1
|
Li X, Li H, Christenson SA, Castro M, Denlinger LC, Erzurum SC, Fahy JV, Gaston BM, Israel E, Jarjour NN, Levy BD, Mauger DT, Moore WC, Zein J, Kaminski N, Wenzel SE, Woodruff PG, Bleecker ER, Meyers DA. Genetic analyses of chr11p15.5 region identify MUC5AC- MUC5B associated with asthma-related phenotypes. J Asthma 2023; 60:1824-1835. [PMID: 36946148 PMCID: PMC10524756 DOI: 10.1080/02770903.2023.2193631] [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: 01/30/2023] [Accepted: 03/16/2023] [Indexed: 03/23/2023]
Abstract
OBJECTIVE Genome-wide association studies (GWASs) have identified single nucleotide polymorphisms (SNPs) in chr11p15.5 region associated with asthma and idiopathic interstitial pneumonias (IIPs). We sought to identify functional genes for asthma by combining SNPs and mRNA expression in bronchial epithelial cells (BEC) in the Severe Asthma Research Program (SARP). METHODS Correlation analyses of mRNA expression of six candidate genes (AP2A2, MUC6, MUC2, MUC5AC, MUC5B, and TOLLIP) and asthma phenotypes were performed in the longitudinal cohort (n = 156) with RNAseq in BEC, and replicated in the cross-sectional cohort (n = 155). eQTL (n = 114) and genetic association analysis of asthma severity (426 severe vs. 531 non-severe asthma) were performed, and compared with previously published GWASs of IIPs and asthma. RESULTS Higher expression of AP2A2 and MUC5AC and lower expression of MUC5B in BEC were correlated with asthma, asthma exacerbations, and T2 biomarkers (P < 0.01). SNPs associated with asthma and IIPs in previous GWASs were eQTL SNPs for MUC5AC, MUC5B, or TOLLIP, however, they were not in strong linkage disequilibrium. The risk alleles for asthma or protective alleles for IIPs were associated with higher expression of MUC5AC and lower expression of MUC5B. rs11603634, rs12788104, and rs28415845 associated with moderate-to-severe asthma or adult onset asthma in previous GWASs were not associated with asthma severity (P > 0.8). CONCLUSIONS SNPs associated with asthma in chr11p15.5 region are not associated with asthma severity neither with IIPs. Higher expression of MUC5AC and lower expression of MUC5B are risk for asthma but protective for IIPs.
Collapse
Affiliation(s)
- Xingnan Li
- Division of Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona, Tucson, Arizona, USA
| | - Huashi Li
- Division of Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona, Tucson, Arizona, USA
| | - Stephanie A. Christenson
- Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, University of California at San Francisco, San Francisco, California, USA
| | - Mario Castro
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Kansas School of Medicine, Kansas City, Kansas, USA
| | - Loren C. Denlinger
- Department of Medicine, University of Wisconsin School of Medicine & Public Health, Madison, Wisconsin, USA
| | - Serpil C. Erzurum
- Lerner Research Institute and the Respiratory Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - John V. Fahy
- Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, University of California at San Francisco, San Francisco, California, USA
| | - Benjamin M. Gaston
- Wells Center for Pediatric Research and Riley Hospital for Children, Indiana University, Indianapolis, Indiana, USA
| | - Elliot Israel
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Nizar N. Jarjour
- Department of Medicine, University of Wisconsin School of Medicine & Public Health, Madison, Wisconsin, USA
| | - Bruce D. Levy
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - David T Mauger
- Department of Public Health Sciences, College of Medicine, Penn State University, Hershey, Pennsylvania, USA
| | - Wendy C. Moore
- Department of Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Joe Zein
- Lerner Research Institute and the Respiratory Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Naftali Kaminski
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Sally E. Wenzel
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Prescott G. Woodruff
- Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, University of California at San Francisco, San Francisco, California, USA
| | - Eugene R. Bleecker
- Division of Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona, Tucson, Arizona, USA
| | - Deborah A. Meyers
- Division of Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona, Tucson, Arizona, USA
| | | |
Collapse
|
2
|
Ren J, Wang XQ, Nakao T, Libby P, Shi GP. Differential Roles of Interleukin-6 in Severe Acute Respiratory Syndrome-Coronavirus-2 Infection and Cardiometabolic Diseases. CARDIOLOGY DISCOVERY 2023; 3:166-182. [PMID: 38152628 PMCID: PMC10750760 DOI: 10.1097/cd9.0000000000000096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
Severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) infection can lead to a cytokine storm, unleashed in part by pyroptosis of virus-infected macrophages and monocytes. Interleukin-6 (IL-6) has emerged as a key participant in this ominous complication of COVID-19. IL-6 antagonists have improved outcomes in patients with COVID-19 in some, but not all, studies. IL-6 signaling involves at least 3 distinct pathways, including classic-signaling, trans-signaling, and trans-presentation depending on the localization of IL-6 receptor and its binding partner glycoprotein gp130. IL-6 has become a therapeutic target in COVID-19, cardiovascular diseases, and other inflammatory conditions. However, the efficacy of inhibition of IL-6 signaling in metabolic diseases, such as obesity and diabetes, may depend in part on cell type-dependent actions of IL-6 in controlling lipid metabolism, glucose uptake, and insulin sensitivity owing to complexities that remain to be elucidated. The present review sought to summarize and discuss the current understanding of how and whether targeting IL-6 signaling ameliorates outcomes following SARS-CoV-2 infection and associated clinical complications, focusing predominantly on metabolic and cardiovascular diseases.
Collapse
Affiliation(s)
- Jingjing Ren
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
| | - Xiao-Qi Wang
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
| | - Tetsushi Nakao
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
| | - Peter Libby
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
| | - Guo-Ping Shi
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
| |
Collapse
|
3
|
Urbani F, Cometa M, Martelli C, Santoli F, Rana R, Ursitti A, Bonato M, Baraldo S, Contoli M, Papi A. Update on virus-induced asthma exacerbations. Expert Rev Clin Immunol 2023; 19:1259-1272. [PMID: 37470413 DOI: 10.1080/1744666x.2023.2239504] [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: 03/07/2023] [Revised: 06/01/2023] [Accepted: 07/18/2023] [Indexed: 07/21/2023]
Abstract
INTRODUCTION Viral infections are common triggers for asthma exacerbation. Subjects with asthma are more susceptible to viral infections and develop more severe or long-lasting lower respiratory tract symptoms than healthy individuals owing to impaired immune responses. Of the many viruses associated with asthma exacerbation, rhinovirus (RV) is the most frequently identified virus in both adults and children. AREAS COVERED We reviewed epidemiological and clinical links and mechanistic studies on virus-associated asthma exacerbations. We included sections on severe acute respiratory syndrome coronavirus 2 (SARS-CoV2), the latest evidence of coronavirus disease 2019 (COVID-19) in asthma patients, and past and future searches for therapeutic and prevention targets. EXPERT OPINION Early treatment or prevention of viral infections might significantly reduce the rate of asthma exacerbation, which is one of the key points of disease management. Although it is hypothetically possible nowadays to interfere with every step of the infectious cycle of respiratory tract viruses, vaccination development has provided some of the most encouraging results. Future research should proceed toward the development of a wider spectrum of vaccines to achieve a better quality of life for patients with asthma and to reduce the economic burden on the healthcare system.
