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1.
Pol J Microbiol ; 72(2): 143-154, 2023 Jun 01.
Article in English | MEDLINE | ID: covidwho-2326672

ABSTRACT

Both pulmonary arterial hypertension (PAH) and chronic obstructive pulmonary disease (COPD) are risk factors for coronavirus disease 2019 (COVID-19). Patients with lung injury and altered pulmonary vascular anatomy or function are more susceptible to infections. The purpose of the study is to ascertain whether individuals with COPD or PAH are affected synergistically by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Data sources for the construction of a protein-protein interaction (PPI) network and the identification of differentially expressed genes (DEGs) included three RNA-seq datasets from the GEO database (GSE147507, GSE106986, and GSE15197). Then, relationships between miRNAs, common DEGs, and transcription factor (TF) genes were discovered. Functional analysis using Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and other databases, as well as the forecasting of antiviral medications for COPD and PAH patients infected with SARS-CoV-2, were also performed. Eleven common DEGs were found in the three datasets, and their biological functions were primarily enriched in the control of protein modification processes, particularly phosphorylation. Growth factor receptor binding reflects molecular function. KEGG analysis indicated that co-DEGs mainly activate Ras, and PI3K-Akt signaling pathways and act on focal adhesions. NFKB1 interacted with HSA-miR-942 in the TF-miRNA-DEGs synergistic regulatory network. Acetaminophen is considered an effective drug candidate. There are some connections between COPD and PAH and the development of COVID-19. This research could aid in developing COVID-19 vaccines and medication candidates that would work well as COVID-19 therapies.


Subject(s)
COVID-19 , MicroRNAs , Pulmonary Arterial Hypertension , Pulmonary Disease, Chronic Obstructive , Humans , COVID-19 Vaccines , Phosphatidylinositol 3-Kinases , SARS-CoV-2/genetics , Pulmonary Disease, Chronic Obstructive/genetics , Signal Transduction/genetics , MicroRNAs/genetics
2.
Biomed Res Int ; 2022: 1806427, 2022.
Article in English | MEDLINE | ID: covidwho-2088968

ABSTRACT

COVID-19 is still prevalent in more world regions and poses a severe threat to human health due to its high pathogenicity. The incidence of COPD patients is gradually increasing, especially in patients over 45 years old. COPD patients are susceptible to COVID-19 due to the specific lung receptor ACE2 of SARS-CoV-2. We attempt to reveal the genetic basis by analyzing the expression of common DEGs of the two diseases through bioinformatics approaches and find potential therapeutic agents based on the target genes. Thus, we search the GEO database for COVID-19 and COPD transcriptomic gene expression. We also study the enrichment of signaling regulatory pathways and hub genes for potential therapeutic treatments. There are 34 common DEGs in the two datasets. The signaling pathways are mainly enriched in intercellular junctions between virus and cytokine regulation. In the PPI network of common DEGs, we extract 5 hub genes. We find that artesunate CTD 00001840, dexverapamil MCF7 UP, and STOCK1N-35696 PC3 DOWN could be therapeutic agents for both diseases. We also analyze the regulatory network of differential genes with transcription factors and miRNAs. Therefore, we conclude that artesunate CTD 00001840, dexverapamil MCF7 UP, and STOCK1N-35696 PC3 DOWN can be therapeutic candidates in COPD combined with COVID-19.


Subject(s)
COVID-19 , Pulmonary Disease, Chronic Obstructive , Artesunate , COVID-19/genetics , Computational Biology , Gene Expression Profiling , Gene Regulatory Networks , Humans , Middle Aged , Pulmonary Disease, Chronic Obstructive/genetics , SARS-CoV-2 , Verapamil
3.
Int J Mol Sci ; 23(14)2022 Jul 13.
Article in English | MEDLINE | ID: covidwho-1964006

ABSTRACT

Airway mucociliary regeneration and function are key players for airway defense and are impaired in chronic obstructive pulmonary disease (COPD). Using transcriptome analysis in COPD-derived bronchial biopsies, we observed a positive correlation between cilia-related genes and microRNA-449 (miR449). In vitro, miR449 was strongly increased during airway epithelial mucociliary differentiation. In vivo, miR449 was upregulated during recovery from chemical or infective insults. miR0449-/- mice (both alleles are deleted) showed impaired ciliated epithelial regeneration after naphthalene and Haemophilus influenzae exposure, accompanied by more intense inflammation and emphysematous manifestations of COPD. The latter occurred spontaneously in aged miR449-/- mice. We identified Aurora kinase A and its effector target HDAC6 as key mediators in miR449-regulated ciliary homeostasis and epithelial regeneration. Aurora kinase A is downregulated upon miR449 overexpression in vitro and upregulated in miR449-/- mouse lungs. Accordingly, imaging studies showed profoundly altered cilia length and morphology accompanied by reduced mucociliary clearance. Pharmacological inhibition of HDAC6 rescued cilia length and coverage in miR449-/- cells, consistent with its tubulin-deacetylating function. Altogether, our study establishes a link between miR449, ciliary dysfunction, and COPD pathogenesis.


