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Xue M, Lin Z, Wen Y, Fan S, Li Y, Qu HQ, Hu Q, Guo Q, Su L, Yang Q, Chen J, Jiang C, Huang H, Zheng P, Li N, Yuan Q, Zhang M, Zhao X, Wu Q, Hu F, Li L, Wang X, Liu P, Hakonarson H, Deng Z, Wang H, Tang X, Sun B. VCL/ICAM-1 pathway is associated with lung inflammatory damage in SARS-CoV-2 Omicron infection. Nat Commun 2025; 16:3801. [PMID: 40268929 PMCID: PMC12019401 DOI: 10.1038/s41467-025-59145-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 04/10/2025] [Indexed: 04/25/2025] Open
Abstract
SARS-CoV-2 variants present diverse clinical manifestations, necessitating deeper insights into their pathogenic effects. This study employs multi-omics approaches to investigate the molecular mechanisms underlying SARS-CoV-2 infection, focusing on vascular damage. Plasma proteomic analysis of unvaccinated participants infected with Omicron BA.2.76 or ancestral variants identifies key signaling pathways associated with endothelial dysfunction, with the vinculin (VCL) pathway emerging as a hallmark of Omicron infections, contributing to lung exudation. Metabolomic analysis of plasma samples from the same cohort reveals disruptions in immune function, cell membrane integrity, and metabolic processes, including altered tricarboxylic acid cycle and glycolysis pathways. An integrated analysis of proteomic and metabolomic data underscores the role of VCL in inflammation and extravasation, highlighting its interactions with adhesion molecules and inflammatory metabolites. A validation cohort of plasma samples from Omicron-infected participants confirms this association by replicating proteomic analysis, showing elevated VCL levels correlated with inflammatory markers. Functional studies in a male rat model of lung injury demonstrate that anti-VCL intervention reduces plasma VCL levels, mitigates alveolar edema, and restores alveolar-capillary barrier integrity, as assessed by histological staining and electron microscopy, thereby illustrating VCL modulation's impact on vascular leakage and extravasation. These findings establish VCL as a potential therapeutic target for mitigating vascular complications in SARS-CoV-2 infections.
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Affiliation(s)
- Mingshan Xue
- Department of Clinical Laboratory, National Center for Respiratory Medicine / National Clinical Research Center for Respiratory Disease / Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510120, China
- State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, Guangdong, 510000, China
- Institute of Infectious Diseases, Guangzhou Eighth Hospital, Guangzhou Medical University, Guangzhou, Guangdong, 510060, China
- Guangzhou Laboratory, XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou, Guangdong, 510005, China
| | - Zhiwei Lin
- Department of Clinical Laboratory, National Center for Respiratory Medicine / National Clinical Research Center for Respiratory Disease / Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510120, China
- State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, Guangdong, 510000, China
| | - Youli Wen
- Zigong First People's Hospital, Sichuan, 643000, China
| | - Shaohui Fan
- The Fifth Affiliated Hospital of Zunyi Medical University, Zhuhai, Guangdong, 519100, China
| | - Youxia Li
- The Fifth Affiliated Hospital of Zunyi Medical University, Zhuhai, Guangdong, 519100, China
| | - Hui-Qi Qu
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Qiurong Hu
- Department of Clinical Laboratory, National Center for Respiratory Medicine / National Clinical Research Center for Respiratory Disease / Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510120, China
| | - Qian Guo
- Department of Clinical Laboratory, National Center for Respiratory Medicine / National Clinical Research Center for Respiratory Disease / Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510120, China
| | - Lijun Su
- Department of Clinical Laboratory, National Center for Respiratory Medicine / National Clinical Research Center for Respiratory Disease / Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510120, China
| | - Qianyue Yang
- Department of Clinical Laboratory, National Center for Respiratory Medicine / National Clinical Research Center for Respiratory Disease / Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510120, China
| | - Jiahong Chen
- Department of Clinical Laboratory, National Center for Respiratory Medicine / National Clinical Research Center for Respiratory Disease / Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510120, China
| | - Chuci Jiang
- Department of Clinical Laboratory, National Center for Respiratory Medicine / National Clinical Research Center for Respiratory Disease / Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510120, China
| | - Huimin Huang
- Department of Clinical Laboratory, National Center for Respiratory Medicine / National Clinical Research Center for Respiratory Disease / Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510120, China
| | - Peiyan Zheng
- Department of Clinical Laboratory, National Center for Respiratory Medicine / National Clinical Research Center for Respiratory Disease / Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510120, China
| | - Ning Li
- Department of Clinical Laboratory, National Center for Respiratory Medicine / National Clinical Research Center for Respiratory Disease / Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510120, China
| | - Quan Yuan
- Zigong First People's Hospital, Sichuan, 643000, China
| | - Meixia Zhang
- Zigong First People's Hospital, Sichuan, 643000, China
| | - Xin Zhao
- Zigong First People's Hospital, Sichuan, 643000, China
| | - Qunhua Wu
- Zigong First People's Hospital, Sichuan, 643000, China
| | - Fengyu Hu
- Institute of Infectious Diseases, Guangzhou Eighth Hospital, Guangzhou Medical University, Guangzhou, Guangdong, 510060, China
| | - Lu Li
- Institute of Infectious Diseases, Guangzhou Eighth Hospital, Guangzhou Medical University, Guangzhou, Guangdong, 510060, China
| | - Xiaowen Wang
- The Fifth Affiliated Hospital of Zunyi Medical University, Zhuhai, Guangdong, 519100, China
| | - Peixin Liu
- Zhuhai People's Hospital, Zhuhai, Guangdong, 519100, China
| | - Hakon Hakonarson
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Division of Human Genetics, Division of Pulmonary Medicine, Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Faculty of Medicine, University of Iceland, 101, Reykjavik, Iceland
| | - Zhiping Deng
- Zigong First People's Hospital, Sichuan, 643000, China
| | - Hongman Wang
- The Fifth Affiliated Hospital of Zunyi Medical University, Zhuhai, Guangdong, 519100, China
| | - Xiaoping Tang
- Department of Clinical Laboratory, National Center for Respiratory Medicine / National Clinical Research Center for Respiratory Disease / Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510120, China
- Institute of Infectious Diseases, Guangzhou Eighth Hospital, Guangzhou Medical University, Guangzhou, Guangdong, 510060, China
- Guangzhou Laboratory, XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou, Guangdong, 510005, China
| | - Baoqing Sun
- Department of Clinical Laboratory, National Center for Respiratory Medicine / National Clinical Research Center for Respiratory Disease / Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510120, China.
- State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, Guangdong, 510000, China.
- Guangzhou Laboratory, XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou, Guangdong, 510005, China.
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Saad MJA, Santos A. The Microbiota and Evolution of Obesity. Endocr Rev 2025; 46:300-316. [PMID: 39673174 PMCID: PMC11894537 DOI: 10.1210/endrev/bnae033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Revised: 09/03/2024] [Accepted: 12/12/2024] [Indexed: 12/16/2024]
Abstract
Obesity is a major global concern and is generally attributed to a combination of genetic and environmental factors. Several hypotheses have been proposed to explain the evolutionary origins of obesity epidemic, including thrifty and drifty genotypes, and changes in thermogenesis. Here, we put forward the hypothesis of metaflammation, which proposes that due to intense selection pressures exerted by environmental pathogens, specific genes that help develop a robust defense mechanism against infectious diseases have had evolutionary advantages and that this may contribute to obesity in modern times due to connections between the immune and energy storage systems. Indeed, incorporating the genetic variations of gut microbiota into the complex genetic framework of obesity makes it more polygenic than previously believed. Thus, uncovering the evolutionary origins of obesity requires a multifaceted approach that considers the complexity of human history, the unique genetic makeup of different populations, and the influence of gut microbiome on host genetics.
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Affiliation(s)
- Mario J A Saad
- Department of Internal Medicine, School of Medical Sciences, University of Campinas, CEP 13083-887 Campinas, SP, Brazil
| | - Andrey Santos
- Department of Internal Medicine, School of Medical Sciences, University of Campinas, CEP 13083-887 Campinas, SP, Brazil
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3
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Meng Z, Zhang C, Liu S, Li W, Wang Y, Zhang Q, Peng B, Ye W, Jiang Y, Song Y, Guo M, Chang X, Shao L. Exploring genetic loci linked to COVID-19 severity and immune response through multi-trait GWAS analyses. Front Genet 2025; 16:1502839. [PMID: 40034745 PMCID: PMC11873281 DOI: 10.3389/fgene.2025.1502839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2024] [Accepted: 01/27/2025] [Indexed: 03/05/2025] Open
Abstract
Introduction COVID-19 severity has been linked to immune factors, with excessive immune responses like cytokine storms contributing to mortality. However, the genetic basis of these immune responses is not well understood. This study aimed to explore the genetic connection between COVID-19 severity and blood cell traits, given their close relationship with immunity. Materials and methods GWAS summary statistics for COVID-19 and blood cell counts were analyzed using Linkage Disequilibrium Score Regression (LDSC) to estimate genetic correlations and heritabilities. For traits with significant correlations, a Multi-Trait GWAS Analysis (MTAG) was performed to identify pleiotropic loci shared between COVID-19 and blood cell counts. Results Our MTAG analysis identified four pleiotropic loci associated with COVID-19 severity, five loci linked to hospitalized cases, and one locus related to general patients. Among these, two novel loci were identified in the high-risk population, with rs55779981 located near RAVER1 and rs73009538 near CARM1. In hospitalized patients, two previously unrecognized loci were detected, namely, rs115545251 near GFI1 and rs3181049 near RAVER1, while in general patients, rs11065822 near CUX2 emerged as a newly identified locus. We also identified potential target genes, including those involved in inflammation signaling (CARM1), endothelial dysfunction (INTS12), and antiviral immune response (RAVER1), which may require further investigation. Conclusion Our study offers insights into the genetic overlap between COVID-19 and immune factors, suggesting potential directions for future research and clinical exploration.
