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Li YK, Wang HY, Chen Y, Shi XQ, Zhang XX, Li K, Fu WP, Sun C. Single‑nucleotide polymorphism rs6592645 confers asthma risk through regulating LRRC32 expression. Exp Ther Med 2023; 26:451. [PMID: 37614425 PMCID: PMC10443064 DOI: 10.3892/etm.2023.12150] [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: 01/31/2023] [Accepted: 06/23/2023] [Indexed: 08/25/2023] Open
Abstract
Asthma is a complex disease, often with evident genetic predisposition; for example, the single-nucleotide polymorphism (SNP) rs7130588 was significantly associated with asthma by genome-wide association study (GWAS). Analysis of 1000 Genomes Project data suggests that there is another SNP, rs6592645, in complete linkage disequilibrium with rs7130588 and should present the same signal in GWAS. However, the causal SNP and the mechanism for the association between rs7130588 and asthma remain to be elucidated. In the presents study, results from dual-luciferase assays indicated that the A/G alleles of rs7130588 failed to present significantly different reporter gene expression. By contrast, A allele of rs6592645 presented a significant increase in relative luciferase activity than G allele, thus suggesting that rs6592645 may be a causal SNP. Using chromosome conformation capture, the enhancer region containing rs6592645 was observed to interact with promoter region of leucine-rich repeat-containing 32 (LRRC32). Gene expression quantification suggested that LRRC32 expression is significantly increased in lung tissue of patients with asthma and is dependent on the genotype of this locus, thus verifying that LRRC32 may be involved in asthma onset and that rs6592645 can regulate LRRC32 expression. Through chromatin immunoprecipitation, transcription factor 3 (TCF3) was identified to bind to rs6592645 surrounding region and the interaction between TCF3 and rs6592645 surrounding region was investigated. Results from the present study may improve our understanding of the mechanism by which the genetic variation in this locus might influence asthma susceptibility.
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Affiliation(s)
- Yi-Kun Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China
| | - Hong-Yan Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China
| | - Ying Chen
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China
| | - Xiao-Qian Shi
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China
| | - Xin-Xin Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China
| | - Ke Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China
| | - Wei-Ping Fu
- Department of Respiratory Critical Care Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
| | - Chang Sun
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China
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Pomés A, Arruda LK. Cockroach allergy: Understanding complex immune responses to develop novel therapies. Mol Immunol 2023; 156:157-169. [PMID: 36930991 PMCID: PMC10134214 DOI: 10.1016/j.molimm.2023.03.001] [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: 10/31/2022] [Revised: 01/24/2023] [Accepted: 03/01/2023] [Indexed: 03/17/2023]
Abstract
Cockroach allergy is associated with the development of asthma. The identification of cockroach allergens, which began in the 1990 s, is an ongoing process that has led to the current listing of 20 official allergen groups in the WHO/IUIS Allergen Nomenclature database. The function and structure of some of these allergens has been determined and define their natural delivery into the environment and their allergenicity. Analysis of antigenic determinants by X-ray crystallography and rational design of site-directed mutagenesis led to the identification of IgE binding sites for the design of molecules with reduced IgE reactivity and T cell modulatory capacity. New developments in recent years include component analyses of B and T cell reactivity and a recent cockroach immunotherapy trial, CRITICAL, that will contribute to understand the immune response to cockroach and to define future directions for cockroach allergy diagnosis and immunotherapy.
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Affiliation(s)
- Anna Pomés
- Director of Basic Research, InBio, 700 Harris Street, Charlottesville, VA 22903, USA.
| | - L Karla Arruda
- Professor of Medicine, Ribeirão Preto Medical School, University of São Paulo, Av. Bandeirantes 3900, Ribeirão Preto, SP 14049-900, Brazil
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3
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Finn PW, Perkins DL. BORN TO WHEEZE OR LEARNED WHEN WE WERE YOUNG: MATERNAL AND ENVIRONMENTAL FACTORS INFLUENCE ATOPIC RISK. TRANSACTIONS OF THE AMERICAN CLINICAL AND CLIMATOLOGICAL ASSOCIATION 2023; 133:181-192. [PMID: 37701609 PMCID: PMC10493753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Abstract
The prevalence of atopic diseases is increasing globally, particularly in children. Heritable genetics can partially explain risk of disease. Evidence also points to acquired genetic material, in the form of the microbiome, as an important factor in disease pathogenesis. The acquisition of the microbiome dynamically changes in response to differences in lifestyle and environmental factors. Also, in utero, maternal and environmental factors influence atopic risk for allergic rhinitis, eczema, asthma, and food allergy. Combining the analytical power of omics, we focus on how the microbiota mediates effects between mother, environment, immunity, and risk of atopic disease. In parallel, we stress that health care disparities impact asthma morbidity and mortality. Efforts to improve asthma outcomes must include multidisciplinary strategies.
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Castellan FS, Irie N. Postnatal depletion of maternal cells biases T lymphocytes and natural killer cells' profiles toward early activation in the spleen. Biol Open 2022; 11:bio059334. [PMID: 36349799 PMCID: PMC9672855 DOI: 10.1242/bio.059334] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 10/11/2022] [Indexed: 08/27/2023] Open
Abstract
The maternal cells transferred into the fetus during gestation persist long after birth in the progeny. These maternal cells have been hypothesized to promote the maturation of the fetal immune system in utero but there are still significant gaps in our knowledge of their potential roles after birth. To provide insights into these maternal cells' postnatal functional roles, we set up a transgenic mouse model to specifically eliminate maternal cells in the neonates by diphtheria toxin injection and confirmed significant depletion in the spleens. We then performed immunophenotyping of the spleens of two-week-old pups by mass cytometry to pinpoint the immune profile differences driven by the depletion of maternal cells in early postnatal life. We observed a heightened expression of markers related to activation and maturation in some natural killer and T cell populations. We hypothesize these results to indicate a potential postnatal regulation of lymphocytic responses by maternal cells. Together, our findings highlight an immunological influence of maternal microchimeric cells postnatally, possibly protecting against adverse hypersensitivity reactions of the neonate at a crucial time of new encounters with self and environmental antigens.
