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Böck A, Urner K, Eckert JK, Salvermoser M, Laubhahn K, Kunze S, Kumbrink J, Hoeppner MP, Kalkbrenner K, Kreimeier S, Beyer K, Hamelmann E, Kabesch M, Depner M, Hansen G, Riedler J, Roponen M, Schmausser-Hechfellner E, Barnig C, Divaret-Chauveau A, Karvonen AM, Pekkanen J, Frei R, Roduit C, Lauener R, Schaub B. An integrated molecular risk score early in life for subsequent childhood asthma risk. Clin Exp Allergy 2024; 54:314-328. [PMID: 38556721 DOI: 10.1111/cea.14475] [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: 08/30/2023] [Revised: 03/05/2024] [Accepted: 03/07/2024] [Indexed: 04/02/2024]
Abstract
BACKGROUND Numerous children present with early wheeze symptoms, yet solely a subgroup develops childhood asthma. Early identification of children at risk is key for clinical monitoring, timely patient-tailored treatment, and preventing chronic, severe sequelae. For early prediction of childhood asthma, we aimed to define an integrated risk score combining established risk factors with genome-wide molecular markers at birth, complemented by subsequent clinical symptoms/diagnoses (wheezing, atopic dermatitis, food allergy). METHODS Three longitudinal birth cohorts (PAULINA/PAULCHEN, n = 190 + 93 = 283, PASTURE, n = 1133) were used to predict childhood asthma (age 5-11) including epidemiological characteristics and molecular markers: genotype, DNA methylation and mRNA expression (RNASeq/NanoString). Apparent (ap) and optimism-corrected (oc) performance (AUC/R2) was assessed leveraging evidence from independent studies (Naïve-Bayes approach) combined with high-dimensional logistic regression models (LASSO). RESULTS Asthma prediction with epidemiological characteristics at birth (maternal asthma, sex, farm environment) yielded an ocAUC = 0.65. Inclusion of molecular markers as predictors resulted in an improvement in apparent prediction performance, however, for optimism-corrected performance only a moderate increase was observed (upto ocAUC = 0.68). The greatest discriminate power was reached by adding the first symptoms/diagnosis (up to ocAUC = 0.76; increase of 0.08, p = .002). Longitudinal analysis of selected mRNA expression in PASTURE (cord blood, 1, 4.5, 6 years) showed that expression at age six had the strongest association with asthma and correlation of genes getting larger over time (r = .59, p < .001, 4.5-6 years). CONCLUSION Applying epidemiological predictors alone showed moderate predictive abilities. Molecular markers from birth modestly improved prediction. Allergic symptoms/diagnoses enhanced the power of prediction, which is important for clinical practice and for the design of future studies with molecular markers.
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Affiliation(s)
- Andreas Böck
- Pediatric Allergology, Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany
- Member of the CHildhood Allergy and Tolerance Consortium (CHAMP), LMU Munich, Munich, Germany
| | - Kathrin Urner
- Pediatric Allergology, Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany
- Member of the CHildhood Allergy and Tolerance Consortium (CHAMP), LMU Munich, Munich, Germany
| | - Jana Kristin Eckert
- Pediatric Allergology, Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany
- Member of the CHildhood Allergy and Tolerance Consortium (CHAMP), LMU Munich, Munich, Germany
| | - Michael Salvermoser
- Pediatric Allergology, Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany
- Member of the CHildhood Allergy and Tolerance Consortium (CHAMP), LMU Munich, Munich, Germany
| | - Kristina Laubhahn
- Pediatric Allergology, Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany
- Comprehensive Pneumology Center - Munich (CPC-M), German Center for Lung Research (DZL), Munich, Germany
| | - Sonja Kunze
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Jörg Kumbrink
- Institute of Pathology, Medical Faculty, LMU Munich, Munich, Germany
| | - Marc P Hoeppner
- Institute of Clinical Molecular Biology, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Kathrin Kalkbrenner
- Pediatric Allergology, Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany
- Member of the CHildhood Allergy and Tolerance Consortium (CHAMP), LMU Munich, Munich, Germany
| | - Simone Kreimeier
- Member of the CHildhood Allergy and Tolerance Consortium (CHAMP), LMU Munich, Munich, Germany
- Department of Health Economics and Health Care Management, School of Public Health, Bielefeld University, Bielefeld, Germany
| | - Kirsten Beyer
- Member of the CHildhood Allergy and Tolerance Consortium (CHAMP), LMU Munich, Munich, Germany
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Eckard Hamelmann
- Member of the CHildhood Allergy and Tolerance Consortium (CHAMP), LMU Munich, Munich, Germany
- Department for Pediatrics, Children's Center Bethel, University Hospital OWL, Bielefeld University, Bielefeld, Germany
| | - Michael Kabesch
- Member of the CHildhood Allergy and Tolerance Consortium (CHAMP), LMU Munich, Munich, Germany
- University Children's Hospital Regensburg (KUNO), St. Hedwig's Hospital of the Order of St. John and the University of Regensburg, Regensburg, Germany
| | - Martin Depner
- Member of the CHildhood Allergy and Tolerance Consortium (CHAMP), LMU Munich, Munich, Germany
- Institute of Asthma and Allergy Prevention, Helmholtz Zentrum München, German Research Centre for Environmental Health, Neuherberg, Germany
| | - Gesine Hansen
- Member of the CHildhood Allergy and Tolerance Consortium (CHAMP), LMU Munich, Munich, Germany
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Member of the German Center for Lung Research (DZL), Hannover, Germany
- Excellence Cluster Resolving Infection Susceptibility RESIST (EXC 2155), Deutsche Forschungsgemeinschaft, Hannover Medical School, Hannover, Germany
| | | | - Marjut Roponen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | - Elisabeth Schmausser-Hechfellner
- Institute of Asthma and Allergy Prevention, Helmholtz Zentrum München, German Research Centre for Environmental Health, Neuherberg, Germany
| | - Cindy Barnig
- Department of Respiratory Disease, University Hospital, Besanҫon, France
- INSERM, EFS BFC, LabEx LipSTIC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, Univ. Bourgogne Franche-Comté, Besançon, France
| | - Amandine Divaret-Chauveau
- Pediatric Allergy Department, Children's Hospital, University Hospital of Nancy, Vandoeuvre les Nancy, France
- EA3450 Development, Adaptation and Handicap (devah), Pediatric Allergy Department, University of Lorraine, Nancy, France
- UMR/CNRS 6249 Chrono-environment, University of Franche Comté, Besançon, France
| | - Anne M Karvonen
- Department of Health Security, Finnish Institute for Health and Welfare, Kuopio, Finland
| | - Juha Pekkanen
- Department of Health Security, Finnish Institute for Health and Welfare, Kuopio, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Remo Frei
- Christine Kühne Center for Allergy Research and Education (CK-CARE), Davos, Switzerland
- Division of Respiratory Medicine and Allergology, Department of Paediatrics, Inselspital, University of Bern, Bern, Switzerland
| | - Caroline Roduit
- Christine Kühne Center for Allergy Research and Education (CK-CARE), Davos, Switzerland
- Division of Respiratory Medicine and Allergology, Department of Paediatrics, Inselspital, University of Bern, Bern, Switzerland
- Children's Hospital of Eastern Switzerland, St. Gallen, Switzerland
- Children's Hospital, University of Zürich, Zürich, Switzerland
| | - Roger Lauener
- Christine Kühne Center for Allergy Research and Education (CK-CARE), Davos, Switzerland
- Children's Hospital of Eastern Switzerland, St. Gallen, Switzerland
| | - Bianca Schaub
- Pediatric Allergology, Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany
- Member of the CHildhood Allergy and Tolerance Consortium (CHAMP), LMU Munich, Munich, Germany
- Comprehensive Pneumology Center - Munich (CPC-M), German Center for Lung Research (DZL), Munich, Germany
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2
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Clay S, Alladina J, Smith NP, Visness CM, Wood RA, O'Connor GT, Cohen RT, Khurana Hershey GK, Kercsmar CM, Gruchalla RS, Gill MA, Liu AH, Kim H, Kattan M, Bacharier LB, Rastogi D, Rivera-Spoljaric K, Robison RG, Gergen PJ, Busse WW, Villani AC, Cho JL, Medoff BD, Gern JE, Jackson DJ, Ober C, Dapas M. Gene-based association study of rare variants in children of diverse ancestries implicates TNFRSF21 in the development of allergic asthma. J Allergy Clin Immunol 2024; 153:809-820. [PMID: 37944567 PMCID: PMC10939893 DOI: 10.1016/j.jaci.2023.10.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 09/25/2023] [Accepted: 10/12/2023] [Indexed: 11/12/2023]
Abstract
BACKGROUND Most genetic studies of asthma and allergy have focused on common variation in individuals primarily of European ancestry. Studying the role of rare variation in quantitative phenotypes and in asthma phenotypes in populations of diverse ancestries can provide additional, important insights into the development of these traits. OBJECTIVE We sought to examine the contribution of rare variants to different asthma- or allergy-associated quantitative traits in children with diverse ancestries and explore their role in asthma phenotypes. METHODS We examined whole-genome sequencing data from children participants in longitudinal studies of asthma (n = 1035; parent-identified as 67% Black and 25% Hispanic) to identify rare variants (minor allele frequency < 0.01). We assigned variants to genes and tested for associations using an omnibus variant-set test between each of 24,902 genes and 8 asthma-associated quantitative traits. On combining our results with external data on predicted gene expression in humans and mouse knockout studies, we identified 3 candidate genes. A burden of rare variants in each gene and in a combined 3-gene score was tested for its associations with clinical phenotypes of asthma. Finally, published single-cell gene expression data in lower airway mucosal cells after allergen challenge were used to assess transcriptional responses to allergen. RESULTS Rare variants in USF1 were significantly associated with blood neutrophil count (P = 2.18 × 10-7); rare variants in TNFRSF21 with total IgE (P = 6.47 × 10-6) and PIK3R6 with eosinophil count (P = 4.10 × 10-5) reached suggestive significance. These 3 findings were supported by independent data from human and mouse studies. A burden of rare variants in TNFRSF21 and in a 3-gene score was associated with allergy-related phenotypes in cohorts of children with mild and severe asthma. Furthermore, TNFRSF21 was significantly upregulated in bronchial basal epithelial cells from adults with allergic asthma but not in adults with allergies (but not asthma) after allergen challenge. CONCLUSIONS We report novel associations between rare variants in genes and allergic and inflammatory phenotypes in children with diverse ancestries, highlighting TNFRSF21 as contributing to the development of allergic asthma.