Subject(s)
Aurora Kinase A/metabolism , Histone Deacetylase 6/metabolism , MicroRNAs , Pulmonary Disease, Chronic Obstructive , Animals , Aurora Kinase A/genetics , Cilia/genetics , Epithelial Cells , Mice , MicroRNAs/genetics , Pulmonary Disease, Chronic Obstructive/genetics , Tubulin/genetics
4.
Addiction ; 117(7): 2027-2036, 2022 Jul.
Article in English | MEDLINE | ID: covidwho-1891443

ABSTRACT

BACKGROUND AND AIMS: Smoking increases the risk of severe COVID-19, but whether lung function or chronic obstructive pulmonary disease (COPD) mediate the underlying associations is unclear. We conducted the largest Mendelian randomization study to date, to our knowledge, to address these questions. DESIGN: Mendelian randomization study using summary statistics from genome-wide association studies (GWAS), FinnGen and UK Biobank. The main analysis was the inverse variance weighted method, and we included a range of sensitivity analyses to assess the robustness of the findings. SETTING: GWAS which included international consortia, FinnGen and UK Biobank. PARTICIPANTS: The sample size ranged from 193 638 to 2 586 691. MEASUREMENTS: Genetic determinants of life-time smoking index, lung function [e.g. forced expiratory volume in 1 sec (FEV1 )], chronic obstructive pulmonary disease (COPD) and different severities of COID-19. RESULTS: Smoking increased the risk of COVID-19 compared with population controls for overall COVID-19 [odds ratio (OR) = 1.19 per standard deviation (SD) of life-time smoking index, 95% confidence interval (CI) = 1.11-1.27], hospitalized COVID-19 (OR = 1.67, 95% CI = 1.42-1.97) or severe COVID-19 (OR = 1.48, 95% CI = 1.10-1.98), with directionally consistent effects from sensitivity analyses. Lung function and COPD liability did not appear to mediate these associations. CONCLUSION: There is genetic evidence that smoking probably increases the risk of severe COVID-19 and possibly also milder forms of COVID-19. Decreased lung function and increased risk of chronic obstructive pulmonary disease do not seem to mediate the effect of smoking on COVID-19 risk.


Subject(s)
COVID-19 , Pulmonary Disease, Chronic Obstructive , COVID-19/genetics , Genome-Wide Association Study , Humans , Lung , Mendelian Randomization Analysis , Polymorphism, Single Nucleotide , Pulmonary Disease, Chronic Obstructive/epidemiology , Pulmonary Disease, Chronic Obstructive/genetics , Risk Factors , Smoking/adverse effects
5.
Int J Chron Obstruct Pulmon Dis ; 17: 13-24, 2022.
Article in English | MEDLINE | ID: covidwho-1623677

ABSTRACT

Purpose: Chronic obstructive pulmonary disease (COPD) is a major cause of death and morbidity worldwide. A better understanding of new biomarkers for COPD patients and their complex mechanisms in the progression of COPD are needed. Methods: An algorithm was conducted to reveal the proportions of 22 subsets of immune cells in COPD samples. Differentially expressed immune-related genes (DE-IRGs) were obtained based on the differentially expressed genes (DEGs) of the GSE57148 dataset, and 1509 immune-related genes (IRGs) were downloaded from the ImmPort database. Functional enrichment analyses of DE-IRGs were conducted by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses and Ingenuity Pathway Analysis (IPA). We defined the DE-IRGs that had correlations with immune cells as hub genes. The potential interactions among the hub genes were explored by a protein-protein interaction (PPI) network. Results: The CIBERSORT results showed that lung tissue of COPD patients contained a greater number of resting NK cells, activated dendritic cells, and neutrophils than normal samples. However, the fractions of follicular helper T cells and resting dendritic cells were relatively lower. Thirty-eight DE-IRGs were obtained for further analysis. Functional enrichment analysis revealed that these DE-IRGs were significantly enriched in several immune-related biological processes and pathways. Notably, we also observed that DE-IRGs were associated with the coronavirus disease COVID-19 in the progression of COPD. After correlation analysis, six DE-IRGs associated with immune cells were considered hub genes, including AHNAK, SLIT2 TNFRRSF10C, CXCR1, CXCR2, and FCGR3B. Conclusion: In the present study, we investigated immune-related genes as novel diagnostic biomarkers and explored the potential mechanism for COPD based on CIBERSORT analysis, providing a new understanding for COPD treatment.