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Affiliation(s)
- Ziang Meng
- Department of Infectious Disease, Central Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Chumeng Zhang
- The Second School of Clinical Medicine of Shandong First Medical University, Tai’an, Shandong, China
| | - Shuai Liu
- Agricultural Products Quality and Safety Center of Jinan, Jinan, Shandong, China
| | - Wen Li
- College of Medical Information and Artificial Intelligence, Shandong First Medical University, Jinan, Shandong, China
| | - Yue Wang
- College of Medical Information and Artificial Intelligence, Shandong First Medical University, Jinan, Shandong, China
| | - Qingyi Zhang
- College of Medical Information and Artificial Intelligence, Shandong First Medical University, Jinan, Shandong, China
| | - Bichen Peng
- College of Medical Information and Artificial Intelligence, Shandong First Medical University, Jinan, Shandong, China
| | - Weiyi Ye
- College of Medical Information and Artificial Intelligence, Shandong First Medical University, Jinan, Shandong, China
| | - Yue Jiang
- College of Medical Information and Artificial Intelligence, Shandong First Medical University, Jinan, Shandong, China
| | - Yingchao Song
- College of Medical Information and Artificial Intelligence, Shandong First Medical University, Jinan, Shandong, China
| | - Miao Guo
- School of Life Sciences, Shandong First Medical University, Shandong, China
| | - Xiao Chang
- College of Medical Information and Artificial Intelligence, Shandong First Medical University, Jinan, Shandong, China
| | - Lei Shao
- Department of Infectious Disease, Central Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
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4
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Talkington GM, Kolluru P, Gressett TE, Ismael S, Meenakshi U, Acquarone M, Solch-Ottaiano RJ, White A, Ouvrier B, Paré K, Parker N, Watters A, Siddeeque N, Sullivan B, Ganguli N, Calero-Hernandez V, Hall G, Longo M, Bix GJ. Neurological sequelae of long COVID: a comprehensive review of diagnostic imaging, underlying mechanisms, and potential therapeutics. Front Neurol 2025; 15:1465787. [PMID: 40046430 PMCID: PMC11881597 DOI: 10.3389/fneur.2024.1465787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Accepted: 11/18/2024] [Indexed: 03/09/2025] Open
Abstract
One lingering effect of the COVID-19 pandemic created by SARS-CoV-2 is the emergence of Long COVID (LC), characterized by enduring neurological sequelae affecting a significant portion of survivors. This review provides a thorough analysis of these neurological disruptions with respect to cognitive dysfunction, which broadly manifest as chronic insomnia, fatigue, mood dysregulation, and cognitive impairments with respect to cognitive dysfunction. Furthermore, we characterize how diagnostic tools such as PET, MRI, EEG, and ultrasonography provide critical insight into subtle neurological anomalies that may mechanistically explain the Long COVID disease phenotype. In this review, we explore the mechanistic hypotheses of these neurological changes, which describe CNS invasion, neuroinflammation, blood-brain barrier disruption, and gut-brain axis dysregulation, along with the novel vascular disruption hypothesis that highlights endothelial dysfunction and hypoperfusion as a core underlying mechanism. We lastly evaluate the clinical treatment landscape, scrutinizing the efficacy of various therapeutic strategies ranging from antivirals to anti-inflammatory agents in mitigating the multifaceted symptoms of LC.
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Affiliation(s)
- Grant McGee Talkington
- Department of Neurosurgery, Clinical Neuroscience Research Center, Tulane University School of Medicine, New Orleans, LA, United States
- Tulane Brain Institute, Tulane University, New Orleans, LA, United States
| | - Paresh Kolluru
- Tulane Brain Institute, Tulane University, New Orleans, LA, United States
| | - Timothy E. Gressett
- Department of Neurosurgery, Clinical Neuroscience Research Center, Tulane University School of Medicine, New Orleans, LA, United States
- Tulane Brain Institute, Tulane University, New Orleans, LA, United States
| | - Saifudeen Ismael
- Department of Neurosurgery, Clinical Neuroscience Research Center, Tulane University School of Medicine, New Orleans, LA, United States
| | - Umar Meenakshi
- Department of Neurosurgery, Clinical Neuroscience Research Center, Tulane University School of Medicine, New Orleans, LA, United States
| | - Mariana Acquarone
- Department of Neurology, Tulane University School of Medicine, New Orleans, LA, United States
| | | | - Amanda White
- Department of Neurosurgery, Clinical Neuroscience Research Center, Tulane University School of Medicine, New Orleans, LA, United States
| | - Blake Ouvrier
- Department of Neurosurgery, Clinical Neuroscience Research Center, Tulane University School of Medicine, New Orleans, LA, United States
- Tulane Brain Institute, Tulane University, New Orleans, LA, United States
| | - Kristina Paré
- Department of Neurosurgery, Clinical Neuroscience Research Center, Tulane University School of Medicine, New Orleans, LA, United States
| | - Nicholas Parker
- Tulane Brain Institute, Tulane University, New Orleans, LA, United States
| | - Amanda Watters
- Tulane Brain Institute, Tulane University, New Orleans, LA, United States
| | - Nabeela Siddeeque
- Tulane Brain Institute, Tulane University, New Orleans, LA, United States
| | - Brooke Sullivan
- Tulane Brain Institute, Tulane University, New Orleans, LA, United States
| | - Nilesh Ganguli
- Tulane Brain Institute, Tulane University, New Orleans, LA, United States
| | | | - Gregory Hall
- Department of Neurosurgery, Clinical Neuroscience Research Center, Tulane University School of Medicine, New Orleans, LA, United States
| | - Michele Longo
- Department of Neurology, Tulane University School of Medicine, New Orleans, LA, United States
| | - Gregory J. Bix
- Department of Neurosurgery, Clinical Neuroscience Research Center, Tulane University School of Medicine, New Orleans, LA, United States
- Tulane Brain Institute, Tulane University, New Orleans, LA, United States
- Department of Neurology, Tulane University School of Medicine, New Orleans, LA, United States
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA, United States
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5
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Mózner O, Szabó E, Kulin A, Várady G, Moldvay J, Vass V, Szentesi A, Jánosi Á, Hegyi P, Sarkadi B. Potential associations of selected polymorphic genetic variants with COVID-19 disease susceptibility and severity. PLoS One 2025; 20:e0316396. [PMID: 39752416 PMCID: PMC11698323 DOI: 10.1371/journal.pone.0316396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2024] [Accepted: 12/10/2024] [Indexed: 01/06/2025] Open
Abstract
In this study, we analyzed the potential associations of selected laboratory and anamnestic parameters, as well as 12 genetic polymorphisms (SNPs), with clinical COVID-19 occurrence and severity in 869 hospitalized patients. The SNPs analyzed by qPCR were selected based on population-wide genetic (GWAS) data previously indicating association with the severity of COVID-19, and additional SNPs that have been shown to be important in cellular processes were also examined. We confirmed the associations of COVID-19 with pre-existing diabetes and found an unexpected association between less severe disease and the loss of smell and taste. Regarding the genetic polymorphisms, a higher allele frequency of the LZTFL1 and IFNAR2 minor variants significantly correlated with greater COVID-19 disease susceptibility (hospitalization) and severity, and a similar tendency was observed for the RAVER1 and the MUC5B variants. Interestingly, the ATP2B4 minor haplotype, protecting against malaria, correlated with an increased disease susceptibility, while in diabetic patients disease susceptibility was lower in the presence of a reduced-function ABCG2 transporter variant. Our current results, which should be reinforced by larger studies, indicate that together with laboratory and anamnestic parameters, genetic polymorphisms may have predictive value for the clinical occurrence and severity of COVID-19.
