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2.
Hum Immunol ; 83(8-9): 613-617, 2022.
Article in English | MEDLINE | ID: covidwho-2179262

ABSTRACT

The NF-κB signaling pathway is a key regulator of inflammation in the response to SARS-CoV-2 infection. This pathway has been implicated in the hyperinflammatory state that characterizes the severe forms of COVID-19. The genetic variation of the NF-κB components might thus explain the predisposition to critical outcomes of this viral disease. We aimed to study the role of the common NFKB1 rs28362491, NFKBIA rs696 and NFKBIZ rs3217713 variants in the risk of developing severe COVID-19 with ICU admission. A total of 470 Spanish patients requiring respiratory support in the ICU were studied (99 deceased and 371 survivors). Compared to healthy population controls (N = 300), the NFKBIA rs696 GG genotype was increased in the patients (p = 0.045; OR = 1.37). The NFKBIZ rs3217713 insertion homozygosis was associated with a significant risk of death (p = 0.02; OR = 1.76) and was also related to increased D-dimer values (p = 0.0078, OR = 1.96). This gene has been implicated in sepsis in mice and rats. Moreover, we found a trend toward lower expression of the NFKBIZ transcript in total blood from II patients. In conclusion, variants in the NF-κB genes might be associated with the risk of developing severe COVID-19, with a significant effect of the NFKBIZ gene on mortality. Our results were based on a limited number of patients and require validation in larger cohorts from other populations.


Subject(s)
COVID-19 , NF-kappa B , Adaptor Proteins, Signal Transducing , COVID-19/genetics , Genetic Association Studies , Genetic Predisposition to Disease , Humans , NF-KappaB Inhibitor alpha/genetics , NF-kappa B/genetics , NF-kappa B p50 Subunit/genetics , Polymorphism, Single Nucleotide , SARS-CoV-2 , Signal Transduction
3.
Patient Educ Couns ; 105(7): 2436-2442, 2022 Jul.
Article in English | MEDLINE | ID: covidwho-2150396

ABSTRACT

OBJECTIVES: Healthy individuals from hereditary cancer families undergoing genetic testing for cancer susceptibility (GTC) report more distress when they perceive their social support as low and suppress their emotions. This study aimed to explore how suppressing emotions and perceiving others as unsupportive are related with cancer-risk distress. METHODS: We performed a regression-based mediation analysis to assess if expressive suppression mediates or is mediated by perceived social support in the relation with cancer-risk distress. Participants were 125 healthy adults aged over 18 (M = 36.07, SD = 12.86), mostly female (72,4%), who undergone GTC to assess the presence of hereditary breast and ovarian cancer or Lynch syndromes. RESULTS: Controlling for age and gender, we found a moderate size indirect effect of social support on cancer-risk distress through expressive suppression (ß = -0.095) and a direct effect of expressive suppression on cancer-risk distress. CONCLUSIONS: When healthy individuals from hereditary cancer families perceive their social network as less responsive, they tend to not express their emotions, which relates to increased distress facing GTC. PRACTICE IMPLICATIONS: Practitioners may assess cancer-risk related distress before the GTC and offer distressed individuals interventions focused on changing emotion regulation strategies in a safe group context.


Subject(s)
Genetic Predisposition to Disease , Neoplasms , Adult , Emotions/physiology , Female , Health Status , Humans , Male , Neoplasms/genetics , Social Support
4.
Am J Respir Crit Care Med ; 206(10): 1220-1229, 2022 Nov 15.
Article in English | MEDLINE | ID: covidwho-2138355

