1
|
Kitaba NT, Østergaard TM, Lønnebotn M, Accordini S, Real FG, Malinovschi A, Oudin A, Benediktsdottir B, González FJC, Gómez LP, Holm M, Jõgi NO, Dharmage SC, Skulstad SM, Schlünssen V, Svanes C, Holloway JW. Father's adolescent body silhouette is associated with offspring asthma, lung function and BMI through DNA methylation. Commun Biol 2025; 8:796. [PMID: 40410506 PMCID: PMC12102279 DOI: 10.1038/s42003-025-08121-9] [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: 09/03/2024] [Accepted: 04/23/2025] [Indexed: 05/25/2025] Open
Abstract
Boys' pubertal overweight associates with future offspring's asthma and low lung function. To identify how paternal overweight is associated with offspring's DNA methylation (DNAm), we conducted an epigenome-wide association study of father's body silhouette (FBS) at three timepoints (age 8, voice break and 30) and change in FBS between these times, with offspring DNAm, in the RHINESSA cohort (N = 339). We identified 2005 differentially methylated cytosine-phosphate-guanine (dmCpG) sites (FDR < 0.05), including dmCpGs associated with offspring asthma (119), lung function (178) and BMI (291). Voice break FBS associated with dmCpGs in loci including KCNJ10, FERMT1, NCK2 and WWP1. Change in FBS across sexual maturation associated with DNAm at loci including NOP10, TRRAP, EFHD1, MRPL17 and NORD59A;ATP5B and showed strong correlation in reduced gene expression in loci NAP1L5, ATP5B, ZNF695, ZNF600, VTRNA2-1, SOAT2 and AGPAT2. We identified 24 imprinted genes including: VTRNA2-1, BLCAP, WT1, NAP1L5 and PTPRN2. Identified pathways relate to lipid and glucose metabolism and adipogenesis. Father's overweight at puberty and during reproductive maturation was strongly associated with offspring DNA, suggesting a key role for epigenetic mechanisms in intergenerational transfer from father to offspring in humans. The results support an important vulnerability window in male puberty for future offspring health.
Collapse
Grants
- We thank all the study participants, fieldworkers and scientists in RHINESSA, Co-ordination of the RHINESSA study has received funding from the Research Council of Norway (Grants No. 274767, 214123, 228174, 230827 and 273838), ERC StG project BRuSH #804199, the European Union's Horizon 2020 research and innovation programme under grant agreement No. 633212 (the ALEC Study), the Bergen Medical Research Foundation, and the Western Norwegian Regional Health Authorities (Grants No. 912011, 911892 and 911631). Study centres have further received local funding from the following: Bergen: the above grants for study establishment and co-ordination, and, in addition, World University Network (REF and Sustainability grants), Norwegian Labour Inspection, and the Norwegian Asthma and Allergy Association. Albacete and Huelva: Sociedad Española de Patología Respiratoria (SEPAR) Fondo de Investigación Sanitaria (FIS PS09). Gøteborg, Umeå and Uppsala: the Swedish Heart and Lung Foundation, the Swedish Asthma and Allergy Association. Reykjavik: Iceland University. Melbourne: National Health and Medical Research Council (NHMRC) of Australia (research grants 299901 and 1021275). Tartu: the Estonian Research Council (Grant No. PUT562). Århus: The Danish Wood Foundation (Grant No. 444508795), the Danish Working Environment Authority (Grant No. 20150067134), Aarhus University (PhD scholarship).
Collapse
Affiliation(s)
- Negusse Tadesse Kitaba
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Toril Mørkve Østergaard
- Department of Global Public Health and Primary Care, Centre for International Health, University of Bergen, Bergen, Norway
| | - Marianne Lønnebotn
- Department of Health and Caring Sciences, Western Norway University of Applied Sciences, Bergen, Norway
| | - Simone Accordini
- Unit of Epidemiology and Medical Statistics, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | | | - Andrei Malinovschi
- Department of Medical Sciences: Clinical Physiology, Uppsala University, Uppsala, Sweden
| | - Anna Oudin
- Section of Sustainable Health, Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | - Bryndis Benediktsdottir
- Department of Allergy, Respiratory Medicine and Sleep, Landspitali University Hospital, Reykjavik, Iceland Faculty of Medicine, University of Iceland, Landspitali, Iceland
| | | | | | - Mathias Holm
- Occupational and Environmental Medicine, School of Public Health and Community Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Nils Oskar Jõgi
- Department of Medical Sciences: Clinical Physiology, Uppsala University, Uppsala, Sweden
| | - Shyamali C Dharmage
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Australia
| | - Svein Magne Skulstad
- Department of Global Public Health and Primary Care, Centre for International Health, University of Bergen, Bergen, Norway
| | - Vivi Schlünssen
- Department of Public Health, Research Unit for Environment, Work and Health, Danish Ramazzini Centre, Aarhus University Denmark, Aarhus, Denmark
| | - Cecilie Svanes
- Department of Global Public Health and Primary Care, Centre for International Health, University of Bergen, Bergen, Norway.
- Department of Occupational Medicine, Haukeland University Hospital, Bergen, Norway.
| | - John W Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
- NIHR Southampton Biomedical Research Centre, University Hospitals Southampton, Southampton, UK
| |
Collapse
|
2
|
Ramonell RP, Oriss TB, McCreary-Partyka JC, Kale SL, Brandon NR, Ross MA, Gauthier MC, Yue M, Nee TJ, Das S, Chen W, Joglekar AV, Ray P, St Croix CM, Rajasundaram D, Wenzel SE, Ray A. CD8+ TEMRAs in severe asthma associate with asthma symptom duration and escape proliferation arrest. JCI Insight 2025; 10:e185061. [PMID: 40048261 PMCID: PMC12016929 DOI: 10.1172/jci.insight.185061] [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: 07/19/2024] [Accepted: 03/04/2025] [Indexed: 04/23/2025] Open
Abstract
Aberrant immune response is a hallmark of asthma, with 5%-10% of patients suffering from severe disease exhibiting poor response to standard treatment. A better understanding of the immune responses contributing to disease heterogeneity is critical for improving asthma management. T cells are major players in the orchestration of asthma, in both mild and severe disease, but it is unclear whether specific T cell subsets influence asthma symptom duration. Here we show a significant association of airway CD8+ effector memory T cells re-expressing CD45RA (TEMRAs), but not CD8+CD45RO+ or tissue-resident memory T cells, with asthma duration in patients with severe asthma (SA) but not mild to moderate asthma (MMA). Higher frequencies of IFN-γ+CD8+ TEMRAs compared with IFN-γ+CD45RO+ T cells were detected in SA airways, and the TEMRAs from patients with SA but not MMA proliferated ex vivo, although both expressed cellular senescence-associated biomarkers. Prompted by the transcriptomic profile of SA CD8+ TEMRAs and proliferative response to IL-15, airway IL15 expression was higher in patients with SA compared with MMA. Additionally, IL15 expression in asthmatic airways negatively correlated with lung function. Our findings add what we believe is a new dimension to understanding asthma heterogeneity, identifying IL-15 as a potential target for treatment.
Collapse
Affiliation(s)
- Richard P. Ramonell
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine
- Asthma and Environmental Lung Health Institute at UPMC
| | - Timothy B. Oriss
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine
| | | | - Sagar L. Kale
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine
| | | | - Mark A. Ross
- Department of Cell Biology
- Center for Biological Imaging
| | - Marc C. Gauthier
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine
- Asthma and Environmental Lung Health Institute at UPMC
| | | | - Taylor J. Nee
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine
- Asthma and Environmental Lung Health Institute at UPMC
| | - Sudipta Das
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine
| | | | | | - Prabir Ray
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine
- Asthma and Environmental Lung Health Institute at UPMC
- Department of Immunology
| | | | | | - Sally E. Wenzel
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine
- Asthma and Environmental Lung Health Institute at UPMC
- Department of Immunology
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Anuradha Ray
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine
- Asthma and Environmental Lung Health Institute at UPMC
- Department of Immunology
| |
Collapse
|
3
|
An J, Park J, Do AR, Seo S, Shin E, Lee JE, Cho YS, Won S, Kim TB. Differential DNA Methylation in Peripheral Blood Mononuclear Cells Reflects Asthma Control Status in Adults. Allergy 2025. [PMID: 40251921 DOI: 10.1111/all.16566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 03/20/2025] [Accepted: 04/10/2025] [Indexed: 04/21/2025]
Affiliation(s)
- Jin An
- Department of Pulmonary, Allergy and Critical Care Medicine, College of Medicine, Kyung Hee University Hospital at Gangdong, Kyung Hee University, Seoul, South Korea
| | - Jaehyun Park
- Interdisciplinary Program of Bioinformatics, Seoul National University, Seoul, South Korea
| | - Ah Ra Do
- Interdisciplinary Program of Bioinformatics, Seoul National University, Seoul, South Korea
| | - Sujin Seo
- Interdisciplinary Program of Bioinformatics, Seoul National University, Seoul, South Korea
| | | | | | - You Sook Cho
- Department of Allergy and Clinical Immunology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Sungho Won
- Department of Public Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, South Korea
- Interdisciplinary Program of Bioinformatics, College of Natural Science, Seoul National University, Seoul, South Korea
- Institute of Health and Environment, Seoul National University, Seoul, South Korea
- Department of Public Health Sciences, Seoul National University, Seoul, Korea
| | - Tae-Bum Kim
- Department of Allergy and Clinical Immunology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| |
Collapse
|
4
|
Makrufardi F, Peng SW, Chung KF, Chadeau-Hyam M, Lee KY, Hsiao TC, Ho KF, Rusmawatiningtyas D, Murni IK, Arguni E, Wang YH, Ho SC, Yang FM, Chuang KJ, Lin SC, Chuang HC. Extreme temperatures modulate gene expression in the airway epithelium of the lungs in mice and asthma patients. Front Med (Lausanne) 2025; 12:1531154. [PMID: 40313552 PMCID: PMC12043461 DOI: 10.3389/fmed.2025.1531154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2024] [Accepted: 03/28/2025] [Indexed: 05/03/2025] Open
Abstract
Background The objective of this study was to examine the effects of extreme temperatures on the gene signature and pathways of airway epithelial cells in mice and asthma patients. Methods We investigated the effects of temperature exposure at normal (22°C), and extreme low (10°C), high (40°C) and temperature fluctuation (40°C for 2 h followed by 10°C for next 2 h) in B6.Sftpc-CreER T2 ;Ai14(RCL-tdT)-D mice and pediatric and adult patient's airway epithelial exposed to extreme temperatures. Results We observed that Mmp8, Sftpb, Cxcl15 and Cd14 were significantly upregulated in airway epithelial cells in mice model. Cma1, Kit, Fdx1, Elf1a, Cdkn2aipnl, Htatsf1, Mfsd13a, Gtf2h5, Tiam2, and Trmt10c were significantly upregulated in 40°C exposure in airway epithelial cells. Sftpc, Gpr171, Sic34a2, Cox14, Lamp3, Luc7l, Nxnl, Tmub2, Tob1, and Cd3e genes were significantly upregulated in 10°C exposure group. Pediatric asthma subjects in the extreme high temperature group consistently showed decreased Wfdc21, Cib3, and Sftpc, at the same time increased Tiam2 and Cma1 expression, while in the extreme low temperature group exhibited consistently higher expression of Sftpc and Nxnl, at the same time decreased Wfdc21, Cib3, Cma1, and Dld expression. Notably, the mice in the extreme temperature fluctuation group showed decreased Wfdc21, Cib3, Gpr171, and Cttnbp2 expression, while increased Hbb-bs expression. Adult asthma subjects in the extreme temperature fluctuation group showed consistently decreased Wfdc21, Cib3, Gpr171, and Cttnbp2 expression, while increased Tiam2 and Cma1 expression. We observed that the mild, moderate, and severe asthma subject in the extreme low temperature group showed increased Tob1, Mub2, Sic34a2, Sftpc, Nxnl, Luc71, Lamp3, Gpr171, Cox14, and Cd3e expression, while in the severe asthma subjects showed increased expression in all temperature exposure group. Conclusion Our study highlights the effects of extreme temperatures on the gene signature of the airway epithelium in both mice and asthma patients. These findings suggest that extreme temperatures modulate gene expression in the airway epithelium, potentially serving as clinical indicators or biomarkers in response to climate change.
Collapse
Affiliation(s)
- Firdian Makrufardi
- International Ph.D. Program in Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
- Department of Child Health, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada – Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | - Syue-Wei Peng
- School of Respiratory Therapy, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Kian Fan Chung
- Imperial College London, National Heart and Lung Institute, London, United Kingdom
| | - Marc Chadeau-Hyam
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, United Kingdom
- MRC Centre for Environment and Health Imperial College London, London, United Kingdom
| | - Kang-Yun Lee
- Division of Pulmonary Medicine, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
- Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
| | - Ta-Chih Hsiao
- Graduate Institute of Environmental Engineering, National Taiwan University, Taipei, Taiwan
| | - Kin-Fai Ho
- JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong, China
| | - Desy Rusmawatiningtyas
- Department of Child Health, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada – Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | - Indah Kartika Murni
- Department of Child Health, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada – Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | - Eggi Arguni
- Department of Child Health, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada – Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | - Yuan-Hung Wang
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
- Department of Medical Research, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
| | - Shu-Chuan Ho
- School of Respiratory Therapy, College of Medicine, Taipei Medical University, Taipei, Taiwan
- Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
| | - Feng-Ming Yang
- School of Respiratory Therapy, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Kai-Jen Chuang
- School of Public Health, College of Public Health, Taipei Medical University, Taipei, Taiwan
- Department of Public Health, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Sheng-Chieh Lin
- Department of Pediatrics, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
- Division of Allergy, Asthma, and Immunology, Department of Pediatrics, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
| | - Hsiao-Chi Chuang
- School of Respiratory Therapy, College of Medicine, Taipei Medical University, Taipei, Taiwan
- Imperial College London, National Heart and Lung Institute, London, United Kingdom
- Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
- Cell Physiology and Molecular Image Research Center, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
| |
Collapse
|
5
|
Rabin RL, Altman MC, Arshad SH, Beger RD, Frischmeyer-Guerrerio PA, Goleva E, Hamilton RG, Khurana Hershey GK, Shamji MH, Sampson HA, Santos AF, Shreffler WG, Togias A, Vieths S, Wambre E, Wenzel SE, Hise K, Lee J, Tripathi A, Slater JE. Biomarker-driven drug development for allergic diseases and asthma: An FDA public workshop. J Allergy Clin Immunol 2025:S0091-6749(25)00329-X. [PMID: 40154576 DOI: 10.1016/j.jaci.2025.03.014] [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: 10/10/2024] [Revised: 03/13/2025] [Accepted: 03/19/2025] [Indexed: 04/01/2025]
Abstract
The US Food and Drug Administration (FDA) hosted a workshop on February 22, 2024, to discuss the status of biomarkers in drug development for allergic asthma and food allergy. The workshop provided a forum for open discussion among regulators, academicians, National Institutes of Health staff and industry to inform stakeholders of the requirements for the FDA to adopt a biomarker as a surrogate end point for a clinical trial, and to inform FDA of the status of various biomarkers in development. The workshop was divided into 3 sessions: (1) FDA and European Union regulators discussing regulatory perspectives on use of biomarkers in drug development programs, (2) investigators discussing biomarkers for pediatric and adult asthma, and (3) investigators discussing biomarkers for food allergy. In this report, we review the information presented at the workshop and summarize the current status of potential biomarkers for these allergic diseases.
Collapse
Affiliation(s)
- Ronald L Rabin
- Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Md.
| | | | - S Hasan Arshad
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Richard D Beger
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Ark
| | | | - Elena Goleva
- Department of Pediatrics, National Jewish Health, Denver, Colo
| | | | | | - Mohamed H Shamji
- Immunomodulation and Tolerance Group, Allergy and Clinical Immunology, Department of National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Hugh A Sampson
- Department of Pediatrics, Jaffe Food Allergy Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Alexandra F Santos
- Department of Women and Children's Health (Pediatric Allergy), School of Life Course and Population Sciences & Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, King's College London, and the Children's Allergy Service, Evelina London Children's Hospital, Guy's and St Thomas' Hospital, London, United Kingdom
| | - Wayne G Shreffler
- Food Allergy Center, Division of Pediatric Allergy and Immunology, and the Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, and the Department of Pediatrics, Harvard Medical School, Boston, Mass
| | - Alkis Togias
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Stefan Vieths
- Molecular Allergology, Paul-Ehrlich-Institut, Langen, Germany
| | - Erik Wambre
- Jaffe Food Allergy Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Sally E Wenzel
- Department of Environmental and Occupational Health, School of Public Health, University of Pittsburgh, Pittsburgh, Pa
| | - Kathleen Hise
- Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Md
| | - Joohee Lee
- Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Md
| | - Anubha Tripathi
- Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Md
| | - Jay E Slater
- Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Md
| |
Collapse
|
6
|
Gauthier M, Kale SL, Ray A. T1-T2 Interplay in the Complex Immune Landscape of Severe Asthma. Immunol Rev 2025; 330:e70011. [PMID: 39991821 PMCID: PMC11849004 DOI: 10.1111/imr.70011] [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: 11/21/2024] [Accepted: 02/11/2025] [Indexed: 02/25/2025]
Abstract
Asthma is orchestrated by an aberrant immune response involving a complex interplay between multiple inflammatory cell types. An increase in Th2 cells in the asthmatic airway is a hallmark of asthma, and biologics blocking their effector functions have been life-changing for many severe asthma patients who poorly respond to immunosuppression by corticosteroids. However, studies in the past decade have highlighted not only other cell types that also produce Th2 cytokines boosting the Type 2/T2 phenotype but also a heightened IFN-γ response, primarily from T cells, referred to as a Type 1/T1 immune response. Data derived from studies of immune cells in the airways and mouse models of severe asthma suggest a role of IFN-γ in corticosteroid resistance, airway hyperreactivity, and also airway remodeling via effects on other cell types including mast cells, eosinophils, airway epithelial cells, and airway smooth muscle cells. The simultaneous presence of T1 and T2 immune responses is detectable in the sickest of asthma patients in whom corticosteroids suppress the T2 but not the T1 response. This article has reviewed our current understanding of the complex T1-T2 interplay in severe asthma highlighting mediators that impact both arms which may be targeted alone or in combination for disease alleviation.
Collapse
Affiliation(s)
- Marc Gauthier
- Pulmonary Allergy Critical Care and Sleep Medicine, Department of MedicineUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
| | - Sagar L. Kale
- Pulmonary Allergy Critical Care and Sleep Medicine, Department of MedicineUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
| | - Anuradha Ray
- Pulmonary Allergy Critical Care and Sleep Medicine, Department of MedicineUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
- Department of ImmunologyUniversity of PittsburghPittsburghPennsylvaniaUSA
| |
Collapse
|
7
|
Zein JG, Zounemat-Kerman N, Adcock IM, Hu B, Attaway A, Castro M, Dahlén SE, Denlinger LC, Erzurum SC, Fahy JV, Gaston B, Hastie AT, Israel E, Jarjour NN, Levy BD, Mauger DT, Moore W, Peters MC, Sumino K, Townsend E, Woodruff P, Ortega VE, Wenzel SE, Meyers DA, Chung KF, Bleecker ER. Development of an asthma health-care burden score as a measure of severity and predictor of remission in SARP III and U-BIOPRED: results from two major longitudinal asthma cohorts. THE LANCET. RESPIRATORY MEDICINE 2025; 13:35-46. [PMID: 39586307 PMCID: PMC11700758 DOI: 10.1016/s2213-2600(24)00250-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 07/15/2024] [Accepted: 08/02/2024] [Indexed: 11/27/2024]
Abstract
BACKGROUND Current asthma guidelines, including those of the European Respiratory Society (ERS) and American Thoracic Society (ATS), suboptimally predict asthma remission, disease severity, and health-care utilisation. We aimed to establish a novel approach to assess asthma severity based on asthma health-care burden data. METHODS We analysed prospectively collected data from the Severe Asthma Research Program III (SARP III; USA) and the European Unbiased Biomarkers for the Prediction of Respiratory Disease Outcomes (U-BIOPRED; 11 European countries) to calculate a composite burden score based on asthma exacerbations and health-care utilisation, which was modified to include the use of short-acting beta agonists (SABAs) to reflect asthma symptom burden. FINDINGS In SARP III, 528 adult participants with asthma were followed up for a mean of 4·4 (SD 1·6) years, and 312 (59%) had severe asthma according to the ERS-ATS definition. Among the 205 participants with asthma who used rescue SABAs daily, 90 used these two or more times a day. In U-BIOPRED, 509 adult participants with asthma were followed up for 1 year, and 421 (83%) had severe asthma. The burden score was less than 1·29 per patient-year in 106 (34%) of 312 SARP III participants and in 80 (19%) of 421 U-BIOPRED participants with severe asthma. By contrast, the burden score was above the median value in 58 (28%) SARP III and 24 (27%) U-BIOPRED participants with non-severe asthma. In both cohorts, the burden score negatively correlated with lung function, asthma control, and quality of life. A burden score of 0·15 or lower predicted asthma remission with a sensitivity greater than 91% and a specificity of 99%. INTERPRETATION Our findings highlight considerable discrepancies between the current definition of asthma severity and our burden score. Although the definition of severe asthma proposed by the ERS-ATS and the and Global Initiative for Asthma (GINA) is based on prescribed asthma medications, our personalised health-care burden score includes patient-centred data that reflect disease severity and accurately predicts asthma remission. Subject to prospective validation, the burden score could help to optimise the management of high-risk individuals with asthma. FUNDING SARP III: US National Heart, Lung, and Blood Institute; AstraZeneca; Boehringer Ingelheim; Genentech; GlaxoSmithKline; Sanofi Genzyme/Regeneron; and Teva Pharmaceuticals. U-BIOPRED Innovative Medicines Initiative Joint Undertaking (EU's Seventh Framework Programme and European Federation of Pharmaceutical Industries and Associations) and eTRIKS project.
