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Kovačić D, Salihović A. Multi-epitope mRNA Vaccine Design that Exploits Variola Virus and Monkeypox Virus Proteins for Elicitation of Long-lasting Humoral and Cellular Protection Against Severe Disease. JOURNAL OF MEDICAL SCIENCE 2022. [DOI: 10.20883/medical.e750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Human monkeypox represents a relatively underexplored infection that has received increased attention since the reported outbreak in May 2022. Due to its clinical similarities with human smallpox, this virus represents a potentially tremendous health problem demanding further research in the context of host-pathogen interactions and vaccine development. Furthermore, the cross-continental spread of monkeypox has reaffirmed the need for devoting attention to human poxviruses in general, as they represent potential bioterrorism agents. Currently, smallpox vaccines are utilized in immunization efforts against monkeypox, an unsurprising fact considering their genomic and phenotypic similarities. Though it offers long-lasting protection against smallpox, its protective effects against human monkeypox continue to be explored, with encouraging results. Taking this into account, this works aims at utilizing in silico tools to identify potent peptide-based epitopes stemming from the variola virus and monkeypox virus proteomes, to devise a vaccine that would offer significant protection against smallpox and monkeypox. In theory, a vaccine that offers cross-protection against variola and monkeypox would also protect against related viruses, at least in severe clinical manifestation. Herein, we introduce a novel multi-epitope mRNA vaccine design that exploits these two viral proteomes to elicit long-lasting humoral and cellular immunity. Special consideration was taken in ensuring that the vaccine candidate elicits a Th1 immune response, correlated with protection against clinically severe disease for both viruses. Immune system simulations and physicochemical and safety analyses characterize our vaccine candidate as antigenically potent, safe, and overall stable. The protein product displays high binding affinity towards relevant immune receptors. Furthermore, the vaccine candidate is to elicit a protective, humoral and Th1-dominated cellular immune response that lasts over five years. Lastly, we build a case about the rapidity and convenience of circumventing the live attenuated vaccine platform using mRNA vaccine technology.
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Germano GV, Braga AF, Camargo RMD, Ballalai PB, Bezerra OC, Manta FSDN, Belone ADFF, Soares CT, Das PK, Moraes MO, Latini ACP, Brito de Souza VN. Association of CD209 (DC-SIGN) rs735240 SNV with paucibacillary leprosy in the Brazilian population and its functional effects. Mem Inst Oswaldo Cruz 2022; 117:e220014. [PMID: 35703715 PMCID: PMC9190517 DOI: 10.1590/0074-02760220014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 04/06/2022] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Leprosy, caused by Mycobacterium leprae, is a public health problem in Brazil that affects peripheral nerves, resulting in physical disabilities. During host-pathogen interactions, the immune response determines leprosy outcomes from a localised (paucibacillary) form to a disseminated (multibacillary) form. The recognition of M. leprae involves the DC-SIGN receptor, which is present on the dendritic cells (DCs) and participates in immune activation. OBJECTIVES To evaluate the association of polymorphisms in the promoter region of the gene encoding DC-SIGN (CD209) and the clinical form of leprosy, and to investigate its functional effects. METHODS The study population included 406 leprosy patients from an endemic area in Brazil [310 multibacillary (MB); 96 paucibacillary (PB)]. A functional evaluation based on the effects of the single nucleotide variant (SNV) associated with PB leprosy on the specific immune response was also performed. RESULTS The GA genotype and the presence of the A allele of rs735240 (-939G>A) were associated with PB leprosy [OR: 2.09 (1.18-3.69) and 1.84 (1.07-3.14), respectively]. Carriers of the A allele showed reduced expression of CD209 and TGF-β1 in leprosy lesions in comparison with individuals with GG genotype, in addition to a higher response to the Mitsuda test. CONCLUSION These data suggest that rs735240 influences the immune response against M. leprae and clinical presentation of leprosy.
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Affiliation(s)
- Giovanna Valle Germano
- Faculdade de Medicina de Botucatu, Programa de Pós-Graduação em Doenças Tropicais, Botucatu, SP, Brasil.,Secretaria de Estado da Saúde de São Paulo, Instituto Lauro de Souza Lima, Bauru, SP, Brasil
| | - André Flores Braga
- Faculdade de Medicina de Botucatu, Programa de Pós-Graduação em Doenças Tropicais, Botucatu, SP, Brasil.,Secretaria de Estado da Saúde de São Paulo, Instituto Lauro de Souza Lima, Bauru, SP, Brasil
| | - Rodrigo Mendes de Camargo
- Faculdade de Medicina de Botucatu, Programa de Pós-Graduação em Doenças Tropicais, Botucatu, SP, Brasil.,Secretaria de Estado da Saúde de São Paulo, Instituto Lauro de Souza Lima, Bauru, SP, Brasil
| | | | - Ohanna Cavalcanti Bezerra
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Hanseníase, Rio de Janeiro, RJ, Brasil
| | | | | | | | - Pranab Kumar Das
- University of Birmingham, College of Medical and Dental Sciences, Division of Infection and Immunity, Department of Clinical Immunology, Edgbaston, UK
| | - Milton Ozório Moraes
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Hanseníase, Rio de Janeiro, RJ, Brasil
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Identification of Aggravation-Predicting Gene Polymorphisms in Coronavirus Disease 2019 Patients Using a Candidate Gene Approach Associated With Multiple Phase Pathogenesis: A Study in a Japanese City of 1 Million People. Crit Care Explor 2021; 3:e0576. [PMID: 34765983 PMCID: PMC8575431 DOI: 10.1097/cce.0000000000000576] [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] [Indexed: 11/26/2022] Open
Abstract
The pathology caused by the coronavirus disease 2019 is mediated by host-mediated lung inflammation, driving severity, and mortality. Polymorphisms in genes encoding host inflammation and immune-related molecules may be associated with the development of serious pathologies, and identifying such gene polymorphisms may lead to the identification of therapeutic targets. OBJECTIVES We attempted to identify aggravation-predicting gene polymorphisms. DESIGN We use a candidate gene approach associated with multiple phase pathogenesis in coronavirus disease 2019 patients among a cohort in Hiroshima, a city with a population of 1 million, in Japan. DNA samples from the study populations were genotyped for 34 functional polymorphisms from 14 distinct candidate genes, which encode proteins related to viral cell entry, regulation of viral replication, innate immune modulators, regulatory cytokines, and effector cytokines. SETTING AND PARTICIPANTS Three core hospitals providing different services for patients with coronavirus disease 2019 under administrative control. A total of 230 patients with coronavirus disease 2019 were recruited from March 1, 2020, to March 31, 2021. MAIN RESULTS AND MEASUREMENTS Among the 14 genes, we found rs1131454 in OAS1 and rs1143627 in IL1B genes as independent genetic factors associated with disease severity (adjusted odds ratio = 7.1 and 4.6 in the dominant model, respectively). Furthermore, we investigated the effect of multiple phase pathogenesis of coronavirus disease 2019 with unbiased multifactor dimensionality reduction analysis and identified a four-gene model with rs1131454 (OAS1), rs1143627 (IL1B), rs2074192 (ACE2), and rs11003125 (MBL). By combining these polygenetic factors with polyclinical factors, including age, sex, higher body mass index, and the presence of diabetes and hypertension, we proposed a composite risk model with a high area under the curve, sensitivity, and probability (0.917, 96.4%, and 74.3%, respectively) in the receiver operating characteristic curve analysis. CONCLUSIONS AND RELEVANCE We successfully identified significant genetic factors in OAS1 and IL1B genes using a candidate gene approach study as valuable information for further mechanistic investigation and predictive model building.
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Darbeheshti F, Mahdiannasser M, Uhal BD, Ogino S, Gupta S, Rezaei N. Interindividual immunogenic variants: Susceptibility to coronavirus, respiratory syncytial virus and influenza virus. Rev Med Virol 2021; 31:e2234. [PMID: 33724604 PMCID: PMC8250219 DOI: 10.1002/rmv.2234] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 02/28/2021] [Accepted: 03/01/2021] [Indexed: 12/12/2022]
Abstract
The coronavirus disease (Covid-19) pandemic is the most serious event of the year 2020, causing considerable global morbidity and mortality. The goal of this review is to provide a comprehensive summary of reported associations between inter-individual immunogenic variants and disease susceptibility or symptoms caused by the coronavirus strains severe acute respiratory syndrome-associated coronavirus, severe acute respiratory syndrome-associated coronavirus-2, and two of the main respiratory viruses, respiratory syncytial virus and influenza virus. The results suggest that the genetic background of the host could affect the levels of proinflammatory and anti-inflammatory cytokines and might modulate the progression of Covid-19 in affected patients. Notably, genetic variations in innate immune components such as toll-like receptors and mannose-binding lectin 2 play critical roles in the ability of the immune system to recognize coronavirus and initiate an early immune response to clear the virus and prevent the development of severe symptoms. This review provides promising clues related to the potential benefits of using immunotherapy and immune modulation for respiratory infectious disease treatment in a personalized manner.
