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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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Fath MK, Naderi M, Hamzavi H, Ganji M, Shabani S, Ghahroodi FN, Khalesi B, Pourzardosht N, Hashemi ZS, Khalili S. Molecular mechanisms and therapeutic effects of different vitamins and minerals in COVID-19 patients. J Trace Elem Med Biol 2022; 73:127044. [PMID: 35901669 PMCID: PMC9297660 DOI: 10.1016/j.jtemb.2022.127044] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 07/10/2022] [Accepted: 07/18/2022] [Indexed: 12/12/2022]
Abstract
COVID-19 is a rapidly spreading disease, which has caught the world by surprise. Millions of people suffer from illness, and the mortality rates are dramatically high. Currently, there is no specific and immediate treatment for this disease. Remedies are limited to supportive regiments and few antiviral and anti-inflammatory drugs. The lack of a definite cure for COVID-19 is the reason behind its high mortality and global prevalence. COVID-19 can lead to a critical illness with severe respiratory distress and cytokine release. Increased oxidative stress and excessive production of inflammatory cytokines are vital components of severe COVID-19. Micronutrients, metalloids, and vitamins such as iron, manganese, selenium, Zinc, Copper, vitamin A, B family, and C are among the essential and trace elements that play a pivotal role in human nutrition and health. They participate in metabolic processes that lead to energy production. In addition, they support immune functions and act as antioxidants. Therefore, maintaining an optimal level of micronutrients intake, particularly those with antioxidant activities, is essential to fight against oxidative stress, modulate inflammation, and boost the immune system. Therefore, these factors could play a crucial role in COVID-19 prevention and treatment. In this review, we aimed to summarize antiviral properties of different vitamins and minerals. Moreover, we will investigate the correlation between them and their effects in COVID-19 patients.
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Affiliation(s)
- Mohsen Karami Fath
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Malihe Naderi
- Department of Microbiology and Microbial Biotechnology, Faculty of life Science and Biotechnology, Shahid Beheshti University, Tehran, Iran; Infectious Diseases Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Hosna Hamzavi
- Department of Biology, Shahed University, Tehran, Iran
| | - Mahmoud Ganji
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Shima Shabani
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Faezeh Noorabad Ghahroodi
- Department of Clinical Biochemistry, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Bahman Khalesi
- Department of Research and Production of Poultry Viral Vaccine, Razi Vaccine and Serum Research Institute, Agricultural Research Education and Extension Organization, Karaj, Iran
| | - Navid Pourzardosht
- Biochemistry Department, Guilan University of Medical Sciences, Rasht, Iran
| | - Zahra Sadat Hashemi
- ATMP Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran. Iran.
| | - Saeed Khalili
- Department of Biology Sciences, Shahid Rajaee Teacher Training University, Tehran, Iran.
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Vavougios GD, Zarogiannis S, Barh D, Breza M, Krogfelt KA, Stamoulis G, Gourgoulianis KI. Innate immunity and metal ion trafficking pathway perturbations in idiopathic Parkinson's disease and Tuberculosis: A comparative transcriptomics approach. BRAIN DISORDERS 2021. [DOI: 10.1016/j.dscb.2021.100025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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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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Andreou A, Trantza S, Filippou D, Sipsas N, Tsiodras S. COVID-19: The Potential Role of Copper and N-acetylcysteine (NAC) in a Combination of Candidate Antiviral Treatments Against SARS-CoV-2. In Vivo 2020; 34:1567-1588. [PMID: 32503814 PMCID: PMC8378025 DOI: 10.21873/invivo.11946] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/15/2020] [Accepted: 05/20/2020] [Indexed: 01/08/2023]
Abstract
BACKGROUND On March 11, 2020, the World Health Organization (WHO) declared the outbreak of coronavirus disease (COVID-19) a pandemic. Since then, thousands of people have suffered and died, making the need for a treatment of severe acute respiratory syndrome-related coronavirus-2 (SARS-CoV-2) more crucial than ever. MATERIALS AND METHODS The authors carried out a search in PubMed, ClinicalTrials.gov and New England Journal of Medicine (NEJM) for COVID-19 to provide information on the most promising treatments against SARS-CoV-2. RESULTS Possible COVID-19 agents with promising efficacy and favorable safety profile were identified. The results support the combination of copper, N-acetylcysteine (NAC), colchicine and nitric oxide (NO) with candidate antiviral agents, remdesivir or EIDD-2801, as a treatment for patients positive for SARS-CoV-2. CONCLUSION The authors propose to study the effects of the combination of copper, NAC, colchicine, NO and currently used experimental antiviral agents, remdesivir or EIDD-2801, as a potential treatment scheme for SARS-COV-2.
