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Nicotra R, Lutz C, Messal HA, Jonkers J. Rat Models of Hormone Receptor-Positive Breast Cancer. J Mammary Gland Biol Neoplasia 2024; 29:12. [PMID: 38913216 PMCID: PMC11196369 DOI: 10.1007/s10911-024-09566-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 06/07/2024] [Indexed: 06/25/2024] Open
Abstract
Hormone receptor-positive (HR+) breast cancer (BC) is the most common type of breast cancer among women worldwide, accounting for 70-80% of all invasive cases. Patients with HR+ BC are commonly treated with endocrine therapy, but intrinsic or acquired resistance is a frequent problem, making HR+ BC a focal point of intense research. Despite this, the malignancy still lacks adequate in vitro and in vivo models for the study of its initiation and progression as well as response and resistance to endocrine therapy. No mouse models that fully mimic the human disease are available, however rat mammary tumor models pose a promising alternative to overcome this limitation. Compared to mice, rats are more similar to humans in terms of mammary gland architecture, ductal origin of neoplastic lesions and hormone dependency status. Moreover, rats can develop spontaneous or induced mammary tumors that resemble human HR+ BC. To date, six different types of rat models of HR+ BC have been established. These include the spontaneous, carcinogen-induced, transplantation, hormone-induced, radiation-induced and genetically engineered rat mammary tumor models. Each model has distinct advantages, disadvantages and utility for studying HR+ BC. This review provides a comprehensive overview of all published models to date.
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Affiliation(s)
- Raquel Nicotra
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, Netherlands
- Oncode Institute, Amsterdam, Netherlands
| | - Catrin Lutz
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, Netherlands.
- Oncode Institute, Amsterdam, Netherlands.
| | - Hendrik A Messal
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, Netherlands.
- Oncode Institute, Amsterdam, Netherlands.
| | - Jos Jonkers
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, Netherlands.
- Oncode Institute, Amsterdam, Netherlands.
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2
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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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3
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Huang S, Carter-Cusack D, Maxwell E, Patkar OL, Irvine KM, Hume DA. Genetic and Immunohistochemistry Tools to Visualize Rat Macrophages In Situ. Methods Mol Biol 2024; 2713:99-115. [PMID: 37639117 DOI: 10.1007/978-1-0716-3437-0_6] [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] [Indexed: 08/29/2023]
Abstract
Macrophages contribute to many aspects of development and homeostasis, innate and acquired immunity, immunopathology, and tissue repair. Every tissue contains an abundant resident macrophage population. Inflammatory stimuli promote the recruitment of monocytes from the blood and their adaptation promotes the removal of the stimulus and subsequent restoration of normal tissue architecture. Dysregulation of this response leads to chronic inflammation and tissue injury. In many tissues, their differentiation and survival are dependent on the colony stimulating factor 1 receptor (CSF1R) signalling axis, which is highly conserved across all vertebrates. Complete loss of either CSF1R or its cognate ligands, colony stimulating factor 1 (CSF1), and interleukin 34 (IL-34), results in the loss of many tissue-resident macrophage populations. This provides a useful paradigm to study macrophages.There are many tools used to visualize tissue-resident macrophages and their precursors, monocytes, in mice and humans. Particularly in mice there are genetic tools available to delete, enhance and manipulate monocytes and macrophages and their gene products to gain insight into phenotype and function. The laboratory rat has many advantages as an experimental model for the understanding of human disease, but the analytical resources are currently more limited than in mice. Here, we describe available genetic models, antibodies, and immunohistochemistry (IHC) methods that may be used to visualize tissue-resident macrophages in rats.
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Affiliation(s)
- Stephen Huang
- Mater Research Institute-UQ, Translational Research Institute, Woolloongabba, Brisbane, QLD, Australia
| | - Dylan Carter-Cusack
- Mater Research Institute-UQ, Translational Research Institute, Woolloongabba, Brisbane, QLD, Australia
| | - Emma Maxwell
- Mater Research Institute-UQ, Translational Research Institute, Woolloongabba, Brisbane, QLD, Australia
| | - Omkar L Patkar
- Mater Research Institute-UQ, Translational Research Institute, Woolloongabba, Brisbane, QLD, Australia
| | - Katharine M Irvine
- Mater Research Institute-UQ, Translational Research Institute, Woolloongabba, Brisbane, QLD, Australia.
| | - David A Hume
- Mater Research Institute-UQ, Translational Research Institute, Woolloongabba, Brisbane, QLD, Australia.
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4
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Vedi M, Nalabolu HS, Lin CW, Hoffman MJ, Smith JR, Brodie K, De Pons JL, Demos WM, Gibson AC, Hayman GT, Hill ML, Kaldunski ML, Lamers L, Laulederkind SJF, Thorat K, Thota J, Tutaj M, Tutaj MA, Wang SJ, Zacher S, Dwinell MR, Kwitek AE. MOET: a web-based gene set enrichment tool at the Rat Genome Database for multiontology and multispecies analyses. Genetics 2022; 220:6516514. [PMID: 35380657 PMCID: PMC8982048 DOI: 10.1093/genetics/iyac005] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 01/03/2022] [Indexed: 12/12/2022] Open
Abstract
Biological interpretation of a large amount of gene or protein data is complex. Ontology analysis tools are imperative in finding functional similarities through overrepresentation or enrichment of terms associated with the input gene or protein lists. However, most tools are limited by their ability to do ontology-specific and species-limited analyses. Furthermore, some enrichment tools are not updated frequently with recent information from databases, thus giving users inaccurate, outdated or uninformative data. Here, we present MOET or the Multi-Ontology Enrichment Tool (v.1 released in April 2019 and v.2 released in May 2021), an ontology analysis tool leveraging data that the Rat Genome Database (RGD) integrated from in-house expert curation and external databases including the National Center for Biotechnology Information (NCBI), Mouse Genome Informatics (MGI), The Kyoto Encyclopedia of Genes and Genomes (KEGG), The Gene Ontology Resource, UniProt-GOA, and others. Given a gene or protein list, MOET analysis identifies significantly overrepresented ontology terms using a hypergeometric test and provides nominal and Bonferroni corrected P-values and odds ratios for the overrepresented terms. The results are shown as a downloadable list of terms with and without Bonferroni correction, and a graph of the P-values and number of annotated genes for each term in the list. MOET can be accessed freely from https://rgd.mcw.edu/rgdweb/enrichment/start.html.