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Affiliation(s)
- Selene Clay
- Department of Human Genetics, University of Chicago, Chicago, Ill.
| | - Jehan Alladina
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Mass; Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, Mass
| | - Neal P Smith
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, Mass; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Mass; Massachusetts General Hospital Cancer Center, Boston, Mass
| | | | - Robert A Wood
- Pediatric Allergy and Immunology Department, Johns Hopkins Bloomberg School of Public Health, Baltimore, Md
| | - George T O'Connor
- Department of Pediatrics, Boston University School of Medicine, Boston, Mass
| | - Robyn T Cohen
- Department of Pediatrics, Boston University School of Medicine, Boston, Mass
| | | | - Carolyn M Kercsmar
- Division of Pulmonary Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Rebecca S Gruchalla
- Internal Medicine and Pediatrics, University of Texas Southwestern Medical Center, Dallas, Tex
| | - Michelle A Gill
- Pediatric Infectious Diseases, St. Louis Children's Hospital, St Louis, Mo
| | - Andrew H Liu
- Breathing Institute, Children's Hospital Colorado, Aurora, Colo
| | - Haejin Kim
- Allergy and Immunology, Henry Ford Health, Detroit, Mich
| | - Meyer Kattan
- Department of Pediatrics, Columbia University Medical Center, New York, NY
| | - Leonard B Bacharier
- Department of Pediatrics, Monroe Carell Jr Children's Hospital at Vanderbilt University Medical Center, Nashville, Tenn
| | - Deepa Rastogi
- Division of Pulmonology and Sleep Medicine, Children's National Hospital, Washington, DC
| | - Katherine Rivera-Spoljaric
- Department of Pediatric Allergy, Immunology, and Pulmonary Medicine, Washington University School of Medicine, St Louis, Mo
| | - Rachel G Robison
- Department of Pediatrics, Monroe Carell Jr Children's Hospital at Vanderbilt University Medical Center, Nashville, Tenn; Ann & Robert H. Lurie Children's Hospital, Chicago, Ill
| | - Peter J Gergen
- National Institute of Allergy and Infectious Diseases, Rockville, Md
| | - William W Busse
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wis
| | - Alexandra-Chloe Villani
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, Mass; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Mass; Massachusetts General Hospital Cancer Center, Boston, Mass
| | - Josalyn L Cho
- Division of Pulmonary, Critical Care and Occupational Medicine, University of Iowa Carver College of Medicine, Iowa City, Iowa
| | - Benjamin D Medoff
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Mass; Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, Mass
| | - James E Gern
- 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
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, Ill
| | - Matthew Dapas
- Department of Human Genetics, University of Chicago, Chicago, Ill
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Erol ÖD, Şenocak Ş, Aerts-Kaya F. The Role of Rab GTPases in the development of genetic and malignant diseases. Mol Cell Biochem 2024; 479:255-281. [PMID: 37060515 DOI: 10.1007/s11010-023-04727-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 04/01/2023] [Indexed: 04/16/2023]
Abstract
Small GTPases have been shown to play an important role in several cellular functions, including cytoskeletal remodeling, cell polarity, intracellular trafficking, cell-cycle, progression and lipid transformation. The Ras-associated binding (Rab) family of GTPases constitutes the largest family of GTPases and consists of almost 70 known members of small GTPases in humans, which are known to play an important role in the regulation of intracellular membrane trafficking, membrane identity, vesicle budding, uncoating, motility and fusion of membranes. Mutations in Rab genes can cause a wide range of inherited genetic diseases, ranging from neurodegenerative diseases, such as Parkinson's disease (PD) and Alzheimer's disease (AD) to immune dysregulation/deficiency syndromes, like Griscelli Syndrome Type II (GS-II) and hemophagocytic lymphohistiocytosis (HLH), as well as a variety of cancers. Here, we provide an extended overview of human Rabs, discussing their function and diseases related to Rabs and Rab effectors, as well as focusing on effects of (aberrant) Rab expression. We aim to underline their importance in health and the development of genetic and malignant diseases by assessing their role in cellular structure, regulation, function and biology and discuss the possible use of stem cell gene therapy, as well as targeting of Rabs in order to treat malignancies, but also to monitor recurrence of cancer and metastasis through the use of Rabs as biomarkers. Future research should shed further light on the roles of Rabs in the development of multifactorial diseases, such as diabetes and assess Rabs as a possible treatment target.
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Affiliation(s)
- Özgür Doğuş Erol
- Department of Stem Cell Sciences, Hacettepe University Graduate School of Health Sciences, 06100, Ankara, Turkey
- Hacettepe University Center for Stem Cell Research and Development, 06100, Ankara, Turkey
| | - Şimal Şenocak
- Department of Stem Cell Sciences, Hacettepe University Graduate School of Health Sciences, 06100, Ankara, Turkey
- Hacettepe University Center for Stem Cell Research and Development, 06100, Ankara, Turkey
| | - Fatima Aerts-Kaya
- Department of Stem Cell Sciences, Hacettepe University Graduate School of Health Sciences, 06100, Ankara, Turkey.
- Hacettepe University Center for Stem Cell Research and Development, 06100, Ankara, Turkey.