Collapse
Affiliation(s)
- Francesca Urbani
- Department of Translational Medicine, University of Ferrara Medical School, University of Ferrara, Sant'anna University Hospital, Ferrara, Italy
| | - Marianna Cometa
- Department of Translational Medicine, University of Ferrara Medical School, University of Ferrara, Sant'anna University Hospital, Ferrara, Italy
| | - Chiara Martelli
- Department of Translational Medicine, University of Ferrara Medical School, University of Ferrara, Sant'anna University Hospital, Ferrara, Italy
| | - Federica Santoli
- Department of Translational Medicine, University of Ferrara Medical School, University of Ferrara, Sant'anna University Hospital, Ferrara, Italy
| | - Roberto Rana
- Department of Translational Medicine, University of Ferrara Medical School, University of Ferrara, Sant'anna University Hospital, Ferrara, Italy
| | - Antonio Ursitti
- Department of Translational Medicine, University of Ferrara Medical School, University of Ferrara, Sant'anna University Hospital, Ferrara, Italy
| | - Matteo Bonato
- Department of Cardiac, Thoracic and Vascular Sciences, University of Padova, Padova, Italy
| | - Simonetta Baraldo
- Department of Cardiac, Thoracic and Vascular Sciences, University of Padova, Padova, Italy
| | - Marco Contoli
- Department of Translational Medicine, University of Ferrara Medical School, University of Ferrara, Sant'anna University Hospital, Ferrara, Italy
| | - Alberto Papi
- Department of Translational Medicine, University of Ferrara Medical School, University of Ferrara, Sant'anna University Hospital, Ferrara, Italy
| |
Collapse
|
4
|
Van Buren E, Radicioni G, Lester S, O’Neal WK, Dang H, Kasela S, Garudadri S, Curtis JL, Han MK, Krishnan JA, Wan ES, Silverman EK, Hastie A, Ortega VE, Lappalainen T, Nawijn MC, van den Berge M, Christenson SA, Li Y, Cho MH, Kesimer M, Kelada SNP. Genetic regulators of sputum mucin concentration and their associations with COPD phenotypes. PLoS Genet 2023; 19:e1010445. [PMID: 37352370 PMCID: PMC10325042 DOI: 10.1371/journal.pgen.1010445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 07/06/2023] [Accepted: 04/26/2023] [Indexed: 06/25/2023] Open
Abstract
Hyper-secretion and/or hyper-concentration of mucus is a defining feature of multiple obstructive lung diseases, including chronic obstructive pulmonary disease (COPD). Mucus itself is composed of a mixture of water, ions, salt and proteins, of which the gel-forming mucins, MUC5AC and MUC5B, are the most abundant. Recent studies have linked the concentrations of these proteins in sputum to COPD phenotypes, including chronic bronchitis (CB) and acute exacerbations (AE). We sought to determine whether common genetic variants influence sputum mucin concentrations and whether these variants are also associated with COPD phenotypes, specifically CB and AE. We performed a GWAS to identify quantitative trait loci for sputum mucin protein concentration (pQTL) in the Sub-Populations and InteRmediate Outcome Measures in COPD Study (SPIROMICS, n = 708 for total mucin, n = 215 for MUC5AC, MUC5B). Subsequently, we tested for associations of mucin pQTL with CB and AE using regression modeling (n = 822-1300). Replication analysis was conducted using data from COPDGene (n = 5740) and by examining results from the UK Biobank. We identified one genome-wide significant pQTL for MUC5AC (rs75401036) and two for MUC5B (rs140324259, rs10001928). The strongest association for MUC5B, with rs140324259 on chromosome 11, explained 14% of variation in sputum MUC5B. Despite being associated with lower MUC5B, the C allele of rs140324259 conferred increased risk of CB (odds ratio (OR) = 1.42; 95% confidence interval (CI): 1.10-1.80) as well as AE ascertained over three years of follow up (OR = 1.41; 95% CI: 1.02-1.94). Associations between rs140324259 and CB or AE did not replicate in COPDGene. However, in the UK Biobank, rs140324259 was associated with phenotypes that define CB, namely chronic mucus production and cough, again with the C allele conferring increased risk. We conclude that sputum MUC5AC and MUC5B concentrations are associated with common genetic variants, and the top locus for MUC5B may influence COPD phenotypes, in particular CB.
Collapse
Affiliation(s)
- Eric Van Buren
- Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Giorgia Radicioni
- Marsico Lung Institute, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Sarah Lester
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Wanda K. O’Neal
- Marsico Lung Institute, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Hong Dang
- Marsico Lung Institute, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Silva Kasela
- New York Genome Center, New York, New York, United States of America
- Department of Systems Biology, Columbia University, New York, New York, United States of America
| | - Suresh Garudadri
- Division of Pulmonary, Critical Care, Allergy, & Sleep Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Jeffrey L. Curtis
- Pulmonary & Critical Care Medicine Division, University of Michigan, Ann Arbor, Michigan, United States of America
- Medical Service, VA Ann Arbor Healthcare System, Ann Arbor, Michigan, United States of America
| | - MeiLan K. Han
- Pulmonary & Critical Care Medicine Division, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Jerry A. Krishnan
- Breathe Chicago Center, University of Illinois, Chicago, Illinois, United States of America
| | - Emily S. Wan
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- VA Boston Healthcare System, Jamaica Plain, Massachusetts, United States of America
| | - Edwin K. Silverman
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Annette Hastie
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Victor E. Ortega
- Department of Internal Medicine, Division of Respiratory Medicine, Mayo Clinic, Scottsdale, Arizona, United States of America
| | - Tuuli Lappalainen
- New York Genome Center, New York, New York, United States of America
- Department of Systems Biology, Columbia University, New York, New York, United States of America
| | - Martijn C. Nawijn
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, Groningen, the Netherlands
| | - Maarten van den Berge
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, Groningen, the Netherlands
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Stephanie A. Christenson
- Division of Pulmonary, Critical Care, Allergy, & Sleep Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Yun Li
- Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Michael H. Cho
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Mehmet Kesimer
- Marsico Lung Institute, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Samir N. P. Kelada
- Marsico Lung Institute, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
| |
Collapse
|
5
|
Xu H, Lin S, Zhou Z, Li D, Zhang X, Yu M, Zhao R, Wang Y, Qian J, Li X, Li B, Wei C, Chen K, Yoshimura T, Wang JM, Huang J. New genetic and epigenetic insights into the chemokine system: the latest discoveries aiding progression toward precision medicine. Cell Mol Immunol 2023:10.1038/s41423-023-01032-x. [PMID: 37198402 DOI: 10.1038/s41423-023-01032-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 04/14/2023] [Indexed: 05/19/2023] Open
Abstract
Over the past thirty years, the importance of chemokines and their seven-transmembrane G protein-coupled receptors (GPCRs) has been increasingly recognized. Chemokine interactions with receptors trigger signaling pathway activity to form a network fundamental to diverse immune processes, including host homeostasis and responses to disease. Genetic and nongenetic regulation of both the expression and structure of chemokines and receptors conveys chemokine functional heterogeneity. Imbalances and defects in the system contribute to the pathogenesis of a variety of diseases, including cancer, immune and inflammatory diseases, and metabolic and neurological disorders, which render the system a focus of studies aiming to discover therapies and important biomarkers. The integrated view of chemokine biology underpinning divergence and plasticity has provided insights into immune dysfunction in disease states, including, among others, coronavirus disease 2019 (COVID-19). In this review, by reporting the latest advances in chemokine biology and results from analyses of a plethora of sequencing-based datasets, we outline recent advances in the understanding of the genetic variations and nongenetic heterogeneity of chemokines and receptors and provide an updated view of their contribution to the pathophysiological network, focusing on chemokine-mediated inflammation and cancer. Clarification of the molecular basis of dynamic chemokine-receptor interactions will help advance the understanding of chemokine biology to achieve precision medicine application in the clinic.
Collapse
Affiliation(s)
- Hanli Xu
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Shuye Lin
- Cancer Research Center, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, 101149, Beijing, China
| | - Ziyun Zhou
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Duoduo Li
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Xiting Zhang
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Muhan Yu
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Ruoyi Zhao
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Yiheng Wang
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Junru Qian
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Xinyi Li
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Bohan Li
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Chuhan Wei
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Keqiang Chen
- Laboratory of Cancer Innovation, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA
| | - Teizo Yoshimura
- Laboratory of Cancer Innovation, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA
| | - Ji Ming Wang
- Laboratory of Cancer Innovation, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA
| | - Jiaqiang Huang
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China.
- Cancer Research Center, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, 101149, Beijing, China.