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Affiliation(s)
- Mahima Vedi
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Harika S Nalabolu
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Chien-Wei Lin
- Division of Biostatistics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Matthew J Hoffman
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jennifer R Smith
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Kent Brodie
- Clinical and Translational Science Institute, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jeffrey L De Pons
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Wendy M Demos
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Adam C Gibson
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - G Thomas Hayman
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Morgan L Hill
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Mary L Kaldunski
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Logan Lamers
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | | | - Ketaki Thorat
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jyothi Thota
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Monika Tutaj
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Marek A Tutaj
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Shur-Jen Wang
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Stacy Zacher
- Information Services, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Melinda R Dwinell
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Anne E Kwitek
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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5
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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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Carreres L, Jílková ZM, Vial G, Marche PN, Decaens T, Lerat H. Modeling Diet-Induced NAFLD and NASH in Rats: A Comprehensive Review. Biomedicines 2021; 9:biomedicines9040378. [PMID: 33918467 PMCID: PMC8067264 DOI: 10.3390/biomedicines9040378] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 03/25/2021] [Accepted: 03/26/2021] [Indexed: 12/12/2022] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is the most common chronic liver disease, characterized by hepatic steatosis without any alcohol abuse. As the prevalence of NAFLD is rapidly increasing worldwide, important research activity is being dedicated to deciphering the underlying molecular mechanisms in order to define new therapeutic targets. To investigate these pathways and validate preclinical study, reliable, simple and reproducible tools are needed. For that purpose, animal models, more precisely, diet-induced NAFLD and nonalcoholic steatohepatitis (NASH) models, were developed to mimic the human disease. In this review, we focus on rat models, especially in the current investigation of the establishment of the dietary model of NAFLD and NASH in this species, compiling the different dietary compositions and their impact on histological outcomes and metabolic injuries, as well as external factors influencing the course of liver pathogenesis.
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Affiliation(s)
- Lydie Carreres
- Institute for Advanced Biosciences, Research Center Inserm U 1209/CNRS 5309, 38700 La Tronche, France; (L.C.); (Z.M.J.); (P.N.M.); (T.D.)
- Université Grenoble-Alpes, 38000 Grenoble, France;
| | - Zuzana Macek Jílková
- Institute for Advanced Biosciences, Research Center Inserm U 1209/CNRS 5309, 38700 La Tronche, France; (L.C.); (Z.M.J.); (P.N.M.); (T.D.)
- Université Grenoble-Alpes, 38000 Grenoble, France;
| | - Guillaume Vial
- Université Grenoble-Alpes, 38000 Grenoble, France;
- Inserm U 1300, Hypoxia PathoPhysiology (HP2), 38000 Grenoble, France
| | - Patrice N. Marche
- Institute for Advanced Biosciences, Research Center Inserm U 1209/CNRS 5309, 38700 La Tronche, France; (L.C.); (Z.M.J.); (P.N.M.); (T.D.)
- Université Grenoble-Alpes, 38000 Grenoble, France;
| | - Thomas Decaens
- Institute for Advanced Biosciences, Research Center Inserm U 1209/CNRS 5309, 38700 La Tronche, France; (L.C.); (Z.M.J.); (P.N.M.); (T.D.)
- Université Grenoble-Alpes, 38000 Grenoble, France;
- Service D’hépato-Gastroentérologie, Pôle Digidune, CHU Grenoble Alpes, 38700 La Tronche, France
| | - Hervé Lerat
- Institute for Advanced Biosciences, Research Center Inserm U 1209/CNRS 5309, 38700 La Tronche, France; (L.C.); (Z.M.J.); (P.N.M.); (T.D.)
- Université Grenoble-Alpes, 38000 Grenoble, France;
- Unité Mixte de Service UGA hTAG, Inserm US 046, CNRS UAR 2019, 38700 La Tronche, France
- Correspondence:
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7
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Virgen-Carrillo CA, de Los Ríos DLH, Torres KR, Moreno AGM. Diagnostic Criteria for Metabolic Syndrome in Diet-Induced Rodent Models: A Systematic Review. Curr Diabetes Rev 2021; 17:e140421192834. [PMID: 33855947 DOI: 10.2174/1573399817666210414103730] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 01/14/2021] [Accepted: 02/09/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Thousands of publications in recent years have addressed the induction of metabolic syndrome (MetS) in rodents. However, the criteria and the reference values for diagnosing this disease have not been defined. OBJECTIVE Our main objective was to carry out a systematic review to gather evidence about the criteria for biochemical and anthropometric parameters in which scientific studies have relied on to report that rats developed MetS from a previous dietary manipulation. METHODS We compiled characteristics and findings of diet-induced MetS with high-fat, high-carbohydrate, high-fat/high-carbohydrates, and cafeteria diet from PubMed and Science Direct databases published in the last 5 years. RESULTS The results on the principal determinants for the syndrome, published in the reviewed articles, were chosen to propose reference values in the rat models of food induction. CONCLUSION The values obtained will serve as reference cut-of points in the development of the disease; in addition, the compilation of data will be useful in planning and executing research protocols in animal models.