Subject(s)
COVID-19 , Pulmonary Disease, Chronic Obstructive , Gene Ontology , Humans , Protein Interaction Maps , Pulmonary Disease, Chronic Obstructive/diagnosis , Pulmonary Disease, Chronic Obstructive/genetics , SARS-CoV-2
6.
Ann Am Thorac Soc ; 19(1): 58-65, 2022 01.
Article in English | MEDLINE | ID: covidwho-1605425

ABSTRACT

Rationale: Both genetic variants and chronic obstructive pulmonary disease (COPD) contribute to the risk of incident severe coronavirus disease (COVID-19). Whether genetic risk of incident severe COVID-19 is the same regardless of preexisting COPD is unknown. Objectives: In this study, we aimed to investigate the potential interaction between genetic risk and COPD in relation to severe COVID-19. Methods: We constructed a polygenic risk score for severe COVID-19 by using 112 single-nucleotide polymorphisms in 430,582 participants from the UK Biobank study. We examined the associations of genetic risk and COPD with severe COVID-19 by using logistic regression models. Results: Of 430,582 participants, 712 developed severe COVID-19 as of February 22, 2021, of whom 19.8% had preexisting COPD. Compared with participants at low genetic risk, those at intermediate genetic risk (odds ratio [OR], 1.34; 95% confidence interval [CI], 1.09-1.66) and high genetic risk (OR, 1.50; 95% CI, 1.18-1.92) had higher risk of severe COVID-19 (P for trend = 0.001), and the association was independent of COPD (P for interaction = 0.76). COPD was associated with a higher risk of incident severe COVID-19 (OR, 1.37; 95% CI, 1.12-1.67; P = 0.002). Participants at high genetic risk and with COPD had a higher risk of severe COVID-19 (OR, 2.05; 95% CI, 1.35-3.04; P < 0.001) than those at low genetic risk and without COPD. Conclusions: The polygenic risk score, which combines multiple risk alleles, can be effectively used in screening for high-risk populations of severe COVID-19. High genetic risk correlates with a higher risk of severe COVID-19, regardless of preexisting COPD.


Subject(s)
COVID-19 , Pulmonary Disease, Chronic Obstructive , Humans , Polymorphism, Single Nucleotide , Pulmonary Disease, Chronic Obstructive/epidemiology , Pulmonary Disease, Chronic Obstructive/genetics , Risk Factors , SARS-CoV-2
7.
Cells ; 11(1)2021 12 22.
Article in English | MEDLINE | ID: covidwho-1580996

ABSTRACT

Patients with COPD may be at an increased risk for severe illness from COVID-19 because of ACE2 upregulation, the entry receptor for SARS-CoV-2. Chronic exposure to cigarette smoke, the main risk factor for COPD, increases pulmonary ACE2. How ACE2 expression is controlled is not known but may involve HuR, an RNA binding protein that increases protein expression by stabilizing mRNA. We hypothesized that HuR would increase ACE2 protein expression. We analyzed scRNA-seq data to profile ELAVL1 expression in distinct respiratory cell populations in COVID-19 and COPD patients. HuR expression and cellular localization was evaluated in COPD lung tissue by multiplex immunohistochemistry and in human lung cells by imaging flow cytometry. The regulation of ACE2 expression was evaluated using siRNA-mediated knockdown of HuR. There is a significant positive correlation between ELAVL1 and ACE2 in COPD cells. HuR cytoplasmic localization is higher in smoker and COPD lung tissue; there were also higher levels of cleaved HuR (CP-1). HuR binds to ACE2 mRNA but knockdown of HuR does not change ACE2 protein levels in primary human lung fibroblasts (HLFs). Our work is the first to investigate the association between ACE2 and HuR. Further investigation is needed to understand the mechanistic underpinning behind the regulation of ACE2 expression.


Subject(s)
Angiotensin-Converting Enzyme 2/genetics , COVID-19/genetics , ELAV-Like Protein 1/genetics , Gene Expression Regulation , Lung/metabolism , Aged , Angiotensin-Converting Enzyme 2/metabolism , COVID-19/metabolism , COVID-19/virology , Cells, Cultured , ELAV-Like Protein 1/metabolism , Female , Fibroblasts/metabolism , Gene Expression Profiling/methods , Humans , Lung/pathology , Lung/virology , Male , Middle Aged , Pulmonary Disease, Chronic Obstructive/genetics , Pulmonary Disease, Chronic Obstructive/metabolism , Pulmonary Disease, Chronic Obstructive/virology , RNA Interference , RNA-Seq/methods , SARS-CoV-2/physiology , Single-Cell Analysis/methods
9.
Genes (Basel) ; 12(7)2021 07 09.
Article in English | MEDLINE | ID: covidwho-1302193