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Kim S, Qin Y, Park HJ, Yue M, Xu Z, Forno E, Chen W, Celedón JC. Methyl-TWAS: A powerful method for in silico transcriptome-wide association studies (TWAS) using long-range DNA methylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.10.566586. [PMID: 38014125 PMCID: PMC10680683 DOI: 10.1101/2023.11.10.566586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
In silico transcriptome-wide association studies (TWAS) are commonly used to test whether expression of specific genes is linked to a complex trait. However, genotype-based in silico TWAS such as PrediXcan, exhibit low prediction accuracy for a majority of genes because genotypic data lack tissue- and disease-specificity and are not affected by the environment. Because methylation is tissue-specific and, like gene expression, can be modified by environment or disease status, methylation should predict gene expression with more accuracy than SNPs. Therefore, we propose Methyl-TWAS, the first approach that utilizes long-range methylation markers to impute gene expression for in silico TWAS through penalized regression. Methyl-TWAS 1) predicts epigenetically regulated/associated expression (eGReX), which incorporates tissue-specific expression and both genetically- (GReX) and environmentally-regulated expression to identify differentially expressed genes (DEGs) that could not be identified by genotype-based methods; and 2) incorporates both cis- and trans- CpGs, including various regulatory regions to identify DEGs that would be missed using cis- methylation only. Methyl-TWAS outperforms PrediXcan and two other methods in imputing gene expression in the nasal epithelium, particularly for immunity-related genes and DEGs in atopic asthma. Methyl-TWAS identified 3,681 (85.2%) of the 4,316 DEGs identified in a previous TWAS of atopic asthma using measured expression, while PrediXcan could not identify any gene. Methyl-TWAS also outperforms PrediXcan for expression imputation as well as in silico TWAS in white blood cells. Methyl-TWAS is a valuable tool for in silico TWAS, leveraging a growing body of publicly available genome-wide DNA methylation data for a variety of human tissues.
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Affiliation(s)
- Soyeon Kim
- Division of Pulmonary Medicine, Department of Pediatrics, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yidi Qin
- Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Hyun Jung Park
- Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Molin Yue
- Department of Biostatistics, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Zhongli Xu
- Division of Pulmonary Medicine, Department of Pediatrics, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA
- School of Medicine, Tsinghua University, Beijing, China
| | - Erick Forno
- Division of Pulmonary Medicine, Department of Pediatrics, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA
| | - Wei Chen
- Division of Pulmonary Medicine, Department of Pediatrics, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA
| | - Juan C. Celedón
- Division of Pulmonary Medicine, Department of Pediatrics, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA
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Zhang L, Chun Y, Irizar H, Arditi Z, Grishina G, Grishin A, Vicencio A, Bunyavanich S. Integrated study of systemic and local airway transcriptomes in asthma reveals causal mediation of systemic effects by airway key drivers. Genome Med 2023; 15:71. [PMID: 37730635 PMCID: PMC10512627 DOI: 10.1186/s13073-023-01222-2] [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: 02/28/2023] [Accepted: 08/18/2023] [Indexed: 09/22/2023] Open
Abstract
BACKGROUND Systemic and local profiles have each been associated with asthma, but parsing causal relationships between system-wide and airway-specific processes can be challenging. We sought to investigate systemic and airway processes in asthma and their causal relationships. METHODS Three hundred forty-one participants with persistent asthma and non-asthmatic controls were recruited and underwent peripheral blood mononuclear cell (PBMC) collection and nasal brushing. Transcriptome-wide RNA sequencing of the PBMC and nasal samples and a series of analyses were then performed using a discovery and independent test set approach at each step to ensure rigor. Analytic steps included differential expression analyses, coexpression and probabilistic causal (Bayesian) network constructions, key driver analyses, and causal mediation models. RESULTS Among the 341 participants, the median age was 13 years (IQR = 10-16), 164 (48%) were female, and 200 (58.7%) had persistent asthma with mean Asthma Control Test (ACT) score 16.6 (SD = 4.2). PBMC genes associated with asthma were enriched in co-expression modules for NK cell-mediated cytotoxicity (fold enrichment = 4.5, FDR = 6.47 × 10-32) and interleukin production (fold enrichment = 2.0, FDR = 1.01 × 10-15). Probabilistic causal network and key driver analyses identified NK cell granule protein (NKG7, fold change = 22.7, FDR = 1.02 × 10-31) and perforin (PRF1, fold change = 14.9, FDR = 1.31 × 10-22) as key drivers predicted to causally regulate PBMC asthma modules. Nasal genes associated with asthma were enriched in the tricarboxylic acid (TCA) cycle module (fold enrichment = 7.5 FDR = 5.09 × 10-107), with network analyses identifying G3BP stress granule assembly factor 1 (G3BP1, fold change = 9.1 FDR = 2.77 × 10-5) and InaD-like protein (INADL, fold change = 5.3 FDR = 2.98 × 10-9) as nasal key drivers. Causal mediation analyses revealed that associations between PBMC key drivers and asthma are causally mediated by nasal key drivers (FDR = 0.0076 to 0.015). CONCLUSIONS Integrated study of the systemic and airway transcriptomes in a well-phenotyped asthma cohort identified causal key drivers of asthma among PBMC and nasal transcripts. Associations between PBMC key drivers and asthma are causally mediated by nasal key drivers.
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Affiliation(s)
- Lingdi Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, USA
| | - Yoojin Chun
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, USA
| | - Haritz Irizar
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, USA
| | - Zoe Arditi
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, USA
| | - Galina Grishina
- Division of Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, USA
| | - Alexander Grishin
- Division of Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, USA
| | - Alfin Vicencio
- Division of Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, USA
| | - Supinda Bunyavanich
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, USA.
- Division of Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, USA.
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6
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Wu W, Chen G, Zhang Z, He M, Li H, Yan F. Construction and verification of atopic dermatitis diagnostic model based on pyroptosis related biological markers using machine learning methods. BMC Med Genomics 2023; 16:138. [PMID: 37330465 PMCID: PMC10276470 DOI: 10.1186/s12920-023-01552-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 05/17/2023] [Indexed: 06/19/2023] Open
Abstract
OBJECTIVE The aim of this study was to construct a model used for the accurate diagnosis of Atopic dermatitis (AD) using pyroptosis related biological markers (PRBMs) through the methods of machine learning. METHOD The pyroptosis related genes (PRGs) were acquired from molecular signatures database (MSigDB). The chip data of GSE120721, GSE6012, GSE32924, and GSE153007 were downloaded from gene expression omnibus (GEO) database. The data of GSE120721 and GSE6012 were combined as the training group, while the others were served as the testing groups. Subsequently, the expression of PRGs was extracted from the training group and differentially expressed analysis was conducted. CIBERSORT algorithm calculated the immune cells infiltration and differentially expressed analysis was conducted. Consistent cluster analysis divided AD patients into different modules according to the expression levels of PRGs. Then, weighted correlation network analysis (WGCNA) screened the key module. For the key module, we used Random forest (RF), support vector machines (SVM), Extreme Gradient Boosting (XGB), and generalized linear model (GLM) to construct diagnostic models. For the five PRBMs with the highest model importance, we built a nomogram. Finally, the results of the model were validated using GSE32924, and GSE153007 datasets. RESULTS Nine PRGs were significant differences in normal humans and AD patients. Immune cells infiltration showed that the activated CD4+ memory T cells and Dendritic cells (DCs) were significantly higher in AD patients than normal humans, while the activated natural killer (NK) cells and the resting mast cells were significantly lower in AD patients than normal humans. Consistent cluster analysis divided the expressing matrix into 2 modules. Subsequently, WGCNA analysis showed that the turquoise module had a significant difference and high correlation coefficient. Then, the machine model was constructed and the results showed that the XGB model was the optimal model. The nomogram was constructed by using HDAC1, GPALPP1, LGALS3, SLC29A1, and RWDD3 five PRBMs. Finally, the datasets GSE32924 and GSE153007 verified the reliability of this result. CONCLUSIONS The XGB model based on five PRBMs can be used for the accurate diagnosis of AD patients.
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Affiliation(s)
- Wenfeng Wu
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Gaofei Chen
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Zhongshan Hospital of Traditional Chinese Medicine Affiliated to Guangzhou University of Traditional Chinese Medicine, Zhongshan, China
| | - Zexin Zhang
- The First Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Meixing He
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Hongyi Li
- Department of Dermatology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine (Guangdong Provincial Hospital of Chinese Medicine), Guangzhou, China.
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.
| | - Fenggen Yan
- Department of Dermatology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine (Guangdong Provincial Hospital of Chinese Medicine), Guangzhou, China.
- Guangdong Provincial Key Laboratory of Chinese Medicine for Prevention and Treatment of Refractory Chronic Diseases, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine (Guangdong Provincial Hospital of Chinese Medicine), Guangzhou, China.
- Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou, China.