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Affiliation(s)
- Carmen Alejandrina Virgen-Carrillo
- Instituto de Investigaciones en Comportamiento Alimentario y Nutrición, Centro Universitario del Sur, Universidad de Guadalajara, Jalisco, Mexico
| | - Diana Laura Hernández de Los Ríos
- Instituto de Investigaciones en Comportamiento Alimentario y Nutrición, Centro Universitario del Sur, Universidad de Guadalajara, Jalisco, Mexico
| | - Karina Ruíz Torres
- Instituto de Investigaciones en Comportamiento Alimentario y Nutrición, Centro Universitario del Sur, Universidad de Guadalajara, Jalisco, Mexico
| | - Alma Gabriela Martínez Moreno
- Instituto de Investigaciones en Comportamiento Alimentario y Nutrición, Centro Universitario del Sur, Universidad de Guadalajara, Jalisco, Mexico
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Kakizaki T, Ohshiro T, Itakura M, Konno K, Watanabe M, Mushiake H, Yanagawa Y. Rats deficient in the GAD65 isoform exhibit epilepsy and premature lethality. FASEB J 2020; 35:e21224. [PMID: 33236473 DOI: 10.1096/fj.202001935r] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/27/2020] [Accepted: 11/11/2020] [Indexed: 02/02/2023]
Abstract
GABA is synthesized by glutamate decarboxylase (GAD), which has two isoforms, namely, GAD65 and GAD67, encoded by the Gad2 and Gad1 genes, respectively. GAD65-deficient (Gad2-/- ) mice exhibit a reduction in brain GABA content after 1 month of age and show spontaneous seizures in adulthood. Approximately 25% of Gad2-/- mice died by 6 months of age. Our Western blot analysis demonstrated that the protein expression ratio of GAD65 to GAD67 in the brain was greater in rats than in mice during postnatal development, suggesting that the contribution of each GAD isoform to GABA functions differs between these two species. To evaluate whether GAD65 deficiency causes different phenotypes between rats and mice, we generated Gad2-/- rats using TALEN genome editing technology. Western blot and immunohistochemical analyses with new antibodies demonstrated that the GAD65 protein was undetectable in the Gad2-/- rat brain. Gad2-/- pups exhibited spontaneous seizures and paroxysmal discharge in EEG at postnatal weeks 3-4. More than 80% of the Gad2-/- rats died at postnatal days (PNDs) 17-23. GABA content in Gad2-/- brains was significantly lower than those in Gad2+/- and Gad2+/+ brains at PND17-19. These results suggest that the low levels of brain GABA content in Gad2-/- rats may lead to epilepsy followed by premature death, and that Gad2-/- rats are more severely affected than Gad2-/- mice. Considering that the GAD65/GAD67 ratio in human brains is more similar to that in rat brains than in mouse brains, Gad2-/- rats would be useful for further investigating the roles of GAD65 in vivo.
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Affiliation(s)
- Toshikazu Kakizaki
- Department of Genetic and Behavioral Neuroscience, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Tomokazu Ohshiro
- Department of Physiology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Makoto Itakura
- Department of Biochemistry, Kitasato University School of Medicine, Sagamihara, Japan
| | - Kohtarou Konno
- Department of Anatomy, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Masahiko Watanabe
- Department of Anatomy, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Hajime Mushiake
- Department of Physiology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yuchio Yanagawa
- Department of Genetic and Behavioral Neuroscience, Gunma University Graduate School of Medicine, Maebashi, Japan
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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: 90] [Impact Index Per Article: 22.5] [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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Wei Z, Yang Y, Li Q, Yin Y, Wei Z, Zhang W, Mu D, Ni J, Sun X, Xu B. The transcriptome of circulating cells indicates potential biomarkers and therapeutic targets in the course of hypertension-related myocardial infarction. Genes Dis 2020; 8:555-568. [PMID: 34179317 PMCID: PMC8209311 DOI: 10.1016/j.gendis.2020.01.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 01/06/2020] [Accepted: 01/08/2020] [Indexed: 12/12/2022] Open
Abstract
Hypertension (HT) is the most common public-health challenge and shows a high incidence around the world. Cardiovascular diseases are the leading cause of mortality and morbidity among the elderly (age > 65 years) in the United States. Now, there is widespread acceptance of the causal link between HT and acute myocardial infarction (MI). This is the first data-mining study to identify co-expressed differentially expressed genes (co-DEGs) between HT and MI (relative to normal control) and to uncover potential biomarkers and therapeutic targets of HT-related MI. In this manuscript, HT-specific DEGs and MI-specific DEGs and differentially expressed microRNAs (DE-miRNAs) were identified in Gene Expression Omnibus (GEO) datasets GSE24752, GSE60993, GSE62646, and GSE24548 after data consolidation and batch correction. Subsequently, enrichment in Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways as well as protein–protein interaction networks were identified, and single-gene gene set enrichment analysis was performed to determine the affected biological categories and networks. Cross-matching of the results on co-DE-miRNAs and predicted miRNAs targeting the co-DEGs was conducted and discussed as well. We found that MYC and HIST1H2BO may be associated with HT, whereas FCGR1A, FYN, KLRD1, KLRB1, and FOLR3 may be implicated in MI. Moreover, co-DEGs FOLR3 and NFE2 with predicted miRNAs and DE-miRNAs, especially miR-7 and miR-548, may be significantly associated and show huge potential as a new set of novel biomarkers and important molecular targets in the course of HT-related MI.
