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Montenegro AFL, Clementino MAF, Yaochite JNU. Type I interferon pathway genetic variants in severe COVID-19. Virus Res 2024; 342:199339. [PMID: 38354910 PMCID: PMC10901847 DOI: 10.1016/j.virusres.2024.199339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 02/09/2024] [Accepted: 02/11/2024] [Indexed: 02/16/2024]
Abstract
Coronavirus Disease 2019 (COVID-19) is an infectious disease caused by SARS-CoV-2. According to the World Health Organization (WHO), there have been over 760 million reported cases and over 6 million deaths caused by this disease worldwide. The severity of COVID-19 is based on symptoms presented by the patient and is divided as asymptomatic, mild, moderate, severe, and critical. The manifestations are interconnected with genetic variations. The innate immunity is the quickest response mechanism of an organism against viruses. Type I interferon pathway plays a key role in antiviral responses due to viral replication inhibition in infected cells and adaptive immunity stimulation induced by interferon molecules. Thus, variants in type I interferon pathway's genes are being studied in different COVID-19 manifestations. This review summarizes the role of variants in type I interferon pathway's genes on prognosis and severity progression of COVID-19.
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Affiliation(s)
- A F L Montenegro
- Laboratório de Imunologia Celular e Molecular, Departamento de Análises Clínicas e Toxicológicas da Faculdade de Farmácia, Odontologia e Enfermagem, Universidade Federal do Ceará - UFC, Rua Pastor Samuel Munguba, 1210 - Rodolfo Teófilo, Fortaleza, Ceará, Brasil
| | - M A F Clementino
- Laboratório de Toxinologia Molecular, NUBIMED - Núcleo de Biomedicina, Universidade Federal do Ceará - UFC. Fortaleza, Ceará, Brasil
| | - J N U Yaochite
- Laboratório de Imunologia Celular e Molecular, Departamento de Análises Clínicas e Toxicológicas da Faculdade de Farmácia, Odontologia e Enfermagem, Universidade Federal do Ceará - UFC, Rua Pastor Samuel Munguba, 1210 - Rodolfo Teófilo, Fortaleza, Ceará, Brasil.
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de Weerd NA, Kurowska A, Mendoza JL, Schreiber G. Structure-function of type I and III interferons. Curr Opin Immunol 2024; 86:102413. [PMID: 38608537 PMCID: PMC11057355 DOI: 10.1016/j.coi.2024.102413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 02/27/2024] [Accepted: 03/29/2024] [Indexed: 04/14/2024]
Abstract
Type I and type III interferons (IFNs) are major components in activating the innate immune response. Common to both are two distinct receptor chains (IFNAR1/IFNAR2 and IFNLR1/IL10R2), which form ternary complexes upon binding their respective ligands. This results in close proximity of the intracellularly associated kinases JAK1 and TYK2, which cross phosphorylate each other, the associated receptor chains, and signal transducer and activator of transcriptions, with the latter activating IFN-stimulated genes. While there are clear similarities in the biological responses toward type I and type III IFNs, differences have been found in their tropism, tuning of activity, and induction of the immune response. Here, we focus on how these differences are embedded in the structure/function relations of these two systems in light of the recent progress that provides in-depth information on the structural assembly of these receptors and their functional implications and how these differ between the mouse and human systems.