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.
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Timing of Blood Sample Processing Affects the Transcriptomic and Epigenomic Profiles in CD4+ T-cells of Atopic Subjects. Cells 2022; 11:cells11192958. [PMID: 36230920 PMCID: PMC9563434 DOI: 10.3390/cells11192958] [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: 07/04/2022] [Revised: 08/10/2022] [Accepted: 09/09/2022] [Indexed: 11/17/2022] Open
Abstract
Optimal pre-analytical conditions for blood sample processing and isolation of selected cell populations for subsequent transcriptomic and epigenomic studies are required to obtain robust and reproducible results. This pilot study was conducted to investigate the potential effects of timing of CD4+ T-cell processing from peripheral blood of atopic and non-atopic adults on their transcriptomic and epigenetic profiles. Two heparinized blood samples were drawn from each of three atopic and three healthy individuals. For each individual, CD4+ T-cells were isolated from the first blood sample within 2 h (immediate) or from the second blood sample after 24 h storage (delayed). RNA sequencing (RNA-Seq) and histone H3K27 acetylation chromatin immunoprecipitation sequencing (ChIP-Seq) analyses were performed. A multiplicity of genes was shown to be differentially expressed in immediately processed CD4+ T-cells from atopic versus healthy subjects. These differences disappeared when comparing delayed processed cells due to a drastic change in expression levels of atopy-related genes in delayed processed CD4+ T-cells from atopic donors. This finding was further validated on the epigenomic level by examining H3K27 acetylation profiles. In contrast, transcriptomic and epigenomic profiles of blood CD4+ T-cells of healthy donors remained rather unaffected. Taken together, for successful transcriptomics and epigenomics studies, detailed standard operation procedures developed on the basis of samples from both healthy and disease conditions are implicitly recommended.
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8
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Lee HW, Baek MG, Choi S, Ahn YH, Bang JY, Sohn KH, Kang MG, Jung JW, Choi JH, Cho SH, Yi H, Kang HR. Peripheral blood transcriptomic clusters uncovered immune phenotypes of asthma. Respir Res 2022; 23:237. [PMID: 36076228 PMCID: PMC9461267 DOI: 10.1186/s12931-022-02156-w] [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: 04/17/2022] [Accepted: 08/01/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Transcriptomic analysis has been used to elucidate the complex pathogenesis of heterogeneous disease and may also contribute to identify potential therapeutic targets by delineating the hub genes. This study aimed to investigate whether blood transcriptomic clustering can distinguish clinical and immune phenotypes of asthmatics, and microbiome in asthmatics. METHODS Transcriptomic expression of peripheral blood mononuclear cells (PBMCs) from 47 asthmatics and 21 non-asthmatics was measured using RNA sequencing. A hierarchical clustering algorithm was used to classify asthmatics. Differentially expressed genes, clinical phenotypes, immune phenotypes, and microbiome of each transcriptomic cluster were assessed. RESULTS In asthmatics, three distinct transcriptomic clusters with numerously different transcriptomic expressions were identified. The proportion of severe asthmatics was highest in cluster 3 as 73.3%, followed by cluster 2 (45.5%) and cluster 1 (28.6%). While cluster 1 represented clinically non-severe T2 asthma, cluster 3 tended to include severe non-T2 asthma. Cluster 2 had features of both T2 and non-T2 asthmatics characterized by the highest serum IgE level and neutrophil-dominant sputum cell population. Compared to non-asthmatics, cluster 1 showed higher CCL23 and IL1RL1 expression while the expression of TREML4 was suppressed in cluster 3. CTSD and ALDH2 showed a significant positive linear relationship across three clusters in the order of cluster 1 to 3. No significant differences in the diversities of lung and gut microbiomes were observed among transcriptomic clusters of asthmatics and non-asthmatics. However, our study has limitations in that small sample size data were analyzed with unmeasured confounding factors and causal relationships or function pathways were not verified. CONCLUSIONS Genetic clustering based on the blood transcriptome may provide novel immunological insight, which can be biomarkers of asthma immune phenotypes. Trial registration Retrospectively registered.
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Affiliation(s)
- Hyun Woo Lee
- Department of Internal Medicine, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, Seoul, Korea
| | - Min-Gyung Baek
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul, Korea
| | - Sungmi Choi
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul, Korea
| | - Yoon Hae Ahn
- Department of Internal Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-Gu, Seoul, 110-744, Korea
| | - Ji-Young Bang
- Department of Translational Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Kyoung-Hee Sohn
- Department of Internal Medicine, Kyung Hee University Hospital, Seoul, Korea
| | - Min-Gyu Kang
- Department of Internal Medicine, Chungbuk National University College of Medicine, Chungbuk National University Hospital, Cheongju, Korea
| | - Jae-Woo Jung
- Department of Internal Medicine, Chung-Ang University College of Medicine, Seoul, Korea
| | - Jeong-Hee Choi
- Department of Pulmonology and Allergy, Allergy and Clinical Immunology Research Center, Hallym University College of Medicine, Chuncheon, Korea
| | - Sang-Heon Cho
- Department of Internal Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-Gu, Seoul, 110-744, Korea.,Institute of Allergy and Clinical Immunology, Seoul National University Medical Research Center, Seoul National University College of Medicine, Seoul, Korea
| | - Hana Yi
- Interdisciplinary Program in Precision Public Health, Korea University, Seoul, Korea. .,School of Biosystems and Biomedical Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, Korea.
| | - Hye-Ryun Kang
- Department of Internal Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-Gu, Seoul, 110-744, Korea. .,Department of Translational Medicine, Seoul National University College of Medicine, Seoul, Korea. .,Institute of Allergy and Clinical Immunology, Seoul National University Medical Research Center, Seoul National University College of Medicine, Seoul, Korea.
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9
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Cai M, Yue M, Chen T, Liu J, Forno E, Lu X, Billiar T, Celedón J, McKennan C, Chen W, Wang J. Robust and accurate estimation of cellular fraction from tissue omics data via ensemble deconvolution. Bioinformatics 2022; 38:3004-3010. [PMID: 35438146 PMCID: PMC9991889 DOI: 10.1093/bioinformatics/btac279] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 03/22/2022] [Accepted: 04/13/2022] [Indexed: 01/04/2023] Open
Abstract
MOTIVATION Tissue-level omics data such as transcriptomics and epigenomics are an average across diverse cell types. To extract cell-type-specific (CTS) signals, dozens of cellular deconvolution methods have been proposed to infer cell-type fractions from tissue-level data. However, these methods produce vastly different results under various real data settings. Simulation-based benchmarking studies showed no universally best deconvolution approaches. There have been attempts of ensemble methods, but they only aggregate multiple single-cell references or reference-free deconvolution methods. RESULTS To achieve a robust estimation of cellular fractions, we proposed EnsDeconv (Ensemble Deconvolution), which adopts CTS robust regression to synthesize the results from 11 single deconvolution methods, 10 reference datasets, 5 marker gene selection procedures, 5 data normalizations and 2 transformations. Unlike most benchmarking studies based on simulations, we compiled four large real datasets of 4937 tissue samples in total with measured cellular fractions and bulk gene expression from different tissues. Comprehensive evaluations demonstrated that EnsDeconv yields more stable, robust and accurate fractions than existing methods. We illustrated that EnsDeconv estimated cellular fractions enable various CTS downstream analyses such as differential fractions associated with clinical variables. We further extended EnsDeconv to analyze bulk DNA methylation data. AVAILABILITY AND IMPLEMENTATION EnsDeconv is freely available as an R-package from https://github.com/randel/EnsDeconv. The RNA microarray data from the TRAUMA study are available and can be accessed in GEO (GSE36809). The demographic and clinical phenotypes can be shared on reasonable request to the corresponding authors. The RNA-seq data from the EVAPR study cannot be shared publicly due to the privacy of individuals that participated in the clinical research in compliance with the IRB approval at the University of Pittsburgh. The RNA microarray data from the FHS study are available from dbGaP (phs000007.v32.p13). The RNA-seq data from ROS study is downloaded from AD Knowledge Portal. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Manqi Cai