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Affiliation(s)
- Farzaneh Darbeheshti
- Department of GeneticsSchool of MedicineTehran University of Medical SciencesTehranIran
- Medical Genetics Network (MeGeNe)Universal Scientific Education and Research Network (USERN)TehranIran
| | - Mojdeh Mahdiannasser
- Department of GeneticsSchool of MedicineTehran University of Medical SciencesTehranIran
| | - Bruce D Uhal
- Department of PhysiologyMichigan State UniversityEast LansingMichiganUSA
| | - Shuji Ogino
- Department of EpidemiologyHarvard T.H. Chan School of Public HealthBostonMassachusettsUSA
- Department of Oncologic PathologyDana‐Farber Cancer InstituteBostonMassachusettsUSA
- Cancer Immunology and Cancer Epidemiology ProgramsDana‐Farber Harvard Cancer CenterBostonMassachusettsUSA
| | - Sudhir Gupta
- Division of Basic and Clinical ImmunologyDepartment of MedicineUniversity of CaliforniaIrvineCaliforniaUSA
| | - Nima Rezaei
- Research Center for ImmunodeficienciesChildren's Medical CenterTehran University of Medical SciencesTehranIran
- Department of ImmunologySchool of MedicineTehran University of Medical SciencesTehranIran
- Network of Immunity in InfectionMalignancy and Autoimmunity (NIIMA)Universal Scientific Education and Research Network (USERN)TehranIran
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Velavan TP, Pallerla SR, Rüter J, Augustin Y, Kremsner PG, Krishna S, Meyer CG. Host genetic factors determining COVID-19 susceptibility and severity. EBioMedicine 2021; 72:103629. [PMID: 34655949 PMCID: PMC8512556 DOI: 10.1016/j.ebiom.2021.103629] [Citation(s) in RCA: 114] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 10/02/2021] [Accepted: 10/03/2021] [Indexed: 12/12/2022] Open
Abstract
The COVID-19 pandemic caused by the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) poses an unprecedented challenge to humanity. SARS-CoV-2 infections range from asymptomatic to severe courses of COVID-19 with acute respiratory distress syndrome (ARDS), multiorgan involvement and death. Risk factors for disease severity include older age, male sex, increased BMI and pre-existing comorbidities. Ethnicity is also relevant to COVID-19 susceptibility and severity. Host genetic predisposition to COVID-19 is now increasingly recognized and whole genome and candidate gene association studies regarding COVID-19 susceptibility have been performed. Several common and rare variants in genes related to inflammation or immune responses have been identified. We summarize research on COVID-19 host genetics and compile genetic variants associated with susceptibility to COVID-19 and disease severity. We discuss candidate genes that should be investigated further to understand such associations and provide insights relevant to pathogenesis, risk classification, therapy response, precision medicine, and drug repurposing.
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Affiliation(s)
- Thirumalaisamy P Velavan
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Wilhelmstrasse 27, Tübingen 72074, Germany; Vietnamese-German Center for Medical Research, VG-CARE, Hanoi, Vietnam.
| | - Srinivas Reddy Pallerla
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Wilhelmstrasse 27, Tübingen 72074, Germany; Vietnamese-German Center for Medical Research, VG-CARE, Hanoi, Vietnam
| | - Jule Rüter
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Wilhelmstrasse 27, Tübingen 72074, Germany
| | - Yolanda Augustin
- Institute of Infection and Immunity, St George's University of London, United Kingdom
| | - Peter G Kremsner
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Wilhelmstrasse 27, Tübingen 72074, Germany; Centre de Recherches Médicales de Lambaréné (CERMEL), Gabon
| | - Sanjeev Krishna
- Institute of Infection and Immunity, St George's University of London, United Kingdom; Centre de Recherches Médicales de Lambaréné (CERMEL), Gabon
| | - Christian G Meyer
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Wilhelmstrasse 27, Tübingen 72074, Germany; Vietnamese-German Center for Medical Research, VG-CARE, Hanoi, Vietnam; Duy Tan University, Da Nang, Vietnam
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Dos Santos ACM, Dos Santos BRC, Dos Santos BB, de Moura EL, Ferreira JM, Dos Santos LKC, Oliveira SP, Dias RBF, Pereira E Silva AC, de Farias KF, de Souza Figueiredo EVM. Genetic polymorphisms as multi-biomarkers in severe acute respiratory syndrome (SARS) by coronavirus infection: A systematic review of candidate gene association studies. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2021; 93:104846. [PMID: 33933633 PMCID: PMC8084602 DOI: 10.1016/j.meegid.2021.104846] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 03/27/2021] [Accepted: 04/01/2021] [Indexed: 12/30/2022]
Abstract
The Severe acute respiratory syndrome may be caused by coronavirus disease which has resulted in a global pandemic. Polymorphisms in the population play a role in susceptibility to severity. We aimed to perform a systematic review related to the effect of single nucleotide polymorphisms in the development of severe acute respiratory syndrome (SARS). Twenty-eight eligible articles published were identified in PubMed, ScienceDirect, Web of Science, PMC Central and Portal BVS and additional records, with 20 studies performed in China. Information on study characteristics, genetic polymorphisms, and comorbidities was extracted. Study quality was assessed by the STrengthening the REporting of Genetic Association (STREGA) guideline. Few studies investigated the presence of polymorphisms in HLA, ACE1, OAS-1, MxA, PKR, MBL, E-CR1, FcγRIIA, MBL2, L-SIGN (CLEC4M), IFNG, CD14, ICAM3, RANTES, IL-12 RB1, TNFA, CXCL10/IP-10, CD209 (DC-SIGN), AHSG, CYP4F3 and CCL2 with the susceptibility or protection to SARS-Cov. This review provides comprehensive evidence of the association between genetic polymorphisms and susceptibility or protection to severity SARS-CoV. The literature about coronavirus infection, susceptibility to severe acute respiratory syndrome (SARS) and genetic variations is scarce. Further studies are necessary to provide more concrete evidence, mainly related to Covid-19.
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Affiliation(s)
- Ana Caroline Melo Dos Santos
- Laboratório de Biologia Molecular e Expressão Gênica, Postgraduate Program in Health Sciences, Federal University of Alagoas, Maceió, Alagoas, Brazil; Instituto de Ciências Biológicas e da Saúde (ICBS), Federal University of Alagoas, Maceió, Alagoas, Brazil
| | - Bárbara Rayssa Correia Dos Santos
- Laboratório de Biologia Molecular e Expressão Gênica, Postgraduate Program in Health Sciences, Federal University of Alagoas, Maceió, Alagoas, Brazil; Instituto de Ciências Biológicas e da Saúde (ICBS), Federal University of Alagoas, Maceió, Alagoas, Brazil
| | - Bruna Brandão Dos Santos
- Laboratório de Biologia Molecular e Expressão Gênica, Postgraduate Program in Health Sciences, Federal University of Alagoas, Maceió, Alagoas, Brazil; Instituto de Ciências Biológicas e da Saúde (ICBS), Federal University of Alagoas, Maceió, Alagoas, Brazil
| | - Edilson Leite de Moura
- Laboratório de Biologia Molecular e Expressão Gênica, Postgraduate Program in Health Sciences, Federal University of Alagoas, Maceió, Alagoas, Brazil; Instituto de Ciências Biológicas e da Saúde (ICBS), Federal University of Alagoas, Maceió, Alagoas, Brazil
| | - Jean Moisés Ferreira
- Laboratório de Biologia Molecular e Expressão Gênica, Postgraduate Program in Health Sciences, Federal University of Alagoas, Maceió, Alagoas, Brazil
| | - Luana Karen Correia Dos Santos
- Laboratório de Biologia Molecular e Expressão Gênica, Postgraduate Program in Health Sciences, Federal University of Alagoas, Maceió, Alagoas, Brazil; Instituto de Ciências Biológicas e da Saúde (ICBS), Federal University of Alagoas, Maceió, Alagoas, Brazil
| | - Susana Paiva Oliveira
- Laboratório de Biologia Molecular e Expressão Gênica, Postgraduate Program in Health Sciences, Federal University of Alagoas, Maceió, Alagoas, Brazil; Instituto de Ciências Biológicas e da Saúde (ICBS), Federal University of Alagoas, Maceió, Alagoas, Brazil
| | - Renise Bastos Farias Dias
- Laboratório de Biologia Molecular e Expressão Gênica, Postgraduate Program in Health Sciences, Federal University of Alagoas, Maceió, Alagoas, Brazil; Instituto de Ciências Biológicas e da Saúde (ICBS), Federal University of Alagoas, Maceió, Alagoas, Brazil
| | - Aline Cristine Pereira E Silva
- Laboratório de Biologia Molecular e Expressão Gênica, Postgraduate Program in Health Sciences, Federal University of Alagoas, Maceió, Alagoas, Brazil
| | - Karol Fireman de Farias
- Laboratório de Biologia Molecular e Expressão Gênica, Postgraduate Program in Health Sciences, Federal University of Alagoas, Maceió, Alagoas, Brazil
| | - Elaine Virgínia Martins de Souza Figueiredo
- Laboratório de Biologia Molecular e Expressão Gênica, Postgraduate Program in Health Sciences, Federal University of Alagoas, Maceió, Alagoas, Brazil; Instituto de Ciências Biológicas e da Saúde (ICBS), Federal University of Alagoas, Maceió, Alagoas, Brazil..
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ALTIOK D, SAVCI EZ, ÖZKARA B, ALKAN K, NAMDAR DS, TUNÇER G, KILINÇ BR, SUİÇMEZ E, ÇETİN G, ÜNAL S, DÖNMÜŞ B, KARAGÜLLEOĞLU ZY, UNCUOĞLU DB, TEKELİ C, MENDİ HA, BENGİ VU, CENGİZ SEVAL G, KILIÇ P, GÜNEŞ ALTUNTAŞ E, DEMİR-DORA D. Host variations in SARS-CoV-2 infection. Turk J Biol 2021; 45:404-424. [PMID: 34803443 PMCID: PMC8573834 DOI: 10.3906/biy-2104-67] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 08/13/2021] [Indexed: 12/12/2022] Open
Abstract
The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the zoonotic pathogen that causes the "Coronavirus Disease of 2019 (COVID-19)", and COVID-19 itself is yet to be thoroughly understood. Both the disease as well as the mechanisms by which the host interacts with the SARS-CoV-2 have not been fully enlightened. The epidemiological factors -e.g. age, sex, race-, the polymorphisms of the host proteins, the blood types and individual differences have all been in discussions about affecting the progression and the course of COVID-19 both individually and collectively, as their effects are mostly interwoven. We focused mainly on the effect of polymorphic variants of the host proteins that have been shown to take part in and/or affect the pathogenesis of COVID-19. Additionally, how the procedures of diagnosing and treating COVID-19 are affected by these variants and what possible changes can be implemented are the other questions, which are sought to be answered.