ABSTRACT

Chronic inflammatory lung diseases are characterized by uncontrolled immune response in the airways as their main pathophysiological manifestation. The lack of specific diagnostic and therapeutic biomarkers for many pulmonary diseases represents a major challenge for pulmonologists. The majority of the currently approved therapeutic approaches are focused on achieving disease remission, although there is no guarantee of complete recovery. It is known that angiotensin-converting enzyme 2 (ACE2), an important counter-regulatory component of the renin-angiotensin-aldosterone system (RAAS), is expressed in the airways. It has been shown that ACE2 plays a role in systemic regulation of the cardiovascular and renal systems, lungs and liver by acting on blood pressure, electrolyte balance control mechanisms and inflammation. Its protective role in the lungs has also been presented, but the exact pathophysiological mechanism of action is still elusive. The aim of this study is to review and discuss recent findings about ACE2, including its potential role in the pathophysiology of chronic inflammatory lung diseases:, i.e., chronic obstructive pulmonary disease, asthma, and pulmonary hypertension. Additionally, in the light of the coronavirus 2019 disease (COVID-19), we will discuss the role of ACE2 in the pathophysiology of this disease, mainly represented by different grades of pulmonary problems. We believe that these insights will open up new perspectives for the future use of ACE2 as a potential biomarker for early diagnosis and monitoring of chronic inflammatory lung diseases.


Subject(s)
Angiotensin-Converting Enzyme 2/metabolism , Asthma/diagnosis , COVID-19 Testing , COVID-19/enzymology , Hypertension, Pulmonary/diagnosis , Lung/enzymology , Pulmonary Disease, Chronic Obstructive/diagnosis , SARS-CoV-2/metabolism , Angiotensin-Converting Enzyme 2/genetics , Asthma/enzymology , Asthma/genetics , COVID-19/genetics , Humans , Hypertension, Pulmonary/enzymology , Hypertension, Pulmonary/genetics , Inflammation/diagnosis , Inflammation/enzymology , Inflammation/genetics , Lung/pathology , Pulmonary Disease, Chronic Obstructive/enzymology , Pulmonary Disease, Chronic Obstructive/genetics , Renin-Angiotensin System
10.
Respir Res ; 22(1): 164, 2021 May 29.
Article in English | MEDLINE | ID: covidwho-1247590

ABSTRACT

BACKGROUND: Chronic obstructive pulmonary disease (COPD) patients are at increased risk of poor outcome from Coronavirus disease (COVID-19). Early data suggest elevated Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) receptor angiotensin converting enzyme 2 (ACE2) expression, but relationships to disease phenotype and downstream regulators of inflammation in the Renin-Angiotensin system (RAS) are unknown. We aimed to determine the relationship between RAS gene expression relevant to SARS-CoV-2 infection in the lung with disease characteristics in COPD, and the regulation of newly identified SARS-CoV-2 receptors and spike-cleaving proteases, important for SARS-CoV-2 infection. METHODS: We quantified gene expression using RNA sequencing of epithelial brushings and bronchial biopsies from 31 COPD and 37 control subjects. RESULTS: ACE2 gene expression (log2-fold change (FC)) was increased in COPD compared to ex-smoking (HV-ES) controls in epithelial brushings (0.25, p = 0.042) and bronchial biopsies (0.23, p = 0.050), and correlated with worse lung function (r = - 0.28, p = 0.0090). ACE2 was further increased in frequent exacerbators compared to infrequent exacerbators (0.51, p = 0.00045) and associated with use of ACE inhibitors (ACEi) (0.50, p = 0.0034), having cardiovascular disease (0.23, p = 0.048) or hypertension (0.34, p = 0.0089), and inhaled corticosteroid use in COPD subjects in bronchial biopsies (0.33, p = 0.049). Angiotensin II receptor type (AGTR)1 and 2 expression was decreased in COPD bronchial biopsies compared to HV-ES controls with log2FC of -0.26 (p = 0.033) and - 0.40, (p = 0.0010), respectively. However, the AGTR1:2 ratio was increased in COPD subjects compared with HV-ES controls, log2FC of 0.57 (p = 0.0051). Basigin, a newly identified potential SARS-CoV-2 receptor was also upregulated in both brushes, log2FC of 0.17 (p = 0.0040), and bronchial biopsies, (log2FC of 0.18 (p = 0.017), in COPD vs HV-ES. Transmembrane protease, serine (TMPRSS)2 was not differentially regulated between control and COPD. However, various other spike-cleaving proteases were, including TMPRSS4 and Cathepsin B, in both epithelial brushes (log2FC of 0.25 (p = 0.0012) and log2FC of 0.56 (p = 5.49E-06), respectively) and bronchial biopsies (log2FC of 0.49 (p = 0.00021) and log2FC of 0.246 (p = 0.028), respectively). CONCLUSION: This study identifies key differences in expression of genes related to susceptibility and aetiology of COVID-19 within the COPD lung. Further studies to understand the impact on clinical course of disease are now required.