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Molin Yue
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Tianmeng Chen
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Jinling Liu
- Department of Engineering Management and Systems Engineering, Missouri University of Science and Technology, Rolla, MO 65409, USA
- Department of Biological Sciences, Missouri University of Science and Technology, Rolla, MO 65409, USA
| | - Erick Forno
- Department of Pediatrics, University of Pittsburgh Medical Center Children’s Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Xinghua Lu
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA 15206, USA
| | - Timothy Billiar
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Juan Celedón
- Department of Pediatrics, University of Pittsburgh Medical Center Children’s Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Chris McKennan
- Department of Statistics, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Wei Chen
- Department of Pediatrics, University of Pittsburgh Medical Center Children’s Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Jiebiao Wang
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA 15261, USA
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10
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Longé C, Bratti M, Kurowska M, Vibhushan S, David P, Desmeure V, Huang JD, Fischer A, de Saint Basile G, Sepulveda FE, Blank U, Ménasché G. Rab44 regulates murine mast cell-driven anaphylaxis through kinesin-1-dependent secretory granule translocation. J Allergy Clin Immunol 2022; 150:676-689. [PMID: 35469841 DOI: 10.1016/j.jaci.2022.04.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/15/2022] [Accepted: 04/08/2022] [Indexed: 11/16/2022]
Abstract
BACKGROUND Mast cells (MCs) are key effectors of the allergic response. Following the cross-linking of IgE receptors (FcεRIs), they release crucial inflammatory mediators through degranulation. Although degranulation depends critically on secretory granule (SG) trafficking towards the plasma membrane, the molecular machinery underlying this transport has not been fully characterized. OBJECTIVE Here, we analyzed the function of Rab44, a large atypical Rab GTPase highly expressed in MC, in MC degranulation process. METHODS Murine KO mouse models (KORab44 and DKOKif5b/Rab44) were used to perform passive cutaneous anaphylaxis (PCA) experiments and analyze granule translocation in derived bone-marrow-derived MCs (BMMCs) during degranulation. RESULTS We demonstrate that mice lacking Rab44 (KORab44) in their BMMCs are impaired in their ability to translocate and degranulate SGs at the plasma membrane upon FcεRI stimulation. Accordingly, KORab44 mice were less sensitive to IgE-mediated passive cutaneous anaphylaxis in vivo. A lack of Rab44 did not impair early FcεRI-stimulated signaling pathways, microtubule reorganization, lipid mediator or cytokine secretion. Mechanistically, Rab44 appears to interact with and function as part of the previously described kinesin-1-dependent transport pathway. CONCLUSIONS Our results highlight a novel role of Rab44 as a regulator of SG transport during degranulation and anaphylaxis acting through the kinesin-1-dependent microtubule transport machinery. Rab44 can thus be considered as a potential target for modulating MC degranulation and inhibiting IgE-mediated allergic reactions.
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Affiliation(s)
- Cyril Longé
- Université Paris Cité, Imagine Institute, Laboratory of Molecular basis of altered immune homeostasis, INSERM UMR1163, F-75015 Paris France
| | - Manuela Bratti
- Université Paris Cité, Centre de Recherche sur l'Inflammation, INSERM UMR1149, CNRS EMR8252, Faculté de Médecine site Bichat, Paris, France; Laboratoire d'Excellence Inflamex, F-75018, Paris, France
| | - Mathieu Kurowska
- Université Paris Cité, Imagine Institute, Laboratory of Molecular basis of altered immune homeostasis, INSERM UMR1163, F-75015 Paris France
| | - Shamila Vibhushan
- Université Paris Cité, Centre de Recherche sur l'Inflammation, INSERM UMR1149, CNRS EMR8252, Faculté de Médecine site Bichat, Paris, France; Laboratoire d'Excellence Inflamex, F-75018, Paris, France
| | - Pierre David
- Transgenesis Facility, Laboratoire d'Expérimentation Animale et Transgénèse (LEAT), Imagine Institute, Structure Fédérative de Recherche Necker INSERM US24/CNRS UMS3633, F-75015, Paris, France
| | - Valère Desmeure
- Université Paris Cité, Imagine Institute, Laboratory of Molecular basis of altered immune homeostasis, INSERM UMR1163, F-75015 Paris France
| | - Jian-Dong Huang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Alain Fischer
- Université Paris Cité, Imagine Institute, Laboratory of Molecular basis of altered immune homeostasis, INSERM UMR1163, F-75015 Paris France; Immunology and Pediatric Hematology Department, Necker Children's Hospital, AP-HP, F-75015 Paris, France; Collège de France, F-75005 Paris, France
| | - Geneviève de Saint Basile
- Université Paris Cité, Imagine Institute, Laboratory of Molecular basis of altered immune homeostasis, INSERM UMR1163, F-75015 Paris France; Centre d'Etude des Déficits Immunitaires, AP-HP, Hôpital Necker-Enfants Malades, F-75015, Paris, France
| | - Fernando E Sepulveda
- Université Paris Cité, Imagine Institute, Laboratory of Molecular basis of altered immune homeostasis, INSERM UMR1163, F-75015 Paris France; Centre National de la Recherche Scientifique, F-75015, Paris. France
| | - Ulrich Blank
- Université Paris Cité, Centre de Recherche sur l'Inflammation, INSERM UMR1149, CNRS EMR8252, Faculté de Médecine site Bichat, Paris, France; Laboratoire d'Excellence Inflamex, F-75018, Paris, France
| | - Gaël Ménasché
- Université Paris Cité, Imagine Institute, Laboratory of Molecular basis of altered immune homeostasis, INSERM UMR1163, F-75015 Paris France
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11
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Xu Z, Forno E, Acosta-Pérez E, Han YY, Rosser F, Manni ML, Canino G, Chen W, Celedón JC. Differential gene expression in nasal airway epithelium from overweight or obese youth with asthma. Pediatr Allergy Immunol 2022; 33:e13776. [PMID: 35470932 PMCID: PMC9047012 DOI: 10.1111/pai.13776] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/07/2022] [Accepted: 04/09/2022] [Indexed: 12/21/2022]
Abstract
BACKGROUND The mechanisms underlying the known link between overweight/obesity and childhood asthma are unclear. We aimed to identify differentially expressed genes and pathways associated with obesity-related asthma through a transcriptomic analysis of nasal airway epithelium. METHODS We compared the whole transcriptome in nasal airway epithelium of youth with overweight or obesity and asthma with that of youth of normal weight and asthma, using RNA sequencing data from a cohort of 235 Puerto Ricans aged 9-20 years (EVA-PR) and an independent cohort of 66 children aged 6-16 years in Pittsburgh (VDKA). Differential expression analysis adjusting for age, sex, sequencing plate number, and sample sorting protocol, and the first five principal components were performed independently in each cohort. Results from the two cohorts were combined in a transcriptome-wide meta-analysis. Gene enrichment and network analyses were performed on top genes. RESULTS In the meta-analysis, 29 genes were associated with obesity-related asthma at an FDR-adjusted p <.05, including pro-inflammatory genes known to be differentially expressed in adipose tissue of obese subjects (e.g., CXCL11, CXCL10, and CXCL9) and several novel genes. Functional enrichment analyses showed that pathways for interferon signaling, and innate and adaptive immune responses were down-regulated in overweight/obese youth with asthma, while pathways related to ciliary structure or function were up-regulated. Upstream regulatory analysis predicted significant inhibition of the IRF7 pathway. Network analyses identified "hub" genes like GBP5 and SOCS1. CONCLUSION Our transcriptome-wide analysis of nasal airway epithelium identified biologically plausible genes and pathways for obesity-related asthma in youth.