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Affiliation(s)
- Doruk ALTIOK
- Faculty of Dentistry, Başkent University, AnkaraTurkey
| | | | - Büşra ÖZKARA
- Faculty of Dentistry, Başkent University, AnkaraTurkey
| | - Kamil ALKAN
- Faculty of Dentistry, Başkent University, AnkaraTurkey
| | | | - Gizem TUNÇER
- Faculty of Dentistry, Başkent University, AnkaraTurkey
| | | | - Evren SUİÇMEZ
- Faculty of Dentistry, Başkent University, AnkaraTurkey
| | - Güneysu ÇETİN
- Faculty of Dentistry, Başkent University, AnkaraTurkey
| | - Sinan ÜNAL
- Faculty of Dentistry, Başkent University, AnkaraTurkey
| | - Beyza DÖNMÜŞ
- Faculty of Dentistry, Başkent University, AnkaraTurkey
| | | | | | - Cansu TEKELİ
- Faculty of Dentistry, Başkent University, AnkaraTurkey
| | | | | | | | - Pelin KILIÇ
- Faculty of Dentistry, Başkent University, AnkaraTurkey
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Cotroneo CE, Mangano N, Dragani TA, Colombo F. Lung expression of genes putatively involved in SARS-CoV-2 infection is modulated in cis by germline variants. Eur J Hum Genet 2021; 29:1019-1026. [PMID: 33649539 PMCID: PMC7917374 DOI: 10.1038/s41431-021-00831-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 12/09/2020] [Accepted: 02/09/2021] [Indexed: 01/10/2023] Open
Abstract
Germline variants in genes involved in SARS-CoV-2 cell entry and in host innate immune responses to viruses may influence the susceptibility to infection. This study used whole-genome analyses of lung tissue to identify polymorphisms acting as expression quantitative trait loci (eQTLs) for 60 genes of relevance to SARS-CoV-2 infection susceptibility. The expression of genes with confirmed or possible roles in viral entry-replication and in host antiviral responses was studied in the non-diseased lung tissue of 408 lung adenocarcinoma patients. No gene was differently expressed by sex, but APOBEC3H levels were higher and PARP12 levels lower in older individuals. A total of 125 cis-eQTLs (false discovery rate < 0.05) was found to modulate mRNA expression of 15 genes (ABO, ANPEP, AP2A2, APOBEC3D, APOBEC3G, BSG, CLEC4G, DDX58, DPP4, FURIN, FYCO1, RAB14, SERINC3, TRIM5, ZCRB1). eQTLs regulating ABO and FYCO1 were found in COVID-19 susceptibility loci. No trans-eQTLs were identified. Genetic control of the expression of these 15 genes, which encode putative virus receptors, proteins required for vesicle trafficking, enzymes that interfere with viral replication, and other restriction factors, may underlie interindividual differences in risk or severity of infection with SARS-CoV-2 or other viruses.
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Affiliation(s)
- Chiara E Cotroneo
- Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Nunzia Mangano
- Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Tommaso A Dragani
- Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy.
| | - Francesca Colombo
- Institute of Biomedical Technologies, National Research Council (ITB-CNR), Segrate, MI, Italy
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Darbeheshti F, Abolhassani H, Bashashati M, Ghavami S, Shahkarami S, Zoghi S, Gupta S, Orange JS, Ochs HD, Rezaei N. Coronavirus: Pure Infectious Disease or Genetic Predisposition. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1318:91-107. [PMID: 33973174 DOI: 10.1007/978-3-030-63761-3_6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes novel coronavirus disease (COVID-19), is the seventh pathogenic coronavirus recently discovered in December 2019 in Wuhan, China. To date, our knowledge about its effect on the human host remains limited. It is well known that host genetic factors account for the individual differences in the susceptibility to infectious diseases. The genetic susceptibility factors to COVID-19 and its severity are associated with several unanswered questions. However, the experience gained from an earlier strain of coronavirus, SARS-CoV-1, which shows 78% genetic similarity to SARS-CoV-2 and uses the same receptor to bind to host cells, could provide some clues. It, therefore, seems possible to assemble new evidence in order to solve a potential genetic predisposition puzzle for COVID-19. In this chapter, the puzzle pieces, including virus entry receptors, immune response, and inflammation-related genes, as well as the probable genetic predisposition models to COVID-19, are discussed.
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Affiliation(s)
- Farzaneh Darbeheshti
- Department of Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Medical Genetics Network (MeGeNe), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Hassan Abolhassani
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institute at Karolinska University Hospital Huddinge, Stockholm, Sweden
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
- Primary Immunodeficiency Diseases Network (PIDNet), Universal Scientific Education and Research Network (USERN), Stockholm, Sweden
| | - Mohammad Bashashati
- Division of Gastroenterology, Department of Internal Medicine, Texas Tech University Health Sciences Center, El Paso, TX, USA
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), El Paso, TX, USA
| | - Saeid Ghavami
- Department of Human Anatomy and Cell Science, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
- Faculty of Medicine, Katowice School of Technology, Katowice, Poland
| | - Sepideh Shahkarami
- Medical Genetics Network (MeGeNe), Universal Scientific Education and Research Network (USERN), Tehran, Iran
- Gene center, Ludwig-Maximilians-University of Munich, Munich, Germany
| | - Samaneh Zoghi
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
| | - Sudhir Gupta
- Department of Medicine, Division of Basic and Clinical Immunology, University of California, Irvine, CA, USA
| | - Jordan S Orange
- Immunology, Allergy, and Rheumatology, Baylor College of Medicine and the Texas Children's Hospital, Houston, TX, USA
| | - Hans D Ochs
- School of Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
- Universal Scientific Education and Research Network (USERN), Seattle, WA, USA
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran.
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran.
- Children's Medical Center Hospital, Tehran, Iran.
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10
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Chen HL, Yan WM, Chen G, Zhang XY, Zeng ZL, Wang XJ, Qi WP, Wang M, Li WN, Ma K, Xu D, Ni M, Huang JQ, Zhu L, Zhang S, Chen L, Wang HW, Ding C, Zhang XP, Chen J, Yu HJ, Ding HF, Wu L, Xing MY, Song JX, Chen T, Luo XP, Guo W, Han MF, Wu D, Ning Q. CAPRL Scoring System for Prediction of 30-day Mortality in 949 Patients with Coronavirus Disease 2019 in Wuhan, China: A Retrospective, Observational Study. INFECTIOUS DISEASES & IMMUNITY 2021; 1:28-35. [PMID: 38630115 PMCID: PMC8057317 DOI: 10.1097/id9.0000000000000001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Indexed: 01/08/2023]
Abstract
Background Coronavirus disease 2019 (COVID-19) is a serious and even lethal respiratory illness. The mortality of critically ill patients with COVID-19, especially short term mortality, is considerable. It is crucial and urgent to develop risk models that can predict the mortality risks of patients with COVID-19 at an early stage, which is helpful to guide clinicians in making appropriate decisions and optimizing the allocation of hospital resoureces. Methods In this retrospective observational study, we enrolled 949 adult patients with laboratory-confirmed COVID-19 admitted to Tongji Hospital in Wuhan between January 28 and February 12, 2020. Demographic, clinical and laboratory data were collected and analyzed. A multivariable Cox proportional hazard regression analysis was performed to calculate hazard ratios and 95% confidence interval for assessing the risk factors for 30-day mortality. Results The 30-day mortality was 11.8% (112 of 949 patients). Forty-nine point nine percent (474) patients had one or more comorbidities, with hypertension being the most common (359 [37.8%] patients), followed by diabetes (169 [17.8%] patients) and coronary heart disease (89 [9.4%] patients). Age above 50 years, respiratory rate above 30 beats per minute, white blood cell count of more than10 × 109/L, neutrophil count of more than 7 × 109/L, lymphocyte count of less than 0.8 × 109/L, platelet count of less than 100 × 109/L, lactate dehydrogenase of more than 400 U/L and high-sensitivity C-reactive protein of more than 50 mg/L were independent risk factors associated with 30-day mortality in patients with COVID-19. A predictive CAPRL score was proposed integrating independent risk factors. The 30-day mortality were 0% (0 of 156), 1.8% (8 of 434), 12.9% (26 of 201), 43.0% (55 of 128), and 76.7% (23 of 30) for patients with 0, 1, 2, 3, ≥4 points, respectively. Conclusions We designed an easy-to-use clinically predictive tool for assessing 30-day mortality risk of COVID-19. It can accurately stratify hospitalized patients with COVID-19 into relevant risk categories and could provide guidance to make further clinical decisions.