- Laboratory of Cancer Innovation, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA.
| |
Collapse
|
6
|
Li X, Guerra S, Ledford JG, Kraft M, Li H, Hastie AT, Castro M, Denlinger LC, Erzurum SC, Fahy JV, Gaston B, Israel E, Jarjour NN, Levy BD, Mauger DT, Moore WC, Zein J, Kaminski N, Wenzel SE, Woodruff PG, Meyers DA, Bleecker ER. Low CC16 mRNA Expression Levels in Bronchial Epithelial Cells Are Associated with Asthma Severity. Am J Respir Crit Care Med 2023; 207:438-451. [PMID: 36066606 PMCID: PMC9940145 DOI: 10.1164/rccm.202206-1230oc] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 09/02/2022] [Indexed: 11/16/2022] Open
Abstract
Rationale: CC16 is a protein mainly produced by nonciliated bronchial epithelial cells (BECs) that participates in host defense. Reduced CC16 protein concentrations in BAL and serum are associated with asthma susceptibility. Objectives: Few studies have investigated the relationship between CC16 and asthma progression, and none has focused on BECs. In this study, we sought to determine if CC16 mRNA expression levels in BECs are associated with asthma severity. Methods: Association analyses between CC16 mRNA expression levels in BECs (242 asthmatics and 69 control subjects) and asthma-related phenotypes in Severe Asthma Research Program were performed using a generalized linear model. Measurements and Main Results: Low CC16 mRNA expression levels in BECs were significantly associated with asthma susceptibility and asthma severity, high systemic corticosteroids use, high retrospective and prospective asthma exacerbations, and low pulmonary function. Low CC16 mRNA expression levels were significantly associated with high T2 inflammation biomarkers (fractional exhaled nitric oxide and sputum eosinophils). CC16 mRNA expression levels were negatively correlated with expression levels of Th2 genes (IL1RL1, POSTN, SERPINB2, CLCA1, NOS2, and MUC5AC) and positively correlated with expression levels of Th1 and inflammation genes (IL12A and MUC5B). A combination of two nontraditional T2 biomarkers (CC16 and IL-6) revealed four asthma endotypes with different characteristics of T2 inflammation, obesity, and asthma severity. Conclusions: Our findings indicate that low CC16 mRNA expression levels in BECs are associated with asthma susceptibility, severity, and exacerbations, partially through immunomodulation of T2 inflammation. CC16 is a potential nontraditional T2 biomarker for asthma development and progression.
Collapse
Affiliation(s)
- Xingnan Li
- Division of Genetics, Genomics, and Precision Medicine, and
| | - Stefano Guerra
- Asthma and Airway Disease Research Center, Department of Medicine, University of Arizona, Tucson, Arizona
| | - Julie G. Ledford
- Asthma and Airway Disease Research Center, Department of Medicine, University of Arizona, Tucson, Arizona
| | - Monica Kraft
- Asthma and Airway Disease Research Center, Department of Medicine, University of Arizona, Tucson, Arizona
| | - Huashi Li
- Division of Genetics, Genomics, and Precision Medicine, and
| | - Annette T. Hastie
- Department of Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Mario Castro
- Division of Pulmonary, Critical Care, and Sleep Medicine, University of Kansas School of Medicine, Kansas City, Kansas
| | - Loren C. Denlinger
- Department of Medicine, University of Wisconsin School of Medicine & Public Health, Madison, Wisconsin
| | - Serpil C. Erzurum
- Lerner Research Institute and the Respiratory Institute, Cleveland Clinic, Cleveland, Ohio
| | - John V. Fahy
- Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of California at San Francisco, San Francisco, California
| | - Benjamin Gaston
- Wells Center for Pediatric Research and Riley Hospital for Children, Indiana University, Indianapolis, Indiana
| | - Elliot Israel
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts
| | - Nizar N. Jarjour
- Department of Medicine, University of Wisconsin School of Medicine & Public Health, Madison, Wisconsin
| | - Bruce D. Levy
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts
| | - David T. Mauger
- Department of Public Health Sciences, College of Medicine, Penn State University, Hershey, Pennsylvania
| | - Wendy C. Moore
- Department of Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Joe Zein
- Lerner Research Institute and the Respiratory Institute, Cleveland Clinic, Cleveland, Ohio
| | - Naftali Kaminski
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut; and
| | - Sally E. Wenzel
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Prescott G. Woodruff
- Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of California at San Francisco, San Francisco, California
| | | | | |
Collapse
|
7
|
Ginebaugh SP, Hagner M, Ray A, Erzurum SC, Comhair SAA, Denlinger LC, Jarjour NN, Castro M, Woodruff PG, Christenson SA, Bleecker ER, Meyers DA, Hastie AT, Moore WC, Mauger DT, Israel E, Levy BD, Wenzel SE, Camiolo MJ. Bronchial epithelial cell transcriptional responses to inhaled corticosteroids dictate severe asthmatic outcomes. J Allergy Clin Immunol 2023:S0091-6749(23)00208-7. [PMID: 36796454 DOI: 10.1016/j.jaci.2023.01.028] [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: 08/18/2022] [Revised: 01/08/2023] [Accepted: 01/12/2023] [Indexed: 02/16/2023]
Abstract
BACKGROUND Inhaled corticosteroids (CSs) are the backbone of asthma treatment, improving quality of life, exacerbation rates, and mortality. Although effective for most, a subset of patients with asthma experience CS-resistant disease despite receiving high-dose medication. OBJECTIVE We sought to investigate the transcriptomic response of bronchial epithelial cells (BECs) to inhaled CSs. METHODS Independent component analysis was performed on datasets, detailing the transcriptional response of BECs to CS treatment. The expression of these CS-response components was examined in 2 patient cohorts and investigated in relation to clinical parameters. Supervised learning was used to predict BEC CS responses using peripheral blood gene expression. RESULTS We identified a signature of CS response that was closely correlated with CS use in patients with asthma. Participants could be separated on the basis of CS-response genes into groups with high and low signature expression. Patients with low expression of CS-response genes, particularly those with a severe asthma diagnosis, showed worse lung function and quality of life. These individuals demonstrated enrichment for T-lymphocyte infiltration in endobronchial brushings. Supervised machine learning identified a 7-gene signature from peripheral blood that reliably identified patients with poor CS-response expression in BECs. CONCLUSIONS Loss of CS transcriptional responses within bronchial epithelium was related to impaired lung function and poor quality of life, particularly in patients with severe asthma. These individuals were identified using minimally invasive blood sampling, suggesting these findings may enable earlier triage to alternative treatments.
Collapse
Affiliation(s)
- Scott P Ginebaugh
- Integrative Systems Biology, University of Pittsburgh, Pittsburgh, Pa
| | | | - Anuradha Ray
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pa; Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pa
| | | | | | - Loren C Denlinger
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wis
| | - Nizar N Jarjour
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wis
| | - Mario Castro
- University of Kansas School of Medicine, Kansas City, Mo
| | - Prescott G Woodruff
- University of California, San Francisco School of Medicine, San Francisco, Calif
| | | | - Eugene R Bleecker
- Division for Genetics, Genomics and Personalized Medicine, University of Arizona College of Medicine, Tucson, Ariz
| | - Deborah A Meyers
- Division for Genetics, Genomics and Personalized Medicine, University of Arizona College of Medicine, Tucson, Ariz
| | | | - Wendy C Moore
- Wake Forest University School of Medicine, Winston-Salem, NC
| | | | - Elliot Israel
- Department of Medicine, Divisions of Pulmonary & Critical Care Medicine & Allergy & Immunology, Brigham & Women's Hospital, Harvard Medical School, Boston, Mass
| | - Bruce D Levy
- Department of Medicine, Divisions of Pulmonary & Critical Care Medicine & Allergy & Immunology, Brigham & Women's Hospital, Harvard Medical School, Boston, Mass
| | - Sally E Wenzel
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pa; Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pa; Department of Environmental Medicine and Occupational Health, Graduate School of Public Health, University of Pittsburgh School of Medicine, Pittsburgh, Pa
| | | |
Collapse
|
8
|
Kottlors J, Fervers P, Geißen S, Gertz RJ, Bremm J, Rinneburger M, Weisthoff M, Shahzad R, Maintz D, Persigehl T. Morphological appearance of the B.1.1.7 mutation of the novel coronavirus 2 (SARS-CoV-2) in chest CT. Quant Imaging Med Surg 2023; 13:1058-1070. [PMID: 36819239 PMCID: PMC9929392 DOI: 10.21037/qims-22-718] [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: 07/07/2022] [Accepted: 12/01/2022] [Indexed: 01/15/2023]
Abstract
Background Diagnosing a coronavirus disease 2019 (COVID-19) infection with high specificity in chest computed tomography (CT) imaging is considered possible due to distinctive imaging features of COVID-19 pneumonia. Since other viral non-COVID pneumonia show mostly a different distribution pattern, it is reasonable to assume that the patterns observed caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are a consequence of its genetically encoded molecular properties when interacting with the respiratory tissue. As more mutations of the initial SARS-CoV-2 wild-type with varying aggressiveness have been detected in the course of 2021, it became obvious that its genome is in a state of transformation and therefore a potential modification of the specific morphological appearance in CT may occur. The aim of this study was to quantitatively analyze the morphological differences of the SARS-CoV-2-B.1.1.7 mutation and wildtype variant in CT scans of the thorax. Methods We analyzed a dataset of 140 patients, which was divided into pneumonias caused by n=40 wildtype variants, n=40 B.1.1.7 variants, n=20 bacterial pneumonias, n=20 viral (non-COVID) pneumonias, and a test group of n=20 unremarkable CT examinations of the thorax. Semiautomated 3D segmentation of the lung tissue was performed for quantification of lung pathologies. The extent, ratio, and specific distribution of inflammatory affected lung tissue in each group were compared in a multivariate group analysis. Results Lung segmentation revealed significant difference between the extent of ground glass opacities (GGO) or consolidation comparing SARS-CoV-2 wild-type and B.1.1.7 variant. Wildtype and B.1.1.7 variant showed both a symmetric distribution pattern of stage-dependent GGO and consolidation within matched COVID-19 stages. Viral non-COVID pneumonias had significantly fewer consolidations than the bacterial, but also than the COVID-19 B.1.1.7 variant groups. Conclusions CT based segmentation showed no significant difference between the morphological appearance of the COVID-19 wild-type variant and the SARS-CoV-2 B.1.1.7 mutation. However, our approach allowed a semiautomatic quantification of bacterial and viral lung pathologies. Quantitative CT image analyses, such as the one presented, appear to be an important component of pandemic preparedness considering an organism with ongoing genetic change, to describe a potential arising change in CT morphological appearance of possible new upcoming COVID-19 variants of concern.