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Affiliation(s)
- Zhongli Xu
- Division of Pediatric Pulmonary Medicine, UPMC Children’s Hospital of Pittsburgh, and Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- School of Medicine, Tsinghua University, Beijing, China
| | - Erick Forno
- Division of Pediatric Pulmonary Medicine, UPMC Children’s Hospital of Pittsburgh, and Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Edna Acosta-Pérez
- Behavioral Sciences Research Institute, University of Puerto Rico, San Juan, PR, USA
| | - Yueh-Ying Han
- Division of Pediatric Pulmonary Medicine, UPMC Children’s Hospital of Pittsburgh, and Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Franziska Rosser
- Division of Pediatric Pulmonary Medicine, UPMC Children’s Hospital of Pittsburgh, and Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Michelle L. Manni
- Division of Pediatric Pulmonary Medicine, UPMC Children’s Hospital of Pittsburgh, and Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Glorisa Canino
- Behavioral Sciences Research Institute, University of Puerto Rico, San Juan, PR, USA
| | - Wei Chen
- Division of Pediatric Pulmonary Medicine, UPMC Children’s Hospital of Pittsburgh, and Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Juan C. Celedón
- Division of Pediatric Pulmonary Medicine, UPMC Children’s Hospital of Pittsburgh, and Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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12
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Mikus MS, Kolmert J, Andersson LI, Östling J, Knowles RG, Gómez C, Ericsson M, Thörngren JO, Khoonsari PE, Dahlén B, Kupczyk M, De Meulder B, Auffray C, Bakke PS, Beghe B, Bel EH, Caruso M, Chanez P, Chawes B, Fowler SJ, Gaga M, Geiser T, Gjomarkaj M, Horváth I, Howarth PH, Johnston SL, Joos G, Krug N, Montuschi P, Musial J, Niżankowska-Mogilnicka E, Olsson HK, Papi A, Rabe KF, Sandström T, Shaw DE, Siafakas NM, Uhlen M, Riley JH, Bates S, Middelveld RJM, Wheelock CE, Chung KF, Adcock IM, Sterk PJ, Djukanovic R, Nilsson P, Dahlén SE, James A. Plasma proteins elevated in severe asthma despite oral steroid use and unrelated to Type-2 inflammation. Eur Respir J 2021; 59:13993003.00142-2021. [PMID: 34737220 PMCID: PMC8850689 DOI: 10.1183/13993003.00142-2021] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 06/24/2021] [Indexed: 12/02/2022]
Abstract
Rationale Asthma phenotyping requires novel biomarker discovery. Objectives To identify plasma biomarkers associated with asthma phenotypes by application of a new proteomic panel to samples from two well-characterised cohorts of severe (SA) and mild-to-moderate (MMA) asthmatics, COPD subjects and healthy controls (HCs). Methods An antibody-based array targeting 177 proteins predominantly involved in pathways relevant to inflammation, lipid metabolism, signal transduction and extracellular matrix was applied to plasma from 525 asthmatics and HCs in the U-BIOPRED cohort, and 142 subjects with asthma and COPD from the validation cohort BIOAIR. Effects of oral corticosteroids (OCS) were determined by a 2-week, placebo-controlled OCS trial in BIOAIR, and confirmed by relation to objective OCS measures in U-BIOPRED. Results In U-BIOPRED, 110 proteins were significantly different, mostly elevated, in SA compared to MMA and HCs. 10 proteins were elevated in SA versus MMA in both U-BIOPRED and BIOAIR (alpha-1-antichymotrypsin, apolipoprotein-E, complement component 9, complement factor I, macrophage inflammatory protein-3, interleukin-6, sphingomyelin phosphodiesterase 3, TNF receptor superfamily member 11a, transforming growth factor-β and glutathione S-transferase). OCS treatment decreased most proteins, yet differences between SA and MMA remained following correction for OCS use. Consensus clustering of U-BIOPRED protein data yielded six clusters associated with asthma control, quality of life, blood neutrophils, high-sensitivity C-reactive protein and body mass index, but not Type-2 inflammatory biomarkers. The mast cell specific enzyme carboxypeptidase A3 was one major contributor to cluster differentiation. Conclusions The plasma proteomic panel revealed previously unexplored yet potentially useful Type-2-independent biomarkers and validated several proteins with established involvement in the pathophysiology of SA. Application of new proteomic panel in two established European asthma cohorts identifies plasma proteins associated with disease severity independently of Type-2 inflammation, suggesting potentially useful novel biomarkers and therapeutic targets.https://bit.ly/3jtTq5m
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Affiliation(s)
- Maria Sparreman Mikus
- Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden .,Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Johan Kolmert
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.,Centre for Allergy Research, Karolinska Institutet, Stockholm, Sweden
| | - Lars I Andersson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.,Centre for Allergy Research, Karolinska Institutet, Stockholm, Sweden
| | | | | | - Cristina Gómez
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.,Centre for Allergy Research, Karolinska Institutet, Stockholm, Sweden
| | - Magnus Ericsson
- Department of Laboratory Medicine, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - John-Olof Thörngren
- Department of Laboratory Medicine, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Payam Emami Khoonsari
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Solna, Sweden
| | - Barbro Dahlén
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.,Centre for Allergy Research, Karolinska Institutet, Stockholm, Sweden.,Department of Medicine, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Maciej Kupczyk
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.,Centre for Allergy Research, Karolinska Institutet, Stockholm, Sweden.,Department of Internal Medicine, Asthma and Allergy, Medical University of Lodz, University of Lodz, Lodz, Poland
| | | | - Charles Auffray
- European Institute for Systems Biology and Medicine, Lyon, France
| | - Per S Bakke
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Bianca Beghe
- Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Elisabeth H Bel
- Department of Respiratory Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Massimo Caruso
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Pascal Chanez
- Assistance Publique des Hôpitaux de Marseille, Clinique des Bronches, Allergies et Sommeil, Aix Marseille Université, Marseille, France
| | - Bo Chawes
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Stephen J Fowler
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, The University of Manchester; Manchester Academic Health Science Centre and NIHR Manchester Biomedical Research Centre, Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Mina Gaga
- Respiratory Medicine Dept and Asthma Centre, Athens Chest Hospital "Sotiria", University of Athens, Athens, Greece
| | - Thomas Geiser
- Department for Pulmonary Medicine, University Hospital and University of Bern, Bern, Switzerland
| | - Mark Gjomarkaj
- Institute for Research and Biomedical Innovation, Italian National Research Council, Palermo, Italy
| | - Ildikó Horváth
- Department of Pulmonology, Semmelweis University, Budapest, Hungary
| | - Peter H Howarth
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, and Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | | | - Guy Joos
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium.,Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Norbert Krug
- Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover, Germany
| | - Paolo Montuschi
- Department of Pharmacology, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Jacek Musial
- Department of Internal Medicine, Jagiellonian University Medical College, Krakow, Poland
| | | | - Henric K Olsson
- Translational Science and Experimental Medicine, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Alberto Papi
- Division of lnternal and Cardiorespiratory Medicine, University of Ferrara, Ferrara, Italy
| | - Klaus F Rabe
- Department of Internal Medicine, Christian Albrechts University Kiel, Kiel, Germany
| | - Thomas Sandström
- Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | - Dominick E Shaw
- Respiratory Research Unit, University of Nottingham, Nottingham, UK
| | - Nikolaos M Siafakas
- Department of Thoracic Medicine, Medical School, University of Crete, Heraklion, Crete, Greece
| | - Mathias Uhlen
- Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden.,Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - John H Riley
- Respiratory Therapeutic Unit, GlaxoSmithKline, London, UK
| | - Stewart Bates
- Respiratory Therapeutic Unit, GlaxoSmithKline, London, UK
| | - Roelinde J M Middelveld
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.,Centre for Allergy Research, Karolinska Institutet, Stockholm, Sweden
| | - Craig E Wheelock
- Centre for Allergy Research, Karolinska Institutet, Stockholm, Sweden.,Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Kian Fan Chung
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Ian M Adcock
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Peter J Sterk
- Department of Respiratory Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Ratko Djukanovic
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, and Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Peter Nilsson
- Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden
| | - Sven-Erik Dahlén
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.,Centre for Allergy Research, Karolinska Institutet, Stockholm, Sweden
| | - Anna James
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.,Centre for Allergy Research, Karolinska Institutet, Stockholm, Sweden
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13
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Endotyping asthma related to three different work exposures. J Allergy Clin Immunol 2021; 148:1072-1080. [PMID: 34331994 DOI: 10.1016/j.jaci.2021.07.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 07/06/2021] [Accepted: 07/22/2021] [Indexed: 11/21/2022]
Abstract
BACKGROUND Work exposures play a significant role in adult-onset asthma, but mechanisms of work-related asthma are not fully elucidated. OBJECTIVE We aimed to reveal the molecular mechanisms of work-related asthma associated with flour (FA), isocyanate (IA) or welding fume (WA) exposures and identify potential biomarkers that distinguish these groups from each other. METHODS We used a combination of clinical tests, transcriptomic analysis and associated pathway analyses to investigate underlying disease mechanisms of the blood immune cells and the airway epithelium of 61 men. RESULTS Compared to the healthy controls, the WA patients had more differentially expressed genes than the FA and IA patients both in the airway epithelia and in the blood immune cells. In the airway epithelia, active inflammation was detected only in WA patients. In contrast, large number of differentially expressed genes were detected in all asthma groups in blood cells. Disease-related immune functions in blood cells were suppressed in all the asthma groups including leukocyte migration and inflammatory responses and decreased expression of upstream cytokines such as TNF and IFNγ. In transcriptome-phenotype correlations, hyperresponsiveness (R∼|0.6|) had the highest clinical relevance and associated with a set of exposure-group specific genes. Finally, biomarker subsets of only 5 genes specifically distinguished each of the asthma exposure group. CONCLUSIONS This study provides novel data on the molecular mechanisms underlying work-related asthma. We identified set of 5 promising biomarkers in asthma related to flour, isocyanate and welding exposure to be tested and clinically validated in future studies.