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Affiliation(s)
- Hui-Long Chen
- Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Wei-Ming Yan
- Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Guang Chen
- Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xiao-Yun Zhang
- Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Zhi-Lin Zeng
- Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xiao-Jing Wang
- Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Wei-Peng Qi
- Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Min Wang
- Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Wei-Na Li
- Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Ke Ma
- Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Dong Xu
- Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Ming Ni
- Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jia-Quan Huang
- Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Lin Zhu
- Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Shen Zhang
- Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Liang Chen
- Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Hong-Wu Wang
- Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Chen Ding
- Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xiao-Ping Zhang
- Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jia Chen
- Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Hai-Jing Yu
- Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Hong-Fang Ding
- Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Liang Wu
- Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Ming-You Xing
- Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | | | - Tao Chen
- Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xiao-Ping Luo
- Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Wei Guo
- Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Mei-Fang Han
- Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Di Wu
- Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Qin Ning
- Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
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11
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Borges RC, Hohmann MS, Borghi SM. Dendritic cells in COVID-19 immunopathogenesis: insights for a possible role in determining disease outcome. Int Rev Immunol 2020; 40:108-125. [PMID: 33191813 DOI: 10.1080/08830185.2020.1844195] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
SARS-CoV-2 is the causative agent of the COVID-19 pandemic. This novel coronavirus emerged in China, quickly spreading to more than 200 countries worldwide. Although most patients are only mildly ill or even asymptomatic, some develop severe pneumonia and become critically ill. One of the biggest unanswered questions is why some develop severe disease, whilst others do not. Insight on the interaction between SARS-CoV-2 and the immune system and the contribution of dysfunctional immune responses to disease progression will be instrumental to the understanding of COVID-19 pathogenesis, risk factors for worst outcome, and rational design of effective therapies and vaccines. In this review we have gathered the knowledge available thus far on the epidemiology of SARS-COV-2 infection, focusing on the susceptibility of older individuals, SARS-CoV-2-host cell interaction during infection and the immune response directed at SARS-CoV-2. Dendritic cells act as crucial messengers linking innate and adaptative immunity against viral infections. Thus, this review also brings a focused discussion on the role of dendritic cells and their immune functions during SARS-CoV-2 infection and how immune evasion strategies of SARS-CoV-2 and advancing age mediate dendritic cell dysfunctions that contribute to COVID-19 pathogenesis and increased susceptibility to worst outcomes. This review brings to light the hypothesis that concomitant occurrence of dendritic cell dysfunction/cytopathic effects induced by SARS-CoV-2 and/or aging may influence disease outcome in the elderly. Lastly, a detailed discussion on the effects and mechanisms of action of drugs currently being tested for COVID-19 on the function of dendritic cells is also provided.
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Affiliation(s)
- Rodrigo Cerqueira Borges
- Avenida Professor Lineu Prestes, University Hospital, University of São Paulo, São Paulo, Brazil
| | - Miriam Sayuri Hohmann
- Departament of Pathology, Biological Sciences Center, Londrina State University, Londrina, Paraná, Brazil
| | - Sergio Marques Borghi
- Departament of Pathology, Biological Sciences Center, Londrina State University, Londrina, Paraná, Brazil.,Center for Research in Health Sciences, University of Northern Paraná - Unopar, Londrina, Paraná, Brazil
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12
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Exploring Host Genetic Polymorphisms Involved in SARS-CoV Infection Outcomes: Implications for Personalized Medicine in COVID-19. Int J Genomics 2020; 2020:6901217. [PMID: 33110916 PMCID: PMC7582067 DOI: 10.1155/2020/6901217] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/19/2020] [Accepted: 10/13/2020] [Indexed: 12/14/2022] Open
Abstract
Objective To systematically explore genetic polymorphisms associated with the clinical outcomes in SARS-CoV infection in humans. Methods This comprehensive literature search comprised available English papers published in PubMed/Medline and SCOPUS databases following the PRISMA-P guidelines and PICO/AXIS criteria. Results Twenty-nine polymorphisms located in 21 genes were identified as associated with SARS-CoV susceptibility/resistance, disease severity, and clinical outcomes predominantly in Asian populations. Thus, genes implicated in key pathophysiological processes such as the mechanisms related to the entry of the virus into the cell and the antiviral immune/inflammatory responses were identified. Conclusions Although caution must be taken, the results of this systematic review suggest that multiple genetic polymorphisms are associated with SARS-CoV infection features by affecting virus pathogenesis and host immune response, which could have important applications for the study and understanding of genetics in SARS-CoV-2/COVID-19 and for personalized translational clinical practice depending on the population studied and associated environments.
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13
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Chen L, Zheng S. Understand variability of COVID-19 through population and tissue variations in expression of SARS-CoV-2 host genes. INFORMATICS IN MEDICINE UNLOCKED 2020; 21:100443. [PMID: 33072849 PMCID: PMC7550072 DOI: 10.1016/j.imu.2020.100443] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/28/2020] [Accepted: 10/04/2020] [Indexed: 12/25/2022] Open
Abstract
An urgent question of coronavirus disease 2019 (COVID-19) is population variation in susceptibility to SARS-CoV-2 infection and symptom severity. We explore the expression profiles of SARS-CoV-2 host genes, their population variations, associated genetic variants, age- and sex-dependency in normal individuals. SARS-CoV-2 host genes are provisionally defined as the human genes that are experimentally validated or bioinformatically predicted to interact with SARS-CoV-2 proteins. Genes exhibiting most variable expression include ACE2, CLEC4G, CLEC4M, CD209 (interact with the SARS-CoV-2 spike protein); REEP6 (a receptor accessory protein expressed in the olfactory epithelium); SLC27A2 and PKP2 (inhibit virus replication); and PTGS2 (mediates fever response). SNP rs4804803, associated with SARS severity, affects expression of CLEC4G and CD209. Genetic variants of proteases associated with SARS-CoV-2 entry (TMPRSS2, CTSB, and CTSL) are strongly associated with their expression variation, suggesting a genetic contribution to phenotypic variations in multiple organs upon virus attack. The most significant age-dependent gene is ACE2, the cellular receptor of SARS-CoV-2. Others include TGF-β family member GDF15, mediating inflammation, and VKORC1, possibly explaining vitamin K deficiency in COVID-19. TIMM10 and ERGIC1 exhibit significant sex differences. In summary, our results show genetic and multiple biological variables may underlie the population variation in SARS-CoV-2 infection and symptom severity.
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Affiliation(s)
- Liang Chen
- Quantitative and Computational Biology, Department of Biological Sciences, University of Southern California, 1050 Childs Way, Los Angeles, CA, 90089, United States
| | - Sika Zheng
- Division of Biomedical Sciences, School of Medicine, University of California Riverside, 900 University Ave, Riverside, CA, 92521, United States
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14
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Smatti MK, Al-Sarraj YA, Albagha O, Yassine HM. Host Genetic Variants Potentially Associated With SARS-CoV-2: A Multi-Population Analysis. Front Genet 2020; 11:578523. [PMID: 33133166 PMCID: PMC7567011 DOI: 10.3389/fgene.2020.578523] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 08/17/2020] [Indexed: 12/27/2022] Open
Abstract
Background Clinical outcomes of coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) showed enormous inter-individual and inter-population differences, possibly due to host genetics differences. Earlier studies identified single nucleotide polymorphisms (SNPs) associated with SARS-CoV-1 in Eastern Asian (EAS) populations. In this report, we aimed at exploring the frequency of a set of genetic polymorphisms that could affect SARS-CoV-2 susceptibility or severity, including those that were previously associated with SARS-CoV-1. Methods We extracted the list of SNPs that could potentially modulate SARS-CoV-2 from the genome wide association studies (GWAS) on SARS-CoV-1 and other viruses. We also collected the expression data of these SNPs from the expression quantitative trait loci (eQTLs) databases. Sequences from Qatar Genome Programme (QGP, n = 6,054) and 1000Genome project were used to calculate and compare allelic frequencies (AF). Results A total of 74 SNPs, located in 10 genes: ICAM3, IFN-γ, CCL2, CCL5, AHSG, MBL, Furin, TMPRSS2, IL4, and CD209 promoter, were identified. Analysis of Qatari genomes revealed significantly lower AF of risk variants linked to SARS-CoV-1 severity (CCL2, MBL, CCL5, AHSG, and IL4) compared to that of 1000Genome and/or the EAS population (up to 25-fold change). Conversely, SNPs in TMPRSS2, IFN-γ, ICAM3, and Furin were more common among Qataris (average 2-fold change). Inter-population analysis showed that the distribution of risk alleles among Europeans differs substantially from Africans and EASs. Remarkably, Africans seem to carry extremely lower frequencies of SARS-CoV-1 susceptibility alleles, reaching to 32-fold decrease compared to other populations. Conclusion Multiple genetic variants, which could potentially modulate SARS-CoV-2 infection, are significantly variable between populations, with the lowest frequency observed among Africans. Our results highlight the importance of exploring population genetics to understand and predict COVID-19 outcomes. Indeed, further studies are needed to validate these findings as well as to identify new genetic determinants linked to SARS-CoV-2.
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Affiliation(s)
- Maria K Smatti
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar.,Biomedical Research Center, Qatar University, Doha, Qatar
| | - Yasser A Al-Sarraj
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Omar Albagha
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar.,Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Hadi M Yassine
- Biomedical Research Center, Qatar University, Doha, Qatar
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15
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Identification of potential mRNA panels for severe acute respiratory syndrome coronavirus 2 (COVID-19) diagnosis and treatment using microarray dataset and bioinformatics methods. 3 Biotech 2020; 10:422. [PMID: 33251083 PMCID: PMC7679428 DOI: 10.1007/s13205-020-02406-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 08/20/2020] [Indexed: 12/15/2022] Open
Abstract
The goal of the present investigation is to identify the differentially expressed genes (DEGs) between SARS-CoV-2 infected and normal control samples to investigate the molecular mechanisms of infection with SARS-CoV-2. The microarray data of the dataset E-MTAB-8871 were retrieved from the ArrayExpress database. Pathway and Gene Ontology (GO) enrichment study, protein–protein interaction (PPI) network, modules, target gene–miRNA regulatory network, and target gene–TF regulatory network have been performed. Subsequently, the key genes were validated using an analysis of the receiver operating characteristic (ROC) curve. In SARS-CoV-2 infection, a total of 324 DEGs (76 up- and 248 down-regulated genes) were identified and enriched in a number of associated SARS-CoV-2 infection pathways and GO terms. Hub and target genes such as TP53, HRAS, MAPK11, RELA, IKZF3, IFNAR2, SKI, TNFRSF13C, JAK1, TRAF6, KLRF2, CD1A were identified from PPI network, target gene–miRNA regulatory network, and target gene–TF regulatory network. Study of the ROC showed that ten genes (CCL5, IFNAR2, JAK2, MX1, STAT1, BID, CD55, CD80, HAL-B, and HLA-DMA) were substantially involved in SARS-CoV-2 patients. The present investigation identified key genes and pathways that deepen our understanding of the molecular mechanisms of SARS-CoV-2 infection, and could be used for SARS-CoV-2 infection as diagnostic and therapeutic biomarkers.