Collapse
Affiliation(s)
- Joe G Zein
- Division of Pulmonary Medicine, Department of Medicine, Mayo Clinic, Scottsdale, AZ, USA.
| | - Nazanin Zounemat-Kerman
- Data Science Institute and National Heart & Lung Institute, Imperial College London, London, UK
| | - Ian M Adcock
- Data Science Institute and National Heart & Lung Institute, Imperial College London, London, UK
| | - Bo Hu
- Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Amy Attaway
- Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Respiratory Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Mario Castro
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Kansas School of Medicine, Kansas City, KS, USA
| | - Sven-Erik Dahlén
- The National Institute of Environmental Medicine, Karolinska Institutet, Solna, Sweden
| | - Loren C Denlinger
- Department of Medicine, University of Wisconsin School of Medicine, Madison, WI, USA
| | - Serpil C Erzurum
- Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Respiratory Institute, Cleveland Clinic, Cleveland, OH, USA
| | - John V Fahy
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of California at San Francisco, San Francisco, CA, USA
| | - Benjamin Gaston
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Annette T Hastie
- Department of Medicine, Wake Forest University, Winston-Salem, NC, USA
| | - Elliot Israel
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Nizar N Jarjour
- Department of Medicine, University of Wisconsin School of Medicine, Madison, WI, USA
| | - Bruce D Levy
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - David T Mauger
- Center for Biostatistics and Epidemiology, Pennsylvania State University School of Medicine, Hershey, PA, USA
| | - Wendy Moore
- Department of Medicine, Wake Forest University, Winston-Salem, NC, USA
| | - Michael C Peters
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of California at San Francisco, San Francisco, CA, USA
| | - Kaharu Sumino
- Division of Pulmonary and Critical Care Medicine, Washington University College of Medicine, Saint Louis, MO, USA
| | - Elizabeth Townsend
- Department of Medicine, University of Wisconsin School of Medicine, Madison, WI, USA
| | - Prescott Woodruff
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of California at San Francisco, San Francisco, CA, USA
| | - Victor E Ortega
- Division of Pulmonary Medicine, Department of Medicine, Mayo Clinic, Scottsdale, AZ, USA
| | - Sally E Wenzel
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Deborah A Meyers
- Division of Pulmonary Medicine, Department of Medicine, Mayo Clinic, Scottsdale, AZ, USA
| | - Kian Fan Chung
- Data Science Institute and National Heart & Lung Institute, Imperial College London, London, UK
| | - Eugene R Bleecker
- Division of Pulmonary Medicine, Department of Medicine, Mayo Clinic, Scottsdale, AZ, USA
| |
Collapse
|
8
|
Plichta J, Majos A, Kuna P, Panek M. Nasal allergen and methacholine provocation tests influence co‑expression patterns of TGF‑β/SMAD and MAPK signaling pathway genes in patients with asthma. Exp Ther Med 2024; 28:445. [PMID: 39386939 PMCID: PMC11462400 DOI: 10.3892/etm.2024.12735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 07/16/2024] [Indexed: 10/12/2024] Open
Abstract
Asthma is characterized by chronic bronchial inflammation and is a highly heterogeneous disease strongly influenced by both specific and non-specific exogenous factors. The present study was performed to assess the effect of nasal allergen provocation tests and methacholine provocation tests on the mRNA co-expression patterns of genes (SMAD1/3/6/7, MPK1/3 and TGFB1/3) involved in SMAD and non-SMAD TGF-β signaling pathways in patients with asthma. Reverse transcription-quantitative PCR was performed on blood samples taken pre-provocation and 1 h post-provocation to assess gene expression changes. Of the 59 patients studied, allergen provocations were administered to 27 patients and methacholine provocations to 32 patients. Correlations between expression levels of studied genes were found to be influenced markedly by the challenge administered, challenge test result and time elapsed since challenge. Importantly, increases in expression levels for four gene pairs (MAPK1-SMAD3, MAPK3-SMAD3, SMAD1-SMAD3 and SMAD3-TGFB1) were found to correlate significantly with asthma occurrence in the allergen provocation cohort, but not in the methacholine provocation cohort. The present study allows us to draw the conclusion that both intranasal allergen and bronchial methacholine challenges influence mRNA co-expression patterns of the SMAD1/3/6/7, MPK1/3 and TGFB1/3 genes.
Collapse
Affiliation(s)
- Jacek Plichta
- Department of Internal Medicine, Asthma and Allergy, Medical University of Lodz, 90-153 Lodz, Poland
| | - Alicja Majos
- Department of Internal Medicine, Asthma and Allergy, Medical University of Lodz, 90-153 Lodz, Poland
- Department of General and Transplant Surgery, Asthma and Allergy, Medical University of Lodz, 90-153 Lodz, Poland
| | - Piotr Kuna
- Department of Internal Medicine, Asthma and Allergy, Medical University of Lodz, 90-153 Lodz, Poland
| | - Michał Panek
- Department of Internal Medicine, Asthma and Allergy, Medical University of Lodz, 90-153 Lodz, Poland
| |
Collapse
|
9
|
Kotrba J, Müller I, Pausder A, Hoffmann A, Camp B, Boehme JD, Müller AJ, Schreiber J, Bruder D, Kahlfuss S, Dudeck A, Stegemann-Koniszewski S. Innate players in Th2 and non-Th2 asthma: emerging roles for the epithelial cell, mast cell, and monocyte/macrophage network. Am J Physiol Cell Physiol 2024; 327:C1373-C1383. [PMID: 39401422 DOI: 10.1152/ajpcell.00488.2024] [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: 07/15/2024] [Revised: 10/03/2024] [Accepted: 10/05/2024] [Indexed: 11/12/2024]
Abstract
Asthma is one of the most common chronic respiratory diseases and is characterized by airway inflammation, increased mucus production, and structural changes in the airways. Recently, there is increasing evidence that the disease is much more heterogeneous than expected, with several distinct asthma endotypes. Based on the specificity of T cells as the best-known driving force in airway inflammation, bronchial asthma is categorized into T helper cell 2 (Th2) and non-Th2 asthma. The most studied effector cells in Th2 asthma include T cells and eosinophils. In contrast to Th2 asthma, much less is known about the pathophysiology of non-Th2 asthma, which is often associated with treatment resistance. Besides T cells, the interaction of myeloid cells such as monocytes/macrophages and mast cells with the airway epithelium significantly contributes to the pathogenesis of asthma. However, the underlying molecular regulation and particularly the specific relevance of this cellular network in certain asthma endotypes remain to be understood. In this review, we summarize recent findings on the regulation of and complex interplay between epithelial cells and the "nonclassical" innate effector cells mast cells and monocytes/macrophages in Th2 and non-Th2 asthma with the ultimate goal of providing the rationale for future research into targeted therapy regimens.
Collapse
Affiliation(s)
- Johanna Kotrba
- Institute for Molecular and Clinical Immunology, Medical Faculty, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
- Health Campus Immunology, Infectiology and Inflammation (GCI3), Medical Faculty, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Ilka Müller
- Experimental Pneumology, Department of Pneumology, University Hospital Magdeburg/Medical Faculty, Otto-von-Guericke University, Magdeburg, Germany
- Health Campus Immunology, Infectiology and Inflammation (GCI3), Medical Faculty, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Alexander Pausder
- Research Group Infection Immunology, Institute of Medical Microbiology and Hospital Hygiene, Medical Faculty, Otto-von-Guericke-University, Magdeburg, Germany
- Health Campus Immunology, Infectiology and Inflammation (GCI3), Medical Faculty, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Aaron Hoffmann
- Institute for Molecular and Clinical Immunology, Medical Faculty, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
- Health Campus Immunology, Infectiology and Inflammation (GCI3), Medical Faculty, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Belinda Camp
- Experimental Pneumology, Department of Pneumology, University Hospital Magdeburg/Medical Faculty, Otto-von-Guericke University, Magdeburg, Germany
- Health Campus Immunology, Infectiology and Inflammation (GCI3), Medical Faculty, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Julia D Boehme
- Research Group Infection Immunology, Institute of Medical Microbiology and Hospital Hygiene, Medical Faculty, Otto-von-Guericke-University, Magdeburg, Germany
- Health Campus Immunology, Infectiology and Inflammation (GCI3), Medical Faculty, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
- Research Group Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Andreas J Müller
- Institute for Molecular and Clinical Immunology, Medical Faculty, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
- Health Campus Immunology, Infectiology and Inflammation (GCI3), Medical Faculty, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
- Center for Health and Medical Prevention (CHaMP), Otto-von-Guericke-University, Magdeburg, Germany
| | - Jens Schreiber
- Experimental Pneumology, Department of Pneumology, University Hospital Magdeburg/Medical Faculty, Otto-von-Guericke University, Magdeburg, Germany
- Health Campus Immunology, Infectiology and Inflammation (GCI3), Medical Faculty, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Dunja Bruder
- Research Group Infection Immunology, Institute of Medical Microbiology and Hospital Hygiene, Medical Faculty, Otto-von-Guericke-University, Magdeburg, Germany
- Health Campus Immunology, Infectiology and Inflammation (GCI3), Medical Faculty, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
- Research Group Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Sascha Kahlfuss
- Institute for Molecular and Clinical Immunology, Medical Faculty, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
- Institute of Medical Microbiology and Hospital Hygiene, Medical Faculty, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
- Health Campus Immunology, Infectiology and Inflammation (GCI3), Medical Faculty, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
- Center for Health and Medical Prevention (CHaMP), Otto-von-Guericke-University, Magdeburg, Germany
| | - Anne Dudeck
- Institute for Molecular and Clinical Immunology, Medical Faculty, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
- Health Campus Immunology, Infectiology and Inflammation (GCI3), Medical Faculty, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
- Center for Health and Medical Prevention (CHaMP), Otto-von-Guericke-University, Magdeburg, Germany
| | - Sabine Stegemann-Koniszewski
- Experimental Pneumology, Department of Pneumology, University Hospital Magdeburg/Medical Faculty, Otto-von-Guericke University, Magdeburg, Germany
- Health Campus Immunology, Infectiology and Inflammation (GCI3), Medical Faculty, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| |
Collapse
|
10
|
Baroni C, D’Agostino I, Renzi G, Kilbile JT, Tamboli Y, Ferraroni M, Carradori S, Capasso C, Carta F, Supuran CT. Lasamide, a Potent Human Carbonic Anhydrase Inhibitor from the Market: Inhibition Profiling and Crystallographic Studies. ACS Med Chem Lett 2024; 15:1749-1755. [PMID: 39411526 PMCID: PMC11472397 DOI: 10.1021/acsmedchemlett.4c00341] [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: 07/15/2024] [Revised: 09/15/2024] [Accepted: 09/20/2024] [Indexed: 10/19/2024] Open
Abstract
Lasamide is a synthetic precursor and a contaminant of the diuretic Furosemide manufacturing process and represents a highly valuable building block for fragment-based drug discovery approaches. We assessed the ability of Lasamide to inhibit in vitro the human-expressed Carbonic Anhydrases by means of the stopped-flow technique, and we assessed its binding modes within hCAs II and XII-mimic catalytic clefts by X-ray crystallography. Interestingly, an unprecedented crystal form for the hCA IX mimic H-tag is reported and discussed herein.
Collapse
Affiliation(s)
- Chiara Baroni
- Department
of Chemistry “Ugo Schiff”, University of Florence, 50019, Sesto Fiorentino, Florence, Italy
| | - Ilaria D’Agostino
- Department
of Pharmacy, University of Pisa, 56126, Pisa, Italy
- Department
of Pharmacy, “G. d’Annunzio”
University of Chieti-Pescara, 66100, Chieti, Italy
- NEUROFARBA
Department, Sezione di Scienze Farmaceutiche e Nutraceutiche, University of Florence, 50019, Sesto Fiorentino, Florence, Italy
| | - Gioele Renzi
- NEUROFARBA
Department, Sezione di Scienze Farmaceutiche e Nutraceutiche, University of Florence, 50019, Sesto Fiorentino, Florence, Italy
| | - Jaydeo T. Kilbile
- University
Department of Basic and Applied Sciences (Chemistry), MGM University, Aurangabad-431003, Maharashtra, India
| | - Yasinalli Tamboli
- King Abdullah
International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry
of National Guard-Health Affairs, Riyadh 14811, Saudi Arabia
| | - Marta Ferraroni
- Department
of Chemistry “Ugo Schiff”, University of Florence, 50019, Sesto Fiorentino, Florence, Italy
| | - Simone Carradori
- Department
of Pharmacy, “G. d’Annunzio”
University of Chieti-Pescara, 66100, Chieti, Italy
| | - Clemente Capasso
- Department
of Biology, Agriculture and Food Sciences, National Research Council
(CNR), Institute of Biosciences and Bioresources, 80131 Naples, Italy
| | - Fabrizio Carta
- NEUROFARBA
Department, Sezione di Scienze Farmaceutiche e Nutraceutiche, University of Florence, 50019, Sesto Fiorentino, Florence, Italy
| | - Claudiu T. Supuran
- NEUROFARBA
Department, Sezione di Scienze Farmaceutiche e Nutraceutiche, University of Florence, 50019, Sesto Fiorentino, Florence, Italy
| |
Collapse
|
11
|
Wu CP, Sleiman J, Fakhry B, Chedraoui C, Attaway A, Bhattacharyya A, Bleecker ER, Erdemir A, Hu B, Kethireddy S, Meyers DA, Rashidi HH, Zein JG. Novel Machine Learning Identifies 5 Asthma Phenotypes Using Cluster Analysis of Real-World Data. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. IN PRACTICE 2024; 12:2084-2091.e4. [PMID: 38685479 PMCID: PMC11340628 DOI: 10.1016/j.jaip.2024.04.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 03/25/2024] [Accepted: 04/19/2024] [Indexed: 05/02/2024]
Abstract
BACKGROUND Asthma classification into different subphenotypes is important to guide personalized therapy and improve outcomes. OBJECTIVES To further explore asthma heterogeneity through determination of multiple patient groups by using novel machine learning (ML) approaches and large-scale real-world data. METHODS We used electronic health records of patients with asthma followed at the Cleveland Clinic between 2010 and 2021. We used k-prototype unsupervised ML to develop a clustering model where predictors were age, sex, race, body mass index, prebronchodilator and postbronchodilator spirometry measurements, and the usage of inhaled/systemic steroids. We applied elbow and silhouette plots to select the optimal number of clusters. These clusters were then evaluated through LightGBM's supervised ML approach on their cross-validated F1 score to support their distinctiveness. RESULTS Data from 13,498 patients with asthma with available postbronchodilator spirometry measurements were extracted to identify 5 stable clusters. Cluster 1 included a young nonsevere asthma population with normal lung function and higher frequency of acute exacerbation (0.8 /patient-year). Cluster 2 had the highest body mass index (mean ± SD, 44.44 ± 7.83 kg/m2), and the highest proportion of females (77.5%) and Blacks (28.9%). Cluster 3 comprised patients with normal lung function. Cluster 4 included patients with lower percent of predicted FEV1 of 77.03 (12.79) and poor response to bronchodilators. Cluster 5 had the lowest percent of predicted FEV1 of 68.08 (15.02), the highest postbronchodilator reversibility, and the highest proportion of severe asthma (44.9%) and blood eosinophilia (>300 cells/μL) (34.8%). CONCLUSIONS Using real-world data and unsupervised ML, we classified asthma into 5 clinically important subphenotypes where group-specific asthma treatment and management strategies can be designed and deployed.
Collapse
Affiliation(s)
- Chao-Ping Wu
- Respiratory Institute, Cleveland Clinic, Cleveland, Ohio
| | - Joelle Sleiman
- Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | - Battoul Fakhry
- Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | | | - Amy Attaway
- Respiratory Institute, Cleveland Clinic, Cleveland, Ohio; Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | | | - Eugene R Bleecker
- Department of Medicine, Division of Pulmonary Medicine, Mayo Clinic, Scottsdale, Ariz
| | - Ahmet Erdemir
- Respiratory Institute, Cleveland Clinic, Cleveland, Ohio
| | - Bo Hu
- Respiratory Institute, Cleveland Clinic, Cleveland, Ohio
| | | | - Deborah A Meyers
- Department of Medicine, Division of Pulmonary Medicine, Mayo Clinic, Scottsdale, Ariz
| | - Hooman H Rashidi
- Pathology and Laboratory Medicine Institute, Cleveland Clinic, Ohio
| | - Joe G Zein
- Department of Medicine, Division of Pulmonary Medicine, Mayo Clinic, Scottsdale, Ariz.
| |
Collapse
|
12
|
Qin R, Long F, Zhang P, Huang R, Hu H, Guo Y, Zheng Z, Xiao J, He L, Peng T, Li J. Presence of sputum IgG against eosinophilic inflammatory proteins in asthma. Front Immunol 2024; 15:1423764. [PMID: 39091502 PMCID: PMC11291201 DOI: 10.3389/fimmu.2024.1423764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 06/24/2024] [Indexed: 08/04/2024] Open
Abstract
Background Sputum immunoglobulin G (Sp-IgG) has been discovered to induce cytolytic extracellular trap cell death in eosinophils, suggesting a potential autoimmune mechanism contributing to asthma. This study aimed to explore the potential origin of Sp-IgG and identify clinically relevant subtypes of Sp-IgG that may indicate autoimmune events in asthma. Methods This study included 165 asthmatic patients and 38 healthy volunteers. We measured Sp-IgG and its five subtypes against eosinophil inflammatory proteins (Sp-IgGEPs), including eosinophil peroxidase, eosinophil major basic protein, eosinophil-derived neurotoxin, eosinophil cationic protein, and Charcot-Leyden Crystal protein in varying asthma severity. Clinical and Mendelian randomization (MR) analyses were conducted. A positive Sp-IgGEPs signature (Sp-IgGEPs+) was defined when any of the five Sp-IgGEPs values exceeded the predefined cutoff thresholds, calculated as the mean values of healthy controls plus twice the standard deviation. Results The levels of Sp-IgG and Sp-IgGEPs were significantly elevated in moderate/severe asthma than those in mild asthma/healthy groups (all p < 0.05). Sp-IgG levels were positively correlated with airway eosinophil and Sp-IgGEPs. MR analysis showed causality between eosinophil and IgG (OR = 1.02, 95%CI = 1.00-1.04, p = 0.020), and elevated IgG was a risk factor for asthma (OR = 2.05, 95%CI = 1.00-4.17, p = 0.049). Subjects with Sp-IgGEPs+ exhibited worse disease severity and served as an independent risk factor contributing to severe asthma (adjusted-OR = 5.818, adjusted-95% CI = 2.193-15.431, adjusted-p < 0.001). Receiver operating characteristic curve analysis demonstrated that the combination of Sp-IgGEPs+ with non-allergic status, an ACT score < 15, and age ≥ 45 years, effectively predicted severe asthma (AUC = 0.84, sensitivity = 86.20%, specificity = 67.80%). Conclusion This study identifies a significant association between airway eosinophilic inflammation, Sp-IgG, and asthma severity. The Sp-IgGEPs panel potentially serves as the specific biomarker reflecting airway autoimmune events in asthma.