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Affiliation(s)
- Orsolya Mózner
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
- Doctoral School, Semmelweis University, Budapest, Hungary
| | - Edit Szabó
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - Anna Kulin
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
- Doctoral School, Semmelweis University, Budapest, Hungary
| | - György Várady
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - Judit Moldvay
- 1 Department of Pulmonology, National Korányi Institute of Pulmonology
- Department of Pulmonology, University of Szeged Albert Szent-Györgyi Medical School
| | - Vivien Vass
- Institute for Translational Medicine, University of Pécs, Medical School, Pécs, Hungary
- Institute of Pancreatic Diseases and Centre for Translational Medicine, Semmelweis University, Budapest, Hungary
| | - Andrea Szentesi
- Institute for Translational Medicine, University of Pécs, Medical School, Pécs, Hungary
| | - Ágoston Jánosi
- Institute for Translational Medicine, University of Pécs, Medical School, Pécs, Hungary
- Heim Pál National Pediatric Institute, Budapest, Hungary
| | - Péter Hegyi
- Institute for Translational Medicine, University of Pécs, Medical School, Pécs, Hungary
- Institute of Pancreatic Diseases and Centre for Translational Medicine, Semmelweis University, Budapest, Hungary
| | - Balázs Sarkadi
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
- Doctoral School, Semmelweis University, Budapest, Hungary
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6
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Alcalde-Herraiz M, Català M, Prats-Uribe A, Paredes R, Xie J, Prieto-Alhambra D. Genome-wide association studies of COVID-19 vaccine seroconversion and breakthrough outcomes in UK Biobank. Nat Commun 2024; 15:8739. [PMID: 39384777 PMCID: PMC11464770 DOI: 10.1038/s41467-024-52890-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 09/23/2024] [Indexed: 10/11/2024] Open
Abstract
Understanding the genetic basis of COVID-19 vaccine seroconversion is crucial to study the role of genetics on vaccine effectiveness. In our study, we used UK Biobank data to find the genetic determinants of COVID-19 vaccine-induced seropositivity and breakthrough infections. We conducted four genome-wide association studies among vaccinated participants for COVID-19 vaccine seroconversion and breakthrough susceptibility and severity. Our findings confirmed a link between the HLA region and seroconversion after the first and second doses. Additionally, we identified 10 genomic regions associated with breakthrough infection (SLC6A20, ST6GAL1, MUC16, FUT6, MXI1, MUC4, HMGN2P18-KRTCAP2, NFKBIZ and APOC1), and one with breakthrough severity (APOE). No significant evidence of genetic colocalisation was found between those traits. Our study highlights the roles of individual genetic make-up in the varied antibody responses to COVID-19 vaccines and provides insights into the potential mechanisms behind breakthrough infections occurred even after the vaccination.
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Affiliation(s)
- Marta Alcalde-Herraiz
- Centre for Statistics in Medicine and NIHR Biomedical Research Centre Oxford, NDORMS, University of Oxford, Oxford, UK
| | - Martí Català
- Centre for Statistics in Medicine and NIHR Biomedical Research Centre Oxford, NDORMS, University of Oxford, Oxford, UK
| | - Albert Prats-Uribe
- Centre for Statistics in Medicine and NIHR Biomedical Research Centre Oxford, NDORMS, University of Oxford, Oxford, UK
| | - Roger Paredes
- Department of Infectious Diseases and Institut de Recerca de la Sida IrsiCaixa, Hospital Universitari Germans Trias i Pujol, Badalona, Catalonia, Spain
- Centre for Global Health and Diseases, Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - JunQing Xie
- Centre for Statistics in Medicine and NIHR Biomedical Research Centre Oxford, NDORMS, University of Oxford, Oxford, UK
| | - Daniel Prieto-Alhambra
- Centre for Statistics in Medicine and NIHR Biomedical Research Centre Oxford, NDORMS, University of Oxford, Oxford, UK.
- Department of Medical Informatics, Erasmus University Medical Centre, Rotterdam, The Netherlands.
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7
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Calcagnile M, Damiano F, Lobreglio G, Siculella L, Bozzetti MP, Forgez P, Malgoyre A, Libert N, Bucci C, Alifano M, Alifano P. In silico evidence that substitution of glycine for valine (p.G8V) in a common variant of TMPRSS2 isoform 1 increases accessibility to an endocytic signal: Implication for SARS-cov-2 entry into host cells and susceptibility to COVID-19. Biochimie 2024; 225:89-98. [PMID: 38754620 DOI: 10.1016/j.biochi.2024.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 05/01/2024] [Accepted: 05/03/2024] [Indexed: 05/18/2024]
Abstract
The TMPRSS2 protease plays a key role in the entry of the SARS-CoV-2 into cells. The TMPRSS2 gene is highly polymorphic in humans, and some polymorphisms may affect the susceptibility to COVID-19 or disease severity. rs75603675 (c.23G > T) is a missense variant that causes the replacement of glycine with valine at position 8 (p.G8V) in the TMPRSS2 isoform 1. According to GnomAD v4.0.0 database, the allele frequency of the rs75603675 on a global scale is 38.10 %, and range from 0.92 % in East Asian to 40.77 % in non-Finnish European (NFE) population. We analyzed the occurrence of the rs75603675 in two cohorts of patients, the first with severe/critical COVID-19 enrolled in a French hospital (42 patients), and the second with predominantly asymptomatic/pauci-symptomatic/mild COVID-19 enrolled in an Italian hospital (69 patients). We found that the TMPRSS2-c.23T minor allele frequency was similar in the two cohorts, 46.43 % and 46.38 %, respectively, and higher than the frequency in the NFE population (40.77 %). Chi-square test provided significant results (p < 0.05) when the genotype data (TMPRSS2-c.23T/c.23T homozygotes + TMPRSS2-c.23G/c.23T heterozygotes vs. TMPRSS2-c.23G/c.23G homozygotes) of the two patient groups were pooled and compared to the expected data for the NFE population, suggesting a possible pathogenetic mechanism of the p.G8V substitution. We explored the possible effects of the p.G8V substitution and found that the N-terminal region of the TMPRSS2 isoform 1 contains a signal for clathrin/AP-2-dependent endocytosis. In silico analysis predicted that the p.G8V substitution may increase the accessibility to the endocytic signal, which could help SARS-CoV-2 enter cells.
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Affiliation(s)
- Matteo Calcagnile
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Fabrizio Damiano
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Giambattista Lobreglio
- Clinical Pathology and Microbiology Unit, Vito Fazzi General Hospital, 73100, Lecce, Italy
| | - Luisa Siculella
- Department of Experimental Medicine, University of Salento, Lecce, Italy
| | - Maria Pia Bozzetti
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Patricia Forgez
- INSERM UMR-S 1124 T3S, Eq 5 CELLULAR HOMEOSTASIS, CANCER and THERAPY, University of Paris, Campus Saint Germain, Paris, France
| | - Alexandra Malgoyre
- Institut de Recherche Biomedicale des Armées, French Armed Forces Health Services, Brétigny sur Orge, France; Ecole Du Val de Grâce, French Armed Forces Health Service, France; Laboratoire de Biologie de L'Exercice pour La Performance et La Santé, Université Evry-Paris-Saclay, Evry, France
| | - Nicolas Libert
- Ecole Du Val de Grâce, French Armed Forces Health Service, France; Hopital D'Instruction des Armées, French Armed Forces Health Services, Clamart, France
| | - Cecilia Bucci
- Department of Experimental Medicine, University of Salento, Lecce, Italy
| | - Marco Alifano
- Thoracic Surgery Department, Cochin Hospital, APHP Centre, University of Paris, France; INSERM U1138 Team «Cancer, Immune Control, and Escape», Cordeliers Research Center, University of Paris, France.
| | - Pietro Alifano
- Department of Experimental Medicine, University of Salento, Lecce, Italy.
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8
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Razavi A, Raei M, Shirato K. Association of IFNAR2 and TYK2 with COVID-19 pathology: current and future. Front Immunol 2024; 15:1462628. [PMID: 39351231 PMCID: PMC11439707 DOI: 10.3389/fimmu.2024.1462628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2024] [Accepted: 09/02/2024] [Indexed: 10/04/2024] Open
Affiliation(s)
- Alireza Razavi
- Student Research Committee, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
- Research Center for Clinical Virology, Tehran University of Medical Science, Tehran, Iran
| | - Maedeh Raei
- Gastrointestinal Cancer Research Center, Non-Communicable Diseases Institute, Mazandaran University of Medical Sciences, Sari, Iran
| | - Ken Shirato
- Department of Molecular Predictive Medicine and Sport Science, Kyorin University Faculty of Medicine, Mitaka, Japan
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9
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da Costa ACA, Albarello Gellen LP, Fernandes MR, Coelho RDCC, Monte N, de Moraes FCA, Calderaro MCL, de Freitas LM, Matos JA, Fernandes TFDS, Aguiar KEC, Vinagre LWMS, dos Santos SEB, dos Santos NPC. Correlation between Genomic Variants and Worldwide COVID-19 Epidemiology. J Pers Med 2024; 14:579. [PMID: 38929800 PMCID: PMC11204818 DOI: 10.3390/jpm14060579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 05/16/2024] [Accepted: 05/21/2024] [Indexed: 06/28/2024] Open
Abstract
COVID-19 is a systemic disease caused by the etiologic agent SARS-CoV-2, first reported in Hubei Province in Wuhan, China, in late 2019. The SARS-CoV-2 virus has evolved over time with distinct transmissibility subvariants from ancestral lineages. The clinical manifestations of the disease vary according to their severity and can range from asymptomatic to severe. Due to the rapid evolution to a pandemic, epidemiological studies have become essential to understand and effectively combat COVID-19, as the incidence and mortality of this disease vary between territories and populations. This study correlated epidemiological data on the incidence and mortality of COVID-19 with frequencies of important SNPs in GWAS studies associated with the susceptibility and mortality of this disease in different populations. Our results indicated significant correlations for 11 genetic variants (rs117169628, rs2547438, rs2271616, rs12610495, rs12046291, rs35705950, rs2176724, rs10774671, rs1073165, rs4804803 and rs7528026). Of these 11 variants, 7 (rs12046291, rs117169628, rs1073165, rs2547438, rs2271616, rs12610495 and rs35705950) were positively correlated with the incidence rate, these variants were more frequent in EUR populations, suggesting that this population is more susceptible to COVID-19. The rs2176724 variant was inversely related to incidence rates; therefore, the higher the frequency of the allele is, the lower the incidence rate. This variant was more frequent in the AFR population, which suggests a protective factor against SARS-CoV-2 infection in this population. The variants rs10774671, rs4804803, and rs7528026 showed a significant relationship with mortality rates. SNPs rs10774671 and rs4804803 were inversely related to mortality rates and are more frequently present in the AFR population. The rs7528026 variant, which is more frequent in the AMR population, was positively related to mortality rates. The study has the potential to identify and correlate the genetic profile with epidemiological data, identify populations that are more susceptible to severe forms of COVID-19, and relate them to incidence and mortality.