ABSTRACT

Rationale: A common MUC5B gene polymorphism, rs35705950-T, is associated with idiopathic pulmonary fibrosis (IPF), but its role in severe acute respiratory syndrome coronavirus 2 infection and disease severity is unclear. Objectives: To assess whether rs35705950-T confers differential risk for clinical outcomes associated with coronavirus disease (COVID-19) infection among participants in the Million Veteran Program (MVP). Methods: The MUC5B rs35705950-T allele was directly genotyped among MVP participants; clinical events and comorbidities were extracted from the electronic health records. Associations between the incidence or severity of COVID-19 and rs35705950-T were analyzed within each ancestry group in the MVP followed by transancestry meta-analysis. Replication and joint meta-analysis were conducted using summary statistics from the COVID-19 Host Genetics Initiative (HGI). Sensitivity analyses with adjustment for additional covariates (body mass index, Charlson comorbidity index, smoking, asbestosis, rheumatoid arthritis with interstitial lung disease, and IPF) and associations with post-COVID-19 pneumonia were performed in MVP subjects. Measurements and Main Results: The rs35705950-T allele was associated with fewer COVID-19 hospitalizations in transancestry meta-analyses within the MVP (Ncases = 4,325; Ncontrols = 507,640; OR = 0.89 [0.82-0.97]; P = 6.86 × 10-3) and joint meta-analyses with the HGI (Ncases = 13,320; Ncontrols = 1,508,841; OR, 0.90 [0.86-0.95]; P = 8.99 × 10-5). The rs35705950-T allele was not associated with reduced COVID-19 positivity in transancestry meta-analysis within the MVP (Ncases = 19,168/Ncontrols = 492,854; OR, 0.98 [0.95-1.01]; P = 0.06) but was nominally significant (P < 0.05) in the joint meta-analysis with the HGI (Ncases = 44,820; Ncontrols = 1,775,827; OR, 0.97 [0.95-1.00]; P = 0.03). Associations were not observed with severe outcomes or mortality. Among individuals of European ancestry in the MVP, rs35705950-T was associated with fewer post-COVID-19 pneumonia events (OR, 0.82 [0.72-0.93]; P = 0.001). Conclusions: The MUC5B variant rs35705950-T may confer protection in COVID-19 hospitalizations.


Subject(s)
COVID-19 , Idiopathic Pulmonary Fibrosis , Humans , COVID-19/epidemiology , COVID-19/genetics , Mucin-5B/genetics , Polymorphism, Genetic , Idiopathic Pulmonary Fibrosis/genetics , Genotype , Hospitalization , Genetic Predisposition to Disease/genetics
5.
Sci Rep ; 12(1): 20167, 2022 Nov 23.
Article in English | MEDLINE | ID: covidwho-2133629

ABSTRACT

To create a scientific resource of expression quantitative trail loci (eQTL), we conducted a genome-wide association study (GWAS) using genotypes obtained from whole genome sequencing (WGS) of DNA and gene expression levels from RNA sequencing (RNA-seq) of whole blood in 2622 participants in Framingham Heart Study. We identified 6,778,286 cis-eQTL variant-gene transcript (eGene) pairs at p < 5 × 10-8 (2,855,111 unique cis-eQTL variants and 15,982 unique eGenes) and 1,469,754 trans-eQTL variant-eGene pairs at p < 1e-12 (526,056 unique trans-eQTL variants and 7233 unique eGenes). In addition, 442,379 cis-eQTL variants were associated with expression of 1518 long non-protein coding RNAs (lncRNAs). Gene Ontology (GO) analyses revealed that the top GO terms for cis-eGenes are enriched for immune functions (FDR < 0.05). The cis-eQTL variants are enriched for SNPs reported to be associated with 815 traits in prior GWAS, including cardiovascular disease risk factors. As proof of concept, we used this eQTL resource in conjunction with genetic variants from public GWAS databases in causal inference testing (e.g., COVID-19 severity). After Bonferroni correction, Mendelian randomization analyses identified putative causal associations of 60 eGenes with systolic blood pressure, 13 genes with coronary artery disease, and seven genes with COVID-19 severity. This study created a comprehensive eQTL resource via BioData Catalyst that will be made available to the scientific community. This will advance understanding of the genetic architecture of gene expression underlying a wide range of diseases.


Subject(s)
Genetic Predisposition to Disease , Genome-Wide Association Study , Quantitative Trait Loci , Humans , DNA , Gene Expression , Quantitative Trait Loci/genetics , Sequence Analysis, RNA
6.
Immunobiology ; 227(6): 152301, 2022 Nov.
Article in English | MEDLINE | ID: covidwho-2119151