Collapse
Affiliation(s)
- Rundong Qin
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health; Department of Allergy and Clinical Immunology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Fei Long
- Sino-French Hoffmann Institute, School of Basic Medical Sciences, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Pingan Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health; Department of Allergy and Clinical Immunology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Renbin Huang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health; Department of Allergy and Clinical Immunology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Hao Hu
- Sino-French Hoffmann Institute, School of Basic Medical Sciences, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Yubiao Guo
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health; Department of Allergy and Clinical Immunology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Zhenyu Zheng
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health; Department of Allergy and Clinical Immunology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jing Xiao
- Sino-French Hoffmann Institute, School of Basic Medical Sciences, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Li He
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health; Department of Allergy and Clinical Immunology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Tao Peng
- Sino-French Hoffmann Institute, School of Basic Medical Sciences, State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Jing Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health; Department of Allergy and Clinical Immunology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| |
Collapse
|
13
|
Bunyavanich S, Becker PM, Altman MC, Lasky-Su J, Ober C, Zengler K, Berdyshev E, Bonneau R, Chatila T, Chatterjee N, Chung KF, Cutcliffe C, Davidson W, Dong G, Fang G, Fulkerson P, Himes BE, Liang L, Mathias RA, Ogino S, Petrosino J, Price ND, Schadt E, Schofield J, Seibold MA, Steen H, Wheatley L, Zhang H, Togias A, Hasegawa K. Analytical challenges in omics research on asthma and allergy: A National Institute of Allergy and Infectious Diseases workshop. J Allergy Clin Immunol 2024; 153:954-968. [PMID: 38295882 PMCID: PMC10999353 DOI: 10.1016/j.jaci.2024.01.014] [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: 12/13/2023] [Revised: 01/19/2024] [Accepted: 01/24/2024] [Indexed: 02/29/2024]
Abstract
Studies of asthma and allergy are generating increasing volumes of omics data for analysis and interpretation. The National Institute of Allergy and Infectious Diseases (NIAID) assembled a workshop comprising investigators studying asthma and allergic diseases using omics approaches, omics investigators from outside the field, and NIAID medical and scientific officers to discuss the following areas in asthma and allergy research: genomics, epigenomics, transcriptomics, microbiomics, metabolomics, proteomics, lipidomics, integrative omics, systems biology, and causal inference. Current states of the art, present challenges, novel and emerging strategies, and priorities for progress were presented and discussed for each area. This workshop report summarizes the major points and conclusions from this NIAID workshop. As a group, the investigators underscored the imperatives for rigorous analytic frameworks, integration of different omics data types, cross-disciplinary interaction, strategies for overcoming current limitations, and the overarching goal to improve scientific understanding and care of asthma and allergic diseases.
Collapse
Affiliation(s)
| | - Patrice M Becker
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Md
| | | | - Jessica Lasky-Su
- Brigham & Women's Hospital and Harvard Medical School, Boston, Mass
| | | | | | | | | | - Talal Chatila
- Boston Children's Hospital and Harvard Medical School, Boston, Mass
| | | | | | | | - Wendy Davidson
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Md
| | - Gang Dong
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Md
| | - Gang Fang
- Icahn School of Medicine at Mount Sinai, New York, NY
| | - Patricia Fulkerson
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Md
| | | | - Liming Liang
- Harvard T. H. Chan School of Public Health, Boston, Mass
| | | | - Shuji Ogino
- Brigham & Women's Hospital and Harvard Medical School, Boston, Mass; Harvard T. H. Chan School of Public Health, Boston, Mass; Broad Institute of MIT and Harvard, Boston, Mass
| | | | | | - Eric Schadt
- Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Max A Seibold
- National Jewish Health, Denver, Colo; University of Colorado School of Medicine, Aurora, Colo
| | - Hanno Steen
- Boston Children's Hospital and Harvard Medical School, Boston, Mass
| | - Lisa Wheatley
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Md
| | - Hongmei Zhang
- School of Public Health, University of Memphis, Memphis, Tenn
| | - Alkis Togias
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Md
| | - Kohei Hasegawa
- Massachusetts General Hospital and Harvard Medical School, Boston, Mass
| |
Collapse
|
14
|
Xu Z, Forno E, Sun Y, Manni ML, Han YY, Kim S, Yue M, Vonk JM, Kersten ETM, Acosta-Perez E, Canino G, Koppelman GH, Chen W, Celedón JC. Nasal epithelial gene expression and total IgE in children and adolescents with asthma. J Allergy Clin Immunol 2024; 153:122-131. [PMID: 37742934 PMCID: PMC10842443 DOI: 10.1016/j.jaci.2023.09.014] [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] [Revised: 08/15/2023] [Accepted: 09/07/2023] [Indexed: 09/26/2023]
Abstract
BACKGROUND Little is known about nasal epithelial gene expression and total IgE in youth. OBJECTIVE We aimed to identify genes whose nasal epithelial expression differs by total IgE in youth, and group them into modules that could be mapped to airway epithelial cell types. METHODS We conducted a transcriptome-wide association study of total IgE in 469 Puerto Ricans aged 9 to 20 years who participated in the Epigenetic Variation and Childhood Asthma in Puerto Ricans study, separately in all subjects and in those with asthma. We then attempted to replicate top findings for each analysis using data from 3 cohorts. Genes with a Benjamini-Hochberg-adjusted P value of less than .05 in the Epigenetic Variation and Childhood Asthma in Puerto Ricans study and a P value of less than .05 in the same direction of association in 1 or more replication cohort were considered differentially expressed genes (DEGs). DEGs for total IgE in subjects with asthma were further dissected into gene modules using coexpression analysis, and such modules were mapped to specific cell types in airway epithelia using public single-cell RNA-sequencing data. RESULTS A higher number of DEGs for total IgE were identified in subjects with asthma (n = 1179 DEGs) than in all subjects (n = 631 DEGs). In subjects with asthma, DEGs were mapped to 11 gene modules. The top module for positive correlation with total IgE was mapped to myoepithelial and mucus secretory cells in lower airway epithelia and was regulated by IL-4, IL5, IL-13, and IL-33. Within this module, hub genes included CDH26, FETUB, NTRK2, CCBL1, CST1, and CST2. Furthermore, an enrichment analysis showed overrepresentation of genes in signaling pathways for synaptogenesis, IL-13, and ferroptosis, supporting interactions between interleukin- and acetylcholine-induced responses. CONCLUSIONS Our findings for nasal epithelial gene expression support neuroimmune coregulation of total IgE in youth with asthma.
Collapse
Affiliation(s)
- Zhongli Xu
- Division of Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pa; Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pa; School of Medicine, Tsinghua University, Beijing, China
| | - Erick Forno
- Division of Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pa; Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pa
| | - Yidan Sun
- Department of Pediatric Pulmonology and Pediatric Allergy, Beatrix Children's Hospital, University Medical Center Groningen, Groningen, The Netherlands; GRIAC Research Institute, University Medical Center Groningen, Groningen, The Netherlands
| | - Michelle L Manni
- Division of Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pa; Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pa
| | - Yueh Ying Han
- Division of Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pa; Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pa
| | - Soyeon Kim
- Division of Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pa; Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pa
| | - Molin Yue
- Division of Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pa; Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pa
| | - Judith M Vonk
- GRIAC Research Institute, University Medical Center Groningen, Groningen, The Netherlands; Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Elin T M Kersten
- Department of Pediatric Pulmonology and Pediatric Allergy, Beatrix Children's Hospital, University Medical Center Groningen, Groningen, The Netherlands; GRIAC Research Institute, University Medical Center Groningen, Groningen, The Netherlands
| | - Edna Acosta-Perez
- Behavioral Sciences Research Institute of Puerto Rico, University of Puerto Rico, San Juan, Puerto Rico
| | - Glorisa Canino
- Behavioral Sciences Research Institute of Puerto Rico, University of Puerto Rico, San Juan, Puerto Rico; Department of Pediatrics, Medical Science Campus, University of Puerto Rico, San Juan, Puerto Rico
| | - Gerard H Koppelman
- Department of Pediatric Pulmonology and Pediatric Allergy, Beatrix Children's Hospital, University Medical Center Groningen, Groningen, The Netherlands; GRIAC Research Institute, University Medical Center Groningen, Groningen, The Netherlands
| | - Wei Chen
- Division of Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pa; Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pa
| | - Juan C Celedón
- Division of Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pa; Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pa.
| |
Collapse
|
15
|
Ahmed DW, Eiken MK, DePalma SJ, Helms AS, Zemans RL, Spence JR, Baker BM, Loebel C. Integrating mechanical cues with engineered platforms to explore cardiopulmonary development and disease. iScience 2023; 26:108472. [PMID: 38077130 PMCID: PMC10698280 DOI: 10.1016/j.isci.2023.108472] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2024] Open
Abstract
Mechanical forces provide critical biological signals to cells during healthy and aberrant organ development as well as during disease processes in adults. Within the cardiopulmonary system, mechanical forces, such as shear, compressive, and tensile forces, act across various length scales, and dysregulated forces are often a leading cause of disease initiation and progression such as in bronchopulmonary dysplasia and cardiomyopathies. Engineered in vitro models have supported studies of mechanical forces in a number of tissue and disease-specific contexts, thus enabling new mechanistic insights into cardiopulmonary development and disease. This review first provides fundamental examples where mechanical forces operate at multiple length scales to ensure precise lung and heart function. Next, we survey recent engineering platforms and tools that have provided new means to probe and modulate mechanical forces across in vitro and in vivo settings. Finally, the potential for interdisciplinary collaborations to inform novel therapeutic approaches for a number of cardiopulmonary diseases are discussed.
Collapse
Affiliation(s)
- Donia W. Ahmed
- Department of Biomedical Engineering, University of Michigan, Lurie Biomedical Engineering Building, 1101 Beal Avenue, Ann Arbor, MI 48109, USA
| | - Madeline K. Eiken
- Department of Biomedical Engineering, University of Michigan, Lurie Biomedical Engineering Building, 1101 Beal Avenue, Ann Arbor, MI 48109, USA
| | - Samuel J. DePalma
- Department of Biomedical Engineering, University of Michigan, Lurie Biomedical Engineering Building, 1101 Beal Avenue, Ann Arbor, MI 48109, USA
| | - Adam S. Helms
- Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Rachel L. Zemans
- Department of Internal Medicine, Division of Pulmonary Sciences and Critical Care Medicine – Gastroenterology, University of Michigan, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA
| | - Jason R. Spence
- Department of Internal Medicine – Gastroenterology, University of Michigan, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA
| | - Brendon M. Baker
- Department of Biomedical Engineering, University of Michigan, Lurie Biomedical Engineering Building, 1101 Beal Avenue, Ann Arbor, MI 48109, USA
| | - Claudia Loebel
- Department of Biomedical Engineering, University of Michigan, Lurie Biomedical Engineering Building, 1101 Beal Avenue, Ann Arbor, MI 48109, USA
- Department of Materials Science & Engineering, University of Michigan, North Campus Research Complex, 2800 Plymouth Road, Ann Arbor, MI 48109, USA
| |
Collapse
|
16
|
Kocatürk E, Abrams EM, Maurer M, Mitri J, Oppenheimer J, Vestergaard C, Zein J. COVID-19 and Its Impact on Common Diseases in the Allergy Clinics. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. IN PRACTICE 2023; 11:3289-3303. [PMID: 37660731 DOI: 10.1016/j.jaip.2023.08.038] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/18/2023] [Accepted: 08/25/2023] [Indexed: 09/05/2023]
Abstract
Coronavirus disease 2019 (COVID-19) is a highly contagious viral disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It has various effects on asthma, allergic rhinitis, atopic dermatitis, and urticaria and may change the course of the disease depending on the severity of the infection and control status of the disease. Conversely, these diseases may also impact the course of COVID-19. Patients with chronic urticaria and atopic dermatitis may have COVID-19-induced disease exacerbations and biological treatments reduce the risk of exacerbations. Poor asthma control is linked to severe COVID-19 while allergic asthma is associated with lower risk of death and a lower rate of hospitalization due to COVID-19 compared with nonallergic asthma. The use of intranasal corticosteroids is associated with lower rates of hospitalization due to COVID-19 in patients with allergic rhinitis, whereas the effect of inhaled corticosteroids is confounded by asthma severity. These observations reinforce the importance of keeping allergic diseases under control during pandemics. The use of biologicals during COVID-19 is generally regarded as safe, but more evidence is needed. The pandemic substantially changed the management of allergic disorders such as home implementation of various biologicals, allergen immunotherapy, food introduction, and increased use of telemedicine and even home management of anaphylaxis to reduce emergency department burden and reduce risk of infection. Physicians need to be aware of the potential impact of COVID-19 on allergic diseases and educate their patients on the importance of continuing prescribed medications and adhering to their treatment plans to maintain optimal control of their disease.
Collapse
Affiliation(s)
- Emek Kocatürk
- Department of Dermatology, Koç University School of Medicine, Istanbul, Turkey; Institute of Allergology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Allergology and Immunology, Berlin, Germany.
| | - Elissa M Abrams
- Department of Pediatrics, Section of Allergy and Clinical Immunology, University of Manitoba, Winnipeg, MB, Canada; Department of Pediatrics, Division of Allergy and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Marcus Maurer
- Institute of Allergology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Allergology and Immunology, Berlin, Germany.
| | - Jad Mitri
- Department of Medicine, Saint Elizabeth Medical Center, Boston, Mass
| | - John Oppenheimer
- UMDNJ-Rutgers Department of Medicine, Division of Allergy and Immunology, Newark, NJ
| | | | - Joe Zein
- The Respiratory Institute, The Cleveland Clinic, Cleveland, Ohio
| |
Collapse
|
17
|
Kim DJ, Lim JE, Jung HU, Chung JY, Baek EJ, Jung H, Kwon SY, Kim HK, Kang JO, Park K, Won S, Kim TB, Oh B. Identification of asthma-related genes using asthmatic blood eQTLs of Korean patients. BMC Med Genomics 2023; 16:259. [PMID: 37875944 PMCID: PMC10599017 DOI: 10.1186/s12920-023-01677-7] [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: 02/03/2023] [Accepted: 09/29/2023] [Indexed: 10/26/2023] Open
Abstract
BACKGROUND More than 200 asthma-associated genetic variants have been identified in genome-wide association studies (GWASs). Expression quantitative trait loci (eQTL) data resources can help identify causal genes of the GWAS signals, but it can be difficult to find an eQTL that reflects the disease state because most eQTL data are obtained from normal healthy subjects. METHODS We performed a blood eQTL analysis using transcriptomic and genotypic data from 433 Korean asthma patients. To identify asthma-related genes, we carried out colocalization, Summary-based Mendelian Randomization (SMR) analysis, and Transcriptome-Wide Association Study (TWAS) using the results of asthma GWASs and eQTL data. In addition, we compared the results of disease eQTL data and asthma-related genes with two normal blood eQTL data from Genotype-Tissue Expression (GTEx) project and a Japanese study. RESULTS We identified 340,274 cis-eQTL and 2,875 eGenes from asthmatic eQTL analysis. We compared the disease eQTL results with GTEx and a Japanese study and found that 64.1% of the 2,875 eGenes overlapped with the GTEx eGenes and 39.0% with the Japanese eGenes. Following the integrated analysis of the asthmatic eQTL data with asthma GWASs, using colocalization and SMR methods, we identified 15 asthma-related genes specific to the Korean asthmatic eQTL data. CONCLUSIONS We provided Korean asthmatic cis-eQTL data and identified asthma-related genes by integrating them with GWAS data. In addition, we suggested these asthma-related genes as therapeutic targets for asthma. We envisage that our findings will contribute to understanding the etiological mechanisms of asthma and provide novel therapeutic targets.
Collapse
Affiliation(s)
- Dong Jun Kim
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Ji Eun Lim
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Hae-Un Jung
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul, Korea
| | - Ju Yeon Chung
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul, Korea
| | | | - Hyein Jung
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul, Korea
| | - Shin Young Kwon
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul, Korea
| | - Han Kyul Kim
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Ji-One Kang
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Kyungtaek Park
- Interdisciplinary Program of Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Sungho Won
- Interdisciplinary Program of Bioinformatics, Seoul National University, Seoul, Republic of Korea
- Department of Public Health Sciences, School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - Tae-Bum Kim
- Department of Allergy and Clinical Immunology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea.
| | - Bermseok Oh
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul, Republic of Korea.
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul, Korea.
- Mendel Inc, Seoul, Republic of Korea.
| |
Collapse
|
18
|
Gerayeli FV, Milne S, Yang CX, Li X, Guinto E, Yang JSW, Cheung CY, Stach TR, Shaipanich T, Leung JM, Sin DD. Single-cell RNA sequencing of bronchoscopy specimens: development of a rapid minimal handling protocol. Biotechniques 2023; 75:157-167. [PMID: 37815826 DOI: 10.2144/btn-2023-0017] [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] [Indexed: 10/11/2023] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) is an important tool for understanding disease pathophysiology, including airway diseases. Currently, the majority of scRNA-seq studies in airway diseases have used invasive methods (airway biopsy, surgical resection), which carry inherent risks and thus present a major limitation to scRNA-seq investigation of airway pathobiology. Bronchial brushing, where the airway mucosa is sampled using a cytological brush, is a viable, less invasive method of obtaining airway cells for scRNA-seq. Here we describe the development of a rapid and minimal handling protocol for preparing single-cell suspensions from bronchial brush specimens for scRNA-seq. Our optimized protocol maximizes cell recovery and cell quality and facilitates large-scale profiling of the airway transcriptome at single-cell resolution.
Collapse
Affiliation(s)
- Firoozeh V Gerayeli
- Center for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, BC, Canada
| | - Stephen Milne
- Center for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, BC, Canada
- Division of Respiratory Medicine, University of British Columbia, Vancouver, BC, Canada
- Sydney Medical School, University of Sydney, Camperdown, New South Wales, Australia
| | - Chen Xi Yang
- Center for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, BC, Canada
| | - Xuan Li
- Center for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, BC, Canada
| | - Elizabeth Guinto
- Center for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, BC, Canada
| | - Julia Shun-Wei Yang
- Center for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, BC, Canada
| | - Chung Yan Cheung
- Center for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, BC, Canada
| | - Tara R Stach
- Biomedical Research Center, School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada
| | - Tawimas Shaipanich
- Division of Respiratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Janice M Leung
- Center for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, BC, Canada
- Division of Respiratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Don D Sin
- Center for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, BC, Canada
- Division of Respiratory Medicine, University of British Columbia, Vancouver, BC, Canada
| |
Collapse
|
19
|
Gonzalez-Uribe V, Romero-Tapia SJ, Castro-Rodriguez JA. Asthma Phenotypes in the Era of Personalized Medicine. J Clin Med 2023; 12:6207. [PMID: 37834850 PMCID: PMC10573947 DOI: 10.3390/jcm12196207] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/19/2023] [Accepted: 09/22/2023] [Indexed: 10/15/2023] Open
Abstract
Asthma is a widespread disease affecting approximately 300-million people globally. This condition leads to significant morbidity, mortality, and economic strain worldwide. Recent clinical and laboratory research advancements have illuminated the immunological factors contributing to asthma. As of now, asthma is understood to be a heterogeneous disease. Personalized medicine involves categorizing asthma by its endotypes, linking observable characteristics to specific immunological mechanisms. Identifying these endotypic mechanisms is paramount in accurately profiling patients and tailoring therapeutic approaches using innovative biological agents targeting distinct immune pathways. This article presents a synopsis of the key immunological mechanisms implicated in the pathogenesis and manifestation of the disease's phenotypic traits and individualized treatments for severe asthma subtypes.