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Affiliation(s)
- Nicole A de Weerd
- Centre for Innate Immunity and Infectious Diseases, Department of Molecular and Translational Science, Hudson Institute of Medical Research and Monash University, Clayton 3168, Victoria, Australia
| | - Aleksandra Kurowska
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Juan L. Mendoza
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
| | - Gideon Schreiber
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel, 76100
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Aliaga-Gaspar P, Hurtado-Guerrero I, Ciano-Petersen NL, Urbaneja P, Brichette-Mieg I, Reyes V, Rodriguez-Bada JL, Alvarez-Lafuente R, Arroyo R, Quintana E, Ramió-Torrentà L, Alonso A, Leyva L, Fernández O, Oliver-Martos B. Soluble Receptor Isoform of IFN-Beta (sIFNAR2) in Multiple Sclerosis Patients and Their Association With the Clinical Response to IFN-Beta Treatment. Front Immunol 2021; 12:778204. [PMID: 34975865 PMCID: PMC8716373 DOI: 10.3389/fimmu.2021.778204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 11/29/2021] [Indexed: 11/25/2022] Open
Abstract
Purpose Interferon beta receptor 2 subunit (IFNAR2) can be produced as a transmembrane protein, but also as a soluble form (sIFNAR2) generated by alternative splicing or proteolytic cleavage, which has both agonist and antagonist activities for IFN-β. However, its role regarding the clinical response to IFN-β for relapsing-remitting multiple sclerosis (RRMS) is unknown. We aim to evaluate the in vitro short-term effects and after 6 and 12 months of IFN-β therapy on sIFNAR2 production and their association with the clinical response in MS patients. Methods Ninety-four RRMS patients were included and evaluated at baseline, 6 and 12 months from treatment onset. A subset of 41 patients were classified as responders and non-responders to IFN-β therapy. sIFNAR2 serum levels were measured by ELISA. mRNA expression for IFNAR1, IFNAR2 splice variants, MxA and proteases were assessed by RT-PCR. The short-term effect was evaluated in PBMC from RRMS patients after IFN-β stimulation in vitro. Results Protein and mRNA levels of sIFNAR2 increased after IFN-β treatment. According to the clinical response, only non-responders increased sIFNAR2 significantly at both protein and mRNA levels. sIFNAR2 gene expression correlated with the transmembrane isoform expression and was 2.3-fold higher. While MxA gene expression increased significantly after treatment, IFNAR1 and IFNAR2 only slightly increased. After short-term IFN-β in vitro induction of PBMC, 6/7 patients increased the sIFNAR2 expression. Conclusions IFN-β administration induces the production of sIFNAR2 in RRMS and higher levels might be associated to the reduction of therapeutic response. Thus, levels of sIFNAR2 could be monitored to optimize an effective response to IFN-β therapy.
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Affiliation(s)
- Pablo Aliaga-Gaspar
- Neuroimmunology and Neuroinflammation Group, Instituto de Investigación Biomédica de Málaga (IBIMA), Unidad de Gestión Clínica (UGC) Neurociencias, Hospital Regional Universitario de Málaga, Málaga, Spain
- Facultad de Medicina, Universidad de Málaga, Málaga, Spain
| | - Isaac Hurtado-Guerrero
- Neuroimmunology and Neuroinflammation Group, Instituto de Investigación Biomédica de Málaga (IBIMA), Unidad de Gestión Clínica (UGC) Neurociencias, Hospital Regional Universitario de Málaga, Málaga, Spain
- Neuroinflammation Unit, Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, Copenhagen Biocentre, University of Copenhagen, Copenhagen, Denmark
| | - Nicolas Lundahl Ciano-Petersen
- Neuroimmunology and Neuroinflammation Group, Instituto de Investigación Biomédica de Málaga (IBIMA), Unidad de Gestión Clínica (UGC) Neurociencias, Hospital Regional Universitario de Málaga, Málaga, Spain
- Red Andaluza de Investigación Clínica y Traslacional en Neurología (Neuro-Reca), Málaga, Spain
| | - Patricia Urbaneja
- Neuroimmunology and Neuroinflammation Group, Instituto de Investigación Biomédica de Málaga (IBIMA), Unidad de Gestión Clínica (UGC) Neurociencias, Hospital Regional Universitario de Málaga, Málaga, Spain
- Red Andaluza de Investigación Clínica y Traslacional en Neurología (Neuro-Reca), Málaga, Spain
| | - Isabel Brichette-Mieg
- Neuroimmunology and Neuroinflammation Group, Instituto de Investigación Biomédica de Málaga (IBIMA), Unidad de Gestión Clínica (UGC) Neurociencias, Hospital Regional Universitario de Málaga, Málaga, Spain
| | - Virginia Reyes