Collapse
Affiliation(s)
- Jonathan Kottlors
- Institute for Diagnostic and Interventional Radiology, Faculty of Medicine and University Hospital Cologne, University of Cologne (UOC), Cologne, Germany
| | - Philipp Fervers
- Institute for Diagnostic and Interventional Radiology, Faculty of Medicine and University Hospital Cologne, University of Cologne (UOC), Cologne, Germany
| | - Simon Geißen
- Division of Cardiology, Pneumology, Angiology and Intensive Care, University of Cologne (UOC), Cologne, Germany
| | - Roman Johannes Gertz
- Institute for Diagnostic and Interventional Radiology, Faculty of Medicine and University Hospital Cologne, University of Cologne (UOC), Cologne, Germany
| | - Johannes Bremm
- Institute for Diagnostic and Interventional Radiology, Faculty of Medicine and University Hospital Cologne, University of Cologne (UOC), Cologne, Germany
| | - Miriam Rinneburger
- Institute for Diagnostic and Interventional Radiology, Faculty of Medicine and University Hospital Cologne, University of Cologne (UOC), Cologne, Germany
| | - Mathilda Weisthoff
- Institute for Diagnostic and Interventional Radiology, Faculty of Medicine and University Hospital Cologne, University of Cologne (UOC), Cologne, Germany
| | - Rahil Shahzad
- Institute for Diagnostic and Interventional Radiology, Faculty of Medicine and University Hospital Cologne, University of Cologne (UOC), Cologne, Germany;,Innovative Technology, Philips Healthcare, Aachen, Germany
| | - David Maintz
- Institute for Diagnostic and Interventional Radiology, Faculty of Medicine and University Hospital Cologne, University of Cologne (UOC), Cologne, Germany
| | - Thorsten Persigehl
- Institute for Diagnostic and Interventional Radiology, Faculty of Medicine and University Hospital Cologne, University of Cologne (UOC), Cologne, Germany
| |
Collapse
|
9
|
Patanavanich R, Siripoon T, Amponnavarat S, Glantz SA. Active Smokers Are at Higher Risk of COVID-19 Death: A Systematic Review and Meta-analysis. NICOTINE & TOBACCO RESEARCH : OFFICIAL JOURNAL OF THE SOCIETY FOR RESEARCH ON NICOTINE AND TOBACCO 2023; 25:177-184. [PMID: 35363877 DOI: 10.1093/ntr/ntac085] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 01/08/2022] [Accepted: 03/29/2022] [Indexed: 01/11/2023]
Abstract
INTRODUCTION Current evidence indicates that smoking worsens COVID-19 outcomes. However, when studies restricted their analyses to current smokers, the risks for COVID-19 severity and death are inconsistent. AIMS AND METHODS This meta-analysis explored the association between current smoking and the risk for mortality based on the studies that reported all three categories of smoking (current, former, and never smokers) to overcome the limitation of the previous meta-analyses which former smokers might have been classified as nonsmokers. We searched PubMed and Embase up to January 1, 2021. We included studies reporting all three categories of smoking behaviors of COVID-19 patients and mortality outcomes. A random-effects meta-analysis and meta-regression were used to examine relationships in the data. RESULTS A total of 34 articles with 35 193 COVID-19 patients was included. The meta-analysis confirmed the association between current smoking (odds ratio [OR] 1.26, 95% confidence interval [CI]: 1.01-1.58) and former smoking (OR 1.76, 95% CI: 1.53-2.03) with COVID-19 mortality. We also found that the risk for COVID-19 death in current smokers does not vary by age, but significantly drops by age in former smokers. Moreover, current smokers in non-high-income countries have higher risks of COVID-19 death compared with high-income countries (OR 3.11, 95% CI: 2.04-4.72 vs. OR 1.14, 95% CI: 0.91-1.43; p = .015). CONCLUSIONS Current and former smokers are at higher risk of dying from COVID-19. Tobacco control should be strengthened to encourage current smokers to quit and prevent the initiation of smoking. Public health professionals should take the COVID-19 pandemic as an opportunity to promote smoking prevention and cession. IMPLICATIONS This study makes an important contribution to the existing literature by distinguishing between current and former smoking and their separate effects on COVID-19 mortality. We also explore the effects by age of patients and country income level. Findings from this study provide empirical evidence against misinformation about the relationship between smoking and COVID-19 mortality.
Collapse
Affiliation(s)
- Roengrudee Patanavanich
- Department of Community Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Tanatorn Siripoon
- Department of Community Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Salin Amponnavarat
- Department of Community Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Stanton A Glantz
- Center for Tobacco Control Research and Education (retired), University of California San Francisco, San Francisco, CA, USA
| |
Collapse
|
10
|
Duarte T, Silva MDM, Michelotti P, Barbosa NBDV, Feltes BC, Dorn M, Rocha JBTD, Dalla Corte CL. The Drosophila melanogaster ACE2 ortholog genes are differently expressed in obesity/diabetes and aging models: Implications for COVID-19 pathology. Biochim Biophys Acta Mol Basis Dis 2022; 1868:166551. [PMID: 36116726 PMCID: PMC9474972 DOI: 10.1016/j.bbadis.2022.166551] [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: 05/06/2022] [Revised: 08/08/2022] [Accepted: 09/12/2022] [Indexed: 11/29/2022]
Abstract
The Spike glycoprotein of SARS-CoV-2, the virus responsible for coronavirus disease 2019, binds to its ACE2 receptor for internalization in the host cells. Elderly individuals or those with subjacent disorders, such as obesity and diabetes, are more susceptible to COVID-19 severity. Additionally, several SARS-CoV-2 variants appear to enhance the Spike-ACE2 interaction, which increases transmissibility and death. Considering that the fruit fly is a robust animal model in metabolic research and has two ACE2 orthologs, Ance and Acer, in this work, we studied the effects of two hypercaloric diets (HFD and HSD) and aging on ACE2 orthologs mRNA expression levels in Drosophila melanogaster. To complement our work, we analyzed the predicted binding affinity between the Spike protein with Ance and Acer. We show for the first time that Ance and Acer genes are differentially regulated and dependent on diet and age in adult flies. At the molecular level, Ance and Acer proteins exhibit the potential to bind to the Spike protein in different regions, as shown by a molecular docking approach. Acer, in particular, interacts with the Spike protein in the same region as in humans. Overall, we suggest that the D. melanogaster is a promising animal model for translational studies on COVID-19 associated risk factors and ACE2.
