGen website contains tools that allow the user to explore qualitative features of individual genes and to see how the gene relates to other genes within a tissue. The PhenoGen database and website continue to grow and to make use of the latest statistical methods for systems genetics creating a national resource for the rat genomics community.
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Affiliation(s)
- Laura Saba
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, 12850 E. Montview Blvd., Aurora, CO, 80045, USA.
| | - Paula Hoffman
- Department of Pharmacology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Boris Tabakoff
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, 12850 E. Montview Blvd., Aurora, CO, 80045, USA
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