Subject(s)
COVID-19/genetics , Lung/metabolism , Pulmonary Disease, Chronic Obstructive/genetics , Transcriptome , Aged , Angiotensin-Converting Enzyme 2/genetics , Angiotensin-Converting Enzyme 2/metabolism , Basigin/genetics , Basigin/metabolism , COVID-19/diagnosis , COVID-19/metabolism , COVID-19/physiopathology , Case-Control Studies , Female , Forced Expiratory Volume , Gene Expression Regulation , Humans , Lung/physiopathology , Male , Middle Aged , Prognosis , Pulmonary Disease, Chronic Obstructive/diagnosis , Pulmonary Disease, Chronic Obstructive/metabolism , Pulmonary Disease, Chronic Obstructive/physiopathology , Receptor, Angiotensin, Type 1/genetics , Receptor, Angiotensin, Type 1/metabolism , Receptor, Angiotensin, Type 2/genetics , Receptor, Angiotensin, Type 2/metabolism , Vital Capacity
11.
Respir Med ; 184: 106466, 2021 08.
Article in English | MEDLINE | ID: covidwho-1230754

ABSTRACT

Alpha1-antitrypsin deficiency arises due to mutations in alpha1-antitrypsin (AAT) gene and represents the most prominent genetic predisposition to chronic obstructive pulmonary disease and emphysema. Since AAT plays important immunomodulatory and tissue-protective roles and since it was suggested to protect from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, we assessed this association in United Kingdom Biobank, a community-based cohort with >500,000 participants. The most common, mild AATD genotypes were associated neither with increased SARS-CoV-2 infection rates nor with increased SARS-CoV-2 fatalities, while the numbers of severe AATD cases were too low to allow definitive conclusions.


Subject(s)
COVID-19/prevention & control , Genetic Predisposition to Disease/genetics , alpha 1-Antitrypsin Deficiency/genetics , Acute Disease , COVID-19/epidemiology , COVID-19/mortality , Cohort Studies , Female , Humans , Male , Mutation , Negative Results , Peptide Fragments/genetics , Peptide Fragments/physiology , Pulmonary Disease, Chronic Obstructive/genetics , Pulmonary Emphysema/genetics , Severity of Illness Index , United Kingdom/epidemiology , alpha 1-Antitrypsin/genetics , alpha 1-Antitrypsin/physiology
12.
Genome Med ; 13(1): 66, 2021 04 21.
Article in English | MEDLINE | ID: covidwho-1197350

ABSTRACT

BACKGROUND: The large airway epithelial barrier provides one of the first lines of defense against respiratory viruses, including SARS-CoV-2 that causes COVID-19. Substantial inter-individual variability in individual disease courses is hypothesized to be partially mediated by the differential regulation of the genes that interact with the SARS-CoV-2 virus or are involved in the subsequent host response. Here, we comprehensively investigated non-genetic and genetic factors influencing COVID-19-relevant bronchial epithelial gene expression. METHODS: We analyzed RNA-sequencing data from bronchial epithelial brushings obtained from uninfected individuals. We related ACE2 gene expression to host and environmental factors in the SPIROMICS cohort of smokers with and without chronic obstructive pulmonary disease (COPD) and replicated these associations in two asthma cohorts, SARP and MAST. To identify airway biology beyond ACE2 binding that may contribute to increased susceptibility, we used gene set enrichment analyses to determine if gene expression changes indicative of a suppressed airway immune response observed early in SARS-CoV-2 infection are also observed in association with host factors. To identify host genetic variants affecting COVID-19 susceptibility in SPIROMICS, we performed expression quantitative trait (eQTL) mapping and investigated the phenotypic associations of the eQTL variants. RESULTS: We found that ACE2 expression was higher in relation to active smoking, obesity, and hypertension that are known risk factors of COVID-19 severity, while an association with interferon-related inflammation was driven by the truncated, non-binding ACE2 isoform. We discovered that expression patterns of a suppressed airway immune response to early SARS-CoV-2 infection, compared to other viruses, are similar to patterns associated with obesity, hypertension, and cardiovascular disease, which may thus contribute to a COVID-19-susceptible airway environment. eQTL mapping identified regulatory variants for genes implicated in COVID-19, some of which had pheWAS evidence for their potential role in respiratory infections. CONCLUSIONS: These data provide evidence that clinically relevant variation in the expression of COVID-19-related genes is associated with host factors, environmental exposures, and likely host genetic variation.