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Large Rab GTPases: Novel Membrane Trafficking Regulators with a Calcium Sensor and Functional Domains. Int J Mol Sci 2021; 22:ijms22147691. [PMID: 34299309 PMCID: PMC8303950 DOI: 10.3390/ijms22147691] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/13/2021] [Accepted: 07/14/2021] [Indexed: 12/28/2022] Open
Abstract
Rab GTPases are major coordinators of intracellular membrane trafficking, including vesicle transport, membrane fission, tethering, docking, and fusion events. Rab GTPases are roughly divided into two groups: conventional “small” Rab GTPases and atypical “large” Rab GTPases that have been recently reported. Some members of large Rab GTPases in mammals include Rab44, Rab45/RASEF, and Rab46. The genes of these large Rab GTPases commonly encode an amino-terminal EF-hand domain, coiled-coil domain, and the carboxyl-terminal Rab GTPase domain. A common feature of large Rab GTPases is that they express several isoforms in cells. For instance, Rab44’s two isoforms have similar functions, but exhibit differential localization. The long form of Rab45 (Rab45-L) is abundantly distributed in epithelial cells. The short form of Rab45 (Rab45-S) is predominantly present in the testes. Both Rab46 (CRACR2A-L) and the short isoform lacking the Rab domain (CRACR2A-S) are expressed in T cells, whereas Rab46 is only distributed in endothelial cells. Although evidence regarding the function of large Rab GTPases has been accumulating recently, there are only a limited number of studies. Here, we report the recent findings on the large Rab GTPase family concerning their function in membrane trafficking, cell differentiation, related diseases, and knockout mouse phenotypes.
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Abstract
PURPOSE OF REVIEW Asthma is the most common chronic disease in pediatric age. Childhood-onset asthma, as opposed to adult-onset asthma, is typically characterized by a personal and often a family history of atopy and related markers of type 2-mediated inflammation. However, the interplay between atopy and asthma development is more complex than a linear dose-response relationship. RECENT FINDINGS Family and personal history of atopic diseases have been confirmed as major risk factors for asthma occurrence and persistence in children. Early life and multiple sensitizations to aeroallergens significantly increase the risk of asthma development in school age. Early life lower respiratory tract viral infections, especially caused by rhinovirus, also increase the susceptibility to atopic asthma in childhood. Human rhinovirus type C receptor CDHR3 polymorphisms have been shown to affect receptor epithelial expression, activation, and asthma development and exacerbation severity in children. Atopic sensitization and respiratory viral infections can synergistically enhance the susceptibility to asthma through multiple mechanisms, including the IgE-mediated inhibition of innate antiviral responses to rhinovirus. Emerging evidence shows that several nonatopic factors are also involved in the asthma pathogenesis in genetically predisposed individuals, including early life exposure to environmental factors, and lung and gut microbiome composition. SUMMARY The current review outlines recent data on the complex role of atopy in asthma pathogenesis and persistence, and addresses new research topics such as the role of epigenetics and the lung microbiome.
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Abstract
Purpose of review Childhood asthma is a heterogeneous inflammatory disease comprising different phenotypes and endotypes and, particularly in its severe forms, has a large impact on the quality-of-life of patients and caregivers. The application of advanced omics technologies provides useful insights into underlying asthma endotypes and may provide potential clinical biomarkers to guide treatment and move towards a precision medicine approach. Recent findings The current article addresses how novel omics approaches have shaped our current understanding of childhood asthma and highlights recent findings from (pharmaco)genomics, epigenomics, transcriptomics, and metabolomics studies on childhood asthma and their potential clinical implications to guide treatment in severe asthmatics. Summary Until now, omics studies have largely expanded our view on asthma heterogeneity, helped understand cellular processes underlying asthma, and brought us closer towards identifying (bio)markers that will allow the prediction of treatment responsiveness and disease progression. There is a clinical need for biomarkers that will guide treatment at the individual level, particularly in the field of biologicals. The integration of multiomics data together with clinical data could be the next promising step towards development individual risk prediction models to guide treatment. However, this requires large-scale collaboration in a multidisciplinary setting.
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Bousquet J, Bedbrook A, Czarlewski W, De Carlo G, Fonseca JA, González Ballester MA, Illario M, Koskinen S, Laatikainen T, Onorato GL, Palkonen S, Patella V, Pham-Thi N, Puggioni F, Ventura MT, Joos G, Kuna P, Louis R, Makris M, Zalud P, Zuberbier T, Bachert C, Brussino L, Carreiro-Martins P, Carrion Y Ribas C, Chalubinski M, Costa EM, de Vries G, Gemicioglu B, Gennimata D, Micheli Y, Niedoszytko M, Regateiro FS, Romantowski J, Taborda-Barata L, Toppila-Salmi S, Tsiligianni I, Viart F, Laune D. Digital Health Europe (DHE) Twinning on severe asthma-kick-off meeting report. J Thorac Dis 2021; 13:3215-3225. [PMID: 34164213 PMCID: PMC8182538 DOI: 10.21037/jtd-21-792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Jean Bousquet
- Charité Universitätsmedizin Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Comprehensive Allergy Center, Department of Dermatology and Allergy, Berlin, Germany.,University Hospital Montpellier, Montpellier, France.,Maladies Chroniques pour un Viellissement Actif, (Macvia-France), Montpellier, France
| | - Anna Bedbrook
- Maladies Chroniques pour un Viellissement Actif, (Macvia-France), Montpellier, France.,Allergic Rhinitis and its Impact on Asthma (ARIA), Montpellier, France.,Mobile Airways Sentinel nekworK (MASK-air), Montpellier, France
| | - Wienczyslawa Czarlewski
- Allergic Rhinitis and its Impact on Asthma (ARIA), Montpellier, France.,Mobile Airways Sentinel nekworK (MASK-air), Montpellier, France.,Medical Consulting Czarlewski, Levallois, France
| | - Giuseppe De Carlo
- European Federation of Allergy and Airways Diseases Patients' Associations, Brussels, Belgium
| | - Joao A Fonseca
- Center for Research in Health Technology and Information Systems, Faculdade de Medicina da Universidade do Porto, Porto, Portugal.,Medida, Lda Porto, Portugal
| | - Miguel A González Ballester
- Department of Information and Communication Technologies, Universitat Pompeu Fabra, Barcelona, Spain, ICREA, Barcelona, Spain
| | - Maddalena Illario
- Division for Health Innovation, Campania Region and Federico II University Hospital Naples (R&D Unit and Department of Public Health), Naples, Italy
| | - Seppo Koskinen
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | | | - Gabrielle L Onorato
- Maladies Chroniques pour un Viellissement Actif, (Macvia-France), Montpellier, France
| | - Susanna Palkonen
- European Federation of Allergy and Airways Diseases Patients' Associations, Brussels, Belgium
| | - Vincenzo Patella
- Division of Allergy and Clinical Immunology, Department of Medicine, Agency of Health ASL Salerno, "Santa Maria della Speranza" Hospital, Battipaglia, Salerno, Italy
| | - Nhân Pham-Thi
- Ecole Polytechnique Palaiseau, IRBA (Institut de Recherche bio-Médicale des Armées), Bretigny, France
| | - Francesca Puggioni
- Personalized Medicine Clinic Asthma & Allergy, Humanitas Clinical and Research Center IRCCS, Rozzano, MI, Italy.,Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, MI, Italy
| | - Maria Teresa Ventura