Collapse
Affiliation(s)
- Tâmie Duarte
- Department of Biochemistry and Molecular Biology, Natural and Exact Sciences Center, Federal University of Santa Maria, 1000 Roraima Avenue, Santa Maria, RS 97105-900, Brazil
| | - Mônica de Medeiros Silva
- Department of Biochemistry and Molecular Biology, Natural and Exact Sciences Center, Federal University of Santa Maria, 1000 Roraima Avenue, Santa Maria, RS 97105-900, Brazil
| | - Paula Michelotti
- Department of Biochemistry and Molecular Biology, Natural and Exact Sciences Center, Federal University of Santa Maria, 1000 Roraima Avenue, Santa Maria, RS 97105-900, Brazil
| | - Nilda Berenice de Vargas Barbosa
- Department of Biochemistry and Molecular Biology, Natural and Exact Sciences Center, Federal University of Santa Maria, 1000 Roraima Avenue, Santa Maria, RS 97105-900, Brazil
| | - Bruno César Feltes
- Institute of Informatics, Federal University of Rio Grande do Sul, 9500 Bento Gonçalves Avenue, Porto Alegre, RS 91501-970, Brazil; Institute of Biosciences, Federal University of Rio Grande do Sul, 9500 Bento Gonçalves Avenue, Porto Alegre, RS 91501-970, Brazil
| | - Márcio Dorn
- Institute of Informatics, Federal University of Rio Grande do Sul, 9500 Bento Gonçalves Avenue, Porto Alegre, RS 91501-970, Brazil; Center of Biotechnology, Federal University of Rio Grande do Sul, 9500 Bento Gonçalves Avenue, Porto Alegre, RS 91501-970, Brazil; National Institute of Science and Technology - Forensic Science, 6681 Ipiranga Avenue, Porto Alegre, RS 90619-900, Brazil
| | - João Batista Teixeira da Rocha
- Department of Biochemistry and Molecular Biology, Natural and Exact Sciences Center, Federal University of Santa Maria, 1000 Roraima Avenue, Santa Maria, RS 97105-900, Brazil
| | - Cristiane Lenz Dalla Corte
- Department of Biochemistry and Molecular Biology, Natural and Exact Sciences Center, Federal University of Santa Maria, 1000 Roraima Avenue, Santa Maria, RS 97105-900, Brazil.
| |
Collapse
|
11
|
Wang QS, Edahiro R, Namkoong H, Hasegawa T, Shirai Y, Sonehara K, Tanaka H, Lee H, Saiki R, Hyugaji T, Shimizu E, Katayama K, Kanai M, Naito T, Sasa N, Yamamoto K, Kato Y, Morita T, Takahashi K, Harada N, Naito T, Hiki M, Matsushita Y, Takagi H, Ichikawa M, Nakamura A, Harada S, Sandhu Y, Kabata H, Masaki K, Kamata H, Ikemura S, Chubachi S, Okamori S, Terai H, Morita A, Asakura T, Sasaki J, Morisaki H, Uwamino Y, Nanki K, Uchida S, Uno S, Nishimura T, Ishiguro T, Isono T, Shibata S, Matsui Y, Hosoda C, Takano K, Nishida T, Kobayashi Y, Takaku Y, Takayanagi N, Ueda S, Tada A, Miyawaki M, Yamamoto M, Yoshida E, Hayashi R, Nagasaka T, Arai S, Kaneko Y, Sasaki K, Tagaya E, Kawana M, Arimura K, Takahashi K, Anzai T, Ito S, Endo A, Uchimura Y, Miyazaki Y, Honda T, Tateishi T, Tohda S, Ichimura N, Sonobe K, Sassa CT, Nakajima J, Nakano Y, Nakajima Y, Anan R, Arai R, Kurihara Y, Harada Y, Nishio K, Ueda T, Azuma M, Saito R, Sado T, Miyazaki Y, Sato R, Haruta Y, Nagasaki T, Yasui Y, Hasegawa Y, Mutoh Y, Kimura T, Sato T, Takei R, Hagimoto S, Noguchi Y, Yamano Y, Sasano H, Ota S, Nakamori Y, Yoshiya K, Saito F, Yoshihara T, Wada D, Iwamura H, Kanayama S, Maruyama S, Yoshiyama T, Ohta K, Kokuto H, Ogata H, Tanaka Y, Arakawa K, Shimoda M, Osawa T, Tateno H, Hase I, Yoshida S, Suzuki S, Kawada M, Horinouchi H, Saito F, Mitamura K, Hagihara M, Ochi J, Uchida T, Baba R, Arai D, Ogura T, Takahashi H, Hagiwara S, Nagao G, Konishi S, Nakachi I, Murakami K, Yamada M, Sugiura H, Sano H, Matsumoto S, Kimura N, Ono Y, Baba H, Suzuki Y, Nakayama S, Masuzawa K, Namba S, Shiroyama T, Noda Y, Niitsu T, Adachi Y, Enomoto T, Amiya S, Hara R, Yamaguchi Y, Murakami T, Kuge T, Matsumoto K, Yamamoto Y, Yamamoto M, Yoneda M, Tomono K, Kato K, Hirata H, Takeda Y, Koh H, Manabe T, Funatsu Y, Ito F, Fukui T, Shinozuka K, Kohashi S, Miyazaki M, Shoko T, Kojima M, Adachi T, Ishikawa M, Takahashi K, Inoue T, Hirano T, Kobayashi K, Takaoka H, Watanabe K, Miyazawa N, Kimura Y, Sado R, Sugimoto H, Kamiya A, Kuwahara N, Fujiwara A, Matsunaga T, Sato Y, Okada T, Hirai Y, Kawashima H, Narita A, Niwa K, Sekikawa Y, Nishi K, Nishitsuji M, Tani M, Suzuki J, Nakatsumi H, Ogura T, Kitamura H, Hagiwara E, Murohashi K, Okabayashi H, Mochimaru T, Nukaga S, Satomi R, Oyamada Y, Mori N, Baba T, Fukui Y, Odate M, Mashimo S, Makino Y, Yagi K, Hashiguchi M, Kagyo J, Shiomi T, Fuke S, Saito H, Tsuchida T, Fujitani S, Takita M, Morikawa D, Yoshida T, Izumo T, Inomata M, Kuse N, Awano N, Tone M, Ito A, Nakamura Y, Hoshino K, Maruyama J, Ishikura H, Takata T, Odani T, Amishima M, Hattori T, Shichinohe Y, Kagaya T, Kita T, Ohta K, Sakagami S, Koshida K, Hayashi K, Shimizu T, Kozu Y, Hiranuma H, Gon Y, Izumi N, Nagata K, Ueda K, Taki R, Hanada S, Kawamura K, Ichikado K, Nishiyama K, Muranaka H, Nakamura K, Hashimoto N, Wakahara K, Koji S, Omote N, Ando A, Kodama N, Kaneyama Y, Maeda S, Kuraki T, Matsumoto T, Yokote K, Nakada TA, Abe R, Oshima T, Shimada T, Harada M, Takahashi T, Ono H, Sakurai T, Shibusawa T, Kimizuka Y, Kawana A, Sano T, Watanabe C, Suematsu R, Sageshima H, Yoshifuji A, Ito K, Takahashi S, Ishioka K, Nakamura M, Masuda M, Wakabayashi A, Watanabe H, Ueda S, Nishikawa M, Chihara Y, Takeuchi M, Onoi K, Shinozuka J, Sueyoshi A, Nagasaki Y, Okamoto M, Ishihara S, Shimo M, Tokunaga Y, Kusaka Y, Ohba T, Isogai S, Ogawa A, Inoue T, Fukuyama S, Eriguchi Y, Yonekawa A, Kan-o K, Matsumoto K, Kanaoka K, Ihara S, Komuta K, Inoue Y, Chiba S, Yamagata K, Hiramatsu Y, Kai H, Asano K, Oguma T, Ito Y, Hashimoto S, Yamasaki M, Kasamatsu Y, Komase Y, Hida N, Tsuburai T, Oyama B, Takada M, Kanda H, Kitagawa Y, Fukuta T, Miyake T, Yoshida S, Ogura S, Abe S, Kono Y, Togashi Y, Takoi H, Kikuchi R, Ogawa S, Ogata T, Ishihara S, Kanehiro A, Ozaki S, Fuchimoto Y, Wada S, Fujimoto N, Nishiyama K, Terashima M, Beppu S, Yoshida K, Narumoto O, Nagai H, Ooshima N, Motegi M, Umeda A, Miyagawa K, Shimada H, Endo M, Ohira Y, Watanabe M, Inoue S, Igarashi A, Sato M, Sagara H, Tanaka A, Ohta S, Kimura T, Shibata Y, Tanino Y, Nikaido T, Minemura H, Sato Y, Yamada Y, Hashino T, Shinoki M, Iwagoe H, Takahashi H, Fujii K, Kishi H, Kanai M, Imamura T, Yamashita T, Yatomi M, Maeno T, Hayashi S, Takahashi M, Kuramochi M, Kamimaki I, Tominaga Y, Ishii T, Utsugi M, Ono A, Tanaka T, Kashiwada T, Fujita K, Saito Y, Seike M, Watanabe H, Matsuse H, Kodaka N, Nakano C, Oshio T, Hirouchi T, Makino S, Egi M, Omae Y, Nannya Y, Ueno T, Takano T, Katayama K, Ai M, Kumanogoh A, Sato T, Hasegawa N, Tokunaga K, Ishii M, Koike R, Kitagawa Y, Kimura A, Imoto S, Miyano S, Ogawa S, Kanai T, Fukunaga K, Okada Y. The whole blood transcriptional regulation landscape in 465 COVID-19 infected samples from Japan COVID-19 Task Force. Nat Commun 2022; 13:4830. [PMID: 35995775 PMCID: PMC9395416 DOI: 10.1038/s41467-022-32276-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 07/25/2022] [Indexed: 11/12/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is a recently-emerged infectious disease that has caused millions of deaths, where comprehensive understanding of disease mechanisms is still unestablished. In particular, studies of gene expression dynamics and regulation landscape in COVID-19 infected individuals are limited. Here, we report on a thorough analysis of whole blood RNA-seq data from 465 genotyped samples from the Japan COVID-19 Task Force, including 359 severe and 106 non-severe COVID-19 cases. We discover 1169 putative causal expression quantitative trait loci (eQTLs) including 34 possible colocalizations with biobank fine-mapping results of hematopoietic traits in a Japanese population, 1549 putative causal splice QTLs (sQTLs; e.g. two independent sQTLs at TOR1AIP1), as well as biologically interpretable trans-eQTL examples (e.g., REST and STING1), all fine-mapped at single variant resolution. We perform differential gene expression analysis to elucidate 198 genes with increased expression in severe COVID-19 cases and enriched for innate immune-related functions. Finally, we evaluate the limited but non-zero effect of COVID-19 phenotype on eQTL discovery, and highlight the presence of COVID-19 severity-interaction eQTLs (ieQTLs; e.g., CLEC4C and MYBL2). Our study provides a comprehensive catalog of whole blood regulatory variants in Japanese, as well as a reference for transcriptional landscapes in response to COVID-19 infection. Genetic mechanisms influencing COVID-19 susceptibility are not well understood. Here, the authors analyzed whole blood RNA-seq data of 465 Japanese individuals with COVID-19, highlighting thousands of fine-mapped variants affecting expression and splicing of genes, as well as the presence of COVID-19 severity-interaction eQTLs.