Collapse
Affiliation(s)
- Victor Gonzalez-Uribe
- Alergia e Inmunología Clínica, Hospital Infantil de México Federico Gómez, Ciudad de Mexico 06720, Mexico;
- Facultad Mexicana de Medicina, Universidad La Salle México, Ciudad de Mexico 14000, Mexico
| | - Sergio J. Romero-Tapia
- Health Sciences Academic Division (DACS), Universidad Juárez Autónoma de Tabasco, Villahermosa 86040, Mexico;
| | - Jose A. Castro-Rodriguez
- Department of Pediatric Pulmonology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
| |
Collapse
|
20
|
Pirmoradi S, Hosseiniyan Khatibi SM, Zununi Vahed S, Homaei Rad H, Khamaneh AM, Akbarpour Z, Seyedrezazadeh E, Teshnehlab M, Chapman KR, Ansarin K. Unraveling the link between PTBP1 and severe asthma through machine learning and association rule mining method. Sci Rep 2023; 13:15399. [PMID: 37717070 PMCID: PMC10505163 DOI: 10.1038/s41598-023-42581-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 09/12/2023] [Indexed: 09/18/2023] Open
Abstract
Severe asthma is a chronic inflammatory airway disease with great therapeutic challenges. Understanding the genetic and molecular mechanisms of severe asthma may help identify therapeutic strategies for this complex condition. RNA expression data were analyzed using a combination of artificial intelligence methods to identify novel genes related to severe asthma. Through the ANOVA feature selection approach, 100 candidate genes were selected among 54,715 mRNAs in blood samples of patients with severe asthmatic and healthy groups. A deep learning model was used to validate the significance of the candidate genes. The accuracy, F1-score, AUC-ROC, and precision of the 100 genes were 83%, 0.86, 0.89, and 0.9, respectively. To discover hidden associations among selected genes, association rule mining was applied. The top 20 genes including the PTBP1, RAB11FIP3, APH1A, and MYD88 were recognized as the most frequent items among severe asthma association rules. The PTBP1 was found to be the most frequent gene associated with severe asthma among those 20 genes. PTBP1 was the gene most frequently associated with severe asthma among candidate genes. Identification of master genes involved in the initiation and development of asthma can offer novel targets for its diagnosis, prognosis, and targeted-signaling therapy.
Collapse
Affiliation(s)
- Saeed Pirmoradi
- Clinical Research Development Unit of Tabriz Valiasr Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Seyed Mahdi Hosseiniyan Khatibi
- Kidney Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Rahat Breath and Sleep Research Center, Tabriz University of Medical Science, Tabriz, Iran
| | | | - Hamed Homaei Rad
- Rahat Breath and Sleep Research Center, Tabriz University of Medical Science, Tabriz, Iran
| | - Amir Mahdi Khamaneh
- Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Zahra Akbarpour
- Rahat Breath and Sleep Research Center, Tabriz University of Medical Science, Tabriz, Iran
| | - Ensiyeh Seyedrezazadeh
- Tuberculosis and Lung Disease Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Teshnehlab
- Department of Electric and Computer Engineering, K.N. Toosi University of Technology, Tehran, Iran
| | - Kenneth R Chapman
- Division of Respiratory Medicine, Department of Medicine, University of Toronto, Toronto, ON, Canada.
| | - Khalil Ansarin
- Rahat Breath and Sleep Research Center, Tabriz University of Medical Science, Tabriz, Iran.
| |
Collapse
|
21
|
Kitaba NT, Knudsen GTM, Johannessen A, Rezwan FI, Malinovschi A, Oudin A, Benediktsdottir B, Martino D, González FJC, Gómez LP, Holm M, Jõgi NO, Dharmage SC, Skulstad SM, Watkins SH, Suderman M, Gómez-Real F, Schlünssen V, Svanes C, Holloway JW. Fathers' preconception smoking and offspring DNA methylation. Clin Epigenetics 2023; 15:131. [PMID: 37649101 PMCID: PMC10469907 DOI: 10.1186/s13148-023-01540-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 07/24/2023] [Indexed: 09/01/2023] Open
Abstract
BACKGROUND Experimental studies suggest that exposures may impact respiratory health across generations via epigenetic changes transmitted specifically through male germ cells. Studies in humans are, however, limited. We aim to identify epigenetic marks in offspring associated with father's preconception smoking. METHODS We conducted epigenome-wide association studies (EWAS) in the RHINESSA cohort (7-50 years) on father's any preconception smoking (n = 875 offspring) and father's pubertal onset smoking < 15 years (n = 304), using Infinium MethylationEPIC Beadchip arrays, adjusting for offspring age, own smoking and maternal smoking. EWAS of maternal and offspring personal smoking were performed for comparison. Father's smoking-associated dmCpGs were checked in subpopulations of offspring who reported no personal smoking and no maternal smoking exposure. RESULTS Father's smoking commencing preconception was associated with methylation of blood DNA in offspring at two cytosine-phosphate-guanine sites (CpGs) (false discovery rate (FDR) < 0.05) in PRR5 and CENPP. Father's pubertal onset smoking was associated with 19 CpGs (FDR < 0.05) mapped to 14 genes (TLR9, DNTT, FAM53B, NCAPG2, PSTPIP2, MBIP, C2orf39, NTRK2, DNAJC14, CDO1, PRAP1, TPCN1, IRS1 and CSF1R). These differentially methylated sites were hypermethylated and associated with promoter regions capable of gene silencing. Some of these sites were associated with offspring outcomes in this cohort including ever-asthma (NTRK2), ever-wheezing (DNAJC14, TPCN1), weight (FAM53B, NTRK2) and BMI (FAM53B, NTRK2) (p < 0.05). Pathway analysis showed enrichment for gene ontology pathways including regulation of gene expression, inflammation and innate immune responses. Father's smoking-associated sites did not overlap with dmCpGs identified in EWAS of personal and maternal smoking (FDR < 0.05), and all sites remained significant (p < 0.05) in analyses of offspring with no personal smoking and no maternal smoking exposure. CONCLUSION Father's preconception smoking, particularly in puberty, is associated with offspring DNA methylation, providing evidence that epigenetic mechanisms may underlie epidemiological observations that pubertal paternal smoking increases risk of offspring asthma, low lung function and obesity.
Collapse
Affiliation(s)
- Negusse Tadesse Kitaba
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK
| | - Gerd Toril Mørkve Knudsen
- Department of Clinical Sciences, University of Bergen, Bergen, Norway
- Department of Occupational Medicine, Haukeland University Hospital, Bergen, Norway
| | - Ane Johannessen
- Centre for International Health, Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Faisal I Rezwan
- Department of Computer Science, Aberystwyth University, Aberystwyth, UK
| | - Andrei Malinovschi
- Department of Medical Sciences: Clinical Physiology, Uppsala University, Uppsala, Sweden
| | - Anna Oudin
- Section of Sustainable Health, Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | - Bryndis Benediktsdottir
- Department of Allergy, Respiratory Medicine and Sleep, Landspitali University Hospital, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - David Martino
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, University of Western Australia, Perth, Australia
| | | | | | - Mathias Holm
- Occupational and Environmental Medicine, School of Public Health and Community Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Nils Oskar Jõgi
- Department of Clinical Sciences, University of Bergen, Bergen, Norway
- Department of Occupational Medicine, Haukeland University Hospital, Bergen, Norway
| | - Shyamali C Dharmage
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Australia
| | - Svein Magne Skulstad
- Department of Occupational Medicine, Haukeland University Hospital, Bergen, Norway
| | - Sarah H Watkins
- University of Bristol, MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, Bristol, UK
| | - Matthew Suderman
- University of Bristol, MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, Bristol, UK
| | - Francisco Gómez-Real
- Department of Clinical Sciences, University of Bergen, Bergen, Norway
- Department of Gynaecology and Obstetrics, Haukeland University Hospital, Bergen, Norway
| | - Vivi Schlünssen
- Department of Public Health, Work, Environment and Health, Danish Ramazzini Centre, Aarhus University Denmark, Aarhus, Denmark
- National Research Center for the Working Environment, Copenhagen, Denmark
| | - Cecilie Svanes
- Department of Occupational Medicine, Haukeland University Hospital, Bergen, Norway
- Centre for International Health, Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - John W Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK.
- NIHR Southampton Biomedical Research Center, University Hospitals Southampton, Southampton, UK.
| |
Collapse
|
22
|
Gauthier M, Kale SL, Oriss TB, Gorry M, Ramonell RP, Dalton K, Ray P, Fahy JV, Seibold MA, Castro M, Jarjour N, Gaston B, Bleecker ER, Meyers DA, Moore W, Hastie AT, Israel E, Levy BD, Mauger D, Erzurum S, Comhair SA, Wenzel SE, Ray A. CCL5 is a potential bridge between type 1 and type 2 inflammation in asthma. J Allergy Clin Immunol 2023; 152:94-106.e12. [PMID: 36893862 PMCID: PMC10330021 DOI: 10.1016/j.jaci.2023.02.028] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 01/06/2023] [Accepted: 02/13/2023] [Indexed: 03/09/2023]
Abstract
BACKGROUND Type 1 (T1) inflammation (marked by IFN-γ expression) is now consistently identified in subsets of asthma cohorts, but how it contributes to disease remains unclear. OBJECTIVE We sought to understand the role of CCL5 in asthmatic T1 inflammation and how it interacts with both T1 and type 2 (T2) inflammation. METHODS CCL5, CXCL9, and CXCL10 messenger RNA expression from sputum bulk RNA sequencing, as well as clinical and inflammatory data were obtained from the Severe Asthma Research Program III (SARP III). CCL5 and IFNG expression from bronchoalveolar lavage cell bulk RNA sequencing was obtained from the Immune Mechanisms in Severe Asthma (IMSA) cohort and expression related to previously identified immune cell profiles. The role of CCL5 in tissue-resident memory T-cell (TRM) reactivation was evaluated in a T1high murine severe asthma model. RESULTS Sputum CCL5 expression strongly correlated with T1 chemokines (P < .001 for CXCL9 and CXCL10), consistent with a role in T1 inflammation. CCL5high participants had greater fractional exhaled nitric oxide (P = .009), blood eosinophils (P < .001), and sputum eosinophils (P = .001) in addition to sputum neutrophils (P = .001). Increased CCL5 bronchoalveolar lavage expression was unique to a previously described T1high/T2variable/lymphocytic patient group in the IMSA cohort, with IFNG trending with worsening lung obstruction only in this group (P = .083). In a murine model, high expression of the CCL5 receptor CCR5 was observed in TRMs and was consistent with a T1 signature. A role for CCL5 in TRM activation was supported by the ability of the CCR5 inhibitor maraviroc to blunt reactivation. CONCLUSION CCL5 appears to contribute to TRM-related T1 neutrophilic inflammation in asthma while paradoxically also correlating with T2 inflammation and with sputum eosinophilia.
Collapse
Affiliation(s)
- Marc Gauthier
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pa.
| | - Sagar Laxman Kale
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pa
| | - Timothy B Oriss
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pa
| | - Michael Gorry
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pa
| | - Richard P Ramonell
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pa
| | - Kathryn Dalton
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pa
| | - Prabir Ray
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pa
| | - John V Fahy
- Division of Pulmonary Allergy and Critical Care, University of California, San Francisco, Calif
| | - Max A Seibold
- Center for Genes, Environment, and Health and Department of Pediatrics, National Jewish Health, Denver, Colo; Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado-Anschutz Medical Campus, Aurora, Colo
| | - Mario Castro
- Pulmonary, Critical Care and Sleep Medicine, University of Kansas School of Medicine, Kansas City, Kan
| | - Nizar Jarjour
- Division of Allergy, Pulmonary and Critical Care Medicine, University of Wisconsin School of Medicine, Madison, Wis
| | - Benjamin Gaston
- Riley Hospital for Children and Indiana University School of Medicine Department of Pediatrics, Indianapolis, Ind
| | - Eugene R Bleecker
- Division of Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona, Tucson, Ariz
| | - Deborah A Meyers
- Division of Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona, Tucson, Ariz
| | - Wendy Moore
- Section on Pulmonary, Critical Care, Allergy & Immunologic Diseases, Wake Forest School of Medicine, Winston-Salem, NC
| | - Annette T Hastie
- Section on Pulmonary, Critical Care, Allergy & Immunologic Diseases, Wake Forest School of Medicine, Winston-Salem, NC
| | - Elliot Israel
- Pulmonary and Critical Care Medicine Division, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass
| | - Bruce D Levy
- Pulmonary and Critical Care Medicine Division, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass
| | - David Mauger
- Division of Statistics and Bioinformatics, Department of Public Health Sciences, Pennsylvania State University, Hershey, Pa
| | - Serpil Erzurum
- Lerner Research Institute, Respiratory Institute, Cleveland Clinic, Cleveland, Ohio
| | - Suzy A Comhair
- Lerner Research Institute, Respiratory Institute, Cleveland Clinic, Cleveland, Ohio
| | - Sally E Wenzel
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pa; Department of Environmental and Occupation Health, University of Pittsburgh School of Public Health, Pittsburgh, Pa
| | - Anuradha Ray
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pa; Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pa
| |
Collapse
|
23
|
Peng Y, Chen SY, Wang ZN, Zhou ZQ, Sun J, Zhang GA, Li J, Wang L, Zhao JC, Tang XX, Wang DY, Zhong NS. Dicoumarol is an effective post-exposure prophylactic for SARS-CoV-2 Omicron infection in human airway epithelium. Signal Transduct Target Ther 2023; 8:242. [PMID: 37301869 PMCID: PMC10256976 DOI: 10.1038/s41392-023-01511-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/08/2023] [Accepted: 05/17/2023] [Indexed: 06/12/2023] Open
Abstract
Repurposing existing drugs to inhibit SARS-CoV-2 infection in airway epithelial cells (AECs) is a quick way to find novel treatments for COVID-19. Computational screening has found dicoumarol (DCM), a natural anticoagulant, to be a potential SARS-CoV-2 inhibitor, but its inhibitory effects and possible working mechanisms remain unknown. Using air-liquid interface culture of primary human AECs, we demonstrated that DCM has potent antiviral activity against the infection of multiple Omicron variants (including BA.1, BQ.1 and XBB.1). Time-of-addition and drug withdrawal assays revealed that early treatment (continuously incubated after viral absorption) of DCM could markedly inhibit Omicron replication in AECs, but DCM did not affect the absorption, exocytosis and spread of viruses or directly eliminate viruses. Mechanistically, we performed single-cell sequencing analysis (a database of 77,969 cells from different airway locations from 10 healthy volunteers) and immunofluorescence staining, and showed that the expression of NAD(P)H quinone oxidoreductase 1 (NQO1), one of the known DCM targets, was predominantly localised in ciliated AECs. We further found that the NQO1 expression level was positively correlated with both the disease severity of COVID-19 patients and virus copy levels in cultured AECs. In addition, DCM treatment downregulated NQO1 expression and disrupted signalling pathways associated with SARS-CoV-2 disease outcomes (e.g., Endocytosis and COVID-19 signalling pathways) in cultured AECs. Collectively, we demonstrated that DCM is an effective post-exposure prophylactic for SARS-CoV-2 infection in the human AECs, and these findings could help physicians formulate novel treatment strategies for COVID-19.
Collapse
Affiliation(s)
- Yang Peng
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, China
- Department of Otolaryngology, Infectious Diseases Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Shi-Ying Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Zhao-Ni Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Zi-Qing Zhou
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jing Sun
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Gui-An Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jia Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, China
- Guangzhou Laboratory, Guangzhou, China
| | - Lei Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, China
- Guangzhou Laboratory, Guangzhou, China
| | - Jin-Cun Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xiao Xiao Tang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, China.
- Guangzhou Laboratory, Guangzhou, China.
| | - De-Yun Wang
- Department of Otolaryngology, Infectious Diseases Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
| | - Nan-Shan Zhong
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong, China.
- Guangzhou Laboratory, Guangzhou, China.
| |
Collapse
|
24
|
Li RB, Yang XH, Zhang JD, Cui W. GAS6-AS1, a long noncoding RNA, functions as a key candidate gene in atrial fibrillation related stroke determined by ceRNA network analysis and WGCNA. BMC Med Genomics 2023; 16:51. [PMID: 36894947 PMCID: PMC9996875 DOI: 10.1186/s12920-023-01478-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 03/03/2023] [Indexed: 03/11/2023] Open
Abstract
BACKGROUND Stroke attributable to atrial fibrillation (AF related stroke, AFST) accounts for 13 ~ 26% of ischemic stroke. It has been found that AFST patients have a higher risk of disability and mortality than those without AF. Additionally, it's still a great challenge to treat AFST patients because its exact mechanism at the molecular level remains unclear. Thus, it's vital to investigate the mechanism of AFST and search for molecular targets of treatment. Long non-coding RNAs (lncRNAs) are related to the pathogenesis of various diseases. However, the role of lncRNAs in AFST remains unclear. In this study, AFST-related lncRNAs are explored using competing endogenous RNA (ceRNA) network analysis and weighted gene co-expression network analysis (WGCNA). METHODS GSE66724 and GSE58294 datasets were downloaded from GEO database. After data preprocessing and probe reannotation, differentially expressed lncRNAs (DELs) and differentially expressed mRNAs (DEMs) between AFST and AF samples were explored. Then, functional enrichment analysis and protein-protein interaction (PPI) network analysis of the DEMs were performed. At the meantime, ceRNA network analysis and WGCNA were performed to identify hub lncRNAs. The hub lncRNAs identified both by ceRNA network analysis and WGCNA were further validated by Comparative Toxicogenomics Database (CTD). RESULTS In all, 19 DELs and 317 DEMs were identified between the AFST and AF samples. Functional enrichment analysis suggested that the DEMs associated with AFST were mainly enriched in the activation of the immune response. Two lncRNAs which overlapped between the three lncRNAs identified by the ceRNA network analysis and the 28 lncRNAs identified by the WGCNA were screened as hub lncRNAs for further validation. Finally, lncRNA GAS6-AS1 turned out to be associated with AFST by CTD validation. CONCLUSION These findings suggested that low expression of GAS6-AS1 might exert an essential role in AFST through downregulating its downstream target mRNAs GOLGA8A and BACH2, and GAS6-AS1 might be a potential target for AFST therapy.
Collapse
Affiliation(s)
- Rui-Bin Li
- Department of Cardiology, The Second Hospital of Hebei Medical University, No. 215 West Heping Road, Shijiazhuang, 050000, Hebei, China
| | - Xiao-Hong Yang
- Department of Cardiology, The Second Hospital of Hebei Medical University, No. 215 West Heping Road, Shijiazhuang, 050000, Hebei, China
| | - Ji-Dong Zhang
- Department of Cardiology, The Second Hospital of Hebei Medical University, No. 215 West Heping Road, Shijiazhuang, 050000, Hebei, China
| | - Wei Cui
- Department of Cardiology, The Second Hospital of Hebei Medical University, No. 215 West Heping Road, Shijiazhuang, 050000, Hebei, China.
| |
Collapse
|
25
|
Herrera-Luis E, Mak ACY, Perez-Garcia J, Martin-Gonzalez E, Eng C, Beckman KB, Huntsman S, Hu D, González-Pérez R, Hernández-Pérez JM, Mederos-Luis E, Sio YY, Poza-Guedes P, Sardón O, Corcuera P, Sánchez-Machín I, Korta-Murua J, Martínez-Rivera C, Mullol J, Muñoz X, Valero A, Sastre J, Garcia-Aymerich J, Llop S, Torrent M, Casas M, Rodríguez-Santana JR, Villar J, del Pozo V, Lorenzo-Diaz F, Williams LK, Melén E, Chew FT, Borrell LN, Burchard EG, Pino-Yanes M. Admixture mapping of severe asthma exacerbations in Hispanic/Latino children and youth. Thorax 2023; 78:233-241. [PMID: 36180068 PMCID: PMC9957797 DOI: 10.1136/thorax-2022-218755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 08/04/2022] [Indexed: 11/04/2022]
Abstract
BACKGROUND In the USA, genetically admixed populations have the highest asthma prevalence and severe asthma exacerbations rates. This could be explained not only by environmental factors but also by genetic variants that exert ethnic-specific effects. However, no admixture mapping has been performed for severe asthma exacerbations. OBJECTIVE We sought to identify genetic variants associated with severe asthma exacerbations in Hispanic/Latino subgroups by means of admixture mapping analyses and fine mapping, and to assess their transferability to other populations and potential functional roles. METHODS We performed an admixture mapping in 1124 Puerto Rican and 625 Mexican American children with asthma. Fine-mapping of the significant peaks was performed via allelic testing of common and rare variants. We performed replication across Hispanic/Latino subgroups, and the transferability to non-Hispanic/Latino populations was assessed in 1001 African Americans, 1250 Singaporeans and 941 Europeans with asthma. The effects of the variants on gene expression and DNA methylation from whole blood were also evaluated in participants with asthma and in silico with data obtained through public databases. RESULTS Genomewide significant associations of Indigenous American ancestry with severe asthma exacerbations were found at 5q32 in Mexican Americans as well as at 13q13-q13.2 and 3p13 in Puerto Ricans. The single nucleotide polymorphism (SNP) rs1144986 (C5orf46) showed consistent effects for severe asthma exacerbations across Hispanic/Latino subgroups, but it was not validated in non-Hispanics/Latinos. This SNP was associated with DPYSL3 DNA methylation and SCGB3A2 gene expression levels. CONCLUSIONS Admixture mapping study of asthma exacerbations revealed a novel locus that exhibited Hispanic/Latino-specific effects and regulated DPYSL3 and SCGB3A2.