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Affiliation(s)
- Zilun Wei
- Department of Cardiology, Nanjing Drum Tower Hospital, Clinical College of Nanjing Medical University, Nanjing, Jiangsu Province, 210008, PR China
| | - Yining Yang
- Department of Cardiology, Nanjing Drum Tower Hospital, Clinical College of Nanjing Medical University, Nanjing, Jiangsu Province, 210008, PR China
| | - Qiaoling Li
- Department of Cardiology, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, Jiangsu Province, 210008, PR China
| | - Yong Yin
- Department of Cardiology, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, Jiangsu Province, 210008, PR China
| | - Zhonghai Wei
- Department of Cardiology, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, Jiangsu Province, 210008, PR China
| | - Wenfeng Zhang
- Department of Cardiology, Nanjing Drum Tower Hospital, Clinical College of Nanjing Medical University, Nanjing, Jiangsu Province, 210008, PR China
| | - Dan Mu
- Department of Cardiology, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, Jiangsu Province, 210008, PR China
| | - Jie Ni
- Department of Cardiology, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, Jiangsu Province, 210008, PR China
| | - Xuan Sun
- Department of Cardiology, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, Jiangsu Province, 210008, PR China
- Corresponding author. Department of Cardiology, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing 210008, China
| | - Biao Xu
- Department of Cardiology, Nanjing Drum Tower Hospital, Clinical College of Nanjing Medical University, Nanjing, Jiangsu Province, 210008, PR China
- Corresponding author. Department of Cardiology, Nanjing Drum Tower Hospital, Clinical College of Nanjing Medical University, Nanjing 210008, China
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11
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Yuan W, Peng S, Wang J, Wei C, Ye Z, Wang Y, Wang M, Xu H, Jiang S, Sun D, Dai C, Jiang L, Li X. Identification and characterization of circRNAs as competing endogenous RNAs for miRNA-mRNA in colorectal cancer. PeerJ 2019; 7:e7602. [PMID: 31579577 PMCID: PMC6754974 DOI: 10.7717/peerj.7602] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 08/01/2019] [Indexed: 12/13/2022] Open
Abstract
Background Recent studies showed that circRNAs are involved in the biological process of some human cancers. However, little is known about their functions in colorectal cancer (CRC). Methods Here we first revealed the expression profiles of circRNAs in the CRC tissues and the adjacent non-tumorous tissues using high-throughput sequencing. The sequence feature, chromosome location, alternative splicing and other characteristics of the circRNAs were also explored. The miRNA and mRNA expression profiles were then obtained by analyzing relevant CRC data retrived from the TCGA database. We obtained and analyzed the competing endogenous RNA (ceRNA) network of the top three pairs of the largest up-regulated and down-regulated circRNAs. Results In this study, we obtained 50,410 circRNAs in the CRC tissue and the adjacent non-tumor tissues, of which 33.7% (16,975) were new, and revealed differential changes in circRNA expression during colorectal carcinogenesis. We have identified six potential key circRNAs (circPIEZO1-3, hsa_circ_0067163, hsa_circ_0140188, hsa_circ_0002632, hsa_circ_0001998 and hsa_circ_0023990) associated with CRC, which play important roles in carcinogenesis as ceRNA for regulation of miRNA-mRNA network. In the subsequent KEGG analysis, several CRC-related pathways were found. Conclusions Our findings advance the understanding of the pathogenesis of CRC from the perspective of circRNAs and provide some circRNAs as candidate diagnostic biomarkers or potential therapeutic targets.
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Affiliation(s)
- Wenliang Yuan
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Shanghai, China.,National Pathogen Collection Center for Aquatic Animals, Ministry of Agriculture of China, Shanghai, China.,International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai, China.,School of Optical-Electric and Computer Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Sihua Peng
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Shanghai, China.,National Pathogen Collection Center for Aquatic Animals, Ministry of Agriculture of China, Shanghai, China.,International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai, China
| | - Jingyu Wang
- Department of Pathology, The First Affiliated Hospital of Jiaxing University, Jiaxing, China
| | - Cai Wei
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Shanghai, China.,National Pathogen Collection Center for Aquatic Animals, Ministry of Agriculture of China, Shanghai, China.,International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai, China
| | - Zhen Ye
- College of Engineering, Lishui University, Lishui, China
| | - Ye Wang
- College of Engineering, Lishui University, Lishui, China
| | - Meiliang Wang
- College of Engineering, Lishui University, Lishui, China
| | - Hao Xu
- College of Engineering, Lishui University, Lishui, China
| | - Shouwen Jiang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Shanghai, China.,National Pathogen Collection Center for Aquatic Animals, Ministry of Agriculture of China, Shanghai, China.,International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai, China
| | - Dan Sun
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Shanghai, China.,National Pathogen Collection Center for Aquatic Animals, Ministry of Agriculture of China, Shanghai, China.,International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai, China
| | - Chaoxu Dai
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Shanghai, China.,National Pathogen Collection Center for Aquatic Animals, Ministry of Agriculture of China, Shanghai, China.,International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai, China
| | - Linhua Jiang
- School of Optical-Electric and Computer Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Xiaobo Li
- College of Engineering, Lishui University, Lishui, China
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12
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Irvine KM, Caruso M, Cestari MF, Davis GM, Keshvari S, Sehgal A, Pridans C, Hume DA. Analysis of the impact of CSF‐1 administration in adult rats using a novel
Csf1r
‐mApple reporter gene. J Leukoc Biol 2019; 107:221-235. [DOI: 10.1002/jlb.ma0519-149r] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 07/04/2019] [Accepted: 07/25/2019] [Indexed: 12/14/2022] Open
Affiliation(s)
| | - Melanie Caruso
- Mater Research The University of Queensland Brisbane Australia
| | | | - Gemma M. Davis
- Faculty of Life Sciences The University of Manchester Manchester United Kingdom
| | - Sahar Keshvari
- Mater Research The University of Queensland Brisbane Australia
| | - Anuj Sehgal
- Mater Research The University of Queensland Brisbane Australia
| | - Clare Pridans
- Centre for Inflammation Research The University of Edinburgh Edinburgh United Kingdom
| | - David A. Hume
- Mater Research The University of Queensland Brisbane Australia
- Centre for Inflammation Research The University of Edinburgh Edinburgh United Kingdom
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13
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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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14
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Goncharov NV, Terpilowski MA, Shmurak VI, Belinskaya DA, Avdonin PV. The Rat (Rattus norvegicus) as a Model Object for Acute Organophosphate Poisoning. 1. Biochemical Aspects. J EVOL BIOCHEM PHYS+ 2019. [DOI: 10.1134/s0022093019020042] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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15
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Wang SJ, Laulederkind SJF, Zhao Y, Hayman GT, Smith JR, Tutaj M, Thota J, Tutaj MA, Hoffman MJ, Bolton ER, De Pons J, Dwinell MR, Shimoyama M. Integrated curation and data mining for disease and phenotype models at the Rat Genome Database. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2019; 2019:5310053. [PMID: 30753478 PMCID: PMC6369425 DOI: 10.1093/database/baz014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 01/18/2019] [Indexed: 11/20/2022]
Abstract
Rats have been used as research models in biomedical research for over 150 years. These disease models arise from naturally occurring mutations, selective breeding and, more recently, genome manipulation. Through the innovation of genome-editing technologies, genome-modified rats provide precision models of disease by disrupting or complementing targeted genes. To facilitate the use of these data produced from rat disease models, the Rat Genome Database (RGD) organizes rat strains and annotates these strains with disease and qualitative phenotype terms as well as quantitative phenotype measurements. From the curated quantitative data, the expected phenotype profile ranges were established through a meta-analysis pipeline using inbred rat strains in control conditions. The disease and qualitative phenotype annotations are propagated to their associated genes and alleles if applicable. Currently, RGD has curated nearly 1300 rat strains with disease/phenotype annotations and about 11% of them have known allele associations. All of the annotations (disease and phenotype) are integrated and displayed on the strain, gene and allele report pages. Finding disease and phenotype models at RGD can be done by searching for terms in the ontology browser, browsing the disease or phenotype ontology branches or entering keywords in the general search. Use cases are provided to show different targeted searches of rat strains at RGD.