Collapse
|
12
|
Mohammadisoleimani E, Firoozi Z, Naghizadeh MM, Ghanbari Asad A, Pezeshki B, Gholampour Y, Mirzaei E, Simin M, Saliani M, Moravej A, Armoon Z, Mansoori Y. Upregulation of hsa_circ_0004812 promotes COVID-19 cytokine storm via hsa-miR-1287-5p/IL6R, RIG-I axis. J Clin Lab Anal 2022; 36:e24666. [PMID: 35989496 PMCID: PMC9538103 DOI: 10.1002/jcla.24666] [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: 06/20/2022] [Revised: 08/03/2022] [Accepted: 08/07/2022] [Indexed: 11/17/2022] Open
Abstract
Background SARS‐CoV‐2 is one of the most contagious viruses in the Coronaviridae (CoV) family, which has become a pandemic. The aim of this study is to understand more about the role of hsa_circ_0004812 in the SARS‐CoV‐2 related cytokine storm and its associated molecular mechanisms. Materials and Methods cDNA synthesis was performed after total RNA was extracted from the peripheral blood mononuclear cells (PBMC) of 46 patients with symptomatic COVID‐19, 46 patients with asymptomatic COVID‐19, and 46 healthy controls. The expression levels of hsa_circ_0004812, hsa‐miR‐1287‐5p, IL6R, and RIG‐I were determined using qRT‐PCR, and the potential interaction between these molecules was confirmed by bioinformatics tools and correlation analysis. Results hsa_circ_0004812, IL6R, and RIG‐I are expressed higher in the severe symptom group compared with the negative control group. Also, the relative expression of these genes in the asymptomatic group is lower than in the severe symptom group. The expression level of hsa‐miR‐1287‐5p was positively correlated with symptoms in patients. The results of the bioinformatics analysis predicted the sponging effect of hsa_circ_0004812 as a competing endogenous RNA on hsa‐miR‐1287‐5p. Moreover, there was a significant positive correlation between hsa_circ_0004812, RIG‐I, and IL‐6R expressions, and also a negative expression correlation between hsa_circ_0004812 and hsa‐miR‐1287‐5p and between hsa‐miR‐1287‐5p, RIG‐I, and IL‐6R. Conclusion The results of this in‐vitro and in silico study show that hsa_circ_0004812/hsa‐miR‐1287‐5p/IL6R, RIG‐I can play an important role in the outcome of COVID‐19.
Collapse
Affiliation(s)
| | - Zahra Firoozi
- Department of Medical Genetics, Fasa University of Medical Sciences, Fasa, Iran
| | | | - Ali Ghanbari Asad
- Department of Medical Biotechnology, Fasa University of Medical Sciences, Fasa, Iran
| | - Babak Pezeshki
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | - Yousef Gholampour
- Department of Internal Medicine, Fasa University of Medical Sciences, Fasa, Iran
| | - Ebrahim Mirzaei
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | | | - Mahsa Saliani
- Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Ali Moravej
- Department of Immunology, Fasa University of Medical Sciences, Fasa, Iran
| | - Zolfaghar Armoon
- Department of Internal Medicine, Fasa University of Medical Sciences, Fasa, Iran
| | - Yaser Mansoori
- Department of Medical Genetics, Fasa University of Medical Sciences, Fasa, Iran.,Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| |
Collapse
|
13
|
COVID-19 Infections and Asthma. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. IN PRACTICE 2022; 10:658-663. [PMID: 34838708 PMCID: PMC8613003 DOI: 10.1016/j.jaip.2021.10.072] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 10/30/2021] [Indexed: 12/15/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2, which causes coronavirus disease 2019 (COVID-19), has infected more than 200 million and led to the deaths of more than 4.3 million people. Although there are known risk factors for severe disease, asthma was initially hypothesized to be a risk factor for severe disease given the association between asthma exacerbations and respiratory viral illnesses in general. Fortunately, clinical outcomes for patients with asthma overall are similar to those for patients without asthma, without convincing evidence that asthma is a risk factor for severe disease. This may be explained in part by the decreasing gradient of angiotensin-converting enzyme-2 receptor from the upper to lower respiratory epithelium and that aeroallergen-sensitized patients with asthma can have up to 50% reduction in angiotensin-converting enzyme-2 receptor expression. Vaccination for patients with asthma is recommended for all without clear contraindications. COVID-19–specific treatment options are available depending on the severity of disease. We caution the use of systemic corticosteroids in patients with asthma not requiring supplemental oxygen given an association with worse outcomes. Postacute COVID-19 syndrome or long-haul COVID does not appear to be more prevalent in the population with asthma, and a multidisciplinary approach to care is a reasonable option.
Collapse
|
14
|
Zein JG, Strauss R, Attaway AH, Hu B, Milinovich A, Jawhari N, Chamat SS, Ortega VE. Eosinophilia Is Associated with Improved COVID-19 Outcomes in Inhaled Corticosteroid-Treated Patients. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. IN PRACTICE 2022; 10:742-750.e14. [PMID: 35033701 PMCID: PMC8757367 DOI: 10.1016/j.jaip.2021.12.034] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 12/18/2021] [Accepted: 12/20/2021] [Indexed: 01/08/2023]
Abstract
BACKGROUND In addition to their proinflammatory effect, eosinophils have antiviral properties. Similarly, inhaled corticosteroids (ICS) were found to suppress coronavirus replication in vitro and were associated with improved outcomes in coronavirus disease 2019 (COVID-19). However, the interplay between the two and its effect on COVID-19 needs further evaluation. OBJECTIVE To determine the associations among preexisting blood absolute eosinophil counts, ICS, and COVID-19-related outcomes. METHODS We analyzed data from the Cleveland Clinic COVID-19 Research Registry (April 1, 2020 to March 31, 2021). Of the 82,096 individuals who tested positive, 46,397 had blood differential cell counts obtained before severe acute respiratory syndrome coronavirus 2 testing dates. Our end points included the need for hospitalization, admission to the intensive care unit (ICU), and in-hospital mortality. The effect of eosinophilia on outcomes was estimated after propensity weighting and adjustment. RESULTS Of the 46,397 patients included in the final analyses, 19,506 had preexisting eosinophilia (>0.15 × 103 cells/μL), 5,011 received ICS, 9,096 (19.6%) were hospitalized, 2,129 required ICU admission (4.6%) and 1,402 died during index hospitalization (3.0%). Adjusted analysis associated eosinophilia with lower odds for hospitalization (odds ratio [OR] [95% confidence interval (CI)]: 0.86 [0.79-0.93]), ICU admission (OR [95% CI]: 0.79 [0.69-0.90]), and mortality (OR [95% CI]: 0.80 [0.68-0.95]) among ICS-treated patients but not untreated ones. The correlation between absolute eosinophil count and the estimated probability of hospitalization, ICU admission, and death was nonlinear (U-shaped) among patients not treated with ICS, and negative in treated patients. CONCLUSIONS The association between eosinophilia and improved COVID-19 outcomes depends on ICS. Future randomized controlled trials are needed to determine the role of ICS and its interaction with eosinophilia in COVID-19 therapy.