Collapse
Affiliation(s)
- Esther Herrera-Luis
- Genomics and Health Group, Department of Biochemistry,
Microbiology, Cell Biology and Genetics, Universidad de La Laguna (ULL), La Laguna,
Tenerife, Spain
| | - Angel C. Y. Mak
- Department of Medicine, University of California San
Francisco, San Francisco, California, U.S.A
| | - Javier Perez-Garcia
- Genomics and Health Group, Department of Biochemistry,
Microbiology, Cell Biology and Genetics, Universidad de La Laguna (ULL), La Laguna,
Tenerife, Spain
| | - Elena Martin-Gonzalez
- Genomics and Health Group, Department of Biochemistry,
Microbiology, Cell Biology and Genetics, Universidad de La Laguna (ULL), La Laguna,
Tenerife, Spain
| | - Celeste Eng
- Department of Medicine, University of California San
Francisco, San Francisco, California, U.S.A
| | | | - Scott Huntsman
- Department of Medicine, University of California San
Francisco, San Francisco, California, U.S.A
| | - Donglei Hu
- Department of Medicine, University of California San
Francisco, San Francisco, California, U.S.A
| | - Ruperto González-Pérez
- Allergy Department, Hospital Universitario de Canarias,
Santa Cruz de Tenerife, Tenerife, Spain,Asthma Unit, Hospital Universitario de Canarias, La Laguna,
Tenerife, Spain
| | - José M. Hernández-Pérez
- Pulmonary Medicine, Hospital Universitario de N.S de
Candelaria, Santa Cruz de Tenerife, Spain,Pulmonary Medicine, Hospital General de La Palma, La Palma,
Santa Cruz de Tenerife, Spain
| | - Elena Mederos-Luis
- Allergy Department, Hospital Universitario de Canarias,
Santa Cruz de Tenerife, Tenerife, Spain
| | - Yang Yie Sio
- Department of Biological Sciences, National University of
Singapore, Singapore
| | - Paloma Poza-Guedes
- Allergy Department, Hospital Universitario de Canarias,
Santa Cruz de Tenerife, Tenerife, Spain,Asthma Unit, Hospital Universitario de Canarias, La Laguna,
Tenerife, Spain
| | - Olaia Sardón
- Division of Pediatric Respiratory Medicine, Hospital
Universitario Donostia, San Sebastián, Spain,Department of Pediatrics, University of the Basque
Country (UPV/EHU), San Sebastián, Spain
| | - Paula Corcuera
- Division of Pediatric Respiratory Medicine, Hospital
Universitario Donostia, San Sebastián, Spain
| | | | - Javier Korta-Murua
- Division of Pediatric Respiratory Medicine, Hospital
Universitario Donostia, San Sebastián, Spain,Department of Pediatrics, University of the Basque
Country (UPV/EHU), San Sebastián, Spain
| | - Carlos Martínez-Rivera
- CIBER de Enfermedades Respiratorias, Instituto de Salud
Carlos III, Madrid, Spain,Servicio de Neumología, Hospital Universitario
Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona,
Spain
| | - Joaquim Mullol
- CIBER de Enfermedades Respiratorias, Instituto de Salud
Carlos III, Madrid, Spain,Rhinology Unit & Smell Clinic, ENT Department;
Clinical & Experimental Respiratory Immunoallergy (IDIBAPS), Universitat de
Barcelona, Barcelona, Spain
| | - Xavier Muñoz
- CIBER de Enfermedades Respiratorias, Instituto de Salud
Carlos III, Madrid, Spain,Servicio de Neumología, Hospital Vall
d’Hebron, Barcelona, Spain
| | - Antonio Valero
- CIBER de Enfermedades Respiratorias, Instituto de Salud
Carlos III, Madrid, Spain,Allergy Unit & Severe Asthma Unit, Pneumonology and
Allergy Department, Hospital Clínic; IDIBAPS; Universitat de
Barcelona.Barcelona, Spain
| | - Joaquín Sastre
- CIBER de Enfermedades Respiratorias, Instituto de Salud
Carlos III, Madrid, Spain,Allergy Department, Hospital Universitario
Fundación Jiménez Díaz, Madrid, Spain
| | - Judith Garcia-Aymerich
- Spanish Consortium for Research on Epidemiology and
Public Health (CIBERESP), Madrid, Spain,ISGlobal, Barcelona, Spain,Universitat Pompeu Fabra, Barcelona, Spain
| | - Sabrina Llop
- Spanish Consortium for Research on Epidemiology and
Public Health (CIBERESP), Madrid, Spain,Epidemiology and Environmental Health Joint Research
Unit, FISABIO–Universitat Jaume I–Universitat de València,
Valencia, Spain
| | | | - Maribel Casas
- ISGlobal, Barcelona, Spain,Universitat Pompeu Fabra, Barcelona, Spain
| | | | - Jesús Villar
- CIBER de Enfermedades Respiratorias, Instituto de Salud
Carlos III, Madrid, Spain,Multidisciplinary Organ Dysfunction Evaluation Research
Network, Research Unit, Hospital Universitario Dr. Negrín, Las Palmas de Gran
Canaria, Spain
| | - Victoria del Pozo
- CIBER de Enfermedades Respiratorias, Instituto de Salud
Carlos III, Madrid, Spain,Immunology Department, Instituto de Investigación
Sanitaria Hospital Universitario Fundación Jiménez Díaz,
Madrid, Spain
| | - Fabian Lorenzo-Diaz
- Genomics and Health Group, Department of Biochemistry,
Microbiology, Cell Biology and Genetics, Universidad de La Laguna (ULL), La Laguna,
Tenerife, Spain,Instituto Universitario de Enfermedades Tropicales y
Salud Pública de Canarias (IUETSPC), Universidad de La Laguna (ULL), La
Laguna, Tenerife, Spain
| | - L. Keoki Williams
- Center for Individualized and Genomic Medicine Research,
Department of Internal Medicine, Henry Ford Health System, Detroit, MI, U.S.A
| | - Erik Melén
- Department of Clinical Sciences and Education,
Södersjukhuset, Karolinska Institutet, Stockholm, Sweden,Sachs’ Children’s Hospital, South General
Hospital, Stockholm, Sweden
| | - Fook Tim Chew
- Department of Biological Sciences, National University of
Singapore, Singapore
| | - Luisa N. Borrell
- Department of Epidemiology & Biostatistics, Graduate
School of Public Health & Health Policy, City University of New York, New York,
NY, U.S.A
| | - Esteban G. Burchard
- UMN Genomics Center, Minneapolis, Minnesota, U.S.A.,Department of Bioengineering and Therapeutic Sciences,
University of California San Francisco, San Francisco, California, U.S.A
| | - Maria Pino-Yanes
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology, and Genetics, Universidad de La Laguna (ULL), La Laguna, Spain .,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.,Instituto de Tecnologías Biomédicas (ITB), Universidad de La Laguna (ULL), La Laguna, Spain
| |
Collapse
|
26
|
Li X, Guerra S, Ledford JG, Kraft M, Li H, Hastie AT, Castro M, Denlinger LC, Erzurum SC, Fahy JV, Gaston B, Israel E, Jarjour NN, Levy BD, Mauger DT, Moore WC, Zein J, Kaminski N, Wenzel SE, Woodruff PG, Meyers DA, Bleecker ER. Low CC16 mRNA Expression Levels in Bronchial Epithelial Cells Are Associated with Asthma Severity. Am J Respir Crit Care Med 2023; 207:438-451. [PMID: 36066606 PMCID: PMC9940145 DOI: 10.1164/rccm.202206-1230oc] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 09/02/2022] [Indexed: 11/16/2022] Open
Abstract
Rationale: CC16 is a protein mainly produced by nonciliated bronchial epithelial cells (BECs) that participates in host defense. Reduced CC16 protein concentrations in BAL and serum are associated with asthma susceptibility. Objectives: Few studies have investigated the relationship between CC16 and asthma progression, and none has focused on BECs. In this study, we sought to determine if CC16 mRNA expression levels in BECs are associated with asthma severity. Methods: Association analyses between CC16 mRNA expression levels in BECs (242 asthmatics and 69 control subjects) and asthma-related phenotypes in Severe Asthma Research Program were performed using a generalized linear model. Measurements and Main Results: Low CC16 mRNA expression levels in BECs were significantly associated with asthma susceptibility and asthma severity, high systemic corticosteroids use, high retrospective and prospective asthma exacerbations, and low pulmonary function. Low CC16 mRNA expression levels were significantly associated with high T2 inflammation biomarkers (fractional exhaled nitric oxide and sputum eosinophils). CC16 mRNA expression levels were negatively correlated with expression levels of Th2 genes (IL1RL1, POSTN, SERPINB2, CLCA1, NOS2, and MUC5AC) and positively correlated with expression levels of Th1 and inflammation genes (IL12A and MUC5B). A combination of two nontraditional T2 biomarkers (CC16 and IL-6) revealed four asthma endotypes with different characteristics of T2 inflammation, obesity, and asthma severity. Conclusions: Our findings indicate that low CC16 mRNA expression levels in BECs are associated with asthma susceptibility, severity, and exacerbations, partially through immunomodulation of T2 inflammation. CC16 is a potential nontraditional T2 biomarker for asthma development and progression.
Collapse
Affiliation(s)
- Xingnan Li
- Division of Genetics, Genomics, and Precision Medicine, and
| | - Stefano Guerra
- Asthma and Airway Disease Research Center, Department of Medicine, University of Arizona, Tucson, Arizona
| | - Julie G. Ledford
- Asthma and Airway Disease Research Center, Department of Medicine, University of Arizona, Tucson, Arizona
| | - Monica Kraft
- Asthma and Airway Disease Research Center, Department of Medicine, University of Arizona, Tucson, Arizona
| | - Huashi Li
- Division of Genetics, Genomics, and Precision Medicine, and
| | - Annette T. Hastie
- Department of Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Mario Castro
- Division of Pulmonary, Critical Care, and Sleep Medicine, University of Kansas School of Medicine, Kansas City, Kansas
| | - Loren C. Denlinger
- Department of Medicine, University of Wisconsin School of Medicine & Public Health, Madison, Wisconsin
| | - Serpil C. Erzurum
- Lerner Research Institute and the Respiratory Institute, Cleveland Clinic, Cleveland, Ohio
| | - John V. Fahy
- Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of California at San Francisco, San Francisco, California
| | - Benjamin Gaston
- Wells Center for Pediatric Research and Riley Hospital for Children, Indiana University, Indianapolis, Indiana
| | - Elliot Israel
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts
| | - Nizar N. Jarjour
- Department of Medicine, University of Wisconsin School of Medicine & Public Health, Madison, Wisconsin
| | - Bruce D. Levy
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts
| | - David T. Mauger
- Department of Public Health Sciences, College of Medicine, Penn State University, Hershey, Pennsylvania
| | - Wendy C. Moore
- Department of Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Joe Zein
- Lerner Research Institute and the Respiratory Institute, Cleveland Clinic, Cleveland, Ohio
| | - Naftali Kaminski
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut; and
| | - Sally E. Wenzel
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Prescott G. Woodruff
- Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of California at San Francisco, San Francisco, California
| | | | | |
Collapse
|
27
|
Liu Y, Li P, Jiang T, Li Y, Wang Y, Cheng Z. Epidermal growth factor receptor in asthma: A promising therapeutic target? Respir Med 2023; 207:107117. [PMID: 36626942 DOI: 10.1016/j.rmed.2023.107117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 01/05/2023] [Accepted: 01/06/2023] [Indexed: 01/09/2023]
Abstract
Activation of the epidermal growth factor receptor (EGFR) pathway is involved in the pathogenesis of asthma. Although decades of intensive research have focused on the role of EGFR in asthma, the specific mechanisms and pathways of EGFR signaling remain unclear. Various reports have indicated that inhibition of EGFR improves the pathological features in asthma models. However, extending these experimental findings to clinical applications is difficult. Several measures can be adopted to promote clinical application of EGFR inhibitors. This review focuses on the role of EGFR in the pathogenesis of asthma and the development of a potentially novel therapeutic target for asthma.
Collapse
Affiliation(s)
- Ye Liu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Pengfei Li
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Tianci Jiang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Yue Li
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Yu Wang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
| | - Zhe Cheng
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
| |
Collapse
|
28
|
Targeting the Semaphorin3E-plexinD1 complex in allergic asthma. Pharmacol Ther 2023; 242:108351. [PMID: 36706796 DOI: 10.1016/j.pharmthera.2023.108351] [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: 03/31/2022] [Revised: 01/09/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023]
Abstract
Asthma is a heterogenous airway disease characterized by airway inflammation and remodeling. It affects more than 300 million people worldwide and poses a significant burden on society. Semaphorins, discovered initially as neural guidance molecules, are ubiquitously expressed in various organs and regulate multiple signaling pathways. Interestingly, Semaphorin3E is a critical molecule in lung pathophysiology through its role in both lung development and homeostasis. Semaphorin3E binds to plexinD1, mediating regulatory effects on cell migration, proliferation, and angiogenesis. Recent in vitro and in vivo studies have demonstrated that the Semaphorin3E-plexinD1 axis is implicated in asthma, impacting inflammatory and structural cells associated with airway inflammation, tissue remodeling, and airway hyperresponsiveness. This review details the Semaphorin3E-plexinD1 axis in various aspects of asthma and highlights future directions in research including its potential role as a therapeutic target in airway allergic diseases.
Collapse
|
29
|
Killian KN, Kosanovich JL, Lipp MA, Empey KM, Oury TD, Perkins TN. RAGE contributes to allergen driven severe neutrophilic airway inflammation via NLRP3 inflammasome activation in mice. Front Immunol 2023; 14:1039997. [PMID: 36776857 PMCID: PMC9910358 DOI: 10.3389/fimmu.2023.1039997] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 01/10/2023] [Indexed: 01/27/2023] Open
Abstract
Background Asthma is a major public healthcare burden, affecting over 300 million people worldwide. While there has been great progress in the treatment of asthma, subsets of patients who present with airway neutrophilia, often have more severe disease, and tend to be resistant to conventional corticosteroid treatments. The receptor for advanced glycation endproducts (RAGE) plays a central role in the pathogenesis of eosinophilic asthma, however, it's role in neutrophilic asthma remains largely uninvestigated. Methods A mouse model of severe steroid resistant neutrophilic airway disease (SSRNAD) using the common fungal allergen Alternaria alternata (AA) was employed to evaluate the effects of genetic ablation of RAGE and pharmacological inhibition of the NLRP3 inflammasome on neutrophilic airway inflammation. Results AA exposure induced robust neutrophil-dominant airway inflammation and increased BALF levels of Th1/Th17 cytokines in wild-type mice, which was significantly reduced in RAGE-/- mice. Serum levels of IgE and IgG1 were increased similarly in both wild-type and RAGE-/- mice. Pharmacological inhibition of NLRP3 blocked the effects of AA exposure and NLRP3 inflammasome activation was RAGE-dependent. Neutrophil extracellular traps were elevated in the BALF of wild-type but not RAGE-/- mice and an atypical population of SiglecF+ neutrophils were identified in the BALF. Lastly, time-course studies found that RAGE expression promoted sustained neutrophil accumulation in the BALF of mice in response to AA.
Collapse
Affiliation(s)
- Katherine N. Killian
- Department of Pathology, University of Pittsburgh, School of Medicine, Pittsburgh, PA, United States
| | - Jessica L. Kosanovich
- Department of Pharmaceutical Sciences, University of Pittsburgh, School of Pharmacy, Pittsburgh, PA, United States
| | - Madeline A. Lipp
- Department of Pharmaceutical Sciences, University of Pittsburgh, School of Pharmacy, Pittsburgh, PA, United States
| | - Kerry M. Empey
- Department of Pharmacy and Therapeutics, University of Pittsburgh, School of Pharmacy, Pittsburgh, PA, United States
- Center for Clinical Pharmaceutical Sciences, University of Pittsburgh, School of Pharmacy, Pittsburgh, PA, United States
- Department of Immunology, University of Pittsburgh, School of Medicine, Pittsburgh, PA, United States
| | - Tim D. Oury
- Department of Pathology, University of Pittsburgh, School of Medicine, Pittsburgh, PA, United States
| | - Timothy N. Perkins
- Department of Pathology, University of Pittsburgh, School of Medicine, Pittsburgh, PA, United States
| |
Collapse
|
30
|
Agache I, Shamji MH, Kermani NZ, Vecchi G, Favaro A, Layhadi JA, Heider A, Akbas DS, Filipaviciute P, Wu LYD, Cojanu C, Laculiceanu A, Akdis CA, Adcock IM. Multidimensional endotyping using nasal proteomics predicts molecular phenotypes in the asthmatic airways. J Allergy Clin Immunol 2023; 151:128-137. [PMID: 36154846 DOI: 10.1016/j.jaci.2022.06.028] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 06/16/2022] [Accepted: 06/27/2022] [Indexed: 02/04/2023]
Abstract
BACKGROUND Unsupervised clustering of biomarkers derived from noninvasive samples such as nasal fluid is less evaluated as a tool for describing asthma endotypes. OBJECTIVE We sought to evaluate whether protein expression in nasal fluid would identify distinct clusters of patients with asthma with specific lower airway molecular phenotypes. METHODS Unsupervised clustering of 168 nasal inflammatory and immune proteins and Shapley values was used to stratify 43 patients with severe asthma (endotype of noneosinophilic asthma) using a 2 "modeling blocks" machine learning approach. This algorithm was also applied to nasal brushings transcriptomics from U-BIOPRED (Unbiased Biomarkers for the Prediction of Respiratory Diseases Outcomes). Feature reduction and functional gene analysis were used to compare proteomic and transcriptomic clusters. Gene set variation analysis provided enrichment scores of the endotype of noneosinophilic asthma protein signature within U-BIOPRED sputum and blood. RESULTS The nasal protein machine learning model identified 2 severe asthma endotypes, which were replicated in U-BIOPRED nasal transcriptomics. Cluster 1 patients had significant airway obstruction, small airways disease, air trapping, decreased diffusing capacity, and increased oxidative stress, although only 4 of 18 were current smokers. Shapley identified 20 cluster-defining proteins. Forty-one proteins were significantly higher in cluster 1. Pathways associated with proteomic and transcriptomic clusters were linked to TH1, TH2, neutrophil, Janus kinase-signal transducer and activator of transcription, TLR, and infection activation. Gene set variation analysis of the nasal protein and gene signatures were enriched in subjects with sputum neutrophilic/mixed granulocytic asthma and in subjects with a molecular phenotype found in sputum neutrophil-high subjects. CONCLUSIONS Protein or gene analysis may indicate molecular phenotypes within the asthmatic lower airway and provide a simple, noninvasive test for non-type 2 immune response asthma that is currently unavailable.