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Affiliation(s)
- Shur-Jen Wang
- Department of Biomedical Engineering, Marquette University and Medical College of Wisconsin, Milwaukee, WI, USA
| | - Stanley J F Laulederkind
- Department of Biomedical Engineering, Marquette University and Medical College of Wisconsin, Milwaukee, WI, USA
| | - Yiqing Zhao
- Department of Biomedical Engineering, Marquette University and Medical College of Wisconsin, Milwaukee, WI, USA
| | - G Thomas Hayman
- Department of Biomedical Engineering, Marquette University and Medical College of Wisconsin, Milwaukee, WI, USA
| | - Jennifer R Smith
- Department of Biomedical Engineering, Marquette University and Medical College of Wisconsin, Milwaukee, WI, USA
| | - Monika Tutaj
- Department of Biomedical Engineering, Marquette University and Medical College of Wisconsin, Milwaukee, WI, USA
| | - Jyothi Thota
- Department of Biomedical Engineering, Marquette University and Medical College of Wisconsin, Milwaukee, WI, USA
| | - Marek A Tutaj
- Department of Biomedical Engineering, Marquette University and Medical College of Wisconsin, Milwaukee, WI, USA
| | - Matthew J Hoffman
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Elizabeth R Bolton
- Department of Biomedical Engineering, Marquette University and Medical College of Wisconsin, Milwaukee, WI, USA
| | - Jeffrey De Pons
- Department of Biomedical Engineering, Marquette University and Medical College of Wisconsin, Milwaukee, WI, USA
| | - Melinda R Dwinell
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Mary Shimoyama
- Department of Biomedical Engineering, Marquette University and Medical College of Wisconsin, Milwaukee, WI, USA
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16
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Singer-Englar T, Barlow G, Mathur R. Obesity, diabetes, and the gut microbiome: an updated review. Expert Rev Gastroenterol Hepatol 2019; 13:3-15. [PMID: 30791839 DOI: 10.1080/17474124.2019.1543023] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Obesity and diabetes are two of the most prevalent health problems and leading causes of death globally. As research on the intestinal microbiome increases, so does our understanding of its intricate relationship to these diseases, although this has yet to be fully elucidated. Areas covered: This review evaluates the role of the gut microbiome in obesity and diabetes, including the influences of internal and environmental factors. Literature searches were performed using the keywords 'diabetes,' 'insulin resistance,' 'gut microbiome,' 'gut microbes,' 'obesity,' and 'weight gain.' Expert commentary: Highlights of recent research include new findings regarding the effects of caloric restriction, which expound the importance of diet in shaping the gut microbiome, and studies reinforcing the lasting implications of antibiotic use for diabetes and obesity, particularly repeated doses in early childhood. Mechanistically, interactions between the microbiome and the host innate immune system, mediated by TLR4-LPS signaling, have been shown to meditate the metabolic benefits of caloric restriction. Further, gut microbes haven now been shown to regulate oxygen availability via butyrate production, thus protecting against the proliferation of pathogens such as E. coli and Salmonella. However, many microbial metabolites remain unidentified and their roles in obesity and diabetes remain to be determined.
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Affiliation(s)
- Tahli Singer-Englar
- a Medically Associated Science and Technology (MAST) Program , Cedars-Sinai Medical Center , Los Angeles , CA , USA
| | - Gillian Barlow
- a Medically Associated Science and Technology (MAST) Program , Cedars-Sinai Medical Center , Los Angeles , CA , USA
| | - Ruchi Mathur
- a Medically Associated Science and Technology (MAST) Program , Cedars-Sinai Medical Center , Los Angeles , CA , USA
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17
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Šedová L, Školníková E, Hodúlová M, Včelák J, Šeda O, Bendlová B. Expression profiling of Nme7 interactome in experimental models of metabolic syndrome. Physiol Res 2018; 67:S543-S550. [PMID: 30484681 DOI: 10.33549/physiolres.934021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Nucleoside diphosphate kinase 7, non-metastatic cells 7 (NME7) is an acknowledged member of ciliome and is involved in the biogenesis or function of cilia. As obesity and diabetes are common in several ciliopathies, we aimed to analyze changes of gene expression within Nme7 interactome in genetically designed rat models of metabolic syndrome. We assessed the liver transcriptome by Affymetrix microarrays in adult males of 14 PXO recombinant inbred rat strains and their two progenitor strains, SHR-Lx and BXH2. In the strains with the lowest expression of Nme7, we have identified significant enrichment of transcripts belonging to Nme7 interactome. In the subsequent network analysis, we have identified three major upstream regulators - Hnf4a, Ppara and Nr1h4 and liver steatosis (p=0.0001) and liver necrosis/cell death (apoptosis of liver cells, p=0.0003) among the most enriched Tox categories. The mechanistic network reaching the top score showed substantial overlap with Assembly of non-motile cilium and Glucose metabolism disorder gene lists. In summary, we show in a genetic model of metabolic syndrome that rat strains with the lowest expression of Nme7 present gene expression shifts of Nme7 interactome that are perturbing networks relevant for carbohydrate and lipid metabolism as well as ciliogenesis.