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Affiliation(s)
- Andri Andreou
- Pharmaceutical Services, Ministry of Health of the Republic of Cyprus, Nicosia, Cyprus
| | | | - Demetrios Filippou
- National Organization for Medicines, Athens, Greece
- Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Nikolaos Sipsas
- Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Sotirios Tsiodras
- Medical School, National and Kapodistrian University of Athens, Athens, Greece
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Qian C, Yun Z, Yao Y, Cao M, Liu Q, Hu S, Zhang S, Luo D. Heterogeneous macrophages: Supersensors of exogenous inducing factors. Scand J Immunol 2019; 90:e12768. [PMID: 31002413 PMCID: PMC6852148 DOI: 10.1111/sji.12768] [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: 01/30/2019] [Revised: 04/01/2019] [Accepted: 04/11/2019] [Indexed: 12/14/2022]
Abstract
As heterogeneous immune cells, macrophages mount effective responses to various internal and external changes during disease progression. Macrophage polarization, rather than macrophage heterogenization, is often used to describe the functional differences between macrophages. While macrophage polarization partially contributes to heterogeneity, it does not completely explain the concept of macrophage heterogeneity. At the same time, there are abundant and sophisticated endogenous and exogenous substances that can affect macrophage heterogeneity. While the research on endogenous factors has been systematically reviewed, the findings on exogenous factors have not been well summarized. Hence, we reviewed the characteristics and inducing factors of heterogeneous macrophages to reveal their functional plasticity as well as their targeting manoeuvreability. In the process of constructing and analysing a network organized by disease-related cells and molecules, paying more attention to heterogeneous macrophages as mediators of this network may help to explore a novel entry point for early prevention of and intervention in disease.
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Affiliation(s)
- Caiyun Qian
- School of Basic Medical Sciences, Nanchang University, Nanchang, Jiangxi, China
| | - Zehui Yun
- Queen Mary School, Nanchang University, Nanchang, Jiangxi, China
| | - Yudi Yao
- School of Basic Medical Sciences, Nanchang University, Nanchang, Jiangxi, China
| | - Minghua Cao
- School of Basic Medical Sciences, Nanchang University, Nanchang, Jiangxi, China
| | - Qiang Liu
- School of Medicine, Nanchang University, Nanchang, Jiangxi, China
| | - Song Hu
- Queen Mary School, Nanchang University, Nanchang, Jiangxi, China
| | - Shuhua Zhang
- Jiangxi Cardiovascular Research Institute, Jiangxi Provincial People's Hospital, Affiliated to Nanchang University, Nanchang, Jiangxi, China
| | - Daya Luo
- School of Basic Medical Sciences, Nanchang University, Nanchang, Jiangxi, China.,Affiliated Infectious Disease Hospital, Nanchang University, Nanchang, Jiangxi, China
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Papathanassiu AE, Ko JH, Imprialou M, Bagnati M, Srivastava PK, Vu HA, Cucchi D, McAdoo SP, Ananieva EA, Mauro C, Behmoaras J. BCAT1 controls metabolic reprogramming in activated human macrophages and is associated with inflammatory diseases. Nat Commun 2017; 8:16040. [PMID: 28699638 PMCID: PMC5510229 DOI: 10.1038/ncomms16040] [Citation(s) in RCA: 142] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 05/24/2017] [Indexed: 12/20/2022] Open
Abstract
Branched-chain aminotransferases (BCAT) are enzymes that initiate the catabolism of branched-chain amino acids (BCAA), such as leucine, thereby providing macromolecule precursors; however, the function of BCATs in macrophages is unknown. Here we show that BCAT1 is the predominant BCAT isoform in human primary macrophages. We identify ERG240 as a leucine analogue that blocks BCAT1 activity. Selective inhibition of BCAT1 activity results in decreased oxygen consumption and glycolysis. This decrease is associated with reduced IRG1 levels and itaconate synthesis, suggesting involvement of BCAA catabolism through the IRG1/itaconate axis within the tricarboxylic acid cycle in activated macrophages. ERG240 suppresses production of IRG1 and itaconate in mice and contributes to a less proinflammatory transcriptome signature. Oral administration of ERG240 reduces the severity of collagen-induced arthritis in mice and crescentic glomerulonephritis in rats, in part by decreasing macrophage infiltration. These results establish a regulatory role for BCAT1 in macrophage function with therapeutic implications for inflammatory conditions.
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Affiliation(s)
| | - Jeong-Hun Ko
- Centre for Complement and Inflammation Research, Imperial College London, London W12 0NN, UK
| | - Martha Imprialou
- Centre for Complement and Inflammation Research, Imperial College London, London W12 0NN, UK
| | - Marta Bagnati
- Centre for Complement and Inflammation Research, Imperial College London, London W12 0NN, UK
| | | | - Hong A. Vu
- Ergon Pharmaceuticals, LLC, P.O. Box 1001, Silver Spring, Maryland 20910, USA
| | - Danilo Cucchi
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
- Institute Pasteur, Fondazione Cenci Bolognetti, Rome 00161, Italy
| | - Stephen P. McAdoo
- Renal and Vascular Inflammation Section, Department of Medicine, Imperial College London, London W12 0NN, UK
| | - Elitsa A. Ananieva
- Biochemistry and Nutrition, Des Moines University, Des Moines, Iowa 50312, USA
| | - Claudio Mauro
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Jacques Behmoaras
- Centre for Complement and Inflammation Research, Imperial College London, London W12 0NN, UK
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