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Affiliation(s)
- Ana Caroline Alves da Costa
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (A.C.A.d.C.); (L.P.A.G.); (M.R.F.); (R.d.C.C.C.); (N.M.); (F.C.A.d.M.); (M.C.L.C.); (L.M.d.F.); (J.A.M.); (K.E.C.A.); (S.E.B.d.S.)
| | - Laura Patrícia Albarello Gellen
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (A.C.A.d.C.); (L.P.A.G.); (M.R.F.); (R.d.C.C.C.); (N.M.); (F.C.A.d.M.); (M.C.L.C.); (L.M.d.F.); (J.A.M.); (K.E.C.A.); (S.E.B.d.S.)
| | - Marianne Rodrigues Fernandes
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (A.C.A.d.C.); (L.P.A.G.); (M.R.F.); (R.d.C.C.C.); (N.M.); (F.C.A.d.M.); (M.C.L.C.); (L.M.d.F.); (J.A.M.); (K.E.C.A.); (S.E.B.d.S.)
- Ophir Loyola Hospital, Pará State Departament of Health, Belém 66063-240, PA, Brazil
| | - Rita de Cássia Calderaro Coelho
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (A.C.A.d.C.); (L.P.A.G.); (M.R.F.); (R.d.C.C.C.); (N.M.); (F.C.A.d.M.); (M.C.L.C.); (L.M.d.F.); (J.A.M.); (K.E.C.A.); (S.E.B.d.S.)
| | - Natasha Monte
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (A.C.A.d.C.); (L.P.A.G.); (M.R.F.); (R.d.C.C.C.); (N.M.); (F.C.A.d.M.); (M.C.L.C.); (L.M.d.F.); (J.A.M.); (K.E.C.A.); (S.E.B.d.S.)
| | - Francisco Cezar Aquino de Moraes
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (A.C.A.d.C.); (L.P.A.G.); (M.R.F.); (R.d.C.C.C.); (N.M.); (F.C.A.d.M.); (M.C.L.C.); (L.M.d.F.); (J.A.M.); (K.E.C.A.); (S.E.B.d.S.)
| | - Maria Clara Leite Calderaro
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (A.C.A.d.C.); (L.P.A.G.); (M.R.F.); (R.d.C.C.C.); (N.M.); (F.C.A.d.M.); (M.C.L.C.); (L.M.d.F.); (J.A.M.); (K.E.C.A.); (S.E.B.d.S.)
| | - Lilian Marques de Freitas
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (A.C.A.d.C.); (L.P.A.G.); (M.R.F.); (R.d.C.C.C.); (N.M.); (F.C.A.d.M.); (M.C.L.C.); (L.M.d.F.); (J.A.M.); (K.E.C.A.); (S.E.B.d.S.)
| | - Juliana Aires Matos
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (A.C.A.d.C.); (L.P.A.G.); (M.R.F.); (R.d.C.C.C.); (N.M.); (F.C.A.d.M.); (M.C.L.C.); (L.M.d.F.); (J.A.M.); (K.E.C.A.); (S.E.B.d.S.)
| | - Thamara Fernanda da Silva Fernandes
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (A.C.A.d.C.); (L.P.A.G.); (M.R.F.); (R.d.C.C.C.); (N.M.); (F.C.A.d.M.); (M.C.L.C.); (L.M.d.F.); (J.A.M.); (K.E.C.A.); (S.E.B.d.S.)
| | - Kaio Evandro Cardoso Aguiar
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (A.C.A.d.C.); (L.P.A.G.); (M.R.F.); (R.d.C.C.C.); (N.M.); (F.C.A.d.M.); (M.C.L.C.); (L.M.d.F.); (J.A.M.); (K.E.C.A.); (S.E.B.d.S.)
| | - Lui Wallacy Morikawa Souza Vinagre
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (A.C.A.d.C.); (L.P.A.G.); (M.R.F.); (R.d.C.C.C.); (N.M.); (F.C.A.d.M.); (M.C.L.C.); (L.M.d.F.); (J.A.M.); (K.E.C.A.); (S.E.B.d.S.)
- Ophir Loyola Hospital, Pará State Departament of Health, Belém 66063-240, PA, Brazil
| | - Sidney Emanuel Batista dos Santos
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (A.C.A.d.C.); (L.P.A.G.); (M.R.F.); (R.d.C.C.C.); (N.M.); (F.C.A.d.M.); (M.C.L.C.); (L.M.d.F.); (J.A.M.); (K.E.C.A.); (S.E.B.d.S.)
- Laboratory of Human and Medical Genetics, Institute of Biological Science, Federal University of Pará, Belém 66077-830, PA, Brazil
| | - Ney Pereira Carneiro dos Santos
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (A.C.A.d.C.); (L.P.A.G.); (M.R.F.); (R.d.C.C.C.); (N.M.); (F.C.A.d.M.); (M.C.L.C.); (L.M.d.F.); (J.A.M.); (K.E.C.A.); (S.E.B.d.S.)
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10
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López-Bielma MF, Falfán-Valencia R, Fierro-Piña A, Abarca-Rojano E, Córdoba-Lanus E, Fricke-Galindo I, Romero-Villaseñor P, Buendía-Roldán I, Chávez-Galán L, Jaime-Capetillo ME, Pérez-Rubio G. Genetic variants in ATP2B2 as risk factors for mortality in patients unrelated but not associated with families with severe COVID-19. Heliyon 2024; 10:e29493. [PMID: 38628728 PMCID: PMC11019202 DOI: 10.1016/j.heliyon.2024.e29493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 04/19/2024] Open
Abstract
Introduction The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of Coronavirus Disease 2019 (COVID-19). The disease has a wide range of clinical manifestations, from asymptomatic to severe. Ancestral contribution, sex, immune response, and genetic factors influence the presentation of the disease. The objective of the present study was to validate these genetic variants in patients with severe COVID-19 who died and in survivor patients. Methods: Single nucleotide variants (SNVs) in six genes: ATPase plasma membrane Ca2+ transporting 2 (ATP2B2), transmembrane serine protease 2 (TMPRSS2), dedicator of cytokinesis 2 (DOCK2), (interferon alpha and beta receptor subunit 2) IFNAR2, tumor necrosis factor receptor superfamily, member 1A (TNFRSF1A), and tumor necrosis factor receptor superfamily, member 1B (TNFRSF1B), were explored in two groups: the first consisted of severe COVID-19-related patients (familial cases from 58 families, n = 130), and the second group of unrelated severe COVID-19 patients (n = 1045). In each study group, death was evaluated as the outcome. Results In non-related patients with severe COVID-19, carriers of GG genotype (rs2289274) in the ATP2B2 gene showed a high-risk probability of non-surviving (OR = 1.43). Survival analysis to 75 days indicates that carriers of GG have a higher risk than GA or AA genotypes (p = 0.0059). The haplotype GG (rs2289273-rs2289274) in ATP2B2 was found to be associated with a high risk of death in severe non-related COVID-19 patients. No significant associations were found between severe COVID-19-related patients and SNVs in ATP2B2, TMPRSS2, DOCK2, IFNAR2, TNFRSF1A, or TNFRSF1B. Conclusions Unrelated patients with severe COVID-19 that carry the GG genotype (rs2289274) in ATP2B2 showed a high death risk. Survival analysis to 75 days indicates that carriers of GG have a higher risk of non-survival compared to GA or AA genotypes.