Collapse
Affiliation(s)
- Ioana Agache
- Faculty of Medicine, Transylvania University, Brasov, Romania; Theramed Healthcare, Brasov, Romania.
| | - Mohamed H Shamji
- National Heart and Lung Institute, Imperial College London, United Kingdom; NIHR Biomedical Research Centre, London, United Kingdom.
| | - Nazanin Zounemat Kermani
- National Heart and Lung Institute, Imperial College London, United Kingdom; Data Science Institute, Imperial College London, United Kingdom
| | | | | | - Janice A Layhadi
- National Heart and Lung Institute, Imperial College London, United Kingdom; NIHR Biomedical Research Centre, London, United Kingdom
| | - Anja Heider
- Christine Kühne-Center for Allergy Research and Education, Davos, Switzerland
| | - Didem Sanver Akbas
- National Heart and Lung Institute, Imperial College London, United Kingdom; NIHR Biomedical Research Centre, London, United Kingdom
| | - Paulina Filipaviciute
- National Heart and Lung Institute, Imperial College London, United Kingdom; NIHR Biomedical Research Centre, London, United Kingdom
| | - Lily Y D Wu
- National Heart and Lung Institute, Imperial College London, United Kingdom; NIHR Biomedical Research Centre, London, United Kingdom
| | - Catalina Cojanu
- Faculty of Medicine, Transylvania University, Brasov, Romania; Theramed Healthcare, Brasov, Romania
| | - Alexandru Laculiceanu
- Faculty of Medicine, Transylvania University, Brasov, Romania; Theramed Healthcare, Brasov, Romania
| | - Cezmi A Akdis
- Christine Kühne-Center for Allergy Research and Education, Davos, Switzerland; Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Ian M Adcock
- National Heart and Lung Institute, Imperial College London, United Kingdom; NIHR Biomedical Research Centre, London, United Kingdom
| |
Collapse
|
31
|
Mori KM, McElroy JP, Weng DY, Chung S, Fadda P, Reisinger SA, Ying KL, Brasky TM, Wewers MD, Freudenheim JL, Shields PG, Song MA. Lung mitochondrial DNA copy number, inflammatory biomarkers, gene transcription and gene methylation in vapers and smokers. EBioMedicine 2022; 85:104301. [PMID: 36215783 PMCID: PMC9561685 DOI: 10.1016/j.ebiom.2022.104301] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 08/31/2022] [Accepted: 09/21/2022] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Mitochondrial DNA copy number (mtCN) maintains cellular function and homeostasis, and is linked to nuclear DNA methylation and gene expression. Increased mtCN in the blood is associated with smoking and respiratory disease, but has received little attention for target organ effects for smoking or electronic cigarette (EC) use. METHODS Bronchoscopy biospecimens from healthy EC users, smokers (SM), and never-smokers (NS) were assessed for associations of mtCN with mtDNA point mutations, immune responses, nuclear DNA methylation and gene expression using linear regression. Ingenuity pathway analysis was used for enriched pathways. GEO and TCGA respiratory disease datasets were used to explore the involvement of mtCN-associated signatures. FINDINGS mtCN was higher in SM than NS, but EC was not statistically different from either. Overall there was a negative association of mtCN with a point mutation in the D-loop but no difference within groups. Positive associations of mtCN with IL-2 and IL-4 were found in EC only. mtCN was significantly associated with 71,487 CpGs and 321 transcripts. 263 CpGs were correlated with nearby transcripts for genes enriched in the immune system. EC-specific mtCN-associated-CpGs and genes were differentially expressed in respiratory diseases compared to controls, including genes involved in cellular movement, inflammation, metabolism, and airway hyperresponsiveness. INTERPRETATION Smoking may elicit a lung toxic effect through mtCN. While the impact of EC is less clear, EC-specific associations of mtCN with nuclear biomarkers suggest exposure may not be harmless. Further research is needed to understand the role of smoking and EC-related mtCN on lung disease risks. FUNDING The National Cancer Institute, the National Heart, Lung, and Blood Institute, the Food and Drug Administration Center for Tobacco Products, the National Center For Advancing Translational Sciences, and Pelotonia Intramural Research Funds.
Collapse
Affiliation(s)
- Kellie M Mori
- Division of Environmental Health Sciences, College of Public Health, The Ohio State University, Columbus, OH, United States
| | - Joseph P McElroy
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH, United States
| | - Daniel Y Weng
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH, United States
| | - Sangwoon Chung
- Pulmonary and Critical Care Medicine, Department of Internal Medicine, The Ohio State University, Columbus, OH, United States
| | - Paolo Fadda
- Genomics Shared Resource, The Ohio State University and James Cancer Hospital, Columbus, OH, United States
| | - Sarah A Reisinger
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH, United States
| | - Kevin L Ying
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH, United States
| | - Theodore M Brasky
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH, United States
| | - Mark D Wewers
- Pulmonary and Critical Care Medicine, Department of Internal Medicine, The Ohio State University, Columbus, OH, United States
| | - Jo L Freudenheim
- Department of Epidemiology and Environmental Health, School of Public Health and Health Professions, University at Buffalo, Buffalo, NY, United States
| | - Peter G Shields
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH, United States.
| | - Min-Ae Song
- Division of Environmental Health Sciences, College of Public Health, The Ohio State University, Columbus, OH, United States.
| |
Collapse
|
32
|
Radzikowska U, Baerenfaller K, Cornejo‐Garcia JA, Karaaslan C, Barletta E, Sarac BE, Zhakparov D, Villaseñor A, Eguiluz‐Gracia I, Mayorga C, Sokolowska M, Barbas C, Barber D, Ollert M, Chivato T, Agache I, Escribese MM. Omics technologies in allergy and asthma research: An EAACI position paper. Allergy 2022; 77:2888-2908. [PMID: 35713644 PMCID: PMC9796060 DOI: 10.1111/all.15412] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 05/30/2022] [Accepted: 06/06/2022] [Indexed: 01/27/2023]
Abstract
Allergic diseases and asthma are heterogenous chronic inflammatory conditions with several distinct complex endotypes. Both environmental and genetic factors can influence the development and progression of allergy. Complex pathogenetic pathways observed in allergic disorders present a challenge in patient management and successful targeted treatment strategies. The increasing availability of high-throughput omics technologies, such as genomics, epigenomics, transcriptomics, proteomics, and metabolomics allows studying biochemical systems and pathophysiological processes underlying allergic responses. Additionally, omics techniques present clinical applicability by functional identification and validation of biomarkers. Therefore, finding molecules or patterns characteristic for distinct immune-inflammatory endotypes, can subsequently influence its development, progression, and treatment. There is a great potential to further increase the effectiveness of single omics approaches by integrating them with other omics, and nonomics data. Systems biology aims to simultaneously and longitudinally understand multiple layers of a complex and multifactorial disease, such as allergy, or asthma by integrating several, separated data sets and generating a complete molecular profile of the condition. With the use of sophisticated biostatistics and machine learning techniques, these approaches provide in-depth insight into individual biological systems and will allow efficient and customized healthcare approaches, called precision medicine. In this EAACI Position Paper, the Task Force "Omics technologies in allergic research" broadly reviewed current advances and applicability of omics techniques in allergic diseases and asthma research, with a focus on methodology and data analysis, aiming to provide researchers (basic and clinical) with a desk reference in the field. The potential of omics strategies in understanding disease pathophysiology and key tools to reach unmet needs in allergy precision medicine, such as successful patients' stratification, accurate disease prognosis, and prediction of treatment efficacy and successful prevention measures are highlighted.
Collapse
Affiliation(s)
- Urszula Radzikowska
- Swiss Institute of Allergy and Asthma Research (SIAF)University of ZurichDavosSwitzerland,Christine‐Kühne Center for Allergy Research and Education (CK‐CARE)DavosSwitzerland
| | - Katja Baerenfaller
- Swiss Institute of Allergy and Asthma Research (SIAF)University of ZurichDavosSwitzerland,Swiss Institute of Bioinformatics (SIB)DavosSwitzerland
| | - José Antonio Cornejo‐Garcia
- Research LaboratoryIBIMA, ARADyAL Instituto de Salud Carlos III, Regional University Hospital of Málaga, UMAMálagaSpain
| | - Cagatay Karaaslan
- Department of Biology, Molecular Biology SectionFaculty of ScienceHacettepe UniversityAnkaraTurkey
| | - Elena Barletta
- Swiss Institute of Allergy and Asthma Research (SIAF)University of ZurichDavosSwitzerland,Swiss Institute of Bioinformatics (SIB)DavosSwitzerland
| | - Basak Ezgi Sarac
- Department of Biology, Molecular Biology SectionFaculty of ScienceHacettepe UniversityAnkaraTurkey
| | - Damir Zhakparov
- Swiss Institute of Allergy and Asthma Research (SIAF)University of ZurichDavosSwitzerland,Swiss Institute of Bioinformatics (SIB)DavosSwitzerland
| | - Alma Villaseñor
- Centre for Metabolomics and Bioanalysis (CEMBIO)Department of Chemistry and BiochemistryFacultad de FarmaciaUniversidad San Pablo‐CEU, CEU UniversitiesMadridSpain,Institute of Applied Molecular Medicine Nemesio Diaz (IMMAND)Department of Basic Medical SciencesFacultad de MedicinaUniversidad San Pablo CEU, CEU UniversitiesMadridSpain
| | - Ibon Eguiluz‐Gracia
- Allergy UnitHospital Regional Universitario de MálagaMálagaSpain,Allergy Research GroupInstituto de Investigación Biomédica de Málaga‐IBIMAMálagaSpain
| | - Cristobalina Mayorga
- Allergy UnitHospital Regional Universitario de MálagaMálagaSpain,Allergy Research GroupInstituto de Investigación Biomédica de Málaga‐IBIMAMálagaSpain,Andalusian Centre for Nanomedicine and Biotechnology – BIONANDMálagaSpain
| | - Milena Sokolowska
- Swiss Institute of Allergy and Asthma Research (SIAF)University of ZurichDavosSwitzerland,Christine‐Kühne Center for Allergy Research and Education (CK‐CARE)DavosSwitzerland
| | - Coral Barbas
- Centre for Metabolomics and Bioanalysis (CEMBIO)Department of Chemistry and BiochemistryFacultad de FarmaciaUniversidad San Pablo‐CEU, CEU UniversitiesMadridSpain
| | - Domingo Barber
- Institute of Applied Molecular Medicine Nemesio Diaz (IMMAND)Department of Basic Medical SciencesFacultad de MedicinaUniversidad San Pablo CEU, CEU UniversitiesMadridSpain
| | - Markus Ollert
- Department of Infection and ImmunityLuxembourg Institute of HealthyEsch‐sur‐AlzetteLuxembourg,Department of Dermatology and Allergy CenterOdense Research Center for AnaphylaxisOdense University Hospital, University of Southern DenmarkOdenseDenmark
| | - Tomas Chivato
- Institute of Applied Molecular Medicine Nemesio Diaz (IMMAND)Department of Basic Medical SciencesFacultad de MedicinaUniversidad San Pablo CEU, CEU UniversitiesMadridSpain,Department of Clinic Medical SciencesFacultad de MedicinaUniversidad San Pablo CEU, CEU UniversitiesMadridSpain
| | | | - Maria M. Escribese
- Institute of Applied Molecular Medicine Nemesio Diaz (IMMAND)Department of Basic Medical SciencesFacultad de MedicinaUniversidad San Pablo CEU, CEU UniversitiesMadridSpain
| |
Collapse
|
33
|
Ahmed MM, Shafat Z, Tazyeen S, Ali R, Almashjary MN, Al-Raddadi R, Harakeh S, Alam A, Haque S, Ishrat R. Identification of pathogenic genes associated with CKD: An integrated bioinformatics approach. Front Genet 2022; 13:891055. [PMID: 36035163 PMCID: PMC9403320 DOI: 10.3389/fgene.2022.891055] [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: 03/16/2022] [Accepted: 06/28/2022] [Indexed: 11/23/2022] Open
Abstract
Chronic kidney disease (CKD) is defined as a persistent abnormality in the structure and function of kidneys and leads to high morbidity and mortality in individuals across the world. Globally, approximately 8%–16% of the population is affected by CKD. Proper screening, staging, diagnosis, and the appropriate management of CKD by primary care clinicians are essential in preventing the adverse outcomes associated with CKD worldwide. In light of this, the identification of biomarkers for the appropriate management of CKD is urgently required. Growing evidence has suggested the role of mRNAs and microRNAs in CKD, however, the gene expression profile of CKD is presently uncertain. The present study aimed to identify diagnostic biomarkers and therapeutic targets for patients with CKD. The human microarray profile datasets, consisting of normal samples and treated samples were analyzed thoroughly to unveil the differentially expressed genes (DEGs). After selection, the interrelationship among DEGs was carried out to identify the overlapping DEGs, which were visualized using the Cytoscape program. Furthermore, the PPI network was constructed from the String database using the selected DEGs. Then, from the PPI network, significant modules and sub-networks were extracted by applying the different centralities methods (closeness, betweenness, stress, etc.) using MCODE, Cytohubba, and Centiserver. After sub-network analysis we identified six overlapped hub genes (RPS5, RPL37A, RPLP0, CXCL8, HLA-A, and ANXA1). Additionally, the enrichment analysis was undertaken on hub genes to determine their significant functions. Furthermore, these six genes were used to find their associated miRNAs and targeted drugs. Finally, two genes CXCL8 and HLA-A were common for Ribavirin drug (the gene-drug interaction), after docking studies HLA-A was selected for further investigation. To conclude our findings, we can say that the identified hub genes and their related miRNAs can serve as potential diagnostic biomarkers and therapeutic targets for CKD treatment strategies.
Collapse
Affiliation(s)
- Mohd Murshad Ahmed
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Zoya Shafat
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Safia Tazyeen
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Rafat Ali
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
- Department of Biosciences, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi, India
| | - Majed N. Almashjary
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Rajaa Al-Raddadi
- Community Medicine Department, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Steve Harakeh
- King Fahd Medical Research Center, and Yousef Abdullatif Jameel Chair of Prophetic Medicine Application, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Aftab Alam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Romana Ishrat
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
- *Correspondence: Romana Ishrat,
| |
Collapse
|
34
|
Cao Y, Wu Y, Lin L, Yang L, Peng X, Chen L. Identifying key genes and functionally enriched pathways in Th2-high asthma by weighted gene co-expression network analysis. BMC Med Genomics 2022; 15:110. [PMID: 35550122 PMCID: PMC9097074 DOI: 10.1186/s12920-022-01241-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 04/14/2022] [Indexed: 12/05/2022] Open
Abstract
Background Asthma is a chronic lung disease characterized by reversible inflammation of the airways. The imbalance of Th1/Th2 cells plays a significant role in the mechanisms of asthma. The aim of this study was to identify asthma-related key genes and functionally enriched pathways in a Th2-high group by using weighted gene coexpression network analysis (WGCNA).
Methods The gene expression profiles of GSE4302, which included 42 asthma patients and 28 controls, were selected from the Gene Expression Omnibus (GEO). A gene network was constructed, and genes were classified into different modules using WGCNA. Gene ontology (GO) was performed to further explore the potential function of the genes in the most related module. In addition, the expression profile and diagnostic capacity (ROC curve) of hub genes of interest were verified by dataset GSE67472. Results In dataset GSE4302, subjects with asthma were divided into Th2-high and Th2-low groups according to the expression of the SERPINB2, POSTN and CLCA1 genes. A weighted gene coexpression network was constructed, and genes were classified into 7 modules. Among them, the red module was most closely associated with Th2-high asthma, which contained 60 genes. These genes were significantly enriched in different biological processes and molecular functions. A total of 8 hub genes (TPSB2, CPA3, ITLN1, CST1, SERPINB10, CEACAM5, CHD26 and P2RY14) were identified, and the expression levels of these genes (except TPSB2) were confirmed in dataset GSE67472. ROC curve analysis validated that the expression of these 8 genes exhibited excellent diagnostic efficiency for Th2-high asthma and Th2-low asthma. Conclusions The study provides a novel perspective on Th2-high asthma by WGCNA, and the hub genes and potential pathways involved may be beneficial for the diagnosis and management of Th2-high asthma. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01241-9.
Collapse
Affiliation(s)
- Yao Cao
- Division of Pediatric Pulmonology and Immunology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, People's Republic of China.,NHC Key Laboratory of Chronobiology (Sichuan University), Chengdu, People's Republic of China
| | - Yi Wu
- Division of Pediatric Pulmonology and Immunology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, People's Republic of China.,NHC Key Laboratory of Chronobiology (Sichuan University), Chengdu, People's Republic of China
| | - Li Lin
- Division of Pediatric Pulmonology and Immunology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, People's Republic of China.,NHC Key Laboratory of Chronobiology (Sichuan University), Chengdu, People's Republic of China
| | - Lin Yang
- Division of Pediatric Pulmonology and Immunology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, People's Republic of China.,NHC Key Laboratory of Chronobiology (Sichuan University), Chengdu, People's Republic of China
| | - Xin Peng
- Division of Pediatric Pulmonology and Immunology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, People's Republic of China.,NHC Key Laboratory of Chronobiology (Sichuan University), Chengdu, People's Republic of China
| | - Lina Chen
- Division of Pediatric Pulmonology and Immunology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, People's Republic of China. .,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, People's Republic of China. .,NHC Key Laboratory of Chronobiology (Sichuan University), Chengdu, People's Republic of China.
| |
Collapse
|
35
|
Guidi R, Xu D, Choy DF, Ramalingam TR, Lee WP, Modrusan Z, Liang Y, Marsters S, Ashkenazi A, Huynh A, Mills J, Flanagan S, Hambro S, Nunez V, Leong L, Cook A, Tran TH, Austin CD, Cao Y, Clarke C, Panettieri RA, Koziol-White C, Jester WF, Wang F, Wilson MS. Steroid-induced fibroblast growth factors drive an epithelial-mesenchymal inflammatory axis in severe asthma. Sci Transl Med 2022; 14:eabl8146. [PMID: 35442706 PMCID: PMC10301263 DOI: 10.1126/scitranslmed.abl8146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Asthma and inflammatory airway diseases restrict airflow in the lung, compromising gas exchange and lung function. Inhaled corticosteroids (ICSs) can reduce inflammation, control symptoms, and improve lung function; however, a growing number of patients with severe asthma do not benefit from ICS. Using bronchial airway epithelial brushings from patients with severe asthma or primary human cells, we delineated a corticosteroid-driven fibroblast growth factor (FGF)-dependent inflammatory axis, with FGF-responsive fibroblasts promoting downstream granulocyte colony-stimulating factor (G-CSF) production, hyaluronan secretion, and neutrophilic inflammation. Allergen challenge studies in mice demonstrate that the ICS, fluticasone propionate, inhibited type 2-driven eosinophilia but induced a concomitant increase in FGFs, G-CSF, hyaluronan, and neutrophil infiltration. We developed a model of steroid-induced neutrophilic inflammation mediated, in part, by induction of an FGF-dependent epithelial-mesenchymal axis, which may explain why some individuals do not benefit from ICS. In further proof-of-concept experiments, we found that combination therapy with pan-FGF receptor inhibitors and corticosteroids prevented both eosinophilic and steroid-induced neutrophilic inflammation. Together, these results establish FGFs as therapeutic targets for severe asthma patients who do not benefit from ICS.