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16
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Di Maria E, Latini A, Borgiani P, Novelli G. Genetic variants of the human host influencing the coronavirus-associated phenotypes (SARS, MERS and COVID-19): rapid systematic review and field synopsis. Hum Genomics 2020; 14:30. [PMID: 32917282 PMCID: PMC7484929 DOI: 10.1186/s40246-020-00280-6] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 08/31/2020] [Indexed: 12/15/2022] Open
Abstract
The COVID-19 pandemic has strengthened the interest in the biological mechanisms underlying the complex interplay between infectious agents and the human host. The spectrum of phenotypes associated with the SARS-CoV-2 infection, ranging from the absence of symptoms to severe systemic complications, raised the question as to what extent the variable response to coronaviruses (CoVs) is influenced by the variability of the hosts' genetic background.To explore the current knowledge about this question, we designed a systematic review encompassing the scientific literature published from Jan. 2003 to June 2020, to include studies on the contemporary outbreaks caused by SARS-CoV-1, MERS-CoV and SARS-CoV-2 (namely SARS, MERS and COVID-19 diseases). Studies were eligible if human genetic variants were tested as predictors of clinical phenotypes.An ad hoc protocol for the rapid review process was designed according to the PRISMA paradigm and registered at the PROSPERO database (ID: CRD42020180860). The systematic workflow provided 32 articles eligible for data abstraction (28 on SARS, 1 on MERS, 3 on COVID-19) reporting data on 26 discovery cohorts. Most studies considered the definite clinical diagnosis as the primary outcome, variably coupled with other outcomes (severity was the most frequently analysed). Ten studies analysed HLA haplotypes (1 in patients with COVID-19) and did not provide consistent signals of association with disease-associated phenotypes. Out of 22 eligible articles that investigated candidate genes (2 as associated with COVID-19), the top-ranked genes in the number of studies were ACE2, CLEC4M (L-SIGN), MBL, MxA (n = 3), ACE, CD209, FCER2, OAS-1, TLR4, TNF-α (n = 2). Only variants in MBL and MxA were found as possibly implicated in CoV-associated phenotypes in at least two studies. The number of studies for each predictor was insufficient to conduct meta-analyses.Studies collecting large cohorts from different ancestries are needed to further elucidate the role of host genetic variants in determining the response to CoVs infection. Rigorous design and robust statistical methods are warranted.
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Affiliation(s)
- Emilio Di Maria
- Department of Health Sciences, University of Genova, Genova, Italy.
- Unit of Medical Genetics, Galliera Hospital, Genova, Italy.
| | - Andrea Latini
- Department of Biomedicine and Prevention, Genetics Unit, University of Roma "Tor Vergata", Roma, Italy
| | - Paola Borgiani
- Department of Biomedicine and Prevention, Genetics Unit, University of Roma "Tor Vergata", Roma, Italy
| | - Giuseppe Novelli
- Department of Biomedicine and Prevention, Genetics Unit, University of Roma "Tor Vergata", Roma, Italy
- IRCCS Neuromed, Pozzilli (IS), Italy
- Department of Pharmacology, School of Medicine, University of Nevada, Reno, NV, 89557, USA
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17
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Ghafouri-Fard S, Noroozi R, Vafaee R, Branicki W, Poṡpiech E, Pyrc K, Łabaj PP, Omrani MD, Taheri M, Sanak M. Effects of host genetic variations on response to, susceptibility and severity of respiratory infections. Biomed Pharmacother 2020; 128:110296. [PMID: 32480226 PMCID: PMC7258806 DOI: 10.1016/j.biopha.2020.110296] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/16/2020] [Accepted: 05/19/2020] [Indexed: 12/13/2022] Open
Abstract
The recent outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has created a global crisis, necessitating the identification of genetic factors that modulate the risk of disorder or its severity. The current data about the role of genetic risk factors in determination of rate of SARS-CoV-2 infection in each ethnic group and the severity of disorder is limited. Moreover, several confounding parameters such as the number of tests performed in each country, the structure of the population especially the age distribution, the presence of risk factors for respiratory disorders such as smoking and other environmental factors might be involved in the variability in disease course or prevalence of infection among different ethnic groups. However, assessment of the role of genetic variants in determination of the course of other respiratory infections might help in recognition of possible candidate for further analysis in patients affected with SARS-CoV-2. In the current review, we summarize the data showing the association between genomic variants and risk of acute respiratory distress syndrome, respiratory infections or severity of these conditions with an especial focus on the SARS-CoV-2.
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Affiliation(s)
- Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Rezvan Noroozi
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Reza Vafaee
- Proteomics Research Center, Student Research Committee, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Wojciech Branicki
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Ewelina Poṡpiech
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Krzysztof Pyrc
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Paweł P Łabaj
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Mir Davood Omrani
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Taheri
- Urogenital Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Marek Sanak
- Department of Internal Medicine, Jagiellonian University Medical College, Krakow, Poland.
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18
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Ovsyannikova IG, Haralambieva IH, Crooke SN, Poland GA, Kennedy RB. The role of host genetics in the immune response to SARS-CoV-2 and COVID-19 susceptibility and severity. Immunol Rev 2020; 296:205-219. [PMID: 32658335 PMCID: PMC7404857 DOI: 10.1111/imr.12897] [Citation(s) in RCA: 149] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 06/14/2020] [Indexed: 01/08/2023]
Abstract
This article provides a review of studies evaluating the role of host (and viral) genetics (including variation in HLA genes) in the immune response to coronaviruses, as well as the clinical outcome of coronavirus-mediated disease. The initial sections focus on seasonal coronaviruses, SARS-CoV, and MERS-CoV. We then examine the state of the knowledge regarding genetic polymorphisms and SARS-CoV-2 and COVID-19. The article concludes by discussing research areas with current knowledge gaps and proposes several avenues for future scientific exploration in order to develop new insights into the immunology of SARS-CoV-2.
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19
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LoPresti M, Beck DB, Duggal P, Cummings DAT, Solomon BD. The Role of Host Genetic Factors in Coronavirus Susceptibility: Review of Animal and Systematic Review of Human Literature. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2020:2020.05.30.20117788. [PMID: 32511629 PMCID: PMC7276057 DOI: 10.1101/2020.05.30.20117788] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
BACKGROUND The recent SARS-CoV-2 pandemic raises many scientific and clinical questions. One set of questions involves host genetic factors that may affect disease susceptibility and pathogenesis. New work is emerging related to SARS-CoV-2; previous work has been conducted on other coronaviruses that affect different species. OBJECTIVES We aimed to review the literature on host genetic factors related to coronaviruses, with a systematic focus on human studies. METHODS We conducted a PubMed-based search and analysis for articles relevant to host genetic factors in coronavirus. We categorized articles, summarized themes related to animal studies, and extracted data from human studies for analyses. RESULTS We identified 1,187 articles of potential relevance. Forty-five studies were related to human host genetic factors related to coronavirus, of which 35 involved analysis of specific genes or loci; aside from one meta-analysis on respiratory infections, all were candidate-driven studies, typically investigating small number of research subjects and loci. Multiple significant loci were identified, including 16 related to susceptibility to coronavirus (of which 7 identified protective alleles), and 16 related to outcomes or clinical variables (of which 3 identified protective alleles). The types of cases and controls used varied considerably; four studies used traditional replication/validation cohorts. Of the other studies, 28 involved both human and non-human host genetic factors related to coronavirus, 174 involved study of non-human (animal) host genetic factors related to coronavirus, 584 involved study of non-genetic host factors related to coronavirus, including involving immunopathogenesis, 16 involved study of other pathogens (not coronavirus), 321 involved other studies of coronavirus, and 18 studies were assigned to the other categories and removed. KEY FINDINGS We have outlined key genes and loci from animal and human host genetic studies that may bear investigation in the nascent host genetic factor studies of COVID-19. Previous human studies to date have been limited by issues that may be less impactful on current endeavors, including relatively low numbers of eligible participants and limited availability of advanced genomic methods.
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20
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Ren J, Wang Z, Chen E. Different Associations between DC-SIGN Promoter-336G/A ( rs4804803) Polymorphism with Severe Dengue in Asians and South-Central Americans: a Meta-Analysis. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16081475. [PMID: 31027310 PMCID: PMC6518176 DOI: 10.3390/ijerph16081475] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 04/02/2019] [Accepted: 04/19/2019] [Indexed: 12/25/2022]
Abstract
Objective: This study was conducted to identify the association between rs4804803 polymorphism in DC-SIGN with the susceptibility of severe dengue. Methods: A comprehensive search was conducted to identify all eligible papers in PubMed, Web of Science, China National Knowledge Infrastructure (CNKI), and Google Scholar. Odds ratios (ORs) and corresponding 95% confidence intervals (95% CIs) were used to assess the association. Subgroup analyses were performed by ethnicity. Sensitivity analyses were performed through employing different statistical models (fixed versus random effect model). Results: A total of nine papers and 12 studies, with 1520 severe dengue and 1496 clinical dengue infection were included. The overall meta-analysis revealed significant associations between rs4804803 and severe dengue under the recession (GG versus GA/AA: OR = 0.44, 95%CI, 0.23–0.82) and a codominant model (GG versus AA: OR = 0.43, 95%CI, 0.23–0.81), but sensitivity analysis indicated that the significant pooled ORs were not robust. The subgroup analysis suggested that the carrier of G in rs4804803 was a risk factor for severe dengue under dominant (GG/GA versus AA: OR = 1.86,95%CI, 1.01–3.45), superdominant (GA versus GG/AA: OR = 1.81,95%CI, 1.02–3.21) and a codominant (GA versus AA: OR=1.82,95%CI, 1.02–3.26) models in Asians, while it was a protective factor for severe dengue in South-central Americans under recessive (GG versus GA/AA: OR = 0.27,95%CI, 0.10–0.70) and codominant (GG versus AA: OR=0.24,95%CI, 0.09–0.64) models. The results from subgroup analysis were robust. Conclusions: Dendritic cell-specific intercellular adhesion molecule-3-grabbing non-integrin (DC-SIGN) promoter-336G/A (rs4804803) polymorphism is association with severe dengue, and it acts in different directions for Asians and South-central Americans.