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Affiliation(s)
- L Šedová
- Laboratory of Transgenic Models of Diseases, Division BIOCEV, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, Czech Republic.
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18
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de Sousa-Pereira P, Abrantes J, Bauernfried S, Pierini V, Esteves PJ, Keppler OT, Pizzato M, Hornung V, Fackler OT, Baldauf HM. The antiviral activity of rodent and lagomorph SERINC3 and SERINC5 is counteracted by known viral antagonists. J Gen Virol 2018; 100:278-288. [PMID: 30566072 DOI: 10.1099/jgv.0.001201] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A first step towards the development of a human immunodeficiency virus (HIV) animal model has been the identification and surmounting of species-specific barriers encountered by HIV along its replication cycle in cells from small animals. Serine incorporator proteins 3 (SERINC3) and 5 (SERINC5) were recently identified as restriction factors that reduce HIV-1 infectivity. Here, we compared the antiviral activity of SERINC3 and SERINC5 among mice, rats and rabbits, and their susceptibility to viral counteraction to their human counterparts. In the absence of viral antagonists, rodent and lagomorph SERINC3 and SERINC5 displayed anti-HIV activity in a similar range to human controls. Vesicular stomatitis virus G protein (VSV-G) pseudotyped virions were considerably less sensitive to restriction by all SERINC3/5 orthologs. Interestingly, HIV-1 Nef, murine leukemia virus (MLV) GlycoGag and equine infectious anemia virus (EIAV) S2 counteracted the antiviral activity of all SERINC3/5 orthologs with similar efficiency. Our results demonstrate that the antiviral activity of SERINC3/5 proteins is conserved in rodents and rabbits, and can be overcome by all three previously reported viral antagonists.
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Affiliation(s)
- Patrícia de Sousa-Pereira
- 3Institute of Medical Virology, University Hospital Frankfurt, Frankfurt, Germany.,1CIBIO/InBIO- Research Network in Biodiversity and Evolutionary Biology, Campus de Vairão, University of Porto, Vairão, Portugal.,5Institute of Virology, Technische Universität München/Helmholtz Zentrum, Munich, Germany.,4Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany.,2Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Joana Abrantes
- 1CIBIO/InBIO- Research Network in Biodiversity and Evolutionary Biology, Campus de Vairão, University of Porto, Vairão, Portugal
| | - Stefan Bauernfried
- 6Gene Center and Department of Biochemistry, LMU München, Munich, Germany
| | - Virginia Pierini
- 7Department of Infectious Diseases, Integrative Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Pedro José Esteves
- 1CIBIO/InBIO- Research Network in Biodiversity and Evolutionary Biology, Campus de Vairão, University of Porto, Vairão, Portugal.,2Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal.,8CITS - Centro de Investigação em Tecnologias de Saúde, CESPU, Gandra, Portugal
| | - Oliver T Keppler
- 3Institute of Medical Virology, University Hospital Frankfurt, Frankfurt, Germany.,4Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany.,5Institute of Virology, Technische Universität München/Helmholtz Zentrum, Munich, Germany
| | - Massimo Pizzato
- 9University of Trento, Centre for Integrative Biology, Trento, Italy
| | - Veit Hornung
- 6Gene Center and Department of Biochemistry, LMU München, Munich, Germany
| | - Oliver T Fackler
- 7Department of Infectious Diseases, Integrative Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Hanna-Mari Baldauf
- 5Institute of Virology, Technische Universität München/Helmholtz Zentrum, Munich, Germany.,3Institute of Medical Virology, University Hospital Frankfurt, Frankfurt, Germany.,4Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany
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19
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Prokop JW, May T, Strong K, Bilinovich SM, Bupp C, Rajasekaran S, Worthey EA, Lazar J. Genome sequencing in the clinic: the past, present, and future of genomic medicine. Physiol Genomics 2018; 50:563-579. [PMID: 29727589 PMCID: PMC6139636 DOI: 10.1152/physiolgenomics.00046.2018] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Genomic sequencing has undergone massive expansion in the past 10 yr, from a rarely used research tool into an approach that has broad applications in a clinical setting. From rare disease to cancer, genomics is transforming our knowledge of biology. The transition from targeted gene sequencing, to whole exome sequencing, to whole genome sequencing has only been made possible due to rapid advancements in technologies and informatics that have plummeted the cost per base of DNA sequencing and analysis. The tools of genomics have resolved the etiology of disease for previously undiagnosable conditions, identified cancer driver gene variants, and have impacted the understanding of pathophysiology for many diseases. However, this expansion of use has also highlighted research's current voids in knowledge. The lack of precise animal models for gene-to-function association, lack of tools for analysis of genomic structural changes, skew in populations used for genetic studies, publication biases, and the "Unknown Proteome" all contribute to voids needing filled for genomics to work in a fast-paced clinical setting. The future will hold the tools to fill in these voids, with new data sets and the continual development of new technologies allowing for expansion of genomic medicine, ushering in the days to come for precision medicine. In this review we highlight these and other points in hopes of advancing and guiding precision medicine into the future for optimal success.