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Affiliation(s)
- Flore S. Castellan
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Naoki Irie
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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Wang Y, Guo D, Chen X, Wang S, Hu J, Liu X. Trends in asthma among adults in the United States, National Health and Nutrition Examination Survey 2005 to 2018. Ann Allergy Asthma Immunol 2022; 129:71-78.e2. [PMID: 35257870 DOI: 10.1016/j.anai.2022.02.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 02/19/2022] [Accepted: 02/22/2022] [Indexed: 01/13/2023]
Abstract
BACKGROUND Asthma is a common chronic disease in American adults. The prevalence of asthma has varied over time, but there are few studies on the long-term trend of asthma in American adults. OBJECTIVE To describe the prevalence and trend of asthma in American adults from 2005 to 2018 and analyze the risk factors for asthma. METHODS Data collection was performed from National Health and Nutrition Examination Survey 2005 to 2018. The unweighted number and weighted percentages of normal participants and patients with asthma and the trends of asthma were calculated. Weighted univariate logistic regression was used to analyze the risk factors for asthma. RESULTS A total of 39,601 adults were included in this study. From 2005 to 2018, the overall prevalence of asthma in American adults was 8.41%, whereas that in young, middle-aged, and elderly adults was 8.30%, 8.70%, and 7.92%, respectively. The estimated prevalence of asthma in the overall adults and young adults increased with time (P for trend = .03, difference = 0.023 and P for trend = .007, difference = 0.060, respectively), and the estimated prevalence of middle-aged and elderly adults remained stable with time (P for trend = .33, difference = 0.015 and P for trend = .80, difference = -0.024, respectively). CONCLUSION Asthma in American adults was on the rise. Female sex, non-Hispanic Blacks, individuals with low annual household income, active smokers, obese patients, patients with hypertension, patients with diabetes, and individuals with positive asthma family history were associated with a higher risk for developing asthma.
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Affiliation(s)
- Yashan Wang
- Department of Epidemiology and Statistics, School of Public Health, Jilin University, Changchun, PR China
| | - Dingjie Guo
- Department of Epidemiology and Statistics, School of Public Health, Jilin University, Changchun, PR China
| | - Xiaofei Chen
- Department of Epidemiology and Statistics, School of Public Health, Jilin University, Changchun, PR China
| | - Song Wang
- Department of Epidemiology and Statistics, School of Public Health, Jilin University, Changchun, PR China
| | - Jiayi Hu
- Department of Epidemiology and Statistics, School of Public Health, Jilin University, Changchun, PR China
| | - Xin Liu
- Department of Epidemiology and Statistics, School of Public Health, Jilin University, Changchun, PR China.
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Clay SM, Schoettler N, Goldstein AM, Carbonetto P, Dapas M, Altman MC, Rosasco MG, Gern JE, Jackson DJ, Im HK, Stephens M, Nicolae DL, Ober C. Fine-mapping studies distinguish genetic risks for childhood- and adult-onset asthma in the HLA region. Genome Med 2022; 14:55. [PMID: 35606880 PMCID: PMC9128203 DOI: 10.1186/s13073-022-01058-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 05/12/2022] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Genome-wide association studies of asthma have revealed robust associations with variation across the human leukocyte antigen (HLA) complex with independent associations in the HLA class I and class II regions for both childhood-onset asthma (COA) and adult-onset asthma (AOA). However, the specific variants and genes contributing to risk are unknown. METHODS We used Bayesian approaches to perform genetic fine-mapping for COA and AOA (n=9432 and 21,556, respectively; n=318,167 shared controls) in White British individuals from the UK Biobank and to perform expression quantitative trait locus (eQTL) fine-mapping in immune (lymphoblastoid cell lines, n=398; peripheral blood mononuclear cells, n=132) and airway (nasal epithelial cells, n=188) cells from ethnically diverse individuals. We also examined putatively causal protein coding variation from protein crystal structures and conducted replication studies in independent multi-ethnic cohorts from the UK Biobank (COA n=1686; AOA n=3666; controls n=56,063). RESULTS Genetic fine-mapping revealed both shared and distinct causal variation between COA and AOA in the class I region but only distinct causal variation in the class II region. Both gene expression levels and amino acid variation contributed to risk. Our results from eQTL fine-mapping and amino acid visualization suggested that the HLA-DQA1*03:01 allele and variation associated with expression of the nonclassical HLA-DQA2 and HLA-DQB2 genes accounted entirely for the most significant association with AOA in GWAS. Our studies also suggested a potentially prominent role for HLA-C protein coding variation in the class I region in COA. We replicated putatively causal variant associations in a multi-ethnic cohort. CONCLUSIONS We highlight roles for both gene expression and protein coding variation in asthma risk and identified putatively causal variation and genes in the HLA region. A convergence of genomic, transcriptional, and protein coding evidence implicates the HLA-DQA2 and HLA-DQB2 genes and HLA-DQA1*03:01 allele in AOA.
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Affiliation(s)
- Selene M Clay
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA.
| | - Nathan Schoettler
- Section of Pulmonary and Critical Care, Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | - Andrew M Goldstein
- Department of Statistics, University of Chicago, Chicago, IL, 60637, USA
| | - Peter Carbonetto
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Matthew Dapas
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Matthew C Altman
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA, 98109, USA
- Systems Immunology Program, Benaroya Research Institute, Seattle, WA, 98101, USA
| | - Mario G Rosasco
- Systems Immunology Program, Benaroya Research Institute, Seattle, WA, 98101, USA
| | - James E Gern
- Department of Pediatrics, University of Wisconsin, School of Medicine and Public Health, Madison, WI, 53706, USA
| | - Daniel J Jackson
- Department of Pediatrics, University of Wisconsin, School of Medicine and Public Health, Madison, WI, 53706, USA
| | - Hae Kyung Im
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | - Matthew Stephens
- Department of Statistics, University of Chicago, Chicago, IL, 60637, USA
| | - Dan L Nicolae
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
- Department of Statistics, University of Chicago, Chicago, IL, 60637, USA
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA.
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7
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Ulrich BJ, Kharwadkar R, Chu M, Pajulas A, Muralidharan C, Koh B, Fu Y, Gao H, Hayes TA, Zhou HM, Goplen NP, Nelson AS, Liu Y, Linnemann AK, Turner MJ, Licona-Limón P, Flavell RA, Sun J, Kaplan MH. Allergic airway recall responses require IL-9 from resident memory CD4 + T cells. Sci Immunol 2022; 7:eabg9296. [PMID: 35302861 PMCID: PMC9295820 DOI: 10.1126/sciimmunol.abg9296] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Asthma is a chronic inflammatory lung disease with intermittent flares predominately mediated through memory T cells. Yet, the identity of long-term memory cells that mediate allergic recall responses is not well defined. In this report, using a mouse model of chronic allergen exposure followed by an allergen-free rest period, we characterized a subpopulation of CD4+ T cells that secreted IL-9 as an obligate effector cytokine. IL-9-secreting cells had a resident memory T cell phenotype, and blocking IL-9 during a recall challenge or deleting IL-9 from T cells significantly diminished airway inflammation and airway hyperreactivity. T cells secreted IL-9 in an allergen recall-specific manner, and secretion was amplified by IL-33. Using scRNA-seq and scATAC-seq, we defined the cellular identity of a distinct population of T cells with a proallergic cytokine pattern. Thus, in a recall model of allergic airway inflammation, IL-9 secretion from a multicytokine-producing CD4+ T cell population was required for an allergen recall response.