ABSTRACT

Coronavirus disease-19 (COVID-19) has recently emerged as a respiratory infection with a significant impact on health and society. The pathogenesis is primarily attributed to a dysregulation of cytokines, especially those with pro-inflammatory and anti-inflammatory effects. Interleukin-38 (IL-38) is a recently identified anti-inflammatory cytokine with a proposed involvement in mediating COVID-19 pathogenesis, while the association between IL38 gene variants and disease susceptibility has not been explored. Therefore, a pilot study was designed to evaluate the association of three gene variants in the promoter region of IL38 gene (rs7599662 T/A/C/G, rs28992497 T/C and rs28992498 C/A/T) with COVID-19 risk. DNA sequencing was performed to identify these variants. The study included 148 Iraqi patients with COVID-19 and 113 healthy controls (HC). Only rs7599662 showed a significant negative association with susceptibility to COVID-19. The mutant T allele was presented at a significantly lower frequency in patients compared to HC. Analysis of recessive, dominant and codominant models demonstrated that rs7599662 TT genotype frequency was significantly lower in patients than in HC. In terms of haplotypes (in order: rs7599662, rs28992497 and rs28992498), frequency of CTC haplotype was significantly increased in patients compared to HC, while TTC haplotype showed significantly lower frequency in patients. The three SNPs influenced serum IL-38 levels and homozygous genotypes of mutant alleles were associated with elevated levels. In conclusion, this study indicated that IL38 gene in terms of promoter variants and haplotypes may have important implications for COVID-19 risk.


Subject(s)
COVID-19 , Humans , COVID-19/epidemiology , COVID-19/genetics , Genotype , Pilot Projects , Iraq , Case-Control Studies , Promoter Regions, Genetic/genetics , Polymorphism, Single Nucleotide , Alleles , Haplotypes , Cytokines/genetics , Interleukins/genetics , Genetic Predisposition to Disease , Gene Frequency
8.
PLoS Genet ; 18(11): e1010367, 2022 11.
Article in English | MEDLINE | ID: covidwho-2098659

ABSTRACT

Host genetics is a key determinant of COVID-19 outcomes. Previously, the COVID-19 Host Genetics Initiative genome-wide association study used common variants to identify multiple loci associated with COVID-19 outcomes. However, variants with the largest impact on COVID-19 outcomes are expected to be rare in the population. Hence, studying rare variants may provide additional insights into disease susceptibility and pathogenesis, thereby informing therapeutics development. Here, we combined whole-exome and whole-genome sequencing from 21 cohorts across 12 countries and performed rare variant exome-wide burden analyses for COVID-19 outcomes. In an analysis of 5,085 severe disease cases and 571,737 controls, we observed that carrying a rare deleterious variant in the SARS-CoV-2 sensor toll-like receptor TLR7 (on chromosome X) was associated with a 5.3-fold increase in severe disease (95% CI: 2.75-10.05, p = 5.41x10-7). This association was consistent across sexes. These results further support TLR7 as a genetic determinant of severe disease and suggest that larger studies on rare variants influencing COVID-19 outcomes could provide additional insights.


Subject(s)
COVID-19 , Exome , Humans , Exome/genetics , Genome-Wide Association Study , COVID-19/genetics , Genetic Predisposition to Disease , Toll-Like Receptor 7/genetics , SARS-CoV-2/genetics
9.
PLoS Genet ; 18(11): e1010253, 2022 11.
Article in English | MEDLINE | ID: covidwho-2098658

ABSTRACT

Genome wide association studies show there is a genetic component to severe COVID-19. We find evidence that the genome-wide genetic association signal with severe COVID-19 is correlated with that of systemic lupus erythematosus (SLE), having formally tested this using genetic correlation analysis by LD score regression. To identify the shared associated loci and gain insight into the shared genetic effects, using summary level data we performed meta-analyses, a local genetic correlation analysis and fine-mapping using stepwise regression and functional annotation. This identified multiple loci shared between the two traits, some of which exert opposing effects. The locus with most evidence of shared association is TYK2, a gene critical to the type I interferon pathway, where the local genetic correlation is negative. Another shared locus is CLEC1A, where the direction of effects is aligned, that encodes a lectin involved in cell signaling, and the anti-fungal immune response. Our analyses suggest that several loci with reciprocal effects between the two traits have a role in the defense response pathway, adding to the evidence that SLE risk alleles are protective against infection.