Collapse
Affiliation(s)
- Joe G Zein
- Department of Pulmonary Medicine, Respiratory Institute, Cleveland Clinic, Cleveland, Ohio; Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio.
| | | | - Amy H Attaway
- Department of Pulmonary Medicine, Respiratory Institute, Cleveland Clinic, Cleveland, Ohio; Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | - Bo Hu
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | - Alex Milinovich
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | | | | | - Victor E Ortega
- Division of Pulmonary Medicine, Department of Medicine, Mayo Clinic, Scottsdale, Ariz
| |
Collapse
|
15
|
Francisco Junior RDS, Temerozo JR, Ferreira CDS, Martins Y, Souza TML, Medina-Acosta E, de Vasconcelos ATR. Differential haplotype expression in class I MHC genes during SARS-CoV-2 infection of human lung cell lines. Front Immunol 2022; 13:1101526. [PMID: 36818472 PMCID: PMC9929942 DOI: 10.3389/fimmu.2022.1101526] [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: 11/17/2022] [Accepted: 12/19/2022] [Indexed: 02/05/2023] Open
Abstract
Introduction Cell entry of SARS-CoV-2 causes genome-wide disruption of the transcriptional profiles of genes and biological pathways involved in the pathogenesis of COVID-19. Expression allelic imbalance is characterized by a deviation from the Mendelian expected 1:1 expression ratio and is an important source of allele-specific heterogeneity. Expression allelic imbalance can be measured by allele-specific expression analysis (ASE) across heterozygous informative expressed single nucleotide variants (eSNVs). ASE reflects many regulatory biological phenomena that can be assessed by combining genome and transcriptome information. ASE contributes to the interindividual variability associated with the disease. We aim to estimate the transcriptome-wide impact of SARS-CoV-2 infection by analyzing eSNVs. Methods We compared ASE profiles in the human lung cell lines Calu-3, A459, and H522 before and after infection with SARS-CoV-2 using RNA-Seq experiments. Results We identified 34 differential ASE (DASE) sites in 13 genes (HLA-A, HLA-B, HLA-C, BRD2, EHD2, GFM2, GSPT1, HAVCR1, MAT2A, NQO2, SUPT6H, TNFRSF11A, UMPS), all of which are enriched in protein binding functions and play a role in COVID-19. Most DASE sites were assigned to the MHC class I locus and were predominantly upregulated upon infection. DASE sites in the MHC class I locus also occur in iPSC-derived airway epithelium basal cells infected with SARS-CoV-2. Using an RNA-Seq haplotype reconstruction approach, we found DASE sites and adjacent eSNVs in phase (i.e., predicted on the same DNA strand), demonstrating differential haplotype expression upon infection. We found a bias towards the expression of the HLA alleles with a higher binding affinity to SARS-CoV-2 epitopes. Discussion Independent of gene expression compensation, SARS-CoV-2 infection of human lung cell lines induces transcriptional allelic switching at the MHC loci. This suggests a response mechanism to SARS-CoV-2 infection that swaps HLA alleles with poor epitope binding affinity, an expectation supported by publicly available proteome data.
Collapse
Affiliation(s)
| | - Jairo R Temerozo
- Laboratory on Thymus Research, Oswaldo Cruz Institute (Fiocruz), Rio de Janeiro, Brazil.,National Institute of Science and Technology on Neuroimmunomodulation, Rio de Janeiro, Brazil
| | - Cristina Dos Santos Ferreira
- Bioinformatics Laboratory (LABINFO), National Laboratory of Scientific Computation (LNCC/MCTIC), Petrópolis, Brazil
| | - Yasmmin Martins
- Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (FCEyN-UBA), Buenos Aires, Argentina
| | - Thiago Moreno L Souza
- Laboratory of Immunopharmacology, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, Brazil.,Center for Technological Development in Health (CDTS), National Institute for Science and Technology on Innovation on Neglected Diseases Neglected Populations (INCT/IDNP), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, Brazil
| | - Enrique Medina-Acosta
- Molecular Identification and Diagnostics Unit (NUDIM), Laboratory of Biotechnology, Center for Biosciences and Biotechnology, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, Brazil
| | | |
Collapse
|
16
|
Nagasaki T, Schuyler AJ, Zhao J, Samovich SN, Yamada K, Deng Y, Ginebaugh SP, Christenson SA, Woodruff PG, Fahy JV, Trudeau JB, Stoyanovsky D, Ray A, Tyurina YY, Kagan VE, Wenzel SE. 15LO1 dictates glutathione redox changes in asthmatic airway epithelium to worsen type-2 inflammation. J Clin Invest 2021; 132:151685. [PMID: 34762602 PMCID: PMC8718153 DOI: 10.1172/jci151685] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 11/10/2021] [Indexed: 11/23/2022] Open
Abstract
Altered redox biology challenges all cells, with compensatory responses often determining a cell’s fate. When 15 lipoxygenase 1 (15LO1), a lipid-peroxidizing enzyme abundant in asthmatic human airway epithelial cells (HAECs), binds phosphatidylethanolamine-binding protein 1 (PEBP1), hydroperoxy-phospholipids, which drive ferroptotic cell death, are generated. Peroxidases, including glutathione peroxidase 4 (GPX4), metabolize hydroperoxy-phospholipids to hydroxy derivatives to prevent ferroptotic death, but consume reduced glutathione (GSH). The cystine transporter SLC7A11 critically restores/maintains intracellular GSH. We hypothesized that high 15LO1, PEBP1, and GPX4 activity drives abnormal asthmatic redox biology, evidenced by lower bronchoalveolar lavage (BAL) fluid and intraepithelial cell GSH:oxidized GSH (GSSG) ratios, to enhance type 2 (T2) inflammatory responses. GSH, GSSG (enzymatic assays), 15LO1, GPX4, SLC7A11, and T2 biomarkers (Western blot and RNA-Seq) were measured in asthmatic and healthy control (HC) cells and fluids, with siRNA knockdown as appropriate. GSSG was higher and GSH:GSSG lower in asthmatic compared with HC BAL fluid, while intracellular GSH was lower in asthma. In vitro, a T2 cytokine (IL-13) induced 15LO1 generation of hydroperoxy-phospholipids, which lowered intracellular GSH and increased extracellular GSSG. Lowering GSH further by inhibiting SLC7A11 enhanced T2 inflammatory protein expression and ferroptosis. Ex vivo, redox imbalances corresponded to 15LO1 and SLC7A11 expression, T2 biomarkers, and worsened clinical outcomes. Thus, 15LO1 pathway–induced redox biology perturbations worsen T2 inflammation and asthma control, supporting 15LO1 as a therapeutic target.