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Affiliation(s)
- Benjamin J Ulrich
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Rakshin Kharwadkar
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Michelle Chu
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Abigail Pajulas
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Charanya Muralidharan
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Byunghee Koh
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Yongyao Fu
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Hongyu Gao
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Tristan A Hayes
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Hong-Ming Zhou
- Department of Dermatology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Richard L. Roudebush VA Medical Center, Indianapolis, IN 46202, USA
| | - Nick P Goplen
- Thoracic Diseases Research Unit, Division of Pulmonary and Critical Care Medicine, Department of Medicine, Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, Rochester, MN 55902, USA
| | - Andrew S Nelson
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Yunlong Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Amelia K Linnemann
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Matthew J Turner
- Department of Dermatology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Richard L. Roudebush VA Medical Center, Indianapolis, IN 46202, USA
| | - Paula Licona-Limón
- Departamento de Biologia Celular y del Desarrollo, Instituto de Fisiologia Celular, Universidad Nacional Autónoma de México, Mexico City 04020, Mexico
| | - Richard A Flavell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
- Howard Hughes Medical Institute, Yale University, New Haven, CT 06510, USA
| | - Jie Sun
- Thoracic Diseases Research Unit, Division of Pulmonary and Critical Care Medicine, Department of Medicine, Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, Rochester, MN 55902, USA
| | - Mark H Kaplan
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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Ye T, Zhang X, Dong Y, Liu J, Zhang W, Wu F, Bo H, Shao H, Zhang R, Shen H. Chemokine CCL17 Affects Local Immune Infiltration Characteristics and Early Prognosis Value of Lung Adenocarcinoma. Front Cell Dev Biol 2022; 10:816927. [PMID: 35321241 PMCID: PMC8936957 DOI: 10.3389/fcell.2022.816927] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 02/11/2022] [Indexed: 12/30/2022] Open
Abstract
CCL17 is an important chemokine that plays a vital immunomodulatory role in the tumor microenvironment (TME). Analysis of lung adenocarcinoma (LUAD) data in Kaplan–Meier plotter databases found that the overall survival of patients in the CCL17 high-expression group was higher than that of the low-expression group, especially for patients with early (stages I and II) LUAD, which has a more positive prognostic value. Expression of CCL17 in LUAD was positively correlated with the proportion of tumor-infiltrating lymphocytes, immunostimulators, and major histocompatibility complexes using the TISIDB databases. Based on the RNA-seq and clinical data of 491 LUAD patients obtained from the TCGA database, 1,455 differential genes were found between the CCL17 high- and low-expression groups. Using WGCNA analysis confirmed that the expression of differential genes in the blue module is negatively correlated with poor survival and clinical stages of LUAD patients, and CCL17 and CCR4 genes belong to the hub genes in the blue module. Further analysis by the ESTIMATE and CIBERSORT algorithm found that the naive B cells and CD8+ T cells in the CCL17 high-expression group have a higher distribution ratio in the early LUAD patients, and the high immune score has a positive relationship with the overall survival rate. Using somatic mutation data of TCGA-LUAD, we found that 1) the tumor mutation burden values of the CCL17 high-expression group were significantly lower than those of the CCL17 low-expression group and 2) the expression levels of CCL17 and the tumor mutation burden values were negatively correlated. Transwell chemotaxis and cytotoxicity assays confirmed that CCL17 contributes to the migration of CCR4-positive lymphocytes into the H1993 LUAD TME and enhances the specific lysis of LUAD cells. In summary, high expression of CCL17 in the LUAD TME promotes local immune cell infiltration and antitumor immune response, which may contribute to the better survival and prognosis of patients with early LUAD.
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Affiliation(s)
- Ting Ye
- Guangdong Provincial Key Laboratory of Biotechnology Candidate Drug Research, School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
| | - Xuefang Zhang
- Department of Radiation Oncology, Dongguan People’s Hospital, Affiliated Dongguan Hospital of Southern Medical University, Dongguan, China
| | - Yongjian Dong
- Guangdong Provincial Key Laboratory of Biotechnology Candidate Drug Research, School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
| | - Jing Liu
- Guangdong Provincial Key Laboratory of Biotechnology Candidate Drug Research, School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
| | - Wenfeng Zhang
- Guangdong Provincial Key Laboratory of Biotechnology Candidate Drug Research, School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
| | - Fenglin Wu
- Guangdong Provincial Key Laboratory of Biotechnology Candidate Drug Research, School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
| | - Huaben Bo
- Guangdong Provincial Key Laboratory of Biotechnology Candidate Drug Research, School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
| | - Hongwei Shao
- Guangdong Provincial Key Laboratory of Biotechnology Candidate Drug Research, School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
| | - Rongxin Zhang
- Guangdong Provincial Key Laboratory of Biotechnology Candidate Drug Research, School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
| | - Han Shen
- Guangdong Provincial Key Laboratory of Biotechnology Candidate Drug Research, School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
- *Correspondence: Han Shen,
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LncRNA functional annotation with improved false discovery rate achieved by disease associations. Comput Struct Biotechnol J 2022; 20:322-332. [PMID: 35035785 PMCID: PMC8724965 DOI: 10.1016/j.csbj.2021.12.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 12/09/2021] [Accepted: 12/11/2021] [Indexed: 12/11/2022] Open
Abstract
The long non‐coding RNAs (lncRNAs) play critical roles in various biological processes and are associated with many diseases. Functional annotation of lncRNAs in diseases attracts great attention in understanding their etiology. However, the traditional co-expression-based analysis usually produces a significant number of false positive function assignments. It is thus crucial to develop a new approach to obtain lower false discovery rate for functional annotation of lncRNAs. Here, a novel strategy termed DAnet which combining disease associations with cis-regulatory network between lncRNAs and neighboring protein-coding genes was developed, and the performance of DAnet was systematically compared with that of the traditional differential expression-based approach. Based on a gold standard analysis of the experimentally validated lncRNAs, the proposed strategy was found to perform better in identifying the experimentally validated lncRNAs compared with the other method. Moreover, the majority of biological pathways (40%∼100%) identified by DAnet were reported to be associated with the studied diseases. In sum, the DAnet is expected to be used to identify the function of specific lncRNAs in a particular disease or multiple diseases.
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10
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Li YK, Zhang XX, Yang Y, Gao J, Shi Q, Liu SD, Fu WP, Sun C. Convergent Evidence Supports TH2LCRR as a Novel Asthma Susceptibility Gene. Am J Respir Cell Mol Biol 2021; 66:283-292. [PMID: 34851809 DOI: 10.1165/rcmb.2020-0481oc] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Asthma is a common complex disease with apparent genetic predispositions, and previous genome-wide association studies suggest that rs1295686 within the IL13 (interleukin 13) gene is significantly associated with asthma. Analysis of the data provided by the 1000 Genomes Project indicated that there are additional four SNPs in nearly complete linkage disequilibrium with rs1295686 in Caucasians. However, the causal SNPs and the associated mechanism remain unclear. To investigate this issue, functional genomics approaches were utilized to analyze the functions of these SNPs. Dual-luciferase assays indicated that the functional SNP is not rs1295686 but a haplotype consisting of other three SNPs, rs1295685, rs848 and rs847. Through chromosome conformation capture, it was found that the enhancer containing the three functional SNPs interacts with the promoter of TH2LCRR (T helper type 2 locus control region associated RNA), a recently identified long non-coding RNA. RNA-seq data analysis indicated that TH2LCRR expression is significantly increased in asthma patients and is dependent on the genotype at this locus, indicating that TH2LCRR is a novel susceptibility gene for asthma and that these SNPs confer asthma risk by regulating TH2LCRR expression. By chromatin immunoprecipitation, the related transcription factors that bind in the region surrounding these three SNPs were identified, and their interactions were investigated by functional genomics approaches. Our effort identified a novel mechanism through which genetic variations at this locus could influence asthma susceptibility.