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Affiliation(s)
- María Fernanda López-Bielma
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, 14080, Mexico
- Sección de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico
| | - Ramcés Falfán-Valencia
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, 14080, Mexico
| | - Aurelio Fierro-Piña
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, 14080, Mexico
| | - Edgar Abarca-Rojano
- Sección de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico
| | - Elizabeth Córdoba-Lanus
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, Universidad de La Laguna, 38296, San Cristóbal de La Laguna, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Ingrid Fricke-Galindo
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, 14080, Mexico
| | - Priscila Romero-Villaseñor
- Translational Research Laboratory on Aging and Pulmonary Fibrosis, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, 14080, Mexico
| | - Ivette Buendía-Roldán
- Translational Research Laboratory on Aging and Pulmonary Fibrosis, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, 14080, Mexico
| | - Leslie Chávez-Galán
- Laboratory of Integrative Immunology, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, 14080, Mexico
| | - María Esther Jaime-Capetillo
- Clinical Laboratory Service, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas, Mexico City, 14080, Mexico
| | - Gloria Pérez-Rubio
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, 14080, Mexico
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11
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Skerenova M, Cibulka M, Dankova Z, Holubekova V, Kolkova Z, Lucansky V, Dvorska D, Kapinova A, Krivosova M, Petras M, Baranovicova E, Baranova I, Novakova E, Liptak P, Banovcin P, Bobcakova A, Rosolanka R, Janickova M, Stanclova A, Gaspar L, Caprnda M, Prosecky R, Labudova M, Gabbasov Z, Rodrigo L, Kruzliak P, Lasabova Z, Matakova T, Halasova E. Host genetic variants associated with COVID-19 reconsidered in a Slovak cohort. Adv Med Sci 2024; 69:198-207. [PMID: 38555007 DOI: 10.1016/j.advms.2024.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 11/15/2023] [Accepted: 03/25/2024] [Indexed: 04/02/2024]
Abstract
We present the results of an association study involving hospitalized coronavirus disease 2019 (COVID-19) patients with a clinical background during the 3rd pandemic wave of COVID-19 in Slovakia. Seventeen single nucleotide variants (SNVs) in the eleven most relevant genes, according to the COVID-19 Host Genetics Initiative, were investigated. Our study confirms the validity of the influence of LZTFL1 and 2'-5'-oligoadenylate synthetase (OAS)1/OAS3 genetic variants on the severity of COVID-19. For two LZTFL1 SNVs in complete linkage disequilibrium, rs17713054 and rs73064425, the odds ratios of baseline allelic associations and logistic regressions (LR) adjusted for age and sex ranged in the four tested designs from 2.04 to 2.41 and from 2.05 to 3.98, respectively. The OAS1/OAS3 haplotype 'gttg' carrying a functional allele G of splice-acceptor variant rs10774671 manifested its protective function in the Delta pandemic wave. Significant baseline allelic associations of two DPP9 variants in all tested designs and two IFNAR2 variants in the Omicron pandemic wave were not confirmed by adjusted LR. Nevertheless, adjusted LR showed significant associations of NOTCH4 rs3131294 and TYK2 rs2304256 variants with severity of COVID-19. Hospitalized patients' reported comorbidities were not correlated with genetic variants, except for obesity, smoking (IFNAR2), and hypertension (NOTCH4). The results of our study suggest that host genetic variations have an impact on the severity and duration of acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Considering the differences in allelic associations between pandemic waves, they support the hypothesis that every new SARS-CoV-2 variant may modify the host immune response by reconfiguring involved pathways.
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Affiliation(s)
- Maria Skerenova
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Michal Cibulka
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Zuzana Dankova
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Veronika Holubekova
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Zuzana Kolkova
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Vincent Lucansky
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Dana Dvorska
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Andrea Kapinova
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Michaela Krivosova
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Martin Petras
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Eva Baranovicova
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Ivana Baranova
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Elena Novakova
- Department of Microbiology and Immunology, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Peter Liptak
- Clinic of Internal Medicine- Gastroenterology, University Hospital in Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Peter Banovcin
- Clinic of Internal Medicine- Gastroenterology, University Hospital in Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Anna Bobcakova
- Clinic of Pneumology and Phthisiology, University Hospital in Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Robert Rosolanka
- Clinic of Infectology and Travel Medicine, University Hospital in Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Maria Janickova
- Clinic of Stomatology and Maxillofacial Surgery, University Hospital in Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Andrea Stanclova
- Department of Pathological Anatomy, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Ludovit Gaspar
- Faculty of Health Sciences, University of Ss. Cyril and Methodius in Trnava, Trnava, Slovakia
| | - Martin Caprnda
- 1st Department of Internal Medicine, Faculty of Medicine, Comenius University and University Hospital, Bratislava, Slovakia
| | - Robert Prosecky
- 2nd Department of Internal Medicine, Faculty of Medicine, Masaryk University and St. Anne'S University Hospital, Brno, Czech Republic; International Clinical Research Centre, St. Anne's University Hospital and Masaryk University, Brno, Czech Republic
| | - Monika Labudova
- Faculty of Health Care and Social Work, University of Trnava in Trnava, Slovakia
| | - Zufar Gabbasov
- National Medical Research Centre for Cardiology, Moscow, Russia
| | - Luis Rodrigo
- Faculty of Medicine, University of Oviedo and Central University Hospital of Asturias (HUCA), Oviedo, Spain
| | - Peter Kruzliak
- Faculty of Medicine, University of Oviedo and Central University Hospital of Asturias (HUCA), Oviedo, Spain; Research and Development Services, Olomouc, Czech Republic.
| | - Zora Lasabova
- Department of Molecular Biology and Genomics, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Tatiana Matakova
- Department of Medical Biochemistry, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Erika Halasova
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia.
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12
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Meng T, Nielsen DE. TAS2R38 haplotypes, COVID-19 infection, and symptomatology: a cross-sectional analysis of data from the Canadian Longitudinal Study on Aging. Sci Rep 2024; 14:4673. [PMID: 38409357 PMCID: PMC10897136 DOI: 10.1038/s41598-024-55428-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 02/23/2024] [Indexed: 02/28/2024] Open
Abstract
The TAS2R38 gene is well known for its function in bitter taste sensitivity, but evidence also suggests a role in innate immunity. TAS2R38 may be relevant in coronavirus disease 2019 (COVID-19), but research findings are inconsistent. The objective of this study was to explore whether common TAS2R38 haplotypes are associated with COVID-19 infection and symptomatology in the Canadian Longitudinal Study on Aging (CLSA). Data from the CLSA COVID-19 Questionnaire and Seroprevalence sub-studies were utilized with CLSA genetic data for common TAS2R38 haplotypes related to bitter taste sensitivity. Haplotypes were categorized into three diplotype groups: [P]AV homozygotes, [P]AV/[A]VI heterozygotes, and [A]VI homozygotes. No significant differences were observed between diplotypes and COVID-19 infection frequency. Among self-reported COVID-19 cases (n = 76), and in uncorrected exploratory analyses, heterozygotes were less likely to report experiencing sinus pain compared to [P]AV homozygotes. Among seroprevalence-confirmed cases (n = 177), [A]VI homozygotes were less likely to report experiencing a sore/scratchy throat compared to [P]AV homozygotes. However, both observations were non-significant upon correction for multiple testing. In this study, TAS2R38 haplotypes were not significantly associated with COVID-19 infection or symptomatology. Nevertheless, in light of some exploratory patterns and conflicting evidence, additional research is warranted to evaluate links between TAS2R38 and innate immunity.
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Affiliation(s)
- Tongzhu Meng
- School of Human Nutrition, McGill University, 21,111 Lakeshore Rd., Room MS2-035, Saint-Anne-de-Bellevue, QC, H9X 3V9, Canada
| | - Daiva E Nielsen
- School of Human Nutrition, McGill University, 21,111 Lakeshore Rd., Room MS2-035, Saint-Anne-de-Bellevue, QC, H9X 3V9, Canada.
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13
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Uslu K, Ozcelik F, Zararsiz G, Eldem V, Cephe A, Sahin IO, Yuksel RC, Sipahioglu H, Ozer Simsek Z, Baspinar O, Akalin H, Simsek Y, Gundogan K, Tutar N, Karayol Akin A, Ozkul Y, Yildiz O, Dundar M. Deciphering the host genetic factors conferring susceptibility to severe COVID-19 using exome sequencing. Genes Immun 2024; 25:14-42. [PMID: 38123822 DOI: 10.1038/s41435-023-00232-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 11/03/2023] [Accepted: 11/09/2023] [Indexed: 12/23/2023]
Abstract
The COVID-19 pandemic remains a significant public health concern despite the new vaccines and therapeutics. The clinical course of acute SARS-CoV-2 infection is highly variable and influenced by several factors related to the virus and the host. Numerous genetic studies, including candidate gene, exome, and genome sequencing studies, genome-wide association studies, and other omics efforts, have proposed various Mendelian and non-Mendelian associations with COVID-19 course. In this study, we conducted whole-exome sequencing on 90 unvaccinated patients from Turkey with no known comorbidities associated with severe COVID-19. Of these patients, 30 had severe, 30 had moderate, and 30 had mild/asymptomatic disease. We identified rare variants in genes associated with SARS-CoV-2 susceptibility and pathogenesis, with an emphasis on genes related to the regulation of inflammation, and discussed these in the context of the clinical course of the patients. In addition, we compared the frequencies of common variants between each group. Even though no variant remained statistically significant after correction for multiple testing, we observed that certain previously associated genes and variants showed significant associations before correction. Our study contributes to the existing literature regarding the genetic susceptibility to SARS-CoV-2. Future studies would be beneficial characterizing the host genetic properties in different populations.
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Affiliation(s)
- Kubra Uslu
- Department of Medical Genetics, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Firat Ozcelik
- Department of Medical Genetics, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Gokmen Zararsiz
- Department of Biostatistics, Faculty of Medicine, Erciyes University, Kayseri, Turkey
- Drug Application and Research Center (ERFARMA), Erciyes University, Kayseri, Turkey
| | - Vahap Eldem
- Department of Biology, Faculty of Science, Istanbul University, Istanbul, Turkey
| | - Ahu Cephe
- Institutional Data Management and Analytics Units, Erciyes University Rectorate, Kayseri, Turkey
| | - Izem Olcay Sahin
- Department of Medical Genetics, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Recep Civan Yuksel
- Division of Intensive Care Medicine, Department of Internal Medicine, Kayseri City Education and Research Hospital, Kayseri, Turkey
| | - Hilal Sipahioglu
- Division of Intensive Care Medicine, Department of Internal Medicine, Kayseri City Education and Research Hospital, Kayseri, Turkey
| | - Zuhal Ozer Simsek
- Division of Intensive Care Medicine, Department of Internal Medicine, Kayseri City Education and Research Hospital, Kayseri, Turkey
| | - Osman Baspinar
- Department of Internal Medicine, Kayseri City Education and Research Hospital, Kayseri, Turkey
| | - Hilal Akalin
- Department of Medical Genetics, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Yasin Simsek
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Kayseri City Education and Research Hospital, Kayseri, Turkey
| | - Kursat Gundogan
- Division of Intensive Care Medicine, Department of Internal Medicine, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Nuri Tutar
- Department of Chest Diseases, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Aynur Karayol Akin
- Department of Anesthesiology and Reanimation, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Yusuf Ozkul
- Department of Medical Genetics, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Orhan Yildiz
- Department of Infectious Diseases, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Munis Dundar
- Department of Medical Genetics, Faculty of Medicine, Erciyes University, Kayseri, Turkey.