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Affiliation(s)
- Jeremy W Prokop
- HudsonAlpha Institute for Biotechnology , Huntsville, Alabama
- Department of Pediatrics and Human Development, Michigan State University , East Lansing, Michigan
- Department of Pharmacology and Toxicology, Michigan State University , East Lansing, Michigan
| | - Thomas May
- HudsonAlpha Institute for Biotechnology , Huntsville, Alabama
- Institute for Health and Aging, University of California San Francisco , San Francisco, California
- Elson S. Floyd College of Medicine, Washington State University , Spokane, Washington
| | - Kim Strong
- HudsonAlpha Institute for Biotechnology , Huntsville, Alabama
| | - Stephanie M Bilinovich
- Department of Pediatrics and Human Development, Michigan State University , East Lansing, Michigan
| | - Caleb Bupp
- Department of Pediatrics and Human Development, Michigan State University , East Lansing, Michigan
- Department of Genetics, Helen DeVos Children's Hospital, Spectrum Health, Grand Rapids, Michigan
| | - Surender Rajasekaran
- Department of Pediatrics and Human Development, Michigan State University , East Lansing, Michigan
- Department of Pediatric Critical Care Medicine, Helen DeVos Children's Hospital, Spectrum Health, Grand Rapids, Michigan
| | | | - Jozef Lazar
- HudsonAlpha Institute for Biotechnology , Huntsville, Alabama
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20
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Foley JF, Phadke DP, Hardy O, Hardy S, Miller V, Madan A, Howard K, Kruse K, Lord C, Ramaiahgari S, Solomon GG, Shah RR, Pandiri AR, Herbert RA, Sills RC, Merrick BA. Whole exome sequencing in the rat. BMC Genomics 2018; 19:487. [PMID: 29925311 PMCID: PMC6011395 DOI: 10.1186/s12864-018-4858-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 06/06/2018] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The rat genome was sequenced in 2004 with the aim to improve human health altered by disease and environmental influences through gene discovery and animal model validation. Here, we report development and testing of a probe set for whole exome sequencing (WES) to detect sequence variants in exons and UTRs of the rat genome. Using an in-silico approach, we designed probes targeting the rat exome and compared captured mutations in cancer-related genes from four chemically induced rat tumor cell lines (C6, FAT7, DSL-6A/C1, NBTII) to validated cancer genes in the human database, Catalogue of Somatic Mutations in Cancer (COSMIC) as well as normal rat DNA. Paired, fresh frozen (FF) and formalin-fixed, paraffin-embedded (FFPE) liver tissue from naive rats were sequenced to confirm known dbSNP variants and identify any additional variants. RESULTS Informatics analysis of available gene annotation from rat RGSC6.0/rn6 RefSeq and Ensembl transcripts provided 223,636 unique exons representing a total of 26,365 unique genes and untranslated regions. Using this annotation and the Rn6 reference genome, an in-silico probe design generated 826,878 probe sequences of which 94.2% were uniquely aligned to the rat genome without mismatches. Further informatics analysis revealed 25,249 genes (95.8%) covered by at least one probe and 23,603 genes (93.5%) had every exon covered by one or more probes. We report high performance metrics from exome sequencing of our probe set and Sanger validation of annotated, highly relevant, cancer gene mutations as cataloged in the human COSMIC database, in addition to several exonic variants in cancer-related genes. CONCLUSIONS An in-silico probe set was designed to enrich the rat exome from isolated DNA. The platform was tested on rat tumor cell lines and normal FF and FFPE liver tissue. The method effectively captured target exome regions in the test DNA samples with exceptional sensitivity and specificity to obtain reliable sequencing data representing variants that are likely chemically induced somatic mutations. Genomic discovery conducted by means of high throughput WES queries should benefit investigators in discovering rat genomic variants in disease etiology and in furthering human translational research.
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Affiliation(s)
- Julie F. Foley
- Biomolecular Screening Branch, National Institute of Environmental Health Sciences, 111 T.W. Alexander Dr. Research Triangle Park, Durham, NC USA
| | | | - Owen Hardy
- Agilent Technologies, Santa Clara, CA USA
| | - Sara Hardy
- Agilent Technologies, Santa Clara, CA USA
| | | | - Anup Madan
- Covance Genomics Laboratory, Redmond, WA USA
| | | | | | - Cara Lord
- Covance Genomics Laboratory, Redmond, WA USA
| | - Sreenivasa Ramaiahgari
- Biomolecular Screening Branch, National Institute of Environmental Health Sciences, 111 T.W. Alexander Dr. Research Triangle Park, Durham, NC USA
| | - Gregory G. Solomon
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC USA
| | | | - Arun R. Pandiri
- Cellular and Molecular Pathology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC USA
| | - Ronald A. Herbert
- Cellular and Molecular Pathology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC USA
| | - Robert C. Sills
- Cellular and Molecular Pathology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC USA
| | - B. Alex Merrick
- Biomolecular Screening Branch, National Institute of Environmental Health Sciences, 111 T.W. Alexander Dr. Research Triangle Park, Durham, NC USA
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21
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Abstract
Rodents (especially Mus musculus and Rattus norvegicus) have been the most widely used models in biomedical research for many years. A notable shift has taken place over the last two decades, with mice taking a more and more prominent role in biomedical science compared to rats. This shift was primarily instigated by the availability of a much larger genetic toolbox for mice, particularly embryonic-stem-cell-based targeting technology for gene disruption. With the recent emergence of tools for altering the rat genome, notably genome-editing technologies, the technological gap between the two organisms is closing, and it is becoming more important to consider the physiological, anatomical, biochemical and pharmacological differences between rats and mice when choosing the right model system for a specific biological question. The aim of this short review and accompanying poster is to highlight some of the most important differences, and to discuss their impact on studies of human diseases, with a special focus on neuropsychiatric disorders.