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Affiliation(s)
- Yi-Kun Li
- Shaanxi Normal University, 12401, College of Life Sciences, Xi'an, China
| | - Xin-Xin Zhang
- Shaanxi Normal University, 12401, College of Life Sciences, Xi'an, China
| | - Yuan Yang
- Shaanxi Normal University, 12401, College of Life Sciences, Xi'an, China
| | - Jing Gao
- Shaanxi Normal University, 12401, College of Life Sciences, Xi'an, China
| | - Qiang Shi
- Shaanxi Normal University, 12401, College of Life Sciences, Xi'an, China
| | - Shao-Dong Liu
- Shaanxi Normal University, 12401, College of Life Sciences, Xi'an, China
| | - Wei-Ping Fu
- Kunming Medical University First Affilliated Hospital, 36657, Kunming, China
| | - Chang Sun
- Shaanxi Normal University, 12401, College of Life Sciences, Xi'an, China;
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11
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Hou JY, Wu JR, Xu D, Chen YB, Shang DD, Liu S, Fan GW, Cui YL. Integration of transcriptomics and system pharmacology to reveal the therapeutic mechanism underlying Qingfei Xiaoyan Wan to treat allergic asthma. JOURNAL OF ETHNOPHARMACOLOGY 2021; 278:114302. [PMID: 34090911 DOI: 10.1016/j.jep.2021.114302] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/23/2021] [Accepted: 06/02/2021] [Indexed: 06/12/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Asthma is a chronic inflammatory disease, characterized by airway inflammation, hyperresponsiveness, and bronchial smooth muscle contraction. Qingfei Xiaoyan Wan (QFXYW), a traditional Chinese formula, has been shown to exert anti-asthma effects and immune response in multiple diseases. AIM OF THIS STUDY In this study, we evaluated the therapeutic mechanism of QFXYW in the suppression of allergic asthma by integrating of transcriptomics and system pharmacology. MATERIALS AND METHODS BALB/c mice were sensitized with ovalbumin (OVA) to establish the allergic asthma model, and its success was confirmed with behavioral observations. Lung histopathological analysis, inflammatory pathology scores, transcription factors were used to evaluate the effects of QFXYW on allergic asthma. The therapeutic mechanism of QFXYW in treating allergic asthma through integrated transcriptomics and system pharmacology was then determined: hub genes were screened out by topological analysis and functional enrichment analysis were performed to identify key signaling pathway. Subsequently, quantitative RP-PCR and protein array were performed to detect the mRNA of hub genes and to predict the key pathway in OVA-induced allergic asthma, respectively. RESULTS Our results demonstrated that QFXYW could significantly attenuate inflammatory cell infiltration, mucus secretion, and epithelial damage. The transcriptomics analysis found the six hub genes with the highest values- CXCL10, CXCL2, CXCL1, IL-6, CCL-5, and CCL-4 were screened out. Functional enrichment analysis showed that the differentially expressed genes (DEGs) were mainly enriched in the inflammatory response and cytokine signaling pathway. Moreover, the quantitative RT-PCR verification experiment found the CXCL2 and CXCL1 were significantly suppressed after treatment with QFXYW. The results of protein array showed that QFXYW inhibited the multi-cytokines of OVA-induced allergic asthma via cytokine signaling pathway. CONCLUSIONS QFXYW may have mediated OVA-induced allergic asthma mainly through the hub genes CXCL2, CXCL1, and the cytokine signaling pathway. This finding will offer a novel strategy to explore effective and safe mechanism of Traditional Chinese Medicine (TCM) formula to treat allergic asthma.
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Affiliation(s)
- Jing-Yi Hou
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China.
| | - Jia-Rong Wu
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China.
| | - Dong Xu
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China.
| | - Yi-Bing Chen
- Tianjin Key Laboratory of Transformation of Traditional Chinese Medicine, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China.
| | - Dan-Dan Shang
- Tianjin Zhongxin Pharmaceutical Group Corporation Limited Darentang Pharmaceutical Factory, Tianjin, 300193, China.
| | - Shu Liu
- Tianjin Zhongxin Pharmaceutical Group Corporation Limited Darentang Pharmaceutical Factory, Tianjin, 300193, China.
| | - Guan-Wei Fan
- Tianjin Key Laboratory of Transformation of Traditional Chinese Medicine, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China.
| | - Yuan-Lu Cui
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China.
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Repetitive aeroallergen challenges elucidate maladaptive epithelial and inflammatory traits that underpin allergic airway diseases. J Allergy Clin Immunol 2021; 148:533-549. [PMID: 33493557 PMCID: PMC8298629 DOI: 10.1016/j.jaci.2021.01.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 01/08/2021] [Accepted: 01/14/2021] [Indexed: 01/09/2023]
Abstract
BACKGROUND Signifying the 2-compartments/1-disease paradigm, allergic rhinoconjunctivitis (ARC) and asthma (AA) are prevalent, comorbid conditions triggered by environmental factors (eg, house dust mites [HDMs]). However, despite the ubiquity of triggers, progression to severe ARC/AA is infrequent, suggesting either resilience or adaptation. OBJECTIVE We sought to determine whether ARC/AA severity relates to maladaptive responses to disease triggers. METHODS Adults with HDM-associated ARC were challenged repetitively with HDMs in an aeroallergen challenge chamber. Mechanistic traits associated with disease severity were identified. RESULTS HDM challenges evoked maladaptive (persistently higher ARC symptoms), adaptive (progressive symptom reduction), and resilient (resistance to symptom induction) phenotypes. Symptom severity in the natural environment was an imprecise correlate of the phenotypes. Nasal airway traits, defined by low inflammation-effectual epithelial integrity, moderate inflammation-effectual epithelial integrity, and higher inflammation-ineffectual epithelial integrity, were hallmarks of the resilient, adaptive, and maladaptive evoked phenotypes, respectively. Highlighting a crosstalk mechanism, peripheral blood inflammatory tone calibrated these traits: ineffectual epithelial integrity associated with CD8+ T cells, whereas airway inflammation associated with both CD8+ T cells and eosinophils. Hallmark peripheral blood maladaptive traits were increased natural killer and CD8+ T cells, lower CD4+ mucosal-associated invariant T cells, and deficiencies along the TLR-IRF-IFN antiviral pathway. Maladaptive traits tracking HDM-associated ARC also contributed to AA risk and severity models. CONCLUSIONS Repetitive challenges with HDMs revealed that maladaptation to disease triggers may underpin ARC/AA disease severity. A combinatorial therapeutic approach may involve reversal of loss-of-beneficial-function traits (ineffectual epithelial integrity, TLR-IRF-IFN deficiencies), mitigation of gain-of-adverse-function traits (inflammation), and blocking of a detrimental crosstalk between the peripheral blood and airway compartments.