Subject(s)
Bronchi , COVID-19/genetics , Respiratory Mucosa , SARS-CoV-2 , Adult , Aged , Aged, 80 and over , Angiotensin-Converting Enzyme 2/genetics , Asthma/genetics , COVID-19/immunology , Cardiovascular Diseases/genetics , Cardiovascular Diseases/immunology , Gene Expression , Genetic Variation , Humans , Middle Aged , Obesity/genetics , Obesity/immunology , Pulmonary Disease, Chronic Obstructive/genetics , Quantitative Trait Loci , Risk Factors , Smoking/genetics
13.
Comput Biol Med ; 128: 104126, 2021 01.
Article in English | MEDLINE | ID: covidwho-996804

ABSTRACT

Genes act in groups known as gene modules, which accomplish different cellular functions in the body. The modular nature of gene networks was used in this study to detect functionally enriched modules in samples obtained from COPD patients. We analyzed modules extracted from COPD samples and identified crucial genes associated with the disease COVID-19. We also extracted modules from a COVID-19 dataset and analyzed a suspected set of genes that may be associated with this deadly disease. We used information available for two other viruses that cause SARS and MERS because their physiology is similar to that of the COVID-19 virus. We report several crucial genes associated with COVID-19: RPA2, POLD4, MAPK8, IRF7, JUN, NFKB1, NFKBIA, CD40LG, FASLG, ICAM1, LIFR, STAT2 and CCR1. Most of these genes are related to the immune system and respiratory organs, which emphasizes the fact that COPD weakens this system and makes patients more susceptible to developing severe COVID-19.


Subject(s)
COVID-19/genetics , Databases, Nucleic Acid , Genetic Predisposition to Disease , Pulmonary Disease, Chronic Obstructive/genetics , SARS-CoV-2/genetics , COVID-19/immunology , Humans , Pulmonary Disease, Chronic Obstructive/immunology , Pulmonary Disease, Chronic Obstructive/virology , SARS-CoV-2/immunology , Severity of Illness Index
14.
Am J Hum Genet ; 108(1): 194-201, 2021 01 07.
Article in English | MEDLINE | ID: covidwho-971875

ABSTRACT

Given the coronavirus disease 2019 (COVID-19) pandemic, investigations into host susceptibility to infectious diseases and downstream sequelae have never been more relevant. Pneumonia is a lung disease that can cause respiratory failure and hypoxia and is a common complication of infectious diseases, including COVID-19. Few genome-wide association studies (GWASs) of host susceptibility and severity of pneumonia have been conducted. We performed GWASs of pneumonia susceptibility and severity in the Vanderbilt University biobank (BioVU) with linked electronic health records (EHRs), including Illumina Expanded Multi-Ethnic Global Array (MEGAEX)-genotyped European ancestry (EA, n= 69,819) and African ancestry (AA, n = 15,603) individuals. Two regions of large effect were identified: the CFTR locus in EA (rs113827944; OR = 1.84, p value = 1.2 × 10-36) and HBB in AA (rs334 [p.Glu7Val]; OR = 1.63, p value = 3.5 × 10-13). Mutations in these genes cause cystic fibrosis (CF) and sickle cell disease (SCD), respectively. After removing individuals diagnosed with CF and SCD, we assessed heterozygosity effects at our lead variants. Further GWASs after removing individuals with CF uncovered an additional association in R3HCC1L (rs10786398; OR = 1.22, p value = 3.5 × 10-8), which was replicated in two independent datasets: UK Biobank (n = 459,741) and 7,985 non-overlapping BioVU subjects, who are genotyped on arrays other than MEGAEX. This variant was also validated in GWASs of COVID-19 hospitalization and lung function. Our results highlight the importance of the host genome in infectious disease susceptibility and severity and offer crucial insight into genetic effects that could potentially influence severity of COVID-19 sequelae.