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Affiliation(s)
- Jiangping Ren
- Zhejiang Provincial Centre for Disease Control and Prevention, Hangzhou 310051, China.
- Key Laboratory of Vaccine, Prevention and Control of Infectious Disease of Zhejiang Province, Hangzhou 310051, China.
- Field Epidemiology Training Program of Zhejiang Province, Hangzhou 310051, China.
| | - Zhengting Wang
- Zhejiang Provincial Centre for Disease Control and Prevention, Hangzhou 310051, China.
| | - Enfu Chen
- Zhejiang Provincial Centre for Disease Control and Prevention, Hangzhou 310051, China.
- Key Laboratory of Vaccine, Prevention and Control of Infectious Disease of Zhejiang Province, Hangzhou 310051, China.
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von Brunn A, Ciesek S, von Brunn B, Carbajo-Lozoya J. Genetic deficiency and polymorphisms of cyclophilin A reveal its essential role for Human Coronavirus 229E replication. Curr Opin Virol 2015; 14:56-61. [PMID: 26318518 PMCID: PMC7102849 DOI: 10.1016/j.coviro.2015.08.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 08/06/2015] [Accepted: 08/10/2015] [Indexed: 12/15/2022]
Abstract
Replication of coronaviruses is inhibited in vitro by cyclosporin A, a well-known immunosuppressive drug which binds to cellular cyclophilins thus inactivating their enzymatic cis-trans peptidyl-prolyl isomerase function. Latter is required for proper folding of cellular proteins and of proteins of several viruses. Here, we summarize present knowledge on the role of cyclophilin A during coronavirus replication. We present data on the effect of cyclophilin A single nucleotide polymorphism mutants on the replication of human CoV-229E demonstrating the requirement of proper cyclophilin A function for virus propagation. Results define cellular cyclophilin A as a host target for inhibition of coronaviruses ranging from relatively mild common cold to highly pathogenic SARS-CoV and MERS-CoV viruses with the perspective of disclosing non-immunosuppressive cyclosporin A analogs to broadly inactivate the coronavirus family.
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Affiliation(s)
- Albrecht von Brunn
- Max-von-Pettenkofer Institute, Ludwig-Maximilians-Universität, München, Germany; German Center for Infection Research (DZIF), Germany.
| | - Sandra Ciesek
- German Center for Infection Research (DZIF), Germany; Department of Gastroenterology, Hepatology und Endocrinology, Medizinische Hochschule Hannover, Hannover, Germany
| | - Brigitte von Brunn
- Max-von-Pettenkofer Institute, Ludwig-Maximilians-Universität, München, Germany; German Center for Infection Research (DZIF), Germany
| | - Javier Carbajo-Lozoya
- Max-von-Pettenkofer Institute, Ludwig-Maximilians-Universität, München, Germany; German Center for Infection Research (DZIF), Germany
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Belopolskaya OB, Smelaya TV, Moroz VV, Golubev AM, Salnikova LE. Clinical associations of host genetic variations in the genes of cytokines in critically ill patients. Clin Exp Immunol 2015; 180:531-41. [PMID: 25619315 DOI: 10.1111/cei.12592] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/16/2015] [Indexed: 12/14/2022] Open
Abstract
Host genetic variations may influence a changing profile of biochemical markers and outcome in patients with trauma/injury. The objective of this study was to assess clinical associations of single nucleotide polymorphisms (SNPs) in the genes of cytokines in critically ill patients. A total of 430 patients were genotyped for SNPs in the genes of pro- (IL1B, IL6, IL8) and anti-inflammatory (IL4, IL10, IL13) cytokines. The main end-points were sepsis, mortality and adult respiratory distress syndrome (ARDS). We evaluated the dynamic levels of bilirubin, blood urea nitrogen, creatine kinase, creatinine and lactate dehydrogenase in five points of measurements (between 1 and 14 days after admission) and correlated them with SNPs. High-producing alleles of proinflammatory cytokines protected patients against sepsis (IL1B -511A and IL8 -251A) and mortality (IL1B -511A). High-producing alleles of anti-inflammatory cytokines IL4 -589T and IL13 431A (144Gln) were less frequent in ARDS patients. The carriers of IL6 -174C/C genotypes were prone to the increased levels of biochemical markers and acute kidney and liver insufficiency. Genotype-dependent differences in the levels of biochemical indicators gradually increased to a maximal value on the 14th day after admission. These findings suggest that genetic variability in pro- and anti-inflammatory cytokines may contribute to different clinical phenotypes in patients at high risk of critical illness.
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Affiliation(s)
- O B Belopolskaya
- N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - T V Smelaya
- V. A. Negovsky Research Institute of General Reanimatology, Russian Academy of Medical Sciences
| | - V V Moroz
- V. A. Negovsky Research Institute of General Reanimatology, Russian Academy of Medical Sciences
| | - A M Golubev
- V. A. Negovsky Research Institute of General Reanimatology, Russian Academy of Medical Sciences
| | - L E Salnikova
- N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia.,V. A. Negovsky Research Institute of General Reanimatology, Russian Academy of Medical Sciences
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Human lectins and their roles in viral infections. Molecules 2015; 20:2229-71. [PMID: 25642836 PMCID: PMC6272597 DOI: 10.3390/molecules20022229] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 01/21/2015] [Accepted: 01/23/2015] [Indexed: 12/20/2022] Open
Abstract
Innate recognition of virus proteins is an important component of the immune response to viral pathogens. A component of this immune recognition is the family of lectins; pattern recognition receptors (PRRs) that recognise viral pathogen-associated molecular patterns (PAMPs) including viral glycoproteins. In this review we discuss the contribution of soluble and membrane-associated PRRs to immunity against virus pathogens, and the potential role of these molecules in facilitating virus replication. These processes are illustrated with examples of viruses including human immunodeficiency virus (HIV), hepatitis C virus (HCV) and Ebola virus (EBOV). We focus on the structure, function and genetics of the well-characterised C-type lectin mannose-binding lectin, the ficolins, and the membrane-bound CD209 proteins expressed on dendritic cells. The potential for lectin-based antiviral therapies is also discussed.
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Wang YT, Hsieh LE, Dai YR, Chueh LL. Polymorphisms in the feline TNFA and CD209 genes are associated with the outcome of feline coronavirus infection. Vet Res 2014; 45:123. [PMID: 25512064 PMCID: PMC4267428 DOI: 10.1186/s13567-014-0123-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 11/26/2014] [Indexed: 01/08/2023] Open
Abstract
Feline infectious peritonitis (FIP), caused by feline coronavirus (FCoV) infection, is a highly lethal disease without effective therapy and prevention. With an immune-mediated disease entity, host genetic variant was suggested to influence the occurrence of FIP. This study aimed at evaluating cytokine-associated single nucleotide polymorphisms (SNPs), i.e., tumor necrosis factor alpha (TNF-α), receptor-associated SNPs, i.e., C-type lectin DC-SIGN (CD209), and the five FIP-associated SNPs identified from Birman cats of USA and Denmark origins and their associations with the outcome of FCoV infection in 71 FIP cats and 93 FCoV infected non-FIP cats in a genetically more diverse cat populations. A promoter variant, fTNFA - 421 T, was found to be a disease-resistance allele. One SNP was identified in the extracellular domain (ECD) of fCD209 at position +1900, a G to A substitution, and the A allele was associated with FIP susceptibility. Three SNPs located in the introns of fCD209, at positions +2276, +2392, and +2713, were identified to be associated with the outcome of FCoV infection, with statistical relevance. In contrast, among the five Birman FIP cat-associated SNPs, no genotype or allele showed significant differences between our FIP and non-FIP groups. As disease resistance is multifactorial and several other host genes could involve in the development of FIP, the five genetic traits identified in this study should facilitate in the future breeding of the disease-resistant animal to reduce the occurrence of cats succumbing to FIP.
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Affiliation(s)
| | | | | | - Ling-Ling Chueh
- Graduate institute of Veterinary Medicine, School of Veterinary Medicine, National Taiwan University, Taipei 10617, Taiwan.
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25
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Khalilullah SA, Harapan H, Hasan NA, Winardi W, Ichsan I, Mulyadi M. Host genome polymorphisms and tuberculosis infection: What we have to say? EGYPTIAN JOURNAL OF CHEST DISEASES AND TUBERCULOSIS 2013; 63:173-185. [PMID: 26966339 DOI: 10.1016/j.ejcdt.2013.12.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Several epidemiology studies suggest that host genetic factors play important roles in susceptibility, protection and progression of tuberculosis infection. Here we have reviewed the implications of some genetic polymorphisms in pathways related to tuberculosis susceptibility, severity and development. Large case-control studies examining single-nucleotide polymorphisms (SNPs) in genes have been performed in tuberculosis patients in some countries. Polymorphisms in natural resistance-associated macrophage protein 1 (NRAMP1), toll-like receptor 2 (TLR2), interleukin-6 (IL-6), tumor necrosis factor alpha (TNF-α), interleukin-1 receptor antagonist (IL-1RA), IL-10, vitamin D receptor (VDR), dendritic cell-specific ICAM-3-grabbing non-integrin (DC-SIGN), monocyte chemoattractant protein-1 (MCP-1), nucleotide oligomerization binding domain 2 (NOD2), interferon-gamma (IFN-γ), inducible nitric oxide synthase (iNOS), mannose-binding lectin (MBL) and surfactant proteins A (SP-A) have been reviewed. These genes have been variably associated with tuberculosis infection and there is strong evidence indicating that host genetic factors play critical roles in tuberculosis susceptibility, severity and development.