Subject(s)
Autoimmune Diseases , COVID-19 , Lupus Erythematosus, Systemic , Humans , Genome-Wide Association Study , Genetic Predisposition to Disease , COVID-19/genetics , Lupus Erythematosus, Systemic/genetics , Autoimmune Diseases/genetics , Polymorphism, Single Nucleotide
10.
Int J Clin Pract ; 2022: 4761631, 2022.
Article in English | MEDLINE | ID: covidwho-2098045

ABSTRACT

Background: Th-17 cells, a proinflammatory subset of CD4 T lymphocytes, have been suggested as a possible cause of coronavirus disease-19 (COVID-19)-related immunological injuries. The aim of this study was to investigate the relationship between IL-17F (rs763780) polymorphism and the susceptibility to and outcomes of COVID-19 infection and to determine the clinical and laboratory predictors of COVID-19 death. Methods: This case-control study included 132 COVID-19 patients and 135 healthy age- and sex-matched controls. The participants were tested for IL-17F rs763780 polymorphism via TaqMan-based genotyping and for the expression of IL-17 by enzyme-linked immunosorbent assay. This study also investigated the predictors for COVID-19 mortality. Results: A non-statistically significant association was observed between IL-17F alleles and genotypes with COVID-19 (P=0.309, P=0.138, respectively). Moreover, no significant difference in the IL-17F genotypes was observed between non-survivors and survivors (P=0.482). In the multivariate analysis, the participants with the following characteristics had 17.7-, 11.2-, 8-, and 17.9-fold higher odds of exhibiting in-hospital mortality, respectively: (1) hypertension, (2) age of >57 years, (3) WBC count of >12.6 × 103/mm3, and (4) D-dimer of >0.9 ng/ml. The ROC curve analysis showed that IL-17 at a cutoff point of >46 pg/ml was a perfect discriminator of COVID-19 patients from control subjects (AUC = 1.0). Conclusion: The findings indicate that the IL-17F H161R variant does not influence the risk of COVID-19. However, the IL-17 level is a perfect discriminator of COVID-19 infection. Hypertension, age of >57 years, white blood cell count of >12.6 × 103/mm3, and D-dimer of >0.9 ng/ml are the independent predictors for death among COVID-19 patients.


Subject(s)
COVID-19 , Hypertension , Humans , Middle Aged , Interleukin-17/genetics , COVID-19/genetics , Genetic Predisposition to Disease , Case-Control Studies , Genotype , Polymorphism, Single Nucleotide
11.
Commun Biol ; 5(1): 1133, 2022 Oct 26.
Article in English | MEDLINE | ID: covidwho-2087324

ABSTRACT

We employed a multifaceted computational strategy to identify the genetic factors contributing to increased risk of severe COVID-19 infection from a Whole Exome Sequencing (WES) dataset of a cohort of 2000 Italian patients. We coupled a stratified k-fold screening, to rank variants more associated with severity, with the training of multiple supervised classifiers, to predict severity based on screened features. Feature importance analysis from tree-based models allowed us to identify 16 variants with the highest support which, together with age and gender covariates, were found to be most predictive of COVID-19 severity. When tested on a follow-up cohort, our ensemble of models predicted severity with high accuracy (ACC = 81.88%; AUCROC = 96%; MCC = 61.55%). Our model recapitulated a vast literature of emerging molecular mechanisms and genetic factors linked to COVID-19 response and extends previous landmark Genome-Wide Association Studies (GWAS). It revealed a network of interplaying genetic signatures converging on established immune system and inflammatory processes linked to viral infection response. It also identified additional processes cross-talking with immune pathways, such as GPCR signaling, which might offer additional opportunities for therapeutic intervention and patient stratification. Publicly available PheWAS datasets revealed that several variants were significantly associated with phenotypic traits such as "Respiratory or thoracic disease", supporting their link with COVID-19 severity outcome.


Subject(s)
COVID-19 , Humans , COVID-19/genetics , Genome-Wide Association Study , Genetic Predisposition to Disease , Whole Exome Sequencing , Phenotype
12.
Sci Rep ; 12(1): 17703, 2022 Oct 21.
Article in English | MEDLINE | ID: covidwho-2087305