Collapse
Affiliation(s)
- Riccardo Guidi
- Immunology Discovery, Genentech, South San Francisco, CA 94080, USA
| | - Daqi Xu
- Immunology Discovery, Genentech, South San Francisco, CA 94080, USA
| | - David F. Choy
- Biomarker Discovery OMNI, Genentech, South San Francisco, CA 94080, USA
| | | | - Wyne P. Lee
- Translational Immunology, Genentech, South San Francisco, CA 94080, USA
| | - Zora Modrusan
- Next Generation Sequencing (NGS), Genentech, South San Francisco, CA 94080, USA
| | - Yuxin Liang
- Next Generation Sequencing (NGS), Genentech, South San Francisco, CA 94080, USA
| | - Scot Marsters
- Cancer Immunology, Genentech, South San Francisco, CA 94080, USA
| | - Avi Ashkenazi
- Cancer Immunology, Genentech, South San Francisco, CA 94080, USA
| | - Alison Huynh
- Necropsy, Genentech, South San Francisco, CA 94080, USA
| | - Jessica Mills
- Necropsy, Genentech, South San Francisco, CA 94080, USA
| | - Sean Flanagan
- Necropsy, Genentech, South San Francisco, CA 94080, USA
| | | | - Victor Nunez
- Necropsy, Genentech, South San Francisco, CA 94080, USA
| | - Laurie Leong
- Pathology, Genentech, South San Francisco, CA 94080, USA
| | - Ashley Cook
- Pathology, Genentech, South San Francisco, CA 94080, USA
| | | | - Cary D. Austin
- Pathology, Genentech, South San Francisco, CA 94080, USA
| | - Yi Cao
- OMNI Bioinformatics, Genentech, South San Francisco, CA 94080, USA
| | - Christine Clarke
- OMNI Bioinformatics, Genentech, South San Francisco, CA 94080, USA
| | - Reynold A. Panettieri
- Institute for Translational Medicine and Science, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Cynthia Koziol-White
- Institute for Translational Medicine and Science, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
| | - William F. Jester
- Institute for Translational Medicine and Science, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Fen Wang
- Center for Cancer Biology and Nutrition, Texas A&M University, Houston, TX 77030, USA
| | - Mark S. Wilson
- Immunology Discovery, Genentech, South San Francisco, CA 94080, USA
| |
Collapse
|
36
|
Lee Y, Chen H, Chen W, Qi Q, Afshar M, Cai J, Daviglus ML, Thyagarajan B, North KE, London SJ, Boerwinkle E, Celedón JC, Kaplan RC, Yu B. Metabolomic Associations of Asthma in the Hispanic Community Health Study/Study of Latinos. Metabolites 2022; 12:metabo12040359. [PMID: 35448546 PMCID: PMC9028429 DOI: 10.3390/metabo12040359] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/02/2022] [Accepted: 04/12/2022] [Indexed: 12/17/2022] Open
Abstract
Asthma disproportionally affects Hispanic and/or Latino backgrounds; however, the relation between circulating metabolites and asthma remains unclear. We conducted a cross-sectional study associating 640 individual serum metabolites, as well as twelve metabolite modules, with asthma in 3347 Hispanic/Latino background participants (514 asthmatics, 15.36%) from the Hispanic/Latino Community Health Study/Study of Latinos. Using survey logistic regression, per standard deviation (SD) increase in 1-arachidonoyl-GPA (20:4) was significantly associated with 32% high odds of asthma after accounting for clinical risk factors (p = 6.27 × 10−5), and per SD of the green module, constructed using weighted gene co-expression network, was suggestively associated with 25% high odds of asthma (p = 0.006). In the stratified analyses by sex and Hispanic and/or Latino backgrounds, the effect of 1-arachidonoyl-GPA (20:4) and the green module was predominantly observed in women (OR = 1.24 and 1.37, p < 0.001) and people of Cuban and Puerto-Rican backgrounds (OR = 1.25 and 1.27, p < 0.01). Mutations in Fatty Acid Desaturase 2 (FADS2) affected the levels of 1-arachidonoyl-GPA (20:4), and Mendelian Randomization analyses revealed that high genetically regulated 1-arachidonoyl-GPA (20:4) levels were associated with increased odds of asthma (p < 0.001). The findings reinforce a molecular basis for asthma etiology, and the potential causal effect of 1-arachidonoyl-GPA (20:4) on asthma provides an opportunity for future intervention.
Collapse
Affiliation(s)
- Yura Lee
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; (Y.L.); (H.C.); (E.B.)
| | - Han Chen
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; (Y.L.); (H.C.); (E.B.)
| | - Wei Chen
- Department of Pediatrics, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15224, USA; (W.C.); (J.C.C.)
| | - Qibin Qi
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA;
| | - Majid Afshar
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI 53726, USA; (M.A.); (R.C.K.)
| | - Jianwen Cai
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA;
| | - Martha L. Daviglus
- Institute of Minority Health Research, University of Illinois College of Medicine, Chicago, IL 60612, USA;
| | - Bharat Thyagarajan
- Department of Laboratory Medicine and Pathology, University of Minnesota, MMC 609, 420 Delaware Street, Minneapolis, MN 55455, USA;
| | - Kari E. North
- Department of Epidemiology and Carolina Center for Genome Sciences, School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA;
| | - Stephanie J. London
- Department of Health and Human Services, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA;
| | - Eric Boerwinkle
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; (Y.L.); (H.C.); (E.B.)
| | - Juan C. Celedón
- Department of Pediatrics, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15224, USA; (W.C.); (J.C.C.)
- Division of Pulmonary Medicine, Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, PA 15224, USA
| | - Robert C. Kaplan
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI 53726, USA; (M.A.); (R.C.K.)
| | - Bing Yu
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; (Y.L.); (H.C.); (E.B.)
- Correspondence:
| |
Collapse
|
37
|
Jin M, Watkins S, Larriba Y, Wallace C, St. Croix C, Zhou X, Zhao J, Peddada S, Wenzel SE. Real-time imaging of asthmatic epithelial cells identifies migratory deficiencies under type-2 conditions. J Allergy Clin Immunol 2022; 149:579-588. [PMID: 34547368 PMCID: PMC8821171 DOI: 10.1016/j.jaci.2021.08.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/05/2021] [Accepted: 08/27/2021] [Indexed: 02/03/2023]
Abstract
BACKGROUND The epithelium is increasingly recognized as a pathologic contributor to asthma and its phenotypes. Although delayed wound closure by asthmatic epithelial cells is consistently observed, underlying mechanisms remain poorly understood, partly due to difficulties in studying dynamic physiologic processes involving polarized multilayered cell systems. Although type-2 immunity has been suggested to play a role, the mechanisms by which repair is diminished are unclear. OBJECTIVES This study sought to develop and utilize primary multilayered polarized epithelial cell systems, derived from patients with asthma, to evaluate cell migration in response to wounding under type-2 and untreated conditions. METHODS A novel wounding device for multilayered polarized cells, along with time-lapse live cell/real-time confocal imaging were evaluated under IL-13 and untreated conditions. The influence of inhibition of 15 lipoxygenase (15LO1), a type-2 enzyme, on the process was also addressed. Cell migration patterns were analyzed by high-dimensional frequency modulated Möbius for statistical comparisons. RESULTS IL-13 stimulation negatively impacts wound healing by altering the total speed, directionality, and acceleration of individual cells. Inhibition 15LO1 partially improved the wound repair through improving total speed. CONCLUSIONS Migration abnormalities contributed to markedly slower wound closure of IL-13 treated cells, which was modestly reversed by 15LO1 inhibition, suggesting its potential as an asthma therapeutic target. These novel methodologies offer new ways to dynamically study cell movements and identify contributing pathologic processes.
Collapse
Affiliation(s)
- Mingzhu Jin
- Department of Environmental and Occupational Health, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, USA,Department of Rhinology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Simon Watkins
- Center for Biologic Imaging, School of Medicine, University of Pittsburgh, Pittsburgh, USA
| | - Yolanda Larriba
- Department of Statistics and Operations Research, Universidad de Valladolid, Valladolid, Spain
| | - Callen Wallace
- Center for Biologic Imaging, School of Medicine, University of Pittsburgh, Pittsburgh, USA
| | - Claudette St. Croix
- Center for Biologic Imaging, School of Medicine, University of Pittsburgh, Pittsburgh, USA
| | - Xiuxia Zhou
- Department of Environmental and Occupational Health, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, USA
| | - Jinming Zhao
- Department of Environmental and Occupational Health, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, USA
| | - Shyamal Peddada
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, USA
| | - Sally E. Wenzel
- Department of Environmental and Occupational Health, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, USA,Asthma and Environmental Lung Health Institute @UPMC, Pittsburgh, USA
| |
Collapse
|
38
|
Guntur VP, Manka LA, Moore CM, Wynn E, Vladar EK, Alam R, Pham TH, Fingerlin TE, Martin RJ. Refractory neutrophilic asthma and ciliary genes. J Allergy Clin Immunol 2022; 149:1970-1980. [PMID: 35034774 DOI: 10.1016/j.jaci.2021.12.761] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 11/12/2021] [Accepted: 12/08/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND Refractory asthma (RA) remains poorly controlled, resulting in high health care utilization despite guideline-based therapies. Patients with RA manifest higher neutrophilia as a result of increased airway inflammation and subclinical infection, the underlying mechanisms of which remain unclear. OBJECTIVE We sought to characterize and clinically correlate gene expression differences between refractory and nonrefractory (NR) asthma to uncover molecular mechanisms driving group distinctions. METHODS Microarray gene expression of paired airway epithelial brush and endobronchial biopsy samples was compared between 60 RA and 30 NR subjects. Subjects were hierarchically clustered to identify subgroups of RA, and biochemical and clinical traits (airway inflammatory molecules, respiratory pathogens, chest imaging) were compared between groups. Weighted gene correlation network analysis was used to identify coexpressed gene modules. Module expression scores were compared between groups using linear regression, controlling for age, sex, and body mass index. RESULTS Differential gene expression analysis showed upregulation of proneutrophilic and downregulation of ciliary function genes/pathways in RA compared to NR. A subgroup of RA with downregulated ciliary gene expression had increased levels of subclinical infections, airway neutrophilia, and eosinophilia as well as higher chest imaging mucus burden compared to other RA, the dominant differences between RA and NR. Weighted gene correlation network analysis identified gene modules related to ciliary function, which were downregulated in RA and were associated with lower pulmonary function and higher airway wall thickness/inflammation, markers of poorer asthma control. CONCLUSIONS Identification of a novel ciliary-deficient subgroup of RA suggests that diminished mucociliary clearance may underlie repeated asthma exacerbations despite adequate treatment, necessitating further exploration of function, mechanism, and therapeutics.
Collapse
Affiliation(s)
- Vamsi P Guntur
- Division of Pulmonary, Critical Care, and Sleep Medicine, National Jewish Health, Denver, Colo; The NJH Cohen Family Asthma Institute, National Jewish Health, Denver, Colo.
| | - Laurie A Manka
- Division of Pulmonary, Critical Care, and Sleep Medicine, National Jewish Health, Denver, Colo; The NJH Cohen Family Asthma Institute, National Jewish Health, Denver, Colo
| | - Camille M Moore
- Center for Genes, Environment and Health, National Jewish Health, Denver, Colo
| | - Elizabeth Wynn
- Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colo
| | - Eszter K Vladar
- Department of Medicine, Division of Pulmonary Sciences and Critical Care Medicine, and the Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, Colo
| | - Rafeul Alam
- The NJH Cohen Family Asthma Institute, National Jewish Health, Denver, Colo; Division of Allergy and Immunology, National Jewish Health, Denver, Colo
| | - Tuyet-Hang Pham
- Translational Science & Experimental Medicine, Research & Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg
| | - Tasha E Fingerlin
- Center for Genes, Environment and Health, National Jewish Health, Denver, Colo; Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colo
| | - Richard J Martin
- Division of Pulmonary, Critical Care, and Sleep Medicine, National Jewish Health, Denver, Colo; The NJH Cohen Family Asthma Institute, National Jewish Health, Denver, Colo
| |
Collapse
|
39
|
Gautam Y, Johansson E, Mersha TB. Multi-Omics Profiling Approach to Asthma: An Evolving Paradigm. J Pers Med 2022; 12:jpm12010066. [PMID: 35055381 PMCID: PMC8778153 DOI: 10.3390/jpm12010066] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/23/2021] [Accepted: 12/28/2021] [Indexed: 02/04/2023] Open
Abstract
Asthma is a complex multifactorial and heterogeneous respiratory disease. Although genetics is a strong risk factor of asthma, external and internal exposures and their interactions with genetic factors also play important roles in the pathophysiology of asthma. Over the past decades, the application of high-throughput omics approaches has emerged and been applied to the field of asthma research for screening biomarkers such as genes, transcript, proteins, and metabolites in an unbiased fashion. Leveraging large-scale studies representative of diverse population-based omics data and integrating with clinical data has led to better profiling of asthma risk. Yet, to date, no omic-driven endotypes have been translated into clinical practice and management of asthma. In this article, we provide an overview of the current status of omics studies of asthma, namely, genomics, transcriptomics, epigenomics, proteomics, exposomics, and metabolomics. The current development of the multi-omics integrations of asthma is also briefly discussed. Biomarker discovery following multi-omics profiling could be challenging but useful for better disease phenotyping and endotyping that can translate into advances in asthma management and clinical care, ultimately leading to successful precision medicine approaches.
Collapse
|
40
|
Jin M, Watkins S, Larriba Y, Wallace C, Croix CS, Zhou X, Zhao J, Peddada S, Wenzel SE. Reply. J Allergy Clin Immunol 2022; 149:1132-1133. [PMID: 35000771 DOI: 10.1016/j.jaci.2021.12.763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 12/10/2021] [Indexed: 11/25/2022]
Affiliation(s)
- Mingzhu Jin
- Department of Environmental and Occupational Health, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pa; Department of Rhinology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Simon Watkins
- Center for Biologic Imaging, School of Medicine, University of Pittsburgh Medical Center, University of Pittsburgh, Pittsburgh, Pa
| | - Yolanda Larriba
- Department of Statistics and Operations Research, Universidad de Valladolid, Valladolid, Spain
| | - Callen Wallace
- Center for Biologic Imaging, School of Medicine, University of Pittsburgh Medical Center, University of Pittsburgh, Pittsburgh, Pa
| | - Claudette St Croix
- Center for Biologic Imaging, School of Medicine, University of Pittsburgh Medical Center, University of Pittsburgh, Pittsburgh, Pa
| | - Xiuxia Zhou
- Department of Environmental and Occupational Health, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pa
| | - Jinming Zhao
- Department of Environmental and Occupational Health, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pa
| | - Shyamal Peddada
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pa
| | - Sally E Wenzel
- Department of Environmental and Occupational Health, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pa; University of Pittsburgh Asthma and Environmental Lung Health Institute @UPMC, Pittsburgh, Pa.
| |
Collapse
|
41
|
Gauthier M, Kale SL, Oriss TB, Scholl K, Das S, Yuan H, Hu S, Chen J, Camiolo M, Ray P, Wenzel S, Ray A. Dual role for CXCR3 and CCR5 in asthmatic type 1 inflammation. J Allergy Clin Immunol 2022; 149:113-124.e7. [PMID: 34146578 PMCID: PMC8674372 DOI: 10.1016/j.jaci.2021.05.044] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 05/17/2021] [Accepted: 05/27/2021] [Indexed: 01/03/2023]
Abstract
BACKGROUND Many patients with severe asthma (SA) fail to respond to type 2 inflammation-targeted therapies. We previously identified a cohort of subjects with SA expressing type 1 inflammation manifesting with IFN-γ expression and variable type 2 responses. OBJECTIVE We investigated the role of the chemotactic receptors C-X-C chemokine receptor 3 (CXCR3) and C-C chemokine receptor 5 (CCR5) in establishing type 1 inflammation in SA. METHODS Bronchoalveolar lavage microarray data from the Severe Asthma Research Program I/II were analyzed for pathway expression and paired with clinical parameters. Wild-type, Cxcr3-/-, and Ccr5-/- mice were exposed to a type 1-high SA model with analysis of whole lung gene expression and histology. Wild-type and Cxcr3-/- mice were treated with a US Food and Drug Administration-approved CCR5 inhibitor (maraviroc) with assessment of airway resistance, inflammatory cell recruitment by flow cytometry, whole lung gene expression, and histology. RESULTS A cohort of subjects with increased IFN-γ expression showed higher asthma severity. IFN-γ expression was correlated with CXCR3 and CCR5 expression, but in Cxcr3-/- and Ccr5-/- mice type 1 inflammation was preserved in a murine SA model, most likely owing to compensation by the other pathway. Incorporation of maraviroc into the experimental model blunted airway hyperreactivity despite only mild effects on lung inflammation. CONCLUSIONS IFNG expression in asthmatic airways was strongly correlated with expression of both the chemokine receptors CXCR3 and CCR5. Although these pathways provide redundancy for establishing type 1 lung inflammation, inhibition of the CCL5/CCR5 pathway with maraviroc provided unique benefits in reducing airway hyperreactivity. Targeting this pathway may be a novel approach for improving lung function in individuals with type 1-high asthma.
Collapse
Affiliation(s)
- Marc Gauthier
- Department of Medicine, Division of Pulmonary Allergy and Critical Care Medicine, Pittsburgh, Pa.
| | - Sagar Laxman Kale
- Department of Medicine, Division of Pulmonary Allergy and Critical Care Medicine, Pittsburgh, Pa
| | - Timothy B Oriss
- Department of Medicine, Division of Pulmonary Allergy and Critical Care Medicine, Pittsburgh, Pa; Department of Immunology, The University of Pittsburgh School of Medicine, Pittsburgh, Pa
| | - Kathryn Scholl
- Department of Medicine, Division of Pulmonary Allergy and Critical Care Medicine, Pittsburgh, Pa
| | - Sudipta Das
- Department of Medicine, Division of Pulmonary Allergy and Critical Care Medicine, Pittsburgh, Pa
| | - Huijuan Yuan
- Department of Medicine, Division of Pulmonary Allergy and Critical Care Medicine, Pittsburgh, Pa
| | - Sanmei Hu
- Department of Medicine, Division of Pulmonary Allergy and Critical Care Medicine, Pittsburgh, Pa
| | - Jie Chen
- Department of Medicine, Division of Pulmonary Allergy and Critical Care Medicine, Pittsburgh, Pa
| | - Matthew Camiolo
- Department of Medicine, Division of Pulmonary Allergy and Critical Care Medicine, Pittsburgh, Pa
| | - Prabir Ray
- Department of Medicine, Division of Pulmonary Allergy and Critical Care Medicine, Pittsburgh, Pa; Department of Immunology, The University of Pittsburgh School of Medicine, Pittsburgh, Pa
| | - Sally Wenzel
- Department of Medicine, Division of Pulmonary Allergy and Critical Care Medicine, Pittsburgh, Pa; The University of Pittsburgh School of Environmental and Occupational Health, Pittsburgh, Pa
| | - Anuradha Ray
- Department of Medicine, Division of Pulmonary Allergy and Critical Care Medicine, Pittsburgh, Pa; Department of Immunology, The University of Pittsburgh School of Medicine, Pittsburgh, Pa.
| |
Collapse
|
42
|
Logotheti M, Agioutantis P, Katsaounou P, Loutrari H. Microbiome Research and Multi-Omics Integration for Personalized Medicine in Asthma. J Pers Med 2021; 11:jpm11121299. [PMID: 34945771 PMCID: PMC8707330 DOI: 10.3390/jpm11121299] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/13/2021] [Accepted: 11/24/2021] [Indexed: 12/12/2022] Open
Abstract
Asthma is a multifactorial inflammatory disorder of the respiratory system characterized by high diversity in clinical manifestations, underlying pathological mechanisms and response to treatment. It is generally established that human microbiota plays an essential role in shaping a healthy immune response, while its perturbation can cause chronic inflammation related to a wide range of diseases, including asthma. Systems biology approaches encompassing microbiome analysis can offer valuable platforms towards a global understanding of asthma complexity and improving patients' classification, status monitoring and therapeutic choices. In the present review, we summarize recent studies exploring the contribution of microbiota dysbiosis to asthma pathogenesis and heterogeneity in the context of asthma phenotypes-endotypes and administered medication. We subsequently focus on emerging efforts to gain deeper insights into microbiota-host interactions driving asthma complexity by integrating microbiome and host multi-omics data. One of the most prominent achievements of these research efforts is the association of refractory neutrophilic asthma with certain microbial signatures, including predominant pathogenic bacterial taxa (such as Proteobacteria phyla, Gammaproteobacteria class, especially species from Haemophilus and Moraxella genera). Overall, despite existing challenges, large-scale multi-omics endeavors may provide promising biomarkers and therapeutic targets for future development of novel microbe-based personalized strategies for diagnosis, prevention and/or treatment of uncontrollable asthma.
Collapse
Affiliation(s)
- Marianthi Logotheti
- G.P. Livanos and M. Simou Laboratories, 1st Department of Critical Care Medicine & Pulmonary Services, Evangelismos Hospital, Medical School, National Kapodistrian University of Athens, 3 Ploutarchou Str., 10675 Athens, Greece; (M.L.); (P.A.)
- Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, 5 Iroon Polytechniou Str., Zografou Campus, 15780 Athens, Greece
| | - Panagiotis Agioutantis
- G.P. Livanos and M. Simou Laboratories, 1st Department of Critical Care Medicine & Pulmonary Services, Evangelismos Hospital, Medical School, National Kapodistrian University of Athens, 3 Ploutarchou Str., 10675 Athens, Greece; (M.L.); (P.A.)
| | - Paraskevi Katsaounou
- Pulmonary Dept First ICU, Evangelismos Hospital, Medical School, National Kapodistrian University of Athens, Ipsilantou 45-7, 10675 Athens, Greece;
| | - Heleni Loutrari
- G.P. Livanos and M. Simou Laboratories, 1st Department of Critical Care Medicine & Pulmonary Services, Evangelismos Hospital, Medical School, National Kapodistrian University of Athens, 3 Ploutarchou Str., 10675 Athens, Greece; (M.L.); (P.A.)