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14
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Esteban ME, Pino D, Romero-Lorca A, Novillo A, Gaibar M, Riancho JA, Rojas-Martínez A, Flores C, Lapunzina P, Carracedo Á, Athanasiadis G, Fernández-Santander A. Worldwide distribution of genetic factors related to severity of COVID-19 infection. Ann Hum Biol 2024; 51:2366248. [PMID: 39012049 DOI: 10.1080/03014460.2024.2366248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 05/28/2024] [Indexed: 07/17/2024]
Abstract
BACKGROUND Genome-wide association studies of COVID-19 severity have been carried out mostly on European or East Asian populations with small representation of other world regions. Here we explore the worldwide distribution and linkage disequilibrium (LD) patterns of genetic variants previously associated with COVID-19 severity. METHODS We followed up the results of a large Spanish genome-wide meta-analysis on 26 populations from the 1000 Genomes Project by calculating allele frequencies and LD scores of the nine most significant SNPs. We also used the entire set of summary statistics to compute polygenic risk scores (PRSs) and carried out comparisons at the population and continental level. RESULTS We observed the strongest differences among continental regions for the five top SNPs in chromosome 3. European, American, and South Asian populations showed similar LD patterns. Average PRSs in South Asian and American populations were consistently higher than those observed in Europeans. While PRS distributions were similar among South Asians, the American populations showed striking differences among them. CONCLUSIONS Considering the caveats of PRS transferability across ethnicities, our analysis showed that American populations present the highest genetic risk score, hence potentially higher propensity, for COVID-19 severity. Independent validation is warranted with additional summary statistics and phenotype data.
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Affiliation(s)
- María Esther Esteban
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, España
| | - Débora Pino
- Helmholtz Pioneer Campus, Helmholtz Munich, Munich, Germany
| | - Alicia Romero-Lorca
- Department of Medicine, Health and Biomedical Science School, Universidad Europea de Madrid, Madrid, Spain
- Human Genetic Variability Group, Hospital La Paz Institute for Health Research-IdiPAZ (La Paz University Hospital-Universidad Autónoma de Madrid-Getafe University Hospital-Universidad Europea de Madrid), Madrid, Spain
| | - Apolonia Novillo
- Human Genetic Variability Group, Hospital La Paz Institute for Health Research-IdiPAZ (La Paz University Hospital-Universidad Autónoma de Madrid-Getafe University Hospital-Universidad Europea de Madrid), Madrid, Spain
- Department of Cell Biology, Faculty of Medicine, Complutense University, Madrid, Spain
| | - María Gaibar
- Human Genetic Variability Group, Hospital La Paz Institute for Health Research-IdiPAZ (La Paz University Hospital-Universidad Autónoma de Madrid-Getafe University Hospital-Universidad Europea de Madrid), Madrid, Spain
- Facultad HM de Ciencias de la Salud, Universidad Camilo José Cela, Instituto de Investigación Sanitaria HM Hospitales, Madrid, España
| | - José A Riancho
- IDIVAL, Santander, Spain
- Universidad de Cantabria, Santander, Spain
- Hospital U M Valdecilla, Santander, Spain
| | - Augusto Rojas-Martínez
- Tecnologico de Monterrey, The Institute for Obesity Research and Escuela de Medicina y Ciencias de la Salud and Hospital San Jose TecSalud, Monterrey, Mexico
| | - Carlos Flores
- Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
- Department of Clinical Sciences, University Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | - Pablo Lapunzina
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz-IDIPAZ, Madrid, Spain
- ERN-ITHACA-European Reference Network, Paris, France
| | - Ángel Carracedo
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Centro Nacional de Genotipado (CEGEN), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain
- Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Fundación Pública Galega de Medicina Xenómica, Sistema Galego de Saúde (SERGAS), Santiago de Compostela, Spain
| | - Georgios Athanasiadis
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona, Spain
| | - Ana Fernández-Santander
- Department of Medicine, Health and Biomedical Science School, Universidad Europea de Madrid, Madrid, Spain
- Human Genetic Variability Group, Hospital La Paz Institute for Health Research-IdiPAZ (La Paz University Hospital-Universidad Autónoma de Madrid-Getafe University Hospital-Universidad Europea de Madrid), Madrid, Spain
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15
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Benmansour R, Tagajdid MR, Lahlou IA, Oumzil H, El Hamzaoui H, Fjouji S, Doghmi N, Houba A, Elkochri S, Aabi R, Elannaz H, Laraqui A, El Mchichi B, Touil N, Ennibi K, Bouhouche A. Implication of IL-12A, IL-12B, IL-6, and TNF single-nucleotide polymorphisms in severity and susceptibility to COVID-19. Int J Immunopathol Pharmacol 2024; 38:3946320241279893. [PMID: 39239824 PMCID: PMC11380133 DOI: 10.1177/03946320241279893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 07/28/2024] [Accepted: 08/12/2024] [Indexed: 09/07/2024] Open
Abstract
BACKGROUND The Coronavirus Disease 2019 (COVID-19) pandemic has led to significant global morbidity and mortality. Understanding the genetic factors that influence disease outcomes can provide critical insights into pathogenesis and potential therapeutic targets. OBJECTIVE This study aimed to investigate the potential correlation between single nucleotide polymorphisms (SNPs) in Interleukin 12 Subunit Alpha (IL-12A), Interleukin 12 Subunit Beta (IL-12B), Interleukin 6 (IL-6), and Tumor Necrosis Factor (TNF) genes and the severity as well as susceptibility to COVID-19 among Moroccan patients. PATIENTS AND METHODS Next-Generation sequencing (NGS) was conducted on 325 Moroccan participants, 207 patients with PCR-confirmed Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection and 118 controls. Among these patients, 51% presented moderate to severe symptoms requiring hospitalization, while 49% were asymptomatic or experienced mild symptoms and did not require hospitalization. Statistical analysis was performed using codominant, dominant, and recessive logistic regression models to assess correlations with the severity and susceptibility to COVID-19 infection. RESULTS No association was found between SNPs of IL-12A, IL-12B, IL-6 or TNF and COVID-19 severity and susceptibility. However, our results unveiled a noteworthy association with IL-6 rs2069840, which exhibited a negative correlation (OR = 0.21, 95% CI = 0.07-0.69, p = .006), suggesting a protective effect against SARS-CoV-2 infection. CONCLUSION Polymorphisms in IL-12A, IL-12B, IL-6, and TNF genes are not correlated to the severity and susceptibility of COVID-19.
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Affiliation(s)
- R. Benmansour
- Center of Virology, Infectious and Tropical Diseases, Mohamed V Military Teaching Hospital, University Mohammed V in Rabat, Rabat, Morocco
| | - M. R. Tagajdid
- Center of Virology, Infectious and Tropical Diseases, Mohamed V Military Teaching Hospital, University Mohammed V in Rabat, Rabat, Morocco
| | - I. A Lahlou
- Center of Virology, Infectious and Tropical Diseases, Mohamed V Military Teaching Hospital, University Mohammed V in Rabat, Rabat, Morocco
| | - H. Oumzil
- Medical Biotechnology Laboratory, School of Medicine and Pharmacy, University Mohammed V in Rabat, Rabat, Morocco
| | - H. El Hamzaoui
- Emergency Department, University Hospital Ibn Sina, School of Medicine and Pharmacy, University Mohammed V in Rabat, Rabat, Morocco
| | - S. Fjouji
- Department of anesthesiology, Mohamed V Military Teaching Hospital, University Mohammed V in Rabat, Rabat, Morocco
| | - N. Doghmi
- Department of anesthesiology, Mohamed V Military Teaching Hospital, University Mohammed V in Rabat, Rabat, Morocco
| | - A. Houba
- Department of anesthesiology, Mohamed V Military Teaching Hospital, University Mohammed V in Rabat, Rabat, Morocco
| | - S. Elkochri
- Center of Virology, Infectious and Tropical Diseases, Mohamed V Military Teaching Hospital, University Mohammed V in Rabat, Rabat, Morocco
| | - R. Aabi
- Center of Virology, Infectious and Tropical Diseases, Mohamed V Military Teaching Hospital, University Mohammed V in Rabat, Rabat, Morocco
| | - H. Elannaz
- Center of Virology, Infectious and Tropical Diseases, Mohamed V Military Teaching Hospital, University Mohammed V in Rabat, Rabat, Morocco
| | - A. Laraqui
- Center of Virology, Infectious and Tropical Diseases, Mohamed V Military Teaching Hospital, University Mohammed V in Rabat, Rabat, Morocco
| | - B. El Mchichi
- Center of Virology, Infectious and Tropical Diseases, Mohamed V Military Teaching Hospital, University Mohammed V in Rabat, Rabat, Morocco
| | - N. Touil
- Center of Virology, Infectious and Tropical Diseases, Mohamed V Military Teaching Hospital, University Mohammed V in Rabat, Rabat, Morocco
| | - K. Ennibi
- Center of Virology, Infectious and Tropical Diseases, Mohamed V Military Teaching Hospital, University Mohammed V in Rabat, Rabat, Morocco
| | - A. Bouhouche
- Human Genetics Laboratory, School of Medicine and Pharmacy, University Mohammed V in Rabat, Rabat, Morocco
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16
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Constantinescu-Bercu A, Lobiuc A, Căliman-Sturdza OA, Oiţă RC, Iavorschi M, Pavăl NE, Șoldănescu I, Dimian M, Covasa M. Long COVID: Molecular Mechanisms and Detection Techniques. Int J Mol Sci 2023; 25:408. [PMID: 38203577 PMCID: PMC10778767 DOI: 10.3390/ijms25010408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/25/2023] [Accepted: 12/26/2023] [Indexed: 01/12/2024] Open
Abstract
Long COVID, also known as post-acute sequelae of SARS-CoV-2 infection (PASC), has emerged as a significant health concern following the COVID-19 pandemic. Molecular mechanisms underlying the occurrence and progression of long COVID include viral persistence, immune dysregulation, endothelial dysfunction, and neurological involvement, and highlight the need for further research to develop targeted therapies for this condition. While a clearer picture of the clinical symptomatology is shaping, many molecular mechanisms are yet to be unraveled, given their complexity and high level of interaction with other metabolic pathways. This review summarizes some of the most important symptoms and associated molecular mechanisms that occur in long COVID, as well as the most relevant molecular techniques that can be used in understanding the viral pathogen, its affinity towards the host, and the possible outcomes of host-pathogen interaction.