ABSTRACT

Autoimmune diseases and coronavirus disease 2019 (COVID-19) share many similarities. Concerns have arisen that autoimmune diseases may increase the susceptibility and severity of COVID-19. We used Mendelian randomization to investigate whether liability to autoimmune diseases is related to COVID-19 susceptibility and severity. Genetic instruments for 8 autoimmune diseases, including type 1 diabetes mellitus, rheumatoid arthritis, systemic lupus erythematosus, psoriasis, multiple sclerosis, primary sclerosing cholangitis, primary biliary cirrhosis and juvenile idiopathic arthritis, were obtained from published genome-wide association studies. Two-sample Mendelian randomization analyses of the associations of liability to each autoimmune disease with COVID-19 infection, hospitalized COVID-19, and very severe COVID-19 were performed using the latest publicly available genome-wide association study for COVID-19. Genetic liability to each of the autoimmune diseases was largely not associated with COVID-19 infection, hospitalized COVID-19, or very severe COVID-19 after accounting for multiple comparison. Sensitivity analysis excluding genetic variants in the human leukocyte antigen gene, which has an important role in the immune response, showed similar results. The autoimmune diseases examined were largely not genetically associated with the susceptibility or severity of COVID-19. Further investigations are warranted.


Subject(s)
Arthritis, Juvenile , Autoimmune Diseases , COVID-19 , Humans , Genetic Predisposition to Disease , COVID-19/epidemiology , COVID-19/genetics , Genome-Wide Association Study , Mendelian Randomization Analysis , Autoimmune Diseases/epidemiology , Autoimmune Diseases/genetics , Arthritis, Juvenile/genetics , HLA Antigens , Polymorphism, Single Nucleotide
13.
Nat Commun ; 13(1): 6336, 2022 Oct 25.
Article in English | MEDLINE | ID: covidwho-2087204

ABSTRACT

Genes with moderate to low expression heritability may explain a large proportion of complex trait etiology, but such genes cannot be sufficiently captured in conventional transcriptome-wide association studies (TWASs), partly due to the relatively small available reference datasets for developing expression genetic prediction models to capture the moderate to low genetically regulated components of gene expression. Here, we introduce a method, the Summary-level Unified Method for Modeling Integrated Transcriptome (SUMMIT), to improve the expression prediction model accuracy and the power of TWAS by using a large expression quantitative trait loci (eQTL) summary-level dataset. We apply SUMMIT to the eQTL summary-level data provided by the eQTLGen consortium. Through simulation studies and analyses of genome-wide association study summary statistics for 24 complex traits, we show that SUMMIT improves the accuracy of expression prediction in blood, successfully builds expression prediction models for genes with low expression heritability, and achieves higher statistical power than several benchmark methods. Finally, we conduct a case study of COVID-19 severity with SUMMIT and identify 11 likely causal genes associated with COVID-19 severity.


Subject(s)
COVID-19 , Transcriptome , Humans , Genome-Wide Association Study/methods , COVID-19/genetics , Quantitative Trait Loci/genetics , Multifactorial Inheritance , Polymorphism, Single Nucleotide , Genetic Predisposition to Disease/genetics
14.
Adv Immunol ; 156: 25-54, 2022.
Article in English | MEDLINE | ID: covidwho-2085835

ABSTRACT

Autoimmune diseases (ADs) often arise from a combination of genetic and environmental triggers that disrupt the immune system's capability to properly tolerate body self-antigens. Familial studies provided the earliest insights into the risk loci of such diseases, while genome-wide association studies (GWAS) significantly broadened the horizons. A drug targeting a prominent pathological pathway can be applied to multiple indications sharing overlapping mechanisms. Advances in genomic technologies used in genetic studies provide critical insights into future research on gene-environment interactions in autoimmunity. This Review summarizes the history and recent advances in the understanding of genetic susceptibility to ADs and related immune disorders, including coronavirus disease 2019 (COVID-19), and their indications for the development of diagnostic or prognostic markers for translational applications.


Subject(s)
Autoimmune Diseases , COVID-19 , Humans , Animals , Autoimmunity/genetics , Genetic Predisposition to Disease , Genome-Wide Association Study , COVID-19/genetics , Autoimmune Diseases/genetics
15.
Yi Chuan ; 44(8): 672-681, 2022 Aug 20.
Article in English | MEDLINE | ID: covidwho-2081137

ABSTRACT

The coronavirus disease 2019 (COVID-19) is a global pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. COVID-19 has a variety of clinical manifestations, ranging from asymptomatic infection or mild symptoms to severe symptoms. Severe COVID-19 patients experience cytokine storm, resulting in multi-organ failure and even death. Male gender, old age, and pre-existing comorbidities (such as hypertension and diabetes ) are risk factors for COVID-19 severity. Recently, a series of studies suggested that genetic defects might also be related to disease severity and the cytokine storm occurence. Genetic variants in key viral immune genes, such as TLR7 and UNC13D, have been identified in severe COVID-19 patients from previous reports. In this review, we summarize the mechanisms underlying immune responses against SARS-CoV-2 and genetic variants that associated with the severity of COVID-19. The study of genetic basis of COVID-19 will be of great benefit for early disease detection and intervention.