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13
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Altman MC, Calatroni A, Ramratnam S, Jackson DJ, Presnell S, Rosasco MG, Gergen PJ, Bacharier LB, O'Connor GT, Sandel MT, Kattan M, Wood RA, Visness CM, Gern JE. Endotype of allergic asthma with airway obstruction in urban children. J Allergy Clin Immunol 2021; 148:1198-1209. [PMID: 33713771 PMCID: PMC8429519 DOI: 10.1016/j.jaci.2021.02.040] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 01/25/2021] [Accepted: 02/01/2021] [Indexed: 12/16/2022]
Abstract
BACKGROUND Black and Hispanic children growing up in disadvantaged urban neighborhoods have the highest rates of asthma and related morbidity in the United States. OBJECTIVES This study sought to identify specific respiratory phenotypes of health and disease in this population, associations with early life exposures, and molecular patterns of gene expression in nasal epithelial cells that underlie clinical disease. METHODS The study population consisted of 442 high-risk urban children who had repeated assessments of wheezing, allergen-specific IgE, and lung function through 10 years of age. Phenotypes were identified by developing temporal trajectories for these data, and then compared to early life exposures and patterns of nasal epithelial gene expression at 11 years of age. RESULTS Of the 6 identified respiratory phenotypes, a high wheeze, high atopy, low lung function group had the greatest respiratory morbidity. In early life, this group had low exposure to common allergens and high exposure to ergosterol in house dust. While all high-atopy groups were associated with increased expression of a type-2 inflammation gene module in nasal epithelial samples, an epithelium IL-13 response module tracked closely with impaired lung function, and a MUC5AC hypersecretion module was uniquely upregulated in the high wheeze, high atopy, low lung function group. In contrast, a medium wheeze, low atopy group showed altered expression of modules of epithelial integrity, epithelial injury, and antioxidant pathways. CONCLUSIONS In the first decade of life, high-risk urban children develop distinct phenotypes of respiratory health versus disease that link early life environmental exposures to childhood allergic sensitization and asthma. Moreover, unique patterns of airway gene expression demonstrate how specific molecular pathways underlie distinct respiratory phenotypes, including allergic and nonallergic asthma.
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Affiliation(s)
- Matthew C Altman
- Immunology Division, Benaroya Research Institute Systems, Seattle, Wash; Department of Medicine, University of Washington, Seattle, Wash.
| | | | - Sima Ramratnam
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, Wis
| | - Daniel J Jackson
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, Wis
| | - Scott Presnell
- Immunology Division, Benaroya Research Institute Systems, Seattle, Wash
| | - Mario G Rosasco
- Immunology Division, Benaroya Research Institute Systems, Seattle, Wash
| | - Peter J Gergen
- National Institute of Allergy and Infectious Diseases, Rockville, Md
| | - Leonard B Bacharier
- Department of Pediatrics, Washington University School of Medicine and St Louis Children's Hospital, St Louis, Mo
| | - George T O'Connor
- Department of Medicine, Boston University School of Medicine, Boston, Mass
| | - Megan T Sandel
- Department of Medicine, Boston University School of Medicine, Boston, Mass
| | - Meyer Kattan
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY
| | - Robert A Wood
- Department of Pediatrics, Johns Hopkins University Medical Center, Baltimore, Md
| | | | - James E Gern
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, Wis
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Cockroach-induced IL9, IL13, and IL31 expression and the development of allergic asthma in urban children. J Allergy Clin Immunol 2021; 147:1974-1977.e3. [PMID: 33712279 DOI: 10.1016/j.jaci.2021.01.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 01/05/2021] [Accepted: 01/08/2021] [Indexed: 11/23/2022]
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15
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Qian Q, Chowdhury BP, Sun Z, Lenberg J, Alam R, Vivier E, Gorska MM. Maternal diesel particle exposure promotes offspring asthma through NK cell-derived granzyme B. J Clin Invest 2021; 130:4133-4151. [PMID: 32407293 DOI: 10.1172/jci130324] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 04/29/2020] [Indexed: 12/31/2022] Open
Abstract
Mothers living near high-traffic roads before or during pregnancy are more likely to have children with asthma. Mechanisms are unknown. Using a mouse model, here we showed that maternal exposure to diesel exhaust particles (DEP) predisposed offspring to allergic airway disease (AAD, murine counterpart of human asthma) through programming of their NK cells; predisposition to AAD did not develop in DEP pups that lacked NK cells and was induced in normal pups receiving NK cells from WT DEP pups. DEP NK cells expressed GATA3 and cosecreted IL-13 and the killer protease granzyme B in response to allergen challenge. Extracellular granzyme B did not kill, but instead stimulated protease-activated receptor 2 (PAR2) to cooperate with IL-13 in the induction of IL-25 in airway epithelial cells. Through loss-of-function and reconstitution experiments in pups, we showed that NK cells and granzyme B were required for IL-25 induction and activation of the type 2 immune response and that IL-25 mediated NK cell effects on type 2 response and AAD. Finally, experiments using human cord blood and airway epithelial cells suggested that DEP might induce an identical pathway in humans. Collectively, we describe an NK cell-dependent endotype of AAD that emerged in early life as a result of maternal exposure to DEP.