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Affiliation(s)
| | - Harapan Harapan
- Medical Research Unit, School of Medicine Syiah Kuala University, Banda Aceh, Indonesia; Tropical Disease Center, School of Medicine Syiah Kuala University, Banda Aceh, Indonesia
| | - Nabeeh A Hasan
- Research Affiliate, Centre for Genes, Environment and Health, National Jewish Health, Denver, CO, USA; Computational Bioscience Program, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Wira Winardi
- Medical Research Unit, School of Medicine Syiah Kuala University, Banda Aceh, Indonesia; Graduate Institute of Medical Science, Taipei Medical University, Taipei, Taiwan
| | - Ichsan Ichsan
- Medical Research Unit, School of Medicine Syiah Kuala University, Banda Aceh, Indonesia; Tropical Disease Center, School of Medicine Syiah Kuala University, Banda Aceh, Indonesia; Institute of Medical Microbiology and National Reference Center for Systemic Mycosis, University Medical Center Goettingen, Goettingen, Germany
| | - Mulyadi Mulyadi
- Pulmonology Department, School of Medicine, Syiah Kuala University, Banda Aceh, Indonesia
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Portman MA, Wiener HW, Silva M, Shendre A, Shrestha S. DC-SIGN gene promoter variants and IVIG treatment response in Kawasaki disease. Pediatr Rheumatol Online J 2013; 11:32. [PMID: 24006904 PMCID: PMC3847673 DOI: 10.1186/1546-0096-11-32] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 08/04/2013] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Genetic variants in the inhibiting FcγRIIB mediate anti-inflammatory responses and influence IVIG refractoriness (IVIG-R). However, these variants are rare in Asian and Hispanic populations so other genes in the pathway could be potentially involved. IVIG is ineffective in mice lacking SIGN-R1, a related molecule to human DC-SIGN. Further, DC-SIGN is a known receptor for sialylated Fc, the component responsible for the anti-inflammatory action of IVIG. Thus, we hypothesized that DC-SIGN would also be involved in the pathway of IVIG response in Kawasaki Disease (KD) patients. FINDINGS A case-control approach was performed to examine the differential distribution of five single nucleotide polymorphisms (SNPs) in DC-SIGN promoter with IVIG-R among White (158 vs. 62), Asian (64 vs. 12) and Hispanic (55 vs. 20) KD patients. Distinct differences in allele frequency distributions of several variants in the DC-SIGN promoter were observed in the three ethnic groups. Further, Asians with the major allele "A" in rs2287886 were more likely (OR = 1.76, p = 0.04) to be IVIG non-responder, but this allele is a minor allele in other two ethnic groups, where the association was not apparent. CONCLUSIONS DC-SIGN can potentially complement the role of FcγRIIB in the anti-inflammatory cascade involved in the IVIG response mechanism.
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Affiliation(s)
- Michael A Portman
- Department of Pediatrics, Center for Developmental Therapeutics, Seattle Children's Research Institute, University of Washington, 1900 9th Avenue, Seattle, WA 98101, USA.
| | - Howard W Wiener
- Department of Epidemiology, University of Alabama at Birmingham, 1665 University Boulevard, RPHB Room 217L, Birmingham 35294-0022, Alabama, USA
| | - Miriam Silva
- Department of Pediatrics, Center for Developmental Therapeutics, Seattle Children’s Research Institute, University of Washington, 1900 9th Avenue, Seattle, WA 98101, USA
| | - Aditi Shendre
- Department of Epidemiology, University of Alabama at Birmingham, 1665 University Boulevard, RPHB Room 217L, Birmingham 35294-0022, Alabama, USA
| | - Sadeep Shrestha
- Department of Epidemiology, University of Alabama at Birmingham, 1665 University Boulevard, RPHB Room 217L, Birmingham 35294-0022, Alabama, USA
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Binding of HIV-1 gp120 to DC-SIGN promotes ASK-1-dependent activation-induced apoptosis of human dendritic cells. PLoS Pathog 2013; 9:e1003100. [PMID: 23382671 PMCID: PMC3561151 DOI: 10.1371/journal.ppat.1003100] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2012] [Accepted: 10/23/2012] [Indexed: 11/19/2022] Open
Abstract
During disease progression to AIDS, HIV-1 infected individuals become increasingly immunosuppressed and susceptible to opportunistic infections. It has also been demonstrated that multiple subsets of dendritic cells (DC), including DC-SIGN(+) cells, become significantly depleted in the blood and lymphoid tissues of AIDS patients, which may contribute to the failure in initiating effective host immune responses. The mechanism for DC depletion, however, is unclear. It is also known that vast quantities of viral envelope protein gp120 are shed from maturing HIV-1 virions and form circulating immune complexes in the serum of HIV-1-infected individuals, but the pathological role of gp120 in HIV-1 pathogenesis remains elusive. Here we describe a previously unrecognized mechanism of DC death in chronic HIV-1 infection, in which ligation of DC-SIGN by gp120 sensitizes DC to undergo accelerated apoptosis in response to a variety of activation stimuli. The cultured monocyte-derived DC and also freshly-isolated DC-SIGN(+) blood DC that were exposed to either cross-linked recombinant gp120 or immune-complex gp120 in HIV(+) serum underwent considerable apoptosis after CD40 ligation or exposure to bacterial lipopolysaccharide (LPS) or pro-inflammatory cytokines such as TNFα and IL-1β. Furthermore, circulating DC-SIGN(+) DC that were isolated directly from HIV-1(+) individuals had actually been pre-sensitized by serum gp120 for activation-induced exorbitant apoptosis. In all cases the DC apoptosis was substantially inhibited by DC-SIGN blockade. Finally, we showed that accelerated DC apoptosis was a direct consequence of excessive activation of the pro-apoptotic molecule ASK-1 and transfection of siRNA against ASK-1 significantly prevented the activation-induced excessive DC death. Our study discloses a previously unknown mechanism of immune modulation by envelope protein gp120, provides new insights into HIV immunopathogenesis, and suggests potential therapeutic approaches to prevent DC depletion in chronic HIV infection. HIV-1 infected individuals become increasingly immunocompromised and susceptible to opportunistic infection during disease progression, which is associated with significant reduction of the dendritic cell number in the peripheral blood or secondary lymphoid tissues. Because dendritic cells are the most powerful antigen-presenting cells, their survival is critical for host defence and inadequate dendritic cell number will fail to induce effective host immune responses. Here we describe a mechanism that may at least partly explain why dendritic cells become significantly depleted in chronic HIV-1 infection. We found that after binding of the HIV-1 envelope protein gp120 to the dendritic cell surface protein DC-SIGN, the subsequent activation by CD40 ligation, or by exposure to bacterial product lipopolysaccharide or pro-inflammatory cytokines such as TNF-α and IL-1β, will lead to overexpression of pro-apoptotic molecule ASK-1, resulting in excessive dendritic cell death. We also confirmed that DC-SIGN(+) dendritic cells in the blood of HIV-1 infected individuals have actually been pre-sensitized by viral gp120, which exists in vast amount in the blood, for activation-induced exorbitant death. Our study thus reveals a previously unknown pathway for dendritic cell depletion and provides clues for potential therapeutic approaches to prevent DC depletion in chronic HIV infection.
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Boily-Larouche G, Milev MP, Zijenah LS, Labbé AC, Zannou DM, Humphrey JH, Ward BJ, Poudrier J, Mouland AJ, Cohen ÉA, Roger M. Naturally-occurring genetic variants in human DC-SIGN increase HIV-1 capture, cell-transfer and risk of mother-to-child transmission. PLoS One 2012; 7:e40706. [PMID: 22808239 PMCID: PMC3393705 DOI: 10.1371/journal.pone.0040706] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Accepted: 06/12/2012] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Mother-to-child transmission (MTCT) is the main cause of HIV-1 infection in children worldwide. Dendritic cell-specific ICAM-3 grabbing-nonintegrin (DC-SIGN, also known as CD209) is an HIV-1 receptor that enhances its transmission to T cells and is expressed on placental macrophages. METHODS AND FINDINGS We have investigated the association between DC-SIGN genetic variants and risk of MTCT of HIV-1 among Zimbabwean infants and characterized the impact of the associated mutations on DC-SIGN expression and interaction with HIV-1. DC-SIGN promoter (p-336C and p-201A) and exon 4 (198Q and 242V) variants were all significantly associated with increased risk of intrauterine (IU) HIV-1 infection. Promoter variants decreased DC-SIGN expression both in vitro and in placental CD163(+) macrophages (Hofbauer cells) of HIV-1 unexposed infants but not of HIV-1 exposed infants. The exon 4 protein-modifying mutations increased HIV-1 capture and transmission to T cells in vitro. CONCLUSION This study provides compelling evidence to support an important role of DC-SIGN in IU HIV-1 infection.