- Neuroimmunology and Neuroinflammation Group, Instituto de Investigación Biomédica de Málaga (IBIMA), Unidad de Gestión Clínica (UGC) Neurociencias, Hospital Regional Universitario de Málaga, Málaga, Spain
- Red Andaluza de Investigación Clínica y Traslacional en Neurología (Neuro-Reca), Málaga, Spain
| | - Jose Luis Rodriguez-Bada
- Neuroimmunology and Neuroinflammation Group, Instituto de Investigación Biomédica de Málaga (IBIMA), Unidad de Gestión Clínica (UGC) Neurociencias, Hospital Regional Universitario de Málaga, Málaga, Spain
| | - Roberto Alvarez-Lafuente
- Grupo de Investigación de Factores Ambientales en Enfermedades Degenerativas, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), Madrid, Spain
- Red Española de Esclerosis Múltiple (REEM), Madrid, Spain
| | - Rafael Arroyo
- Servicio de Neurología, Hospital Universitario Quirónsalud, Madrid, Spain
| | - Ester Quintana
- Red Española de Esclerosis Múltiple (REEM), Madrid, Spain
- Servicio de Neurología, Hospital Universitari de Girona Doctor Josep Trueta, Girona, Spain
| | - Lluis Ramió-Torrentà
- Red Española de Esclerosis Múltiple (REEM), Madrid, Spain
- Servicio de Neurología, Hospital Universitari de Girona Doctor Josep Trueta, Girona, Spain
- Girona Biomedical Research Institute (IDIBGI), Girona, Spain
- Medical Sciences Department, University of Girona, Girona, Spain
| | - Ana Alonso
- Neuroimmunology and Neuroinflammation Group, Instituto de Investigación Biomédica de Málaga (IBIMA), Unidad de Gestión Clínica (UGC) Neurociencias, Hospital Regional Universitario de Málaga, Málaga, Spain
- Red Andaluza de Investigación Clínica y Traslacional en Neurología (Neuro-Reca), Málaga, Spain
| | - Laura Leyva
- Neuroimmunology and Neuroinflammation Group, Instituto de Investigación Biomédica de Málaga (IBIMA), Unidad de Gestión Clínica (UGC) Neurociencias, Hospital Regional Universitario de Málaga, Málaga, Spain
- Red Española de Esclerosis Múltiple (REEM), Madrid, Spain
| | - Oscar Fernández
- Departmento de Farmacología, Facultad de Medicina, Universidad de Málaga, Málaga, Spain
- *Correspondence: Begoña Oliver-Martos, ; Oscar Fernández,
| | - Begoña Oliver-Martos
- Neuroimmunology and Neuroinflammation Group, Instituto de Investigación Biomédica de Málaga (IBIMA), Unidad de Gestión Clínica (UGC) Neurociencias, Hospital Regional Universitario de Málaga, Málaga, Spain
- Red Andaluza de Investigación Clínica y Traslacional en Neurología (Neuro-Reca), Málaga, Spain
- Red Española de Esclerosis Múltiple (REEM), Madrid, Spain
- Departamento de Biología Celular, Genética y Fisiología, Área de Fisiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
- *Correspondence: Begoña Oliver-Martos, ; Oscar Fernández,
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Baranova A, Cao H, Zhang F. Unraveling Risk Genes of COVID-19 by Multi-Omics Integrative Analyses. Front Med (Lausanne) 2021; 8:738687. [PMID: 34557504 PMCID: PMC8452849 DOI: 10.3389/fmed.2021.738687] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 08/17/2021] [Indexed: 11/13/2022] Open
Abstract
Objectives: Uncovering the genetic basis of COVID-19 may shed insight into its pathogenesis and help to improve treatment measures. We aimed to investigate the host genetic variants associated with COVID-19. Methods: The summary result of a COVID-19 GWAS (9,373 hospitalized COVID-19 cases and 1,197,256 controls) was obtained from the COVID-19 Host Genetic Initiative GWAS meta-analyses. We tested colocalization of the GWAS signals of COVID-19 with expression and methylation quantitative traits loci (eQTL and mQTL, respectively) using the summary data-based Mendelian randomization (SMR) analysis. Four eQTL and two mQTL datasets were utilized in the SMR analysis, including CAGE blood eQTL data (n = 2,765), GTEx v7 blood (n = 338) and lung (n = 278) eQTL data, Geuvadis lymphoblastoid cells eQTL data, LBC-BSGS blood mQTL data (n = 1,980), and Hannon blood mQTL summary data (n = 1,175). We conducted a transcriptome-wide association study (TWAS) on COVID-19 with precomputed prediction models of GTEx v8 eQTL in lung and blood using S-PrediXcan. Results: Our SMR analyses identified seven protein-coding genes (TYK2, IFNAR2, OAS1, OAS3, XCR1, CCR5, and MAPT) associated with COVID-19, including two novel risk genes, CCR5 and tau-encoding MAPT. The TWAS revealed four genes for COVID-19 (CXCR6, CCR5, CCR9, and PIGN), including two novel risk genes, CCR5 and PIGN. Conclusion: Our study highlighted the functional relevance of some known genome-wide risk genes of COVID-19 and revealed novel genes contributing to differential outcomes of COVID-19 disease.