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Affiliation(s)
- Adela Constantinescu-Bercu
- Department of Biomedical Sciences, Faculty of Medicine and Biological Sciences, “Ştefan cel Mare” University of Suceava, 720229 Suceava, Romania; (A.C.-B.); (O.A.C.-S.); (M.I.); (N.-E.P.); (M.C.)
| | - Andrei Lobiuc
- Department of Biomedical Sciences, Faculty of Medicine and Biological Sciences, “Ştefan cel Mare” University of Suceava, 720229 Suceava, Romania; (A.C.-B.); (O.A.C.-S.); (M.I.); (N.-E.P.); (M.C.)
| | - Olga Adriana Căliman-Sturdza
- Department of Biomedical Sciences, Faculty of Medicine and Biological Sciences, “Ştefan cel Mare” University of Suceava, 720229 Suceava, Romania; (A.C.-B.); (O.A.C.-S.); (M.I.); (N.-E.P.); (M.C.)
- Suceava Emergency Clinical County Hospital, 720224 Suceava, Romania
| | - Radu Cristian Oiţă
- Integrated Center for Research, Development and Innovation for Advanced Materials, Nanotechnologies, Manufacturing and Control Distributed Systems (MANSiD), Ştefan cel Mare University of Suceava, 720229 Suceava, Romania; (R.C.O.); (I.Ș.); (M.D.)
| | - Monica Iavorschi
- Department of Biomedical Sciences, Faculty of Medicine and Biological Sciences, “Ştefan cel Mare” University of Suceava, 720229 Suceava, Romania; (A.C.-B.); (O.A.C.-S.); (M.I.); (N.-E.P.); (M.C.)
| | - Naomi-Eunicia Pavăl
- Department of Biomedical Sciences, Faculty of Medicine and Biological Sciences, “Ştefan cel Mare” University of Suceava, 720229 Suceava, Romania; (A.C.-B.); (O.A.C.-S.); (M.I.); (N.-E.P.); (M.C.)
| | - Iuliana Șoldănescu
- Integrated Center for Research, Development and Innovation for Advanced Materials, Nanotechnologies, Manufacturing and Control Distributed Systems (MANSiD), Ştefan cel Mare University of Suceava, 720229 Suceava, Romania; (R.C.O.); (I.Ș.); (M.D.)
| | - Mihai Dimian
- Integrated Center for Research, Development and Innovation for Advanced Materials, Nanotechnologies, Manufacturing and Control Distributed Systems (MANSiD), Ştefan cel Mare University of Suceava, 720229 Suceava, Romania; (R.C.O.); (I.Ș.); (M.D.)
- Department of Computers, Electronics and Automation, Ştefan cel Mare University of Suceava, 720229 Suceava, Romania
| | - Mihai Covasa
- Department of Biomedical Sciences, Faculty of Medicine and Biological Sciences, “Ştefan cel Mare” University of Suceava, 720229 Suceava, Romania; (A.C.-B.); (O.A.C.-S.); (M.I.); (N.-E.P.); (M.C.)
- Department of Basic Medical Sciences, College of Osteopathic Medicine, Western University of Health Sciences, Pomona, CA 91711, USA
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17
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Corpas M, de Mendoza C, Moreno-Torres V, Pintos I, Seoane P, Perkins JR, Ranea JA, Fatumo S, Korcsmaros T, Martín-Villa JM, Barreiro P, Corral O, Soriano V. Genetic signature detected in T cell receptors from patients with severe COVID-19. iScience 2023; 26:107735. [PMID: 37720084 PMCID: PMC10504482 DOI: 10.1016/j.isci.2023.107735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/21/2023] [Accepted: 08/23/2023] [Indexed: 09/19/2023] Open
Abstract
Characterization of host genetic factors contributing to COVID-19 severity promises advances on drug discovery to fight the disease. Most genetic analyses to date have identified genome-wide significant associations involving loss-of-function variants for immune response pathways. Despite accumulating evidence supporting a role for T cells in COVID-19 severity, no definitive genetic markers have been found to support an involvement of T cell responses. We analyzed 205 whole exomes from both a well-characterized cohort of hospitalized severe COVID-19 patients and controls. Significantly enriched high impact alleles were found for 25 variants within the T cell receptor beta (TRB) locus on chromosome 7. Although most of these alleles were found in heterozygosis, at least three or more in TRBV6-5, TRBV7-3, TRBV7-6, TRBV7-7, and TRBV10-1 suggested a possible TRB loss of function via compound heterozygosis. This loss-of-function in TRB genes supports suboptimal or dysfunctional T cell responses as a major contributor to severe COVID-19 pathogenesis.
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Affiliation(s)
- Manuel Corpas
- School of Life Sciences, University of Westminster, London, UK
- Cambridge Precision Medicine Limited, ideaSpace, University of Cambridge Biomedical Innovation Hub, Cambridge, UK
- UNIR Health Sciences School & Medical Center, Madrid, Spain
- Institute of Continuing Education, University of Cambridge, Cambridge, UK
| | - Carmen de Mendoza
- Puerta de Hierro University Hospital & Research Institute, Majadahonda, Spain
| | - Víctor Moreno-Torres
- UNIR Health Sciences School & Medical Center, Madrid, Spain
- Puerta de Hierro University Hospital & Research Institute, Majadahonda, Spain
| | - Ilduara Pintos
- Puerta de Hierro University Hospital & Research Institute, Majadahonda, Spain
| | - Pedro Seoane
- Department of Molecular Biology and Biochemistry, University of Málaga, Málaga, Spain
- CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - James R. Perkins
- Department of Molecular Biology and Biochemistry, University of Málaga, Málaga, Spain
- CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- The Biomedical Research Institute of Málaga (IBIMA), Málaga, Spain
| | - Juan A.G. Ranea
- Department of Molecular Biology and Biochemistry, University of Málaga, Málaga, Spain
- CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- The Biomedical Research Institute of Málaga (IBIMA), Málaga, Spain
- Spanish National Bioinformatics Institute (INB/ELIXIR-ES), Madrid, Spain
| | - Segun Fatumo
- The African Computational Genomics (TACG) Research Group, MRC/UVRI and LSHTM, Entebbe, Uganda
- London School of Hygiene and Tropical Medicine, London, UK
- H3Africa Bioinformatics Network (H3ABioNet) Node, Centre for Genomics Research and Innovation, NABDA/FMST, Abuja, Nigeria
| | - Tamas Korcsmaros
- Faculty of Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | | | - Pablo Barreiro
- UNIR Health Sciences School & Medical Center, Madrid, Spain
- Emergency Hospital Isabel Zendal, Madrid, Spain
| | - Octavio Corral
- UNIR Health Sciences School & Medical Center, Madrid, Spain
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18
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Breno M, Noris M, Rubis N, Parvanova AI, Martinetti D, Gamba S, Liguori L, Mele C, Piras R, Orisio S, Valoti E, Alberti M, Diadei O, Bresin E, Rigoldi M, Prandini S, Gamba T, Stucchi N, Carrara F, Daina E, Benigni A, Remuzzi G, on behalf of the ORIGIN study group. A GWAS in the pandemic epicenter highlights the severe COVID-19 risk locus introgressed by Neanderthals. iScience 2023; 26:107629. [PMID: 37731612 PMCID: PMC10507134 DOI: 10.1016/j.isci.2023.107629] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/29/2023] [Accepted: 08/11/2023] [Indexed: 09/22/2023] Open
Abstract
Large GWAS indicated that genetic factors influence the response to SARS-CoV-2. However, sex, age, concomitant diseases, differences in ancestry, and uneven exposure to the virus impacted the interpretation of data. We aimed to perform a GWAS of COVID-19 outcome in a homogeneous population who experienced a high exposure to the virus and with a known infection status. We recruited inhabitants of Bergamo province-that in spring 2020 was the epicenter of the SARS-Cov-2 pandemic in Europe-via an online questionnaire followed by personal interviews. Cases and controls were matched by age, sex and risk factors. We genotyped 1195 individuals and replicated the association at the 3p21.31 locus with severity, but with a stronger effect size that further increased in gravely ill patients. Transcriptome-wide association study highlighted eQTLs for LZTFL1 and CCR9. We also identified 17 loci not previously reported, suggestive for an association with either COVID-19 severity or susceptibility.