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Affiliation(s)
- Geneviève Boily-Larouche
- Laboratoire d’Immunogénétique, Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, Canada
- Département de Microbiologie et Immunologie, Université de Montréal, Montréal, Canada
| | - Miroslav P. Milev
- Department of Medicine, McGill University, The Lady Davis Institute for Medical Research and McGill AIDS Center, Montreal, Canada
| | - Lynn S. Zijenah
- Department of Immunology, University of Zimbabwe College of Health Sciences, Harare, Zimbabwe
| | - Annie-Claude Labbé
- Département de Microbiologie et Immunologie, Université de Montréal, Montréal, Canada
- Département de Microbiologie de l’hôpital Maisonneuve-Rosemont, Montréal, Canada
| | - Djimon M. Zannou
- Centre National Hospitalier Universitaire, Université d’Abomey Calavi, Cotonou, Bénin
| | - Jean H. Humphrey
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Brian J. Ward
- Research Institute of the McGill University Health Centre, Montreal, Canada
| | - Johanne Poudrier
- Laboratoire d’Immunogénétique, Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, Canada
- Département de Microbiologie et Immunologie, Université de Montréal, Montréal, Canada
| | - Andrew J. Mouland
- Department of Medicine, McGill University, The Lady Davis Institute for Medical Research and McGill AIDS Center, Montreal, Canada
| | - Éric A. Cohen
- Département de Microbiologie et Immunologie, Université de Montréal, Montréal, Canada
- Institut de Recherches Cliniques de Montréal, Montréal, Canada
| | - Michel Roger
- Laboratoire d’Immunogénétique, Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, Canada
- Département de Microbiologie et Immunologie, Université de Montréal, Montréal, Canada
- * E-mail:
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Sainz J, Lupiáñez CB, Segura-Catena J, Vazquez L, Ríos R, Oyonarte S, Hemminki K, Försti A, Jurado M. Dectin-1 and DC-SIGN polymorphisms associated with invasive pulmonary Aspergillosis infection. PLoS One 2012; 7:e32273. [PMID: 22384201 PMCID: PMC3288082 DOI: 10.1371/journal.pone.0032273] [Citation(s) in RCA: 110] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Accepted: 01/24/2012] [Indexed: 12/22/2022] Open
Abstract
The recognition of pathogen-derived structures by C-type lectins and the chemotactic activity mediated by the CCL2/CCR2 axis are critical steps in determining the host immune response to fungi. The present study was designed to investigate whether the presence of single nucleotide polymorphisms (SNPs) within DC-SIGN, Dectin-1, Dectin-2, CCL2 and CCR2 genes influence the risk of developing Invasive Pulmonary Aspergillosis (IPA). Twenty-seven SNPs were selected using a hybrid functional/tagging approach and genotyped in 182 haematological patients, fifty-seven of them diagnosed with proven or probable IPA according to the 2008 EORTC/MSG criteria. Association analysis revealed that carriers of the Dectin-1(rs3901533 T/T) and Dectin-1(rs7309123 G/G) genotypes and DC-SIGN(rs4804800 G), DC-SIGN(rs11465384 T), DC-SIGN(7248637 A) and DC-SIGN(7252229 C) alleles had a significantly increased risk of IPA infection (OR = 5.59 95%CI 1.37-22.77; OR = 4.91 95%CI 1.52-15.89; OR = 2.75 95%CI 1.27-5.95; OR = 2.70 95%CI 1.24-5.90; OR = 2.39 95%CI 1.09-5.22 and OR = 2.05 95%CI 1.00-4.22, respectively). There was also a significantly increased frequency of galactomannan positivity among patients carrying the Dectin-1(rs3901533_T) allele and Dectin-1(rs7309123_G/G) genotype. In addition, healthy individuals with this latter genotype showed a significantly decreased level of Dectin-1 mRNA expression compared to C-allele carriers, suggesting a role of the Dectin-1(rs7309123) polymorphism in determining the levels of Dectin-1 and, consequently, the level of susceptibility to IPA infection. SNP-SNP interaction (epistasis) analysis revealed significant interactions models including SNPs in Dectin-1, Dectin-2, CCL2 and CCR2 genes, with synergistic genetic effects. Although these results need to be further validated in larger cohorts, they suggest that Dectin-1, DC-SIGN, Dectin-2, CCL2 and CCR2 genetic variants influence the risk of IPA infection and might be useful in developing a risk-adapted prophylaxis.
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Affiliation(s)
- Juan Sainz
- Genomic Oncology Area, Genyo, Pfizer-University of Granada-Andalusian Government Centre for Genomics and Oncological Research, Granada, Spain.
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Kutikhin AG, Yuzhalin AE. C-type lectin receptors and RIG-I-like receptors: new points on the oncogenomics map. Cancer Manag Res 2012; 4:39-53. [PMID: 22427730 PMCID: PMC3304337 DOI: 10.2147/cmar.s28983] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The group of pattern recognition receptors includes families of Toll-like receptors, NOD-like receptors, C-type lectin receptors, and RIG-I-like receptors. They are key sensors for a number of infectious agents, some of which are oncogenic, and they launch an immune response against them, normally promoting their eradication. Inherited variations in genes encoding these receptors and proteins and their signaling pathways may affect their function, possibly modulating cancer risk and features of cancer progression. There are numerous studies investigating the association of single nucleotide polymorphisms within or near genes encoding Toll-like receptors and NOD-like receptors, cancer risk, and features of cancer progression. However, there is an almost total absence of articles analyzing the correlation between polymorphisms of genes encoding C-type lectin receptors and RIG-I-like receptors and cancer risk or progression. Nevertheless, there is some evidence supporting the hypothesis that inherited C-type lectin receptor and RIG-I-like receptor variants can be associated with increased cancer risk. Certain C-type lectin receptors and RIG-I-like receptors recognize pathogen-associated molecular patterns of potentially oncogenic infectious agents, and certain polymorphisms of genes encoding C-type lectin receptors and RIG-I-like receptors may have functional consequences at the molecular level that can lead to association of such single nucleotide polymorphisms with risk or progression of some diseases that may modulate cancer risk, so these gene polymorphisms may affect cancer risk indirectly. Polymorphisms of genes encoding C-type lectin receptors and RIG-I-like receptors thereby may be correlated with a risk of lung, oral, esophageal, gastric, colorectal, and liver cancer, as well as nasopharyngeal carcinoma, glioblastoma, multiple myeloma, and lymphoma. The list of the most promising polymorphisms for oncogenomic investigations may include rs1926736, rs2478577, rs2437257, rs691005, rs2287886, rs735239, rs4804803, rs16910526, rs36055726, rs11795404, and rs10813831.
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Affiliation(s)
- Anton G Kutikhin
- Department of Epidemiology, Kemerovo State Medical Academy, Kemerovo, Russian Federation
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Abstract
In the immune system, C-type lectins and CTLDs have been shown to act both as adhesion and as pathogen recognition receptors. The Dendritic cell-specific ICAM-3 grabbing non-integrin (DC-SIGN) and its homologs in human and mouse represent an important C-type lectin family. DC-SIGN contains a lectin domain that recognizes in a Ca2+-dependent manner carbohydrates such as mannose-containing structures present on glycoproteins such as ICAM-2 and ICAM-3. DC-SIGN is a prototype C-type lectin organized in microdomains, which have their role as pathogen recognition receptors in sensing microbes. Although the integrin LFA-1 is a counter-receptor for both ICAM-2 and ICAM-3 on DC, DC-SIGN is the high affinity adhesion receptor for ICAM-2/-3. While cell–cell contact is a primary function of selectins, collectins are specialized in recognition of pathogens. Interestingly, DC-SIGN is a cell adhesion receptor as well as a pathogen recognition receptor. As adhesion receptor, DC-SIGN mediates the contact between dendritic cells (DCs) and T lymphocytes, by binding to ICAM-3, and mediates rolling of DCs on endothelium, by interacting with ICAM-2. As pathogen receptor, DC-SIGN recognizes a variety of microorganisms, including viruses, bacteria, fungi and several parasites (Cambi et al. 2005). The natural ligands of DC-SIGN consist of mannose oligosaccharides or fucose-containing Lewis-type determinants. In this chapter, we shall focus on the structure and functions of DC-SIGN and related CTLDs in the recognition of pathogens, the molecular and structural determinants that regulate the interaction with pathogen-associated molecular patterns. The heterogeneity of carbohydrate residues exposed on cellular proteins and pathogens regulates specific binding of DC-expressed C-type lectins that contribute to the diversity of immune responses created by DCs (van Kooyk et al. 2003a; Cambi et al. 2005).
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Barkhash AV, Perelygin AA, Babenko VN, Brinton MA, Voevoda MI. Single nucleotide polymorphism in the promoter region of the CD209 gene is associated with human predisposition to severe forms of tick-borne encephalitis. Antiviral Res 2012; 93:64-8. [DOI: 10.1016/j.antiviral.2011.10.017] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2011] [Revised: 09/05/2011] [Accepted: 10/19/2011] [Indexed: 12/14/2022]
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Zheng R, Zhou Y, Qin L, Jin R, Wang J, Lu J, Wang W, Tang S, Hu Z. Relationship between polymorphism of DC-SIGN (CD209) gene and the susceptibility to pulmonary tuberculosis in an eastern Chinese population. Hum Immunol 2010; 72:183-6. [PMID: 21081145 PMCID: PMC7132724 DOI: 10.1016/j.humimm.2010.11.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2010] [Revised: 10/25/2010] [Accepted: 11/08/2010] [Indexed: 01/27/2023]
Abstract
Dendritic cell–specific intracellular adhesion molecule–3–grabbing nonintegrin (DC-SIGN) is an important receptor for Mycobacterium tuberculosis on human dendritic cells. Previous studies have shown that the variation, especially the −871A/G and −336A/G in DC-SIGN promoter influenced the susceptibility to tuberculosis. We therefore investigated whether polymorphisms in the DC-SIGN gene were associated with susceptibility to tuberculosis in an eastern Chinese population. A total of 237 culture-positive pulmonary tuberculosis case patients and 244 controls were genotyped for −871A/G and −336A/G by pyrosequencing. Our results suggested that the 2 promoter variants of DC-SIGN gene were not associated with susceptibility to tuberculosis in Chinese. Further analysis showed that the allele -336G was associated with a protective effect against fever in pulmonary tuberculosis patients, but not against cavity formation. In addition, we compared the allelic frequencies of −871A/G and −336A/G in African, Caucasian, and Asian groups. The results showed that the tw forms of allelic frequencies detected Chinese individuals in our study were similar to the reported frequencies in other Asian populations but differed significantly from those in the African and Caucasian groups studied.
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Affiliation(s)
- Ruijuan Zheng
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
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