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Affiliation(s)
- Ancha Baranova
- School of Systems Biology, George Mason University, Manassas, VA, United States.,Research Centre for Medical Genetics, Moscow, Russia
| | - Hongbao Cao
- School of Systems Biology, George Mason University, Manassas, VA, United States
| | - Fuquan Zhang
- Institute of Neuropsychiatry, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, China.,Department of Psychiatry, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, China
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Rao S, Baranova A, Cao H, Chen J, Zhang X, Zhang F. Genetic mechanisms of COVID-19 and its association with smoking and alcohol consumption. Brief Bioinform 2021; 22:6326524. [PMID: 34308962 DOI: 10.1093/bib/bbab284] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 07/01/2021] [Accepted: 07/04/2021] [Indexed: 11/14/2022] Open
Abstract
We aimed to investigate the genetic mechanisms associated with coronavirus disease of 2019 (COVID-19) outcomes in the host and to evaluate the possible associations between smoking and drinking behavior and three COVID-19 outcomes: severe COVID-19, hospitalized COVID-19 and COVID-19 infection. We described the genomic loci and risk genes associated with the COVID-19 outcomes, followed by functional analyses of the risk genes. Then, a summary data-based Mendelian randomization (SMR) analysis, and a transcriptome-wide association study (TWAS) were performed for the severe COVID-19 dataset. A two-sample Mendelian randomization (MR) analysis was used to evaluate the causal associations between various measures of smoking and alcohol consumption and the COVID-19 outcomes. A total of 26 protein-coding genes, enriched in chemokine binding, cytokine binding and senescence-related functions, were associated with either severe COVID-19 or hospitalized COVID-19. The SMR and the TWAS analyses highlighted functional implications of some GWAS hits and identified seven novel genes for severe COVID-19, including CCR5, CCR5AS, IL10RB, TAC4, RMI1 and TNFSF15, some of which are targets of approved or experimental drugs. According to our studies, increasing consumption of cigarettes per day by 1 standard deviation is related to a 2.3-fold increase in susceptibility to severe COVID-19 and a 1.6-fold increase in COVID-19-induced hospitalization. Contrarily, no significant links were found between alcohol consumption or binary smoking status and COVID-19 outcomes. Our study revealed some novel COVID-19 related genes and suggested that genetic liability to smoking may quantitatively contribute to an increased risk for a severe course of COVID-19.
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Affiliation(s)
- Shuquan Rao
- Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, China
| | - Ancha Baranova
- School of Systems Biology, George Mason University, China
| | - Hongbao Cao
- School of Systems Biology, George Mason University, China
| | - Jiu Chen
- Affiliated Brain Hospital of Nanjing Medical University, China
| | - Xiangrong Zhang
- Affiliated Brain Hospital of Nanjing Medical University, China
| | - Fuquan Zhang
- Affiliated Brain Hospital of Nanjing Medical University, China
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