Subject(s)
COVID-19/complications , COVID-19/genetics , Host-Pathogen Interactions/genetics , Pneumonia, Viral/complications , Pneumonia, Viral/genetics , Bronchitis/genetics , COVID-19/pathology , COVID-19/physiopathology , Cystic Fibrosis Transmembrane Conductance Regulator/genetics , Databases, Genetic , Electronic Health Records , Female , Genome-Wide Association Study , Genotype , Hemoglobins/genetics , Humans , Inpatients , Linkage Disequilibrium , Male , Outpatients , Pneumonia, Viral/pathology , Pneumonia, Viral/physiopathology , Polymorphism, Single Nucleotide/genetics , Principal Component Analysis , Pulmonary Disease, Chronic Obstructive/genetics , Reproducibility of Results , United Kingdom
15.
J Allergy Clin Immunol ; 147(2): 510-519.e5, 2021 Feb.
Article in English | MEDLINE | ID: covidwho-872184

ABSTRACT

BACKGROUND: The mechanisms underlying altered susceptibility and propensity to severe Coronavirus disease 2019 (COVID-19) disease in at-risk groups such as patients with chronic obstructive pulmonary disease (COPD) are poorly understood. Inhaled corticosteroids (ICSs) are widely used in COPD, but the extent to which these therapies protect or expose patients to risk of severe COVID-19 is unknown. OBJECTIVE: The aim of this study was to evaluate the effect of ICSs following pulmonary expression of the SARS-CoV-2 viral entry receptor angiotensin-converting enzyme-2 (ACE2). METHODS: We evaluated the effect of ICS administration on pulmonary ACE2 expression in vitro in human airway epithelial cell cultures and in vivo in mouse models of ICS administration. Mice deficient in the type I IFN-α/ß receptor (Ifnar1-/-) and administration of exogenous IFN-ß were used to study the functional role of type-I interferon signaling in ACE2 expression. We compared sputum ACE2 expression in patients with COPD stratified according to use or nonuse of ICS. RESULTS: ICS administration attenuated ACE2 expression in mice, an effect that was reversed by exogenous IFN-ß administration, and Ifnar1-/- mice had reduced ACE2 expression, indicating that type I interferon contributes mechanistically to this effect. ICS administration attenuated expression of ACE2 in airway epithelial cell cultures from patients with COPD and in mice with elastase-induced COPD-like changes. Compared with ICS nonusers, patients with COPD who were taking ICSs also had reduced sputum expression of ACE2. CONCLUSION: ICS therapies in COPD reduce expression of the SARS-CoV-2 entry receptor ACE2. This effect may thus contribute to altered susceptibility to COVID-19 in patients with COPD.


Subject(s)
Adrenal Cortex Hormones/administration & dosage , Angiotensin-Converting Enzyme 2/antagonists & inhibitors , COVID-19 , Interferon Type I/antagonists & inhibitors , Pulmonary Disease, Chronic Obstructive/immunology , SARS-CoV-2 , Administration, Inhalation , Aged , Angiotensin-Converting Enzyme 2/genetics , Angiotensin-Converting Enzyme 2/immunology , Animals , Bronchi/cytology , Cells, Cultured , Disease Susceptibility , Down-Regulation/drug effects , Epithelial Cells/drug effects , Epithelial Cells/immunology , Female , Humans , Interferon Type I/immunology , Lung/drug effects , Lung/immunology , Male , Mice, Inbred C57BL , Mice, Knockout , Middle Aged , Pulmonary Disease, Chronic Obstructive/genetics , Receptor, Interferon alpha-beta/genetics , Serine Endopeptidases/genetics
16.
Sci Adv ; 6(33): eabb7238, 2020 08.
Article in English | MEDLINE | ID: covidwho-733188

ABSTRACT

Cigarette smoking, the leading cause of chronic obstructive pulmonary disease (COPD), has been implicated as a risk factor for severe disease in patients infected with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Here we show that mice with lung epithelial cell-specific loss of function of Miz1, which we identified as a negative regulator of nuclear factor κB (NF-κB) signaling, spontaneously develop progressive age-related changes resembling COPD. Furthermore, loss of Miz1 up-regulates the expression of Ace2, the receptor for SARS-CoV-2. Concomitant partial loss of NF-κB/RelA prevented the development of COPD-like phenotype in Miz1-deficient mice. Miz1 protein levels are reduced in the lungs from patients with COPD, and in the lungs of mice exposed to chronic cigarette smoke. Our data suggest that Miz1 down-regulation-induced sustained activation of NF-κB-dependent inflammation in the lung epithelium is sufficient to induce progressive lung and airway destruction that recapitulates features of COPD, with implications for COVID-19.