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Affiliation(s)
- Qian Qian
- Division of Allergy and Clinical Immunology, Department of Medicine, National Jewish Health (NJH), Denver, Colorado, USA
| | - Bidisha Paul Chowdhury
- Division of Allergy and Clinical Immunology, Department of Medicine, National Jewish Health (NJH), Denver, Colorado, USA
| | - Zehua Sun
- Division of Allergy and Clinical Immunology, Department of Medicine, National Jewish Health (NJH), Denver, Colorado, USA
| | - Jerica Lenberg
- Division of Allergy and Clinical Immunology, Department of Medicine, National Jewish Health (NJH), Denver, Colorado, USA
| | - Rafeul Alam
- Division of Allergy and Clinical Immunology, Department of Medicine, National Jewish Health (NJH), Denver, Colorado, USA.,Division of Allergy and Clinical Immunology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Eric Vivier
- Innate Pharma Research Labs, Innate Pharma, Marseille, France.,Centre d'Immunologie de Marseille-Luminy, CNRS, INSERM, Aix Marseille University, Marseille, France.,Service d'Immunologie, Marseille Immunopole, Hôpital de la Timone, Assistance Publique des Hôpitaux de Marseille, Marseille, France
| | - Magdalena M Gorska
- Division of Allergy and Clinical Immunology, Department of Medicine, National Jewish Health (NJH), Denver, Colorado, USA.,Division of Allergy and Clinical Immunology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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Expression quantitative trait locus fine mapping of the 17q12-21 asthma locus in African American children: a genetic association and gene expression study. THE LANCET RESPIRATORY MEDICINE 2020; 8:482-492. [PMID: 32380068 DOI: 10.1016/s2213-2600(20)30011-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 01/08/2020] [Accepted: 01/13/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND African ancestry is associated with a higher prevalence and greater severity of asthma than European ancestries, yet genetic studies of the most common locus associated with childhood-onset asthma, 17q12-21, in African Americans have been inconclusive. The aim of this study was to leverage both the phenotyping of the Children's Respiratory and Environmental Workgroup (CREW) birth cohort consortium, and the reduced linkage disequilibrium in African Americans, to fine map the 17q12-21 locus. METHODS We first did a genetic association study and meta-analysis using 17q12-21 tag single-nucleotide polymorphisms (SNPs) for childhood-onset asthma in 1613 European American and 870 African American children from the CREW consortium. Nine tag SNPs were selected based on linkage disequilibrium patterns at 17q12-21 and their association with asthma, considering the effect allele under an additive model (0, 1, or 2 effect alleles). Results were meta-analysed with publicly available summary data from the EVE consortium (on 4303 European American and 3034 African American individuals) for seven of the nine SNPs of interest. Subsequently, we tested for expression quantitative trait loci (eQTLs) among the SNPs associated with childhood-onset asthma and the expression of 17q12-21 genes in resting peripheral blood mononuclear cells (PBMCs) from 85 African American CREW children and in upper airway epithelial cells from 246 African American CREW children; and in lower airway epithelial cells from 44 European American and 72 African American adults from a case-control study of asthma genetic risk in Chicago (IL, USA). FINDINGS 17q12-21 SNPs were broadly associated with asthma in European Americans. Only two SNPs (rs2305480 in gasdermin-B [GSDMB] and rs8076131 in ORMDL sphingolipid biosynthesis regulator 3 [ORMDL3]) were associated with asthma in African Americans, at a Bonferroni-corrected threshold of p<0·0055 (for rs2305480_G, odds ratio [OR] 1·36 [95% CI 1·12-1·65], p=0·0014; and for rs8076131_A, OR 1·37 [1·13-1·67], p=0·0010). In upper airway epithelial cells from African American children, genotype at rs2305480 was the most significant eQTL for GSDMB (eQTL effect size [β] 1·35 [95% CI 1·25-1·46], p<0·0001), and to a lesser extent showed an eQTL effect for post-GPI attachment to proteins phospholipase 3 (β 1·15 [1·08-1·22], p<0·0001). No SNPs were eQTLs for ORMDL3. By contrast, in PBMCs, the five core SNPs were associated only with expression of GSDMB and ORMDL3. Genotype at rs12936231 (in zona pellucida binding protein 2) showed the strongest associations across both genes (for GSDMB, eQTLβ 1·24 [1·15-1·32], p<0·0001; and for ORMDL3 (β 1·19 [1·12-1·24], p<0·0001). The eQTL effects of rs2305480 on GSDMB expression were replicated in lower airway cells from African American adults (β 1·29 [1·15-1·44], p<0·0001). INTERPRETATION Our study suggests that SNPs regulating GSDMB expression in airway epithelial cells have a major role in childhood-onset asthma, whereas SNPs regulating the expression levels of 17q12-21 genes in resting blood cells are not central to asthma risk. Our genetic and gene expression data in African Americans and European Americans indicated GSDMB to be the leading candidate gene at this important asthma locus. FUNDING National Institutes of Health, Office of the Director.
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17
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Chang YS, Turturice B, Schott C, Finn P, Perkins D. Immune network dysregulation precedes clinical diagnosis of asthma. Sci Rep 2020; 10:12784. [PMID: 32732938 PMCID: PMC7393349 DOI: 10.1038/s41598-020-69494-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Accepted: 07/10/2020] [Indexed: 02/05/2023] Open
Abstract
Allergic asthma is a chronic disease beginning in childhood that is characterized by dominant T-helper 2 cell activation without adequate counter-regulation by T-helper 1 cell and regulatory T cell activity. Prior transcriptomic studies of childhood asthma have primarily investigated subjects who already have a disease diagnosis, and have generally taken an approach of differential gene expression as opposed to differential gene interactions. The immune states that predispose towards allergic sensitization and disease development remain ill defined. We thus characterize immune networks of asthmatic predisposition in children at the age of 2, prior to the diagnosis of allergic asthma, who are subsequently diagnosed with asthma at the age of 7. We show extensive differences of gene expression networks and gene regulatory networks in children who develop asthma versus those who do not using transcriptomic data from stimulated peripheral blood mononuclear cells. Moreover, transcription factors that bind proximally to one another share patterns of dysregulation, suggesting that network differences prior to asthma diagnosis result from altered accessibility of gene targets. In summary, we demonstrate non-allergen-specific immune network dysregulation in individuals long before clinical asthma diagnosis.
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Affiliation(s)
- Yi-Shin Chang
- Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois at Chicago College of Medicine, Chicago, IL, USA
- Department of Bioengineering, University of Illinois at Chicago College of Medicine, Chicago, IL, USA
| | - Benjamin Turturice
- Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois at Chicago College of Medicine, Chicago, IL, USA
- Department of Microbiology and Immunology, University of Illinois at Chicago College of Medicine, Chicago, IL, USA
| | - Cody Schott
- Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois at Chicago College of Medicine, Chicago, IL, USA
- Department of Microbiology and Immunology, University of Illinois at Chicago College of Medicine, Chicago, IL, USA
| | - Patricia Finn
- Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois at Chicago College of Medicine, Chicago, IL, USA
- Department of Bioengineering, University of Illinois at Chicago College of Medicine, Chicago, IL, USA
- Department of Microbiology and Immunology, University of Illinois at Chicago College of Medicine, Chicago, IL, USA
| | - David Perkins
- Department of Bioengineering, University of Illinois at Chicago College of Medicine, Chicago, IL, USA.
- Division of Nephrology, Department of Medicine, University of Illinois at Chicago College of Medicine, Chicago, IL, USA.
- Department of Surgery, University of Illinois at Chicago College of Medicine, Chicago, IL, USA.
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18
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Long A, Bunning B, Sampath V, DeKruyff RH, Nadeau KC. Epigenetics and the Environment in Airway Disease: Asthma and Allergic Rhinitis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1253:153-181. [PMID: 32445095 DOI: 10.1007/978-981-15-3449-2_6] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Asthma and rhinitis are complex, heterogeneous diseases characterized by chronic inflammation of the upper and lower airways. While genome-wide association studies (GWAS) have identified a number of susceptible loci and candidate genes associated with the pathogenesis of asthma and allergic rhinitis (AR), the risk-associated alleles account for only a very small percent of the genetic risk. In allergic airway and other complex diseases, it is thought that epigenetic modifications, including DNA methylation, histone modifications, and non-coding microRNAs, caused by complex interactions between the underlying genome and the environment may account for some of this "missing heritability" and may explain the high degree of plasticity in immune responses. In this chapter, we will focus on the current knowledge of classical epigenetic modifications, DNA methylation and histone modifications, and their potential role in asthma and AR. In particular, we will review epigenetic variations associated with maternal airway disease, demographics, environment, and non-specific associations. The role of specific genetic haplotypes in environmentally induced epigenetic changes are also discussed. A major limitation of many of the current studies of asthma epigenetics is that they evaluate epigenetic modifications in both allergic and non-allergic asthma, making it difficult to distinguish those epigenetic modifications that mediate allergic asthma from those that mediate non-allergic asthma. Additionally, most DNA methylation studies in asthma use peripheral or cord blood due to poor accessibility of airway cells or tissue. Unlike DNA sequences, epigenetic alterations are quite cell- and tissue-specific, and epigenetic changes found in airway tissue or cells may be discordant from that of circulating blood. These two confounding factors should be considered when reviewing epigenetic studies in allergic airway disease.