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Affiliation(s)
- Bart Ellenbroek
- School of Psychology, Victoria University of Wellington, PO Box 600, Wellington 6041, New Zealand
| | - Jiun Youn
- School of Psychology, Victoria University of Wellington, PO Box 600, Wellington 6041, New Zealand
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22
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Mullins LJ, Conway BR, Menzies RI, Denby L, Mullins JJ. Renal disease pathophysiology and treatment: contributions from the rat. Dis Model Mech 2017; 9:1419-1433. [PMID: 27935823 PMCID: PMC5200898 DOI: 10.1242/dmm.027276] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The rat has classically been the species of choice for pharmacological studies and disease modeling, providing a source of high-quality physiological data on cardiovascular and renal pathophysiology over many decades. Recent developments in genome engineering now allow us to capitalize on the wealth of knowledge acquired over the last century. Here, we review rat models of hypertension, diabetic nephropathy, and acute and chronic kidney disease. These models have made important contributions to our understanding of renal diseases and have revealed key genes, such as Ace and P2rx7, involved in renal pathogenic processes. By targeting these genes of interest, researchers are gaining a better understanding of the etiology of renal pathologies, with the promised potential of slowing disease progression or even reversing the damage caused. Some, but not all, of these target genes have proved to be of clinical relevance. However, it is now possible to generate more sophisticated and appropriate disease models in the rat, which can recapitulate key aspects of human renal pathology. These advances will ultimately be used to identify new treatments and therapeutic targets of much greater clinical relevance. Summary: This Review highlights the key role that the rat continues to play in improving our understanding of the etiologies of renal pathologies, and how these insights have opened up new therapeutic avenues.
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Affiliation(s)
- Linda J Mullins
- University of Edinburgh/British Heart Foundation Centre for Cardiovascular Science, Queen's Medical Research Institute, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Bryan R Conway
- University of Edinburgh/British Heart Foundation Centre for Cardiovascular Science, Queen's Medical Research Institute, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Robert I Menzies
- University of Edinburgh/British Heart Foundation Centre for Cardiovascular Science, Queen's Medical Research Institute, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Laura Denby
- University of Edinburgh/British Heart Foundation Centre for Cardiovascular Science, Queen's Medical Research Institute, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - John J Mullins
- University of Edinburgh/British Heart Foundation Centre for Cardiovascular Science, Queen's Medical Research Institute, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
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23
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Aquarius R, Smits D, Gounis MJ, Leenders WPJ, de Vries J. Flow diverter implantation in a rat model of sidewall aneurysm: a feasibility study. J Neurointerv Surg 2017; 10:88-92. [DOI: 10.1136/neurintsurg-2016-012878] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 01/12/2017] [Accepted: 01/13/2017] [Indexed: 11/04/2022]
Abstract
BackgroundMore challenging animal models are needed to elucidate the efficacy of flow diverter (FD) designs and the mechanisms behind observed complications. The purpose of this study is to demonstrate the feasibility of implanting a FD in a sidewall aneurysm rat model.MethodsAn end-to-side anastomosis was created in the abdominal aorta of 36 rats using a decellularized donor pouch. A FD was subsequently implanted.ResultsAfter up to 3 months of follow-up, we observed that rats displayed normal growth and behavior. Mortality within the groups was low (2 rats, 5.6%). All aneurysms thrombosed after FD implantation and showed progressive soft tissue replacement of the thrombus during follow-up. The abdominal aortas remained patent.ConclusionsThis model can be used to test the effects of FDs in future studies.
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Moreno-Moral A, Petretto E. From integrative genomics to systems genetics in the rat to link genotypes to phenotypes. Dis Model Mech 2016; 9:1097-1110. [PMID: 27736746 PMCID: PMC5087832 DOI: 10.1242/dmm.026104] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Complementary to traditional gene mapping approaches used to identify the hereditary components of complex diseases, integrative genomics and systems genetics have emerged as powerful strategies to decipher the key genetic drivers of molecular pathways that underlie disease. Broadly speaking, integrative genomics aims to link cellular-level traits (such as mRNA expression) to the genome to identify their genetic determinants. With the characterization of several cellular-level traits within the same system, the integrative genomics approach evolved into a more comprehensive study design, called systems genetics, which aims to unravel the complex biological networks and pathways involved in disease, and in turn map their genetic control points. The first fully integrated systems genetics study was carried out in rats, and the results, which revealed conserved trans-acting genetic regulation of a pro-inflammatory network relevant to type 1 diabetes, were translated to humans. Many studies using different organisms subsequently stemmed from this example. The aim of this Review is to describe the most recent advances in the fields of integrative genomics and systems genetics applied in the rat, with a focus on studies of complex diseases ranging from inflammatory to cardiometabolic disorders. We aim to provide the genetics community with a comprehensive insight into how the systems genetics approach came to life, starting from the first integrative genomics strategies [such as expression quantitative trait loci (eQTLs) mapping] and concluding with the most sophisticated gene network-based analyses in multiple systems and disease states. Although not limited to studies that have been directly translated to humans, we will focus particularly on the successful investigations in the rat that have led to primary discoveries of genes and pathways relevant to human disease.
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Affiliation(s)
- Aida Moreno-Moral
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore (NUS) Medical School, Singapore
| | - Enrico Petretto
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore (NUS) Medical School, Singapore
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25
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Abstract
Future prospects continue to be strong for research using the rat as a model organism. New technology has enabled the proliferation of many new transgenic and knockout rat strains, the genomes of more than 40 rat strains have been sequenced, publications using the rat as a model continue to be produced at a steady rate, and discoveries of disease-associated genes and mechanisms from rat experiments abound, frequently with conservation of function between rats and humans. However, advances in genome technology have led to increasing insights into human disease directly from human genetic studies, pulling more and more researchers into the human genetics arena and placing funding for model organisms and their databases under threat. This, therefore, is a pivotal time for rat-based biomedical research - a timely moment to review progress and prospects - providing the inspiration for a new Special Collection focused on the impact of the model on translational science, launched in this issue of Disease Models & Mechanisms. What disease areas are most appropriate for research using rats? Why should the rat be favoured over other model organisms, and should the present levels of funding be continued? Which approaches should we expect to yield biologically and medically useful insights in the coming years? These are key issues that are addressed in the original Research Articles and reviews published in this Special Collection, and in this introductory Editorial. These exemplar articles serve as a landmark for the present status quo after a decade of major advances using the rat model and could help to guide the direction of rat research in the coming decade.
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Affiliation(s)
- Tim Aitman
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Paraminder Dhillon
- Disease Models & Mechanisms, The Company of Biologists, Bidder Building, Station Road, Histon, Cambridge CB24 9LF, UK
| | - Aron M Geurts
- Department of Physiology and Genome Editing Rat Resource Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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