Collapse
Affiliation(s)
- Tadao Nagasaki
- Department of Respiratory Medicine, Graduate School of Medicine Kyoto University, Kyoto, Japan
| | - Alexander J Schuyler
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, United States of America
| | - Jinming Zhao
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, United States of America
| | - Svetlana N Samovich
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, United States of America
| | - Kazuhiro Yamada
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, United States of America
| | - Yanhan Deng
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, United States of America
| | - Scott P Ginebaugh
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, United States of America
| | - Stephanie A Christenson
- Department of Medicine, University of California, San Francisco, San Francisco, United States of America
| | - Prescott G Woodruff
- Department of Medicine, University of California, San Francisco, San Francisco, United States of America
| | - John V Fahy
- Department of Medicine, University of California, San Francisco, San Francisco, United States of America
| | - John B Trudeau
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, United States of America
| | - Detcho Stoyanovsky
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, United States of America
| | - Anuradha Ray
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh Asthma and Environmental Lung Health Institute, Pittsburgh, United States of America
| | - Yulia Y Tyurina
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, United States of America
| | - Valerian E Kagan
- Department of Environmental and Occupational Health, University of Pittsburgh Asthma and Environmental Lung Health Institute, Pittsburgh, United States of America
| | - Sally E Wenzel
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh Asthma Institute at UPMC, Pittsburgh, United States of America
| |
Collapse
|
17
|
Strauss R, Jawhari N, Attaway AH, Hu B, Jehi L, Milinovich A, Ortega VE, Zein JG. Intranasal Corticosteroids Are Associated with Better Outcomes in Coronavirus Disease 2019. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. IN PRACTICE 2021; 9:3934-3940.e9. [PMID: 34438103 PMCID: PMC8381621 DOI: 10.1016/j.jaip.2021.08.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/14/2021] [Accepted: 08/04/2021] [Indexed: 01/08/2023]
Abstract
BACKGROUND Sites of entry for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are highly expressed in nasal epithelial cells; however, little is known about the impact of intranasal corticosteroids (INCS) on coronavirus disease 2019 (COVID-19)-related outcomes. OBJECTIVE To determine the association between baseline INCS use and COVID-19-related outcomes. METHODS Using the Cleveland Clinic COVID-19 Research Registry, we performed a propensity score matching for treatment with INCS before SARS-CoV-2 infection (April 1, 2020, to March 31, 2021). Of the 82,096 individuals who tested positive, 72,147 met inclusion criteria. Our endpoints included the need for hospitalization, admission to the intensive care unit (ICU), or in-hospital mortality. RESULTS Of the 12,608 (17.5%) who were hospitalized, 2935 (4.1%) required ICU admission and 1880 (2.6%) died during hospitalization. A significant proportion (n = 10,187; 14.1%) were using INCS before SARS-CoV-2 infection. Compared with nonusers, INCS users demonstrated lower risk for hospitalization (adjusted odds ratio [OR] [95% confidence interval (CI)]: 0.78 [0.72; 0.85]), ICU admission (adjusted OR [95% CI]: 0.77 [0.65; 0.92]), and in-hospital mortality (adjusted OR [95% CI]: 0.76 [0.61; 0.94]). These findings were replicated in sensitivity analyses where patients on inhaled corticosteroids and those with allergic rhinitis were excluded. The beneficial effect of INCS was significant after adjustment for baseline blood eosinophil count (measured before SARS-CoV-2 testing) in a subset of 30,289 individuals. CONCLUSION INCS therapy is associated with a lower risk for COVID-19-related hospitalization, ICU admission, or death. Future randomized control trials are needed to determine if INCS reduces the risk for severe outcomes related to COVID-19.
Collapse
Affiliation(s)
- Ronald Strauss
- The Cleveland Allergy and Asthma Center, Cleveland, Ohio
| | | | - Amy H. Attaway
- Respiratory Institute, Cleveland Clinic, Cleveland, Ohio,Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | - Bo Hu
- Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | - Lara Jehi
- Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | - Alex Milinovich
- Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | - Victor E. Ortega
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Wake Forest School of Medicine, Winston-Salem, NC
| | - Joe G. Zein
- Respiratory Institute, Cleveland Clinic, Cleveland, Ohio,Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio,Corresponding author: Joe G. Zein, MD, PhD, Cleveland Clinic Main Campus, 9500 Euclid Avenue, Mail Box: A90, Cleveland, OH 44195
| |
Collapse
|
18
|
Pushparaj PN, Abdulkareem AA, Naseer MI. Identification of Novel Gene Signatures using Next-Generation Sequencing Data from COVID-19 Infection Models: Focus on Neuro-COVID and Potential Therapeutics. Front Pharmacol 2021; 12:688227. [PMID: 34531741 PMCID: PMC8438179 DOI: 10.3389/fphar.2021.688227] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 07/16/2021] [Indexed: 12/23/2022] Open
Abstract
SARS-CoV-2 is the causative agent for coronavirus disease-19 (COVID-19) and belongs to the family Coronaviridae that causes sickness varying from the common cold to more severe illnesses such as severe acute respiratory syndrome, sudden stroke, neurological complications (Neuro-COVID), multiple organ failure, and mortality in some patients. The gene expression profiles of COVID-19 infection models can be used to decipher potential therapeutics for COVID-19 and related pathologies, such as Neuro-COVID. Here, we used the raw RNA-seq reads (Single-End) in quadruplicates derived using Illumina Next Seq 500 from SARS-CoV-infected primary human bronchial epithelium (NHBE) and mock-treated NHBE cells obtained from the Gene Expression Omnibus (GEO) (GSE147507), and the quality control (QC) was evaluated using the CLC Genomics Workbench 20.0 (Qiagen, United States) before the RNA-seq analysis using BioJupies web tool and iPathwayGuide for gene ontologies (GO), pathways, upstream regulator genes, small molecules, and natural products. Additionally, single-cell transcriptomics data (GSE163005) of meta clusters of immune cells from the cerebrospinal fluid (CSF), such as T-cells/natural killer cells (NK) (TcMeta), dendritic cells (DCMeta), and monocytes/granulocyte (monoMeta) cell types for comparison, namely, Neuro-COVID versus idiopathic intracranial hypertension (IIH), were analyzed using iPathwayGuide. L1000 fireworks display (L1000FWD) and L1000 characteristic direction signature search engine (L1000 CDS2) web tools were used to uncover the small molecules that could potentially reverse the COVID-19 and Neuro-COVID-associated gene signatures. We uncovered small molecules such as camptothecin, importazole, and withaferin A, which can potentially reverse COVID-19 associated gene signatures. In addition, withaferin A, trichostatin A, narciclasine, camptothecin, and JQ1 have the potential to reverse Neuro-COVID gene signatures. Furthermore, the gene set enrichment analysis (GSEA) preranked method and Metascape web tool were used to decipher and annotate the gene signatures that were potentially reversed by these small molecules. In conclusion, our study unravels a rapid approach for applying next-generation knowledge discovery (NGKD) platforms to discover small molecules with therapeutic potential against COVID-19 and its related disease pathologies.
Collapse
Affiliation(s)
- Peter Natesan Pushparaj
- Center of Excellence in Genomic Medicine Research, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Angham Abdulrahman Abdulkareem
- Center of Excellence in Genomic Medicine Research, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Muhammad Imran Naseer
- Center of Excellence in Genomic Medicine Research, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| |
Collapse
|
19
|
Coden ME, Loffredo LF, Abdala-Valencia H, Berdnikovs S. Comparative Study of SARS-CoV-2, SARS-CoV-1, MERS-CoV, HCoV-229E and Influenza Host Gene Expression in Asthma: Importance of Sex, Disease Severity, and Epithelial Heterogeneity. Viruses 2021; 13:1081. [PMID: 34198852 PMCID: PMC8226441 DOI: 10.3390/v13061081] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 05/24/2021] [Accepted: 05/26/2021] [Indexed: 02/07/2023] Open
Abstract
Epithelial characteristics underlying the differential susceptibility of chronic asthma to SARS-CoV-2 (COVID-19) and other viral infections are currently unclear. By revisiting transcriptomic data from patients with Th2 low versus Th2 high asthma, as well as mild, moderate, and severe asthmatics, we characterized the changes in expression of human coronavirus and influenza viral entry genes relative to sex, airway location, and disease endotype. We found sexual dimorphism in the expression of SARS-CoV-2-related genes ACE2, TMPRSS2, TMPRSS4, and SLC6A19. ACE2 receptor downregulation occurred specifically in females in Th2 high asthma, while proteases broadly assisting coronavirus and influenza viral entry, TMPRSS2, and TMPRSS4, were highly upregulated in both sexes. Overall, changes in SARS-CoV-2-related gene expression were specific to the Th2 high molecular endotype of asthma and different by asthma severity and airway location. The downregulation of ACE2 (COVID-19, SARS) and ANPEP (HCoV-229E) viral receptors wascorrelated with loss of club and ciliated cells in Th2 high asthma. Meanwhile, the increase in DPP4 (MERS-CoV), ST3GAL4, and ST6GAL1 (influenza) was associated with increased goblet and basal activated cells. Overall, this study elucidates sex, airway location, disease endotype, and changes in epithelial heterogeneity as potential factors underlying asthmatic susceptibility, or lack thereof, to SARS-CoV-2.
Collapse
Affiliation(s)
- Mackenzie E. Coden
- Division of Allergy and Immunology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; (M.E.C.); (L.F.L.)
| | - Lucas F. Loffredo
- Division of Allergy and Immunology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; (M.E.C.); (L.F.L.)
| | - Hiam Abdala-Valencia
- Division of Pulmonary and Critical Care, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA;
| | - Sergejs Berdnikovs
- Division of Allergy and Immunology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; (M.E.C.); (L.F.L.)
| |
Collapse
|