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Affiliation(s)
- Andrew Long
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research at Stanford University, Stanford, CA, 94305, USA.,Department of Pharmacy, Lucile Packard Children's Hospital, Stanford, CA, 94304, USA
| | - Bryan Bunning
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research at Stanford University, Stanford, CA, 94305, USA
| | - Vanitha Sampath
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research at Stanford University, Stanford, CA, 94305, USA
| | - Rosemarie H DeKruyff
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research at Stanford University, Stanford, CA, 94305, USA
| | - Kari C Nadeau
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research at Stanford University, Stanford, CA, 94305, USA.
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Larson D, Patel P, Salapatek AM, Couroux P, Whitehouse D, Pina A, Johnson JL, Sever ML, Sanda S, Poyser J, Allio T, Scadding GW, Qin T, Shamji MH, Kwok WW, James EA, French D, Lelic A, Larché M, Altman MC, Togias A, Durham SR. Nasal allergen challenge and environmental exposure chamber challenge: A randomized trial comparing clinical and biological responses to cat allergen. J Allergy Clin Immunol 2020; 145:1585-1597. [PMID: 32169380 DOI: 10.1016/j.jaci.2020.02.024] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 02/25/2020] [Accepted: 02/27/2020] [Indexed: 11/15/2022]
Abstract
BACKGROUND The direct-instillation nasal allergen challenge (NAC) and the environmental exposure chamber (EEC) are 2 methods of conducting controlled allergen provocations. The clinical and biological comparability of these methods has not been thoroughly investigated. OBJECTIVE We sought to compare clinical and immunologic responses to cat allergen in NAC versus EEC. METHODS Twenty-four participants were randomized to receive either NAC followed by a 2-day challenge in an EEC or a 2-day challenge in an EEC followed by NAC. Challenges were separated by 28-day washout periods. We measured total nasal symptom scores, peak nasal inspiratory flow, nasal (0-8 hours) and serum cytokines, serum antibodies, peripheral blood antigen-specific T lymphocytes, and gene expression in nasal scrapings. The primary outcome was the total nasal symptom score area under the curve for the first 3 hours after allergen exposure in NAC or after initiation of exposure in EEC. RESULTS Both challenges increased IL-5 and IL-13 in nasal fluids and serum and resulted in altered nasal cell expression of gene modules related to mucosal biology and transcriptional regulation. Changes in gene modules, more so than cytokine measurements, showed significant associations with total nasal symptom score and peak nasal inspiratory flow. Overall, EEC exposure generated larger responses and more early terminations compared with NAC. Although the 2 challenges did not correlate in symptom magnitude or temporality, striking correlations were observed in cytokine levels. CONCLUSIONS Although clinical outcomes of NAC and EEC were temporally different and nonequivalent in magnitude, immunologic responses were similar. Selection of a particular allergen challenge method should depend on considerations of study objectives and cost.
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Affiliation(s)
| | - Piyush Patel
- Inflamax Research Limited, DBA Cliantha Research, Mississauga, Canada
| | | | - Peter Couroux
- Inflamax Research Limited, DBA Cliantha Research, Mississauga, Canada
| | | | - Adela Pina
- Rho Federal Systems Division, Durham, NC
| | | | | | | | - Julian Poyser
- National Institute of Allergy and Infectious Diseases, Bethesda, Md
| | - Theresa Allio
- National Institute of Allergy and Infectious Diseases, Bethesda, Md
| | - Guy W Scadding
- MRC and Asthma UK, Centre in Allergic Mechanisms of Asthma, London, United Kingdom
| | - Tielin Qin
- The Immune Tolerance Network, Bethesda, Md
| | - Mohamed H Shamji
- MRC and Asthma UK, Centre in Allergic Mechanisms of Asthma, London, United Kingdom; Immunomodulation and Tolerance Group, Allergy and Clinical Immunology, Section of Inflammation Repair and Development, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - William W Kwok
- Benaroya Research Institute, Department of Translational Research, Seattle, Wash
| | - Eddie A James
- Benaroya Research Institute, Department of Translational Research, Seattle, Wash
| | | | - Alina Lelic
- Human Immunology Testing Suite, McMaster University, Hamilton, Ontario, Canada
| | - Mark Larché
- McMaster University, Hamilton, Ontario, Canada; Divisions of Clinical Immunology & Allergy and Respirology, Department of Medicine, Firestone Institute of Respiratory Health, The Research Institute, St Joe's Hamilton, Hamilton, Canada
| | - Matthew C Altman
- Department of Medicine, University of Washington, Seattle, Wash; Benaroya Research Institute, Systems Immunology Division, Seattle, Wash
| | - Alkis Togias
- National Institute of Allergy and Infectious Diseases, Bethesda, Md
| | - Stephen R Durham
- MRC and Asthma UK, Centre in Allergic Mechanisms of Asthma, London, United Kingdom; Immunomodulation and Tolerance Group, Allergy and Clinical Immunology, Section of Inflammation Repair and Development, National Heart and Lung Institute, Imperial College London, London, United Kingdom
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Altered Frequency of NK Cells and Treg Cells by Astragalus Polysaccharide Combined with Budesonide in Asthma Model Mice. ADVANCES IN POLYMER TECHNOLOGY 2020. [DOI: 10.1155/2020/1763245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Objective. We investigated the efficacy of astragalus polysaccharide (APS) combined with budesonide and the effect on expressions of peripheral NK cells and Treg cells and the molecular mechanism in mice with bronchial asthma. Methods. In this study, we established a mouse model of asthma. Four groups of BaLB/C mice were developed; control group had no asthma induction, and the other three groups of mice were sensitized by OVA (Ovalbumin), OVA + budesonide, and OVA + APS + budesonide. Flow cytometry was used to determine the proportion of NK cells and Treg cells. Levels of cytokines IL-4 and IL-10 were detected using RT-PCR and ELISA. Results. Asthma mice treated with APS + budesonide showed alleviated airway resistance compared to model mice (P<0.05). The percentage of dendritic cells (DCs) was reduced (P<0.05), while anti-inflammatory NK cells and Treg cells significantly increased after APS + budesonide treatment (P<0.05). Further, APS + budesonide treatment resulted in improvements in IL-4 and IL-10 mRNA and protein levels (P<0.05). Conclusion. APS combined with budesonide medication may regulate expressions of DCs cells and related cytokines, reliving clinical symptom of bronchial asthma.