Subject(s)
COVID-19 , Humans , Male , COVID-19/genetics , Genetic Predisposition to Disease , Cytokine Release Syndrome/genetics , SARS-CoV-2/genetics , Membrane Proteins
16.
Sci Rep ; 12(1): 13483, 2022 08 05.
Article in English | MEDLINE | ID: covidwho-2077085

ABSTRACT

COVID-19 has caused the recent pandemic of respiratory infection, which threatened global health. The severity of the symptoms varies among affected individuals, from asymptotic or mild signs to severe or critical illness. Genetic predisposition explains the variation in disease severity among patients who suffer from severe symptoms without any known background risk factors. The present study was performed to show the association between APOE genotype and the severity of COVID-19 disease. The APOE genotype of 201 COVID-19 patients (101 patients with asymptomatic to mild form of the disease as the control group and 100 patients with severe to critical illness without any known background risk factors as the case group) were detected via multiplex tetra-primer ARMS-PCR method. Results showed that the e4 allele increased the risk of the COVID-19 infection severity more than five times and the e4/e4 genotype showed a 17-fold increase in the risk of severe disease. In conclusion, since our study design was based on the exclusion of patients with underlying diseases predisposing to severe form of COVID-19 and diseases related to the APOE gene in the study population, our results showed that the e4 genotype is independently associated with the severity of COVID-19 disease. However, further studies are needed to confirm these findings in other nations and to demonstrate the mechanisms behind the role of these alleles in disease severity.


Subject(s)
Apolipoproteins E , COVID-19 , Alleles , Apolipoprotein E4/genetics , Apolipoproteins E/genetics , COVID-19/genetics , Critical Illness , Genetic Predisposition to Disease , Genotype , Humans , Severity of Illness Index
17.
Int J Environ Res Public Health ; 19(19)2022 Oct 02.
Article in English | MEDLINE | ID: covidwho-2066024

ABSTRACT

The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 virus (SARS-CoV-2), has triggered an enormous scientific response. Many studies have focused on understanding the entry of the SARS-CoV-2 virus into the host cell. The angiotensin-converting enzyme-2 (ACE2) is recognized as the host receptor used by SARS-CoV-2 to enter its target cells. Recent studies suggest that ACE2 gene polymorphisms might be candidates for genetic susceptibility to SARS-CoV-2 infection. The aim of this study is to evaluate the influence of ACE2 polymorphisms on COVID-19 disease risk and severity. In our study, we confirmed that there is a statistically significant increased risk of a more severe disease course of SARS-CoV-2 infection associated with the need for hospitalization in intensive care for patients with specific polymorphisms of the ACE2 gene. The most significant correlation was found for variant ACE2 rs2285666 (AA allele, OR = 2.12, p = 0.0189) and ACE2 rs2074192 (TT allele, OR = 2.05, p = 0.0016), and for ACE2 rs4646174 (GG allele, OR = 1.93, p = 0.0016), ACE2 rs4646156 (TT allele OR = 1.71, p = 0.008) and ACE2 rs2158083 (TT allele OR = 1.84, p = 0.0025). In conclusion, our findings identify that certain ACE2 polymorphisms impact the severity of COVID-19 disease independently of other well-known risk factors.