Subject(s)
Epithelial Cells/metabolism , Kruppel-Like Transcription Factors/metabolism , Lung/metabolism , Peptidyl-Dipeptidase A/metabolism , Phenotype , Protein Inhibitors of Activated STAT/genetics , Pulmonary Disease, Chronic Obstructive/genetics , Ubiquitin-Protein Ligases/genetics , Up-Regulation/genetics , Angiotensin-Converting Enzyme 2 , Animals , Betacoronavirus , COVID-19 , Coronavirus Infections/metabolism , Coronavirus Infections/virology , Gene Knockout Techniques , Humans , Mice , Mice, Inbred C57BL , Mice, Knockout , Pandemics , Pneumonia, Viral/metabolism , Pneumonia, Viral/virology , Protein Inhibitors of Activated STAT/metabolism , Pulmonary Disease, Chronic Obstructive/etiology , Pulmonary Disease, Chronic Obstructive/metabolism , SARS-CoV-2 , Signal Transduction/genetics , Smoking/adverse effects , Transcription Factor RelA/metabolism , Ubiquitin-Protein Ligases/metabolism
17.
Eur J Clin Invest ; 50(10): e13382, 2020 Oct.
Article in English | MEDLINE | ID: covidwho-706530

ABSTRACT

In barely nine months, the pandemic known as COVID-19 has spread over 200 countries, affecting more than 22 million people and causing over than 786 000 deaths. Elderly people and patients with previous comorbidities such as hypertension and diabetes are at an increased risk to suffer a poor prognosis after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Although the same could be expected from patients with chronic obstructive pulmonary disease (COPD), current epidemiological data are conflicting. This could lead to a reduction of precautionary measures in these patients, in the context of a particularly complex global health crisis. Most COPD patients have a long history of smoking or exposure to other harmful particles or gases, capable of impairing pulmonary defences even years after the absence of exposure. Moreover, COPD is characterized by an ongoing immune dysfunction, which affects both pulmonary and systemic cellular and molecular inflammatory mediators. Consequently, increased susceptibility to viral respiratory infections have been reported in COPD, often worsened by bacterial co-infections and leading to serious clinical outcomes. The present paper is an up-to-date review that discusses the available research regarding the implications of coronavirus infection in COPD. Although validation in large studies is still needed, COPD likely increases SARS-CoV-2 susceptibility and increases COVID-19 severity. Hence, specific mechanisms to monitor and assess COPD patients should be addressed in the current pandemic.


Subject(s)
Coronavirus Infections/epidemiology , Pneumonia, Viral/epidemiology , Pulmonary Disease, Chronic Obstructive/epidemiology , Betacoronavirus , Biomass , COVID-19 , Coronavirus Infections/immunology , Coronavirus Infections/physiopathology , Disease Susceptibility , Environmental Exposure/statistics & numerical data , Genetic Predisposition to Disease , Humans , Pandemics , Particulate Matter , Pneumonia, Viral/immunology , Pneumonia, Viral/physiopathology , Pulmonary Disease, Chronic Obstructive/genetics , Pulmonary Disease, Chronic Obstructive/immunology , SARS-CoV-2 , Severity of Illness Index , Smoke , Smoking/epidemiology , Smoking/immunology
19.
J Infect Dis ; 222(4): 556-563, 2020 07 23.
Article in English | MEDLINE | ID: covidwho-593365

ABSTRACT

Patients who died from COVID-19 often had comorbidities, such as hypertension, diabetes, and chronic obstructive lung disease. Although angiotensin-converting enzyme 2 (ACE2) is crucial for SARS-CoV-2 to bind and enter host cells, no study has systematically assessed the ACE2 expression in the lungs of patients with these diseases. Here, we analyzed over 700 lung transcriptome samples from patients with comorbidities associated with severe COVID-19 and found that ACE2 was highly expressed in these patients compared to control individuals. This finding suggests that patients with such comorbidities may have higher chances of developing severe COVID-19. Correlation and network analyses revealed many potential regulators of ACE2 in the human lung, including genes related to histone modifications, such as HAT1, HDAC2, and KDM5B. Our systems biology approach offers a possible explanation for increased COVID-19 severity in patients with certain comorbidities.


Subject(s)
Coronavirus Infections/epidemiology , Lung/enzymology , Peptidyl-Dipeptidase A/metabolism , Pneumonia, Viral/epidemiology , Angiotensin-Converting Enzyme 2 , COVID-19 , Case-Control Studies , Cerebrovascular Disorders/epidemiology , Cerebrovascular Disorders/genetics , Comorbidity , Coronary Disease/epidemiology , Coronary Disease/genetics , Coronavirus Infections/enzymology , Coronavirus Infections/genetics , Diabetes Complications/epidemiology , Diabetes Complications/genetics , Epigenomics , Female , Humans , Hypertension/epidemiology , Hypertension/genetics , Male , Pandemics , Peptidyl-Dipeptidase A/genetics , Pneumonia, Viral/enzymology , Pneumonia, Viral/genetics , Pulmonary Disease, Chronic Obstructive/epidemiology , Pulmonary Disease, Chronic Obstructive/genetics , Severity of Illness Index , Systems Biology , Transcriptome
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