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Affiliation(s)
- Matteo Breno
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Marina Noris
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Nadia Rubis
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Aneliya Ilieva Parvanova
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Davide Martinetti
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Sara Gamba
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Lucia Liguori
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Caterina Mele
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Rossella Piras
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Silvia Orisio
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Elisabetta Valoti
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Marta Alberti
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Olimpia Diadei
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Elena Bresin
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Miriam Rigoldi
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Silvia Prandini
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Tiziano Gamba
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Nadia Stucchi
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Fabiola Carrara
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Erica Daina
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Ariela Benigni
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
| | - Giuseppe Remuzzi
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Clinical Research Center for Rare Diseases Aldo e Cele Daccò and Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso, Bergamo, Italy
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Tripathy AS, Wagh P, Vishwakarma S, Akolkar K, Tripathy S, Jali P, Kakrani AL, Barthwal M, Gurav Y, Kadgi N, Nakate L, Abraham P. Association of human leukocyte antigen class I and class II alleles and haplotypes in COVID-19 infection in a western Indian population. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 113:105468. [PMID: 37331496 PMCID: PMC10273771 DOI: 10.1016/j.meegid.2023.105468] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 05/22/2023] [Accepted: 06/15/2023] [Indexed: 06/20/2023]
Affiliation(s)
| | - Priyanka Wagh
- ICMR-National Institute of Virology, Pune, Maharashtra, India
| | | | | | - Srikanth Tripathy
- Dr. D. Y. Patil Medical College, Hospital & Research Centre, Pune, India
| | - Priyanka Jali
- Dr. D. Y. Patil Medical College, Hospital & Research Centre, Pune, India
| | - Arjun Lal Kakrani
- Dr. D. Y. Patil Medical College, Hospital & Research Centre, Pune, India
| | | | - Yogesh Gurav
- ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Nalini Kadgi
- BJMC and Sassoon General Hospital, Pune, Maharashtra, India
| | - Leena Nakate
- BJMC and Sassoon General Hospital, Pune, Maharashtra, India
| | - Priya Abraham
- ICMR-National Institute of Virology, Pune, Maharashtra, India
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20
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Eshetie S, Jullian P, Benyamin B, Lee SH. Host genetic determinants of COVID-19 susceptibility and severity: A systematic review and meta-analysis. Rev Med Virol 2023; 33:e2466. [PMID: 37303119 DOI: 10.1002/rmv.2466] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/29/2023] [Accepted: 06/01/2023] [Indexed: 06/13/2023]
Abstract
Genome-wide association studies (GWASs) have identified single nucleotide polymorphisms (SNPs) associated with susceptibility and severity of coronavirus disease 2019 (COVID-19). However, identified SNPs are inconsistent across studies, and there is no compelling consensus that COVID-19 status is determined by genetic factors. Here, we conducted a systematic review and meta-analysis to determine the effect of genetic factors on COVID-19. A random-effect meta-analysis was performed to estimate pooled odds ratios (ORs) of SNP effects, and SNP-based heritability (SNP-h2 ) of COVID-19. The analyses were performed using meta-R package, and Stata version 17. The meta-analysis included a total of 96,817 COVID-19 cases and 6,414,916 negative controls. The meta-analysis showed that a cluster of highly correlated 9 SNPs (R2 > 0.9) at 3p21.31 gene locus covering LZTFL1 and SLC6A20 genes was significantly associated with COVID-19 severity, with a pooled OR of 1.8 [1.5-2.0]. Meanwhile, another 3 SNPs (rs2531743-G, rs2271616-T, and rs73062389-A) within the locus was associated with COVID-19 susceptibility, with pooled estimates of 0.95 [0.93-0.96], 1.23 [1.19-1.27] and 1.15 [1.13-1.17], respectively. Interestingly, SNPs associated with susceptibility and SNPs associated with severity in this locus are in linkage equilibrium (R2 < 0.026). The SNP-h2 on the liability scale for severity and susceptibility was estimated at 7.6% (Se = 3.2%) and 4.6% (Se = 1.5%), respectively. Genetic factors contribute to COVID-19 susceptibility and severity. In the 3p21.31 locus, SNPs that are associated with susceptibility are not in linkage disequilibrium (LD) with SNPs that are associated with severity, indicating within-locus heterogeneity.
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Affiliation(s)
- Setegn Eshetie
- Australian Centre for Precision Health and UniSA Allied Health & Human Performance, University of South Australia, Adelaide, South Australia, Australia
- Department of Medical Microbiology, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
- South Australian Health and Medical Research Institute (SAHMRI), University of South Australia, Adelaide, South Australia, Australia
| | - Pastor Jullian
- Australian Centre for Precision Health and UniSA Allied Health & Human Performance, University of South Australia, Adelaide, South Australia, Australia
- South Australian Health and Medical Research Institute (SAHMRI), University of South Australia, Adelaide, South Australia, Australia
| | - Beben Benyamin
- Australian Centre for Precision Health and UniSA Allied Health & Human Performance, University of South Australia, Adelaide, South Australia, Australia
- South Australian Health and Medical Research Institute (SAHMRI), University of South Australia, Adelaide, South Australia, Australia
| | - S Hong Lee
- Australian Centre for Precision Health and UniSA Allied Health & Human Performance, University of South Australia, Adelaide, South Australia, Australia
- South Australian Health and Medical Research Institute (SAHMRI), University of South Australia, Adelaide, South Australia, Australia
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Perez DM. α 1-Adrenergic Receptors: Insights into Potential Therapeutic Opportunities for COVID-19, Heart Failure, and Alzheimer's Disease. Int J Mol Sci 2023; 24:4188. [PMID: 36835598 PMCID: PMC9963459 DOI: 10.3390/ijms24044188] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/06/2023] [Accepted: 02/08/2023] [Indexed: 02/22/2023] Open
Abstract
α1-Adrenergic receptors (ARs) are members of the G-Protein Coupled Receptor superfamily and with other related receptors (β and α2), they are involved in regulating the sympathetic nervous system through binding and activation by norepinephrine and epinephrine. Traditionally, α1-AR antagonists were first used as anti-hypertensives, as α1-AR activation increases vasoconstriction, but they are not a first-line use at present. The current usage of α1-AR antagonists increases urinary flow in benign prostatic hyperplasia. α1-AR agonists are used in septic shock, but the increased blood pressure response limits use for other conditions. However, with the advent of genetic-based animal models of the subtypes, drug design of highly selective ligands, scientists have discovered potentially newer uses for both agonists and antagonists of the α1-AR. In this review, we highlight newer treatment potential for α1A-AR agonists (heart failure, ischemia, and Alzheimer's disease) and non-selective α1-AR antagonists (COVID-19/SARS, Parkinson's disease, and posttraumatic stress disorder). While the studies reviewed here are still preclinical in cell lines and rodent disease models or have undergone initial clinical trials, potential therapeutics discussed here should not be used for non-approved conditions.
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Affiliation(s)
- Dianne M Perez
- The Lerner Research Institute, The Cleveland Clinic Foundation, 9500 Euclid Ave, Cleveland, OH 44195, USA
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Dumenil T, Le TT, Rawle DJ, Yan K, Tang B, Nguyen W, Bishop C, Suhrbier A. Warmer ambient air temperatures reduce nasal turbinate and brain infection, but increase lung inflammation in the K18-hACE2 mouse model of COVID-19. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 859:160163. [PMID: 36395835 PMCID: PMC9659553 DOI: 10.1016/j.scitotenv.2022.160163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 11/04/2022] [Accepted: 11/09/2022] [Indexed: 06/16/2023]
Abstract
Warmer climatic conditions have been associated with fewer COVID-19 cases. Herein we infected K18-hACE2 mice housed at the standard animal house temperature of ∼22 °C, or at ∼31 °C, which is considered to be thermoneutral for mice. On day 2 post infection, RNA-Seq analyses showed no significant differential gene expression lung in lungs of mice housed at the two temperatures, with almost identical viral loads and type I interferon responses. There was also no significant difference in viral loads in lungs on day 5, but RNA-Seq and histology analyses showed clearly elevated inflammatory signatures and infiltrates. Thermoneutrality thus promoted lung inflammation. On day 2 post infection mice housed at 31 °C showed reduced viral loads in nasal turbinates, consistent with increased mucociliary clearance at the warmer ambient temperature. These mice also had reduced virus levels in the brain, and an ensuing amelioration of weight loss and a delay in mortality. Warmer air temperatures may thus reduce infection of the upper respiratory track and the olfactory epithelium, resulting in reduced brain infection. Potential relevance for anosmia and neurological sequelae in COVID-19 patients is discussed.
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Affiliation(s)
- Troy Dumenil
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | - Thuy T Le
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | - Daniel J Rawle
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | - Kexin Yan
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | - Bing Tang
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | - Wilson Nguyen
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | - Cameron Bishop
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | - Andreas Suhrbier
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia; Australian Infectious Disease Research Centre, GVN Center of Excellence, Brisbane, Queensland 4029, 4072, Australia.
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