Subject(s)
Angiotensin-Converting Enzyme 2/genetics , COVID-19 , Angiotensins/genetics , COVID-19/epidemiology , COVID-19/genetics , Genetic Predisposition to Disease , Humans , Pandemics , Peptidyl-Dipeptidase A/genetics , SARS-CoV-2/genetics
18.
Cell Stem Cell ; 29(10): 1475-1490.e6, 2022 10 06.
Article in English | MEDLINE | ID: covidwho-2061891

ABSTRACT

Population-based studies to identify disease-associated risk alleles typically require samples from a large number of individuals. Here, we report a human-induced pluripotent stem cell (hiPSC)-based screening strategy to link human genetics with viral infectivity. A genome-wide association study (GWAS) identified a cluster of single-nucleotide polymorphisms (SNPs) in a cis-regulatory region of the NDUFA4 gene, which was associated with susceptibility to Zika virus (ZIKV) infection. Loss of NDUFA4 led to decreased sensitivity to ZIKV, dengue virus, and SARS-CoV-2 infection. Isogenic hiPSC lines carrying non-risk alleles of SNPs or deletion of the cis-regulatory region lower sensitivity to viral infection. Mechanistic studies indicated that loss/reduction of NDUFA4 causes mitochondrial stress, which leads to the leakage of mtDNA and thereby upregulation of type I interferon signaling. This study provides proof-of-principle for the application of iPSC arrays in GWAS and identifies NDUFA4 as a previously unknown susceptibility locus for viral infection.


Subject(s)
COVID-19 , Dengue , Electron Transport Complex IV , Zika Virus Infection , Humans , Alleles , COVID-19/genetics , DNA, Mitochondrial/metabolism , Electron Transport Complex IV/genetics , Genetic Predisposition to Disease , Genome-Wide Association Study , Induced Pluripotent Stem Cells/metabolism , Interferon Type I/metabolism , Polymorphism, Single Nucleotide , SARS-CoV-2 , Zika Virus , Zika Virus Infection/genetics , Dengue/genetics
19.
Int J Mycobacteriol ; 11(3): 318-322, 2022.
Article in English | MEDLINE | ID: covidwho-2055700

ABSTRACT

Background: The aim of the present study was to investigate the susceptibility of purified protein derivative (PPD) plus health-care workers to SARS-CoV-2 (COVID-19). For this reason, single-nucleotide polymorphism (SNP) of interferon-gamma (IFN-γ) gene at position +2109 and IFN-γ receptor 1 (R1) at position -56 was assessed in PPD plus group before and after COVID-19 infection (2017-2018; 2020-2021). Methods: The selected study cases (n = 100) that were working in tuberculosis (TB) unite (5-10 years) with PPD positivity >15 mm (16-20 mm) were included in this investigation. Sampling was done twice, once before and after the COVID-19 pandemic. Group A contains 50 samples collected from the GenBank TB laboratory that belong to TB staff before the pandemic (2017-2018). The other sample (Group B; 2021) was collected from the same unite during the COVID-19 pandemic. The SNP in the IFN-γ gene (+2109; 670 bp) and IFN-γ R 1 (-56; 366 bp) was performed using a specific primer and the polymerase chain reaction products were digested using restriction enzyme Fau I and Bts I, respectively. Statistical analyses were used to obtain the frequency of alleles among all studied cases. The confidence intervals (CIs) and t-test were calculated using the SPSS and GraphPad Prism software. Results: In overall, the most frequent genotype in Group A was AA (41/50; 82%) and Group B was 76% (38/50) in position + 2109 (odds ratio [OR] = 0.69, 95% CI, 0.26-1.83, and P = 0.46). Although in position -56, the most frequent genotype in Group A was TT (35/50; 70%) which significantly was than Group B TT (15/50; 30%) (OR = 0.184, 95% CI, 0.78-0.43, and P = 0.00). The frequency of allele A was more in both groups at position + 2109 (OR = 0.815, 95% CI, 0.23-2.86, and P = 0.75), whereas the dominate allele at position -56 was T in Group A (OR = 1.37, 95% CI, 0.62-3.02, and P = 0.42). Conclusion: No significant differences were observed in + 2109 in genotype among Group A and B. The main differences were seen in IFN-γ R1 at position (-56) between Group A and B. Hence, the IFN-γ R1 may play important role in COVID-19 infection. However, more study is needed to clear the IFN-γ correlation to COVID-19 infection.


Subject(s)
COVID-19 , Tuberculosis , Humans , Case-Control Studies , COVID-19/genetics , Genetic Predisposition to Disease , Genotype , Interferon-gamma/genetics , Pandemics , Polymorphism, Single Nucleotide , SARS-CoV-2/genetics , Tuberculin , Tuberculosis/genetics
20.
Nat Rev Rheumatol ; 18(10): 552, 2022 10.
Article in English | MEDLINE | ID: covidwho-2050408
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