- University of Bari Medical School, Unit of Geriatric Immunoallergology, Bari, Italy
| | - Guy Joos
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Piotr Kuna
- Division of Internal Medicine, Asthma and Allergy, Barlicki University Hospital, Medical University of Lodz, Lodz, Poland
| | - Renaud Louis
- Department of Pulmonary Medicine, CHU Sart-Tilman, and GIGA I3 Research Group, Liege, Belgium
| | - Michael Makris
- Allergy Unit "D Kalogeromitros", 2nd Department of Dermatology and Venereology, National & Kapodistrian University of Athens, "Attikon" University Hospital, Athens, Greece
| | | | - Torsten Zuberbier
- Charité Universitätsmedizin Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Comprehensive Allergy Center, Department of Dermatology and Allergy, Berlin, Germany
| | - Claus Bachert
- Upper Airways Research Laboratory, ENT Department, Ghent University Hospital, Ghent, Belgium.,International Airway Research Center, First Affiliated Hospital, Sun Yat-sen University, Guangzou, China.,Division of ENT Diseases, CLINTEC, Karolinska Institutet, Stockholm, Sweden.,Department of ENT Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Luisa Brussino
- Department of Medical Sciences, Allergy and Clinical Immunology Unit, University of Torino & Mauriziano Hospital, Torino, Italy
| | - Pedro Carreiro-Martins
- Serviço de Imunoalergologia, Hospital de Dona Estefânia, Centro Hospitalar de Lisboa Central, Lisbon, Portugal.,CEDOC, Faculdade de Ciências Médicas (FCM), Universidade Nova de Lisboa, Lisbon, Portugal
| | - Carme Carrion Y Ribas
- School of Health Sciences and UOC eHealth Center, Universitat Oberta de Catalunya, Barcelona, Spain
| | - Maciej Chalubinski
- Department of Immunology and Allergy, Medical University of Lodz, Lodz, Poland
| | - Elisio M Costa
- Faculty of Pharmacy and Competence Center on Active and Healthy Ageing of University of Porto (Porto4Ageing), Porto, Portugal
| | | | - Bilun Gemicioglu
- Department of Pulmonary Diseases, Istanbul University-Cerrahpasa, Cerrahpasa Faculty of Medicine, Istanbul, Turkey
| | - Dimitra Gennimata
- Department of Pharmacy, Athens General Hospital "Korgialenio-Benakio" Hellenic Red Cross, Athens, Greece
| | | | - Marek Niedoszytko
- Medical University of Gdańsk, Department of Allergology, Gdańsk, Poland
| | - Frederico S Regateiro
- Allergy and Clinical Immunology Unit, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal.,Institute of Immunology, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Jan Romantowski
- Medical University of Gdańsk, Department of Allergology, Gdańsk, Poland
| | - Luis Taborda-Barata
- Health Sciences, University of Beira Interior, Covilhã, Portugal.,Department of Immunoallergology, Cova da Beira University Hospital Centre, Covilhã, Portugal
| | - Sanna Toppila-Salmi
- Skin and Allergy Hospital, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Ioanna Tsiligianni
- Health Planning Unit, Department of Social Medicine, Faculty of Medicine, University of Crete, Crete, Greece.,International Primary Care Respiratory Group IPCRG, Aberdeen, Scotland
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Abstract
Allergic rhinitis (AR) is caused by immunoglobulin E (IgE)-mediated reactions to inhaled allergens and is one of the most common chronic conditions globally. AR often co-occurs with asthma and conjunctivitis and is a global health problem causing major burden and disability worldwide. Risk factors include inhalant and occupational allergens, as well as genetic factors. AR impairs quality of life, affects social life, school and work, and is associated with substantial economic costs. The Allergic Rhinitis and its Impact on Asthma (ARIA) initiative classified AR into intermittent or persistent and mild or moderate/severe. The diagnosis is based on the clinical history and, if needed in patients with uncontrolled rhinitis despite medications or with long-lasting symptoms, on skin tests or the presence of serum-specific IgE antibodies to allergens. The most frequently used pharmacological treatments include oral, intranasal or ocular H1-antihistamines, intranasal corticosteroids or a fixed combination of intranasal H1-antihistamines and corticosteroids. Allergen immunotherapy prescribed by a specialist using high-quality extracts in stratified patients is effective in patients with persistent symptoms. Real-world data obtained by mobile technology offer new insights into AR phenotypes and management. The outlook for AR includes a better understanding of novel multimorbid phenotypes, health technology assessment and patient-centred shared decision-making.
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Lemonnier N, Melén E, Jiang Y, Joly S, Ménard C, Aguilar D, Acosta‐Perez E, Bergström A, Boutaoui N, Bustamante M, Canino G, Forno E, Ramon González J, Garcia‐Aymerich J, Gruzieva O, Guerra S, Heinrich J, Kull I, Ibarluzea Maurolagoitia J, Santa‐Marina Rodriguez L, Thiering E, Wickman M, Akdis C, Akdis M, Chen W, Keil T, Koppelman GH, Siroux V, Xu C, Hainaut P, Standl M, Sunyer J, Celedón JC, Maria Antó J, Bousquet J. A novel whole blood gene expression signature for asthma, dermatitis, and rhinitis multimorbidity in children and adolescents. Allergy 2020; 75:3248-3260. [PMID: 32277847 DOI: 10.1111/all.14314] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 03/25/2020] [Accepted: 03/30/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND Allergic diseases often occur in combination (multimorbidity). Human blood transcriptome studies have not addressed multimorbidity. Large-scale gene expression data were combined to retrieve biomarkers and signaling pathways to disentangle allergic multimorbidity phenotypes. METHODS Integrated transcriptomic analysis was conducted in 1233 participants with a discovery phase using gene expression data (Human Transcriptome Array 2.0) from whole blood of 786 children from three European birth cohorts (MeDALL), and a replication phase using RNA Sequencing data from an independent cohort (EVA-PR, n = 447). Allergic diseases (asthma, atopic dermatitis, rhinitis) were considered as single disease or multimorbidity (at least two diseases), and compared with no disease. RESULTS Fifty genes were differentially expressed in allergic diseases. Thirty-two were not previously described in allergy. Eight genes were consistently overexpressed in all types of multimorbidity for asthma, dermatitis, and rhinitis (CLC, EMR4P, IL5RA, FRRS1, HRH4, SLC29A1, SIGLEC8, IL1RL1). All genes were replicated the in EVA-PR cohort. RT-qPCR validated the overexpression of selected genes. In MeDALL, 27 genes were differentially expressed in rhinitis alone, but none was significant for asthma or dermatitis alone. The multimorbidity signature was enriched in eosinophil-associated immune response and signal transduction. Protein-protein interaction network analysis identified IL5/JAK/STAT and IL33/ST2/IRAK/TRAF as key signaling pathways in multimorbid diseases. Synergistic effect of multimorbidity on gene expression levels was found. CONCLUSION A signature of eight genes identifies multimorbidity for asthma, rhinitis, and dermatitis. Our results have clinical and mechanistic implications, and suggest that multimorbidity should be considered differently than allergic diseases occurring alone.
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Barbetta C, Mazza F, Caminati M. Small airways dysfunction: is there any involvement in patients with atopy? THE LANCET RESPIRATORY MEDICINE 2020; 7:e26. [PMID: 31486394 DOI: 10.1016/s2213-2600(19)30244-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 06/27/2019] [Indexed: 10/26/2022]
Affiliation(s)
- Carlo Barbetta
- Department of Pulmonary Medicine, Ospedale Santa Maria degli Angeli, 33170 Pordenone, Italy.
| | - Francesco Mazza
- Department of Pulmonary Medicine, Ospedale Santa Maria degli Angeli, 33170 Pordenone, Italy
| | - Marco Caminati
- Asthma Center and Allergy Unit and Department of Medicine, University of Verona, Verona, Italy
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