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Saglani S, Custovic A. Childhood Asthma: Advances Using Machine Learning and Mechanistic Studies. Am J Respir Crit Care Med 2020; 199:414-422. [PMID: 30571146 DOI: 10.1164/rccm.201810-1956ci] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
A paradigm shift brought by the recognition that childhood asthma is an aggregated diagnosis that comprises several different endotypes underpinned by different pathophysiology, coupled with advances in understanding potentially important causal mechanisms, offers a real opportunity for a step change to reduce the burden of the disease on individual children, families, and society. Data-driven methodologies facilitate the discovery of "hidden" structures within "big healthcare data" to help generate new hypotheses. These findings can be translated into clinical practice by linking discovered "phenotypes" to specific mechanisms and clinical presentations. Epidemiological studies have provided important clues about mechanistic avenues that should be pursued to identify interventions to prevent the development or alter the natural history of asthma-related diseases. Findings from cohort studies followed by mechanistic studies in humans and in neonatal mouse models provided evidence that environments such as traditional farming may offer protection by modulating innate immune responses and that impaired innate immunity may increase susceptibility. The key question of which component of these exposures can be translated into interventions requires confirmation. Increasing mechanistic evidence is demonstrating that shaping the microbiome in early life may modulate immune function to confer protection. Iterative dialogue and continuous interaction between experts with different but complementary skill sets, including data scientists who generate information about the hidden structures within "big data" assets, and medical professionals, epidemiologists, basic scientists, and geneticists who provide critical clinical and mechanistic insights about the mechanisms underpinning the architecture of the heterogeneity, are keys to delivering mechanism-based stratified treatments and prevention.
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Affiliation(s)
| | - Adnan Custovic
- 2 Section of Paediatrics, Department of Medicine, Imperial College London, London, United Kingdom
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22
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Kozik A, Huang YJ. Ecological interactions in asthma: from environment to microbiota and immune responses. Curr Opin Pulm Med 2020; 26:27-32. [PMID: 31567329 PMCID: PMC7147973 DOI: 10.1097/mcp.0000000000000632] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
PURPOSE OF REVIEW Asthma is a heterogeneous condition shaped not only by genetics but also host conditioning by environmental factors. Recognizing the ecological context of microbe-immune interactions across environments and body sites is a necessary step toward better understanding how human microbiota influence or drive the pathogenesis and pathophysiology of asthma in its various presentations. RECENT FINDINGS There is increasing evidence of a critical role for microbiota in asthma pathogenesis and outcomes across various body compartments, including the upper and lower airways, and gut. We discuss recent studies from this area including: development of a method to quantify microbial farm-effect in nonfarm environments, relationships between environmental microbial exposures and asthma prevalence across different geographies, microbiome-mediated responses to ozone, and microbiome-immune interactions within and across body compartments. Beyond bacteria, recent reports of asthma-associated differences in archaea and fungal organisms also are highlighted. SUMMARY Collective evidence warrants application of an ecological framework to advance mechanistic insights into microbiota-immune interactions in asthma. This is necessary to achieve goals of developing successful therapeutic interventions targeting modification of microbiomes.
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Affiliation(s)
- Ariangela Kozik
- University of Michigan, Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, 6301B MSRB3/SPC5642, 1150 W. Medical Center Drive, Ann Arbor, MI 48109-5642
| | - Yvonne J. Huang
- University of Michigan, Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, 6301B MSRB3/SPC5642, 1150 W. Medical Center Drive, Ann Arbor, MI 48109-5642
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23
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Bacharier LB, Mori A, Kita H. Advances in asthma, asthma-COPD overlap, and related biologics in 2018. J Allergy Clin Immunol 2019; 144:906-919. [PMID: 31476323 DOI: 10.1016/j.jaci.2019.08.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/23/2019] [Accepted: 08/26/2019] [Indexed: 01/14/2023]
Abstract
Over the past year, numerous important advances in our understanding of multiple aspects of asthma, ranging from disease pathogenesis to epidemiology to therapeutics, have been reported. This review is a compilation of highlights from articles published largely in the Journal of Allergy and Clinical Immunology and supplemented by articles published elsewhere that have substantially advanced the fields of asthma, chronic obstructive pulmonary disease (COPD), and asthma-COPD overlap and biologic therapies for these disorders. The intention of this article is not to provide a comprehensive review but rather to focus on several areas that have developed quickly and/or received extensive attention from our readers.
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Affiliation(s)
- Leonard B Bacharier
- Division of Pediatric Allergy, Immunology and Pulmonary Medicine, Department of Pediatrics, Washington University School of Medicine and St Louis Children's Hospital, St Louis, Mo.
| | - Akio Mori
- Department of Advanced Medicine, Clinical Research Center for Allergy and Rheumatology, National Hospital Organization Sagamihara National Hospital, Sagamihara, Japan
| | - Hirohito Kita
- Division of Allergic Diseases, Department of Medicine and Department of Immunology, Mayo Clinic, Rochester, Minn; Division of Allergic Diseases, Department of Medicine and Department of Immunology, Mayo Clinic, Scottsdale
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24
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Lu G, Ren JH, Hu B, He CH, Wu PQ, Jiang WH. Sample procedure in peripheral blood mononuclear cells RNA sequencing. J Allergy Clin Immunol 2019; 143:2334. [PMID: 30979656 DOI: 10.1016/j.jaci.2019.03.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Accepted: 03/06/2019] [Indexed: 10/27/2022]
Affiliation(s)
- Gen Lu
- Department of Respiration, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Jian-Hua Ren
- Department of Orthopedics, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Bo Hu
- Department of Central Laboratory, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Chun-Hui He
- Department of Respiration, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Pei-Qiong Wu
- Department of Respiration, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Wen-Hui Jiang
- Department of Respiration, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China.
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25
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Altman MC, Gern JE. Reply. J Allergy Clin Immunol 2019; 143:2334-2335. [PMID: 30979657 DOI: 10.1016/j.jaci.2019.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 03/06/2019] [Indexed: 11/24/2022]
Affiliation(s)
- Matthew C Altman
- Benaroya Research Institute Systems Immunology Division, Seattle, Wash.
| | - James E Gern
- University of Wisconsin School of Medicine and Public Health, Madison, Wis
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26
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Yang D, Liu C. Can natural killer cells represent an early life immune response in development of allergic asthma? More precise data analysis should be considered. J Allergy Clin Immunol 2018; 142:712-713. [PMID: 29945813 DOI: 10.1016/j.jaci.2018.04.036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Accepted: 04/24/2018] [Indexed: 02/05/2023]
Affiliation(s)
- Dan Yang
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, China.
| | - Chuntao Liu
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, China
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27
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Reply. J Allergy Clin Immunol 2018; 142:713. [PMID: 29945814 DOI: 10.1016/j.jaci.2018.04.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 04/24/2018] [Indexed: 11/22/2022]
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