- Correspondence:
| |
Collapse
|
43
|
Moghbeli K, Valenzi E, Naramore R, Sembrat JC, Chen K, Rojas MM, Wenzel SE, Lafyatis R, Modena B, Weathington NM. β-Agonist exposure preferentially impacts lung macrophage cyclic AMP-related gene expression in asthma and asthma COPD overlap syndrome. Am J Physiol Lung Cell Mol Physiol 2021; 321:L837-L843. [PMID: 34494468 DOI: 10.1152/ajplung.00260.2021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Bronchoalveolar lavage (BAL) samples from Severe Asthma Research Program (SARP) patients display suppression of a module of genes involved in cAMP-signaling pathways (BALcAMP) correlating with severity, therapy, and macrophage constituency. We sought to establish if gene expression changes were specific to macrophages and compared gene expression trends from multiple sources. Datasets included single-cell RNA sequencing (scRNA-seq) from lung specimens including a fatal exacerbation of severe Asthma COPD Overlap Syndrome (ACOS) after intense therapy and controls without lung disease, bulk RNA sequencing from cultured macrophage (THP-1) cells after acute or prolonged β-agonist exposure, SARP datasets, and data from the Immune Modulators of Severe Asthma (IMSA) cohort. THP monocytes suppressed BALcAMP network gene expression after prolonged relative to acute β-agonist exposure, corroborating SARP observations. scRNA-seq from healthy and diseased lung tissue revealed 13 cell populations enriched for macrophages. In severe ACOS, BALcAMP gene network expression scores were decreased in many cell populations, most significantly for macrophage populations (P < 3.9e-111). Natural killer (NK) cells and type II alveolar epithelial cells displayed less robust network suppression (P < 9.2e-8). Alveolar macrophages displayed the most numerous individual genes affected and the highest amplitude of modulation. Key BALcAMP genes demonstrate significantly decreased expression in severe asthmatics in the IMSA cohort. We conclude that suppression of the BALcAMP gene module identified from SARP BAL samples is validated in the IMSA patient cohort with physiological parallels observed in a monocytic cell line and in a severe ACOS patient sample with effects preferentially localizing to macrophages.
Collapse
Affiliation(s)
- Kaveh Moghbeli
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Eleanor Valenzi
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Rachel Naramore
- Division of General Internal Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - John Charles Sembrat
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Kong Chen
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Mauricio M Rojas
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Ohio State University, Columbus, Ohio
| | - Sally E Wenzel
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania.,Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Robert Lafyatis
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Brian Modena
- Allergy & Rheumatology Medical Clinic, Scripps Research Institute, La Jolla, California
| | - Nathaniel M Weathington
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| |
Collapse
|
44
|
Soliai MM, Kato A, Helling BA, Stanhope CT, Norton JE, Naughton KA, Klinger AI, Thompson EE, Clay SM, Kim S, Celedón JC, Gern JE, Jackson DJ, Altman MC, Kern RC, Tan BK, Schleimer RP, Nicolae DL, Pinto JM, Ober C. Multi-omics colocalization with genome-wide association studies reveals a context-specific genetic mechanism at a childhood onset asthma risk locus. Genome Med 2021; 13:157. [PMID: 34629083 PMCID: PMC8504130 DOI: 10.1186/s13073-021-00967-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 09/10/2021] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Genome-wide association studies (GWASs) have identified thousands of variants associated with asthma and other complex diseases. However, the functional effects of most of these variants are unknown. Moreover, GWASs do not provide context-specific information on cell types or environmental factors that affect specific disease risks and outcomes. To address these limitations, we used an upper airway epithelial cell (AEC) culture model to assess transcriptional and epigenetic responses to rhinovirus (RV), an asthma-promoting pathogen, and provide context-specific functional annotations to variants discovered in GWASs of asthma. METHODS Genome-wide genetic, gene expression, and DNA methylation data in vehicle- and RV-treated upper AECs were collected from 104 individuals who had a diagnosis of airway disease (n=66) or were healthy participants (n=38). We mapped cis expression and methylation quantitative trait loci (cis-eQTLs and cis-meQTLs, respectively) in each treatment condition (RV and vehicle) in AECs from these individuals. A Bayesian test for colocalization between AEC molecular QTLs and adult onset asthma and childhood onset asthma GWAS SNPs, and a multi-ethnic GWAS of asthma, was used to assign the function to variants associated with asthma. We used Mendelian randomization to demonstrate DNA methylation effects on gene expression at asthma colocalized loci. RESULTS Asthma and allergic disease-associated GWAS SNPs were specifically enriched among molecular QTLs in AECs, but not in GWASs from non-immune diseases, and in AEC eQTLs, but not among eQTLs from other tissues. Colocalization analyses of AEC QTLs with asthma GWAS variants revealed potential molecular mechanisms of asthma, including QTLs at the TSLP locus that were common to both the RV and vehicle treatments and to both childhood onset and adult onset asthma, as well as QTLs at the 17q12-21 asthma locus that were specific to RV exposure and childhood onset asthma, consistent with clinical and epidemiological studies of these loci. CONCLUSIONS This study provides evidence of functional effects for asthma risk variants in AECs and insight into RV-mediated transcriptional and epigenetic response mechanisms that modulate genetic effects in the airway and risk for asthma.
Collapse
Affiliation(s)
- Marcus M Soliai
- Departments of Human Genetics, University of Chicago, Chicago, IL, USA.
- Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, IL, USA.
| | - Atsushi Kato
- Departments of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Britney A Helling
- Departments of Human Genetics, University of Chicago, Chicago, IL, USA
| | | | - James E Norton
- Departments of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | | | - Aiko I Klinger
- Departments of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Emma E Thompson
- Departments of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Selene M Clay
- Departments of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Soyeon Kim
- Division of Pediatric Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA
| | - Juan C Celedón
- Division of Pediatric Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, 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
| | - Matthew C Altman
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA, USA
- Systems Immunology Program, Benaroya Research Institute, Seattle, WA, USA
| | - Robert C Kern
- Department of Otolaryngology-Head and Neck Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Bruce K Tan
- Department of Otolaryngology-Head and Neck Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Robert P Schleimer
- Departments of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Dan L Nicolae
- Department of Statistics, University of Chicago, Chicago, IL, USA
| | - Jayant M Pinto
- Department of Surgery, University of Chicago, Chicago, IL, USA
| | - Carole Ober
- Departments of Human Genetics, University of Chicago, Chicago, IL, USA.
- Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, IL, USA.
| |
Collapse
|
45
|
Du L, Chen F, Xu C, Tan W, Shi J, Tang L, Xiao L, Xie C, Zeng Z, Liang Y, Guo Y. Increased MMP12 mRNA expression in induced sputum was correlated with airway eosinophilic inflammation in asthma patients: evidence from bioinformatic analysis and experiment verification. Gene 2021; 804:145896. [PMID: 34384863 DOI: 10.1016/j.gene.2021.145896] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 08/03/2021] [Accepted: 08/06/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Asthma is a common chronic airway inflammatory disease worldwide. Studies on gene expression profiles in induced sputum may provide noninvasive diagnostic biomarkers and therapeutic targets for asthma. OBJECTIVE To investigate mRNA expression of MMP12 in induced sputum and its relationship with asthma airway eosinophilic inflammation. METHODS GSE76262 dataset was analyzed using R software, weighted gene coexpression network analysis (WGCNA), and protein-protein interaction (PPI) network construction. The top ten hub genes were screened with Cytoscape software (version 3.8.4). We then verified the mRNA expression of MMP12 in two other datasets (GSE137268 and GSE74075) via ROC curve estimates and our induced sputum samples using real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR). Finally, we explored the correlation between MMP12 with asthmatic eosinophilic-related indicators. RESULTS We obtained the top ten hub genes, namely, CCL17, CCL2, CSF1, CCL22, CCR3, CD69, FCGR2B, CD1C, CD1E, and MMP12 via expression profile screening and validation on the GSE76262 dataset. MMP12 was selected as the candidate gene through further validation on GSE137268 and GSE74075 datasets. Finally, we demonstrated that the mRNA expression of MMP12 is significantly upregulated in induced sputum of asthmatic patients (p<0.05) and significantly correlated with eosinophilic-related indicators (p<0.05). These findings indicated that MMP12 can act as a diagnostic biomarker for asthma. CONCLUSION Our study successfully identified and demonstrated that MMP12 is a potential diagnostic biomarker for asthma due to its high expression and association with eosinophilic-related indicators. The results of this study can provide novel insights into asthmatic diagnosis and therapy in the future.
Collapse
Affiliation(s)
- Lijuan Du
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Sun Yat-Sen University, No. 58 Zhongshan 2nd Road, Guangzhou 510080, Guangdong, China; Institute of Respiratory Diseases of Sun Yat-Sen University, No. 58 Zhongshan 2nd Road, Guangzhou 510080, Guangdong, China
| | - Fengjia Chen
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Sun Yat-Sen University, No. 58 Zhongshan 2nd Road, Guangzhou 510080, Guangdong, China; Institute of Respiratory Diseases of Sun Yat-Sen University, No. 58 Zhongshan 2nd Road, Guangzhou 510080, Guangdong, China
| | - Changyi Xu
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Sun Yat-Sen University, No. 58 Zhongshan 2nd Road, Guangzhou 510080, Guangdong, China; Institute of Respiratory Diseases of Sun Yat-Sen University, No. 58 Zhongshan 2nd Road, Guangzhou 510080, Guangdong, China
| | - Weiping Tan
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Sun Yat-Sen University, No. 58 Zhongshan 2nd Road, Guangzhou 510080, Guangdong, China; Institute of Respiratory Diseases of Sun Yat-Sen University, No. 58 Zhongshan 2nd Road, Guangzhou 510080, Guangdong, China
| | - Jia Shi
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Sun Yat-Sen University, No. 58 Zhongshan 2nd Road, Guangzhou 510080, Guangdong, China; Institute of Respiratory Diseases of Sun Yat-Sen University, No. 58 Zhongshan 2nd Road, Guangzhou 510080, Guangdong, China
| | - Lu Tang
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Sun Yat-Sen University, No. 58 Zhongshan 2nd Road, Guangzhou 510080, Guangdong, China; Institute of Respiratory Diseases of Sun Yat-Sen University, No. 58 Zhongshan 2nd Road, Guangzhou 510080, Guangdong, China
| | - Lisha Xiao
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Sun Yat-Sen University, No. 58 Zhongshan 2nd Road, Guangzhou 510080, Guangdong, China; Institute of Respiratory Diseases of Sun Yat-Sen University, No. 58 Zhongshan 2nd Road, Guangzhou 510080, Guangdong, China
| | - Canmao Xie
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Sun Yat-Sen University, No. 58 Zhongshan 2nd Road, Guangzhou 510080, Guangdong, China; Institute of Respiratory Diseases of Sun Yat-Sen University, No. 58 Zhongshan 2nd Road, Guangzhou 510080, Guangdong, China
| | - Zhimin Zeng
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Sun Yat-Sen University, No. 58 Zhongshan 2nd Road, Guangzhou 510080, Guangdong, China; Institute of Respiratory Diseases of Sun Yat-Sen University, No. 58 Zhongshan 2nd Road, Guangzhou 510080, Guangdong, China.
| | - Yuxia Liang
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Sun Yat-Sen University, No. 58 Zhongshan 2nd Road, Guangzhou 510080, Guangdong, China; Institute of Respiratory Diseases of Sun Yat-Sen University, No. 58 Zhongshan 2nd Road, Guangzhou 510080, Guangdong, China.
| | - Yubiao Guo
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Sun Yat-Sen University, No. 58 Zhongshan 2nd Road, Guangzhou 510080, Guangdong, China; Institute of Respiratory Diseases of Sun Yat-Sen University, No. 58 Zhongshan 2nd Road, Guangzhou 510080, Guangdong, China.
| |
Collapse
|
46
|
Jerome JA, Wenzel SE, Trejo Bittar HE. Digital Imaging Analysis Reveals Reduced Alveolar α-Smooth Muscle Actin Expression in Severe Asthma. Appl Immunohistochem Mol Morphol 2021; 29:506-512. [PMID: 33710120 PMCID: PMC8373652 DOI: 10.1097/pai.0000000000000926] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 01/27/2021] [Indexed: 10/21/2022]
Abstract
Expansion of α-smooth muscle actin (α-SMA)-expressing airway smooth muscle of the large airways in asthma is well-studied. However, the contribution of α-SMA-expressing cells in the more distal alveolated parenchyma, including pericytes and myofibroblasts within the alveolar septum, to asthma pathophysiology remains relatively unexplored. The objective of this study was to evaluate α-SMA expression in the alveolated parenchyma of individuals with severe asthma (SA), compared with healthy controls or individuals with chronic obstructive pulmonary disease. Using quantitative digital image analysis and video-assisted thoracoscopic surgery lung biopsies, we show that alveolated parenchyma α-SMA expression is markedly reduced in SA in comparison to healthy controls (mean %positive pixels: 12% vs. 23%, P=0.005). Chronic obstructive pulmonary disease cases showed a similar, but trending, decrease in α-SMA positivity compared with controls (mean %positivity: 17% vs. 23%, P=0.107), which may suggest loss of α-SMA expression is a commonality of obstructive lung diseases. The SA group had similar staining for ETS-related gene protein, a specific endothelial marker, comparatively to controls (mean %positive nuclei: 34% vs. 42%, P=0.218), which suggests intact capillary endothelium and likely intact capillary-associated, α-SMA-positive pericytes. These findings suggest that the loss of α-SMA expression in SA may be because of changes in myofibroblast α-SMA expression or cell number. Further study is necessary to fully evaluate possible mechanisms and consequences of this phenomenon.
Collapse
Affiliation(s)
| | - Sally E Wenzel
- Department of Environmental and Occupational Health, Graduate School of Public Health, University of Pittsburgh
| | | |
Collapse
|
47
|
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: 1.3] [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.
Collapse
|
48
|
Banerjee P, Balraj P, Ambhore NS, Wicher SA, Britt RD, Pabelick CM, Prakash YS, Sathish V. Network and co-expression analysis of airway smooth muscle cell transcriptome delineates potential gene signatures in asthma. Sci Rep 2021; 11:14386. [PMID: 34257337 PMCID: PMC8277837 DOI: 10.1038/s41598-021-93845-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 06/28/2021] [Indexed: 02/06/2023] Open
Abstract
Airway smooth muscle (ASM) is known for its role in asthma exacerbations characterized by acute bronchoconstriction and remodeling. The molecular mechanisms underlying multiple gene interactions regulating gene expression in asthma remain elusive. Herein, we explored the regulatory relationship between ASM genes to uncover the putative mechanism underlying asthma in humans. To this end, the gene expression from human ASM was measured with RNA-Seq in non-asthmatic and asthmatic groups. The gene network for the asthmatic and non-asthmatic group was constructed by prioritizing differentially expressed genes (DEGs) (121) and transcription factors (TFs) (116). Furthermore, we identified differentially connected or co-expressed genes in each group. The asthmatic group showed a loss of gene connectivity due to the rewiring of major regulators. Notably, TFs such as ZNF792, SMAD1, and SMAD7 were differentially correlated in the asthmatic ASM. Additionally, the DEGs, TFs, and differentially connected genes over-represented in the pathways involved with herpes simplex virus infection, Hippo and TGF-β signaling, adherens junctions, gap junctions, and ferroptosis. The rewiring of major regulators unveiled in this study likely modulates the expression of gene-targets as an adaptive response to asthma. These multiple gene interactions pointed out novel targets and pathways for asthma exacerbations.
Collapse
Affiliation(s)
- Priyanka Banerjee
- Department of Pharmaceutical Sciences, North Dakota State University, Fargo, ND, USA
| | - Premanand Balraj
- Department of Pharmaceutical Sciences, North Dakota State University, Fargo, ND, USA
| | | | - Sarah A Wicher
- Department of Anesthesiology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Rodney D Britt
- Center for Perinatal Research, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Christina M Pabelick
- Department of Anesthesiology, Mayo Clinic College of Medicine, Rochester, MN, USA
- Department of Physiology and Biomedical Engineering, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Y S Prakash
- Department of Anesthesiology, Mayo Clinic College of Medicine, Rochester, MN, USA
- Department of Physiology and Biomedical Engineering, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Venkatachalem Sathish
- Department of Pharmaceutical Sciences, North Dakota State University, Fargo, ND, USA.
- Department of Pharmaceutical Sciences, School of Pharmacy, College of Health Professions, North Dakota State University, Sudro 108A, Fargo, ND, 58108-6050, USA.
| |
Collapse
|
49
|
Ano S, Kikuchi N, Matsuyama M, Nakajima M, Kondo Y, Masuda M, Osawa H, Ishii Y, Hizawa N. Transcriptome genetic differences between responders and non-responders before bronchial thermoplasty. J Asthma 2021; 59:1641-1651. [PMID: 34143700 DOI: 10.1080/02770903.2021.1945088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Bronchial thermoplasty (BT) is an endoscopic therapy used for the treatment of refractory asthma. Some predictive factors, for example the number of activations and severity of disease at baseline, have been used to determine the effectiveness of BT in treating patients with asthma. The aim of the present study was to comprehensively analyze RNA samples from the airway bronchial tissues of patients with severe asthma treated by BT, and to characterize each patient as a BT responder or non-responder. METHODS Eight patients with severe asthma scheduled to undergo BT and bronchus biopsies were recruited before the procedures were conducted. Extracted RNA samples from bronchial tissues were sequenced and differential gene expression analysis was carried out.Results/discussion: Subjects with Asthma Quality of Life Questionnaire score changes ≥0.5 for a period of 12 months were considered BT responders. Non-responders had score changes <0.5 for 12 months. Histopathology findings were similar to those reported previously, and no significant differences in the expression of α-smooth muscle actin and protein gene product 9.5 were observed between responders and non-responders. Transcriptome analysis at baseline identified 67 genes that were differentially expressed between responders and non-responders, including SLPI, MMP3, and MUC19, which were upregulated in responders. Although the differentially expressed gene products may have conflicting effects, genes in the airway epithelium and extracellular matrix of patients with severe asthma may determine the BT response. Our results identified possible transcriptomic changes that could be used to identify BT responders.
Collapse
Affiliation(s)
- Satoshi Ano
- The Department of Respiratory Medicine, National Hospital Organization Kasumigaura Medical Center, Tsuchiura, Japan
| | - Norihiro Kikuchi
- The Department of Respiratory Medicine, National Hospital Organization Kasumigaura Medical Center, Tsuchiura, Japan
| | - Masashi Matsuyama
- The Department of Respiratory Medicine, University of Tsukuba, Tsukuba, Japan
| | - Masayuki Nakajima
- The Department of Respiratory Medicine, University of Tsukuba, Tsukuba, Japan
| | - Yuzuru Kondo
- The Department of Diagnostic Pathology, National Hospital Organization Kasumigaura Medical Center, Tsuchiura, Japan
| | - Michiko Masuda
- The Department of Respiratory Medicine, National Hospital Organization Kasumigaura Medical Center, Tsuchiura, Japan
| | - Hajime Osawa
- The Department of Respiratory Medicine, National Hospital Organization Kasumigaura Medical Center, Tsuchiura, Japan.,The Department of Respiratory Medicine, University of Tsukuba, Tsukuba, Japan
| | - Yukio Ishii
- The Department of Respiratory Medicine, National Hospital Organization Kasumigaura Medical Center, Tsuchiura, Japan.,The Department of Respiratory Medicine, University of Tsukuba, Tsukuba, Japan
| | - Nobuyuki Hizawa
- The Department of Respiratory Medicine, University of Tsukuba, Tsukuba, Japan
| |
Collapse
|
50
|
Sim S, Choi Y, Park HS. Potential Metabolic Biomarkers in Adult Asthmatics. Metabolites 2021; 11:metabo11070430. [PMID: 34209139 PMCID: PMC8306564 DOI: 10.3390/metabo11070430] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/25/2021] [Accepted: 06/25/2021] [Indexed: 12/05/2022] Open
Abstract
Asthma is the most common chronic airway inflammation, with multiple phenotypes caused by complicated interactions of genetic, epigenetic, and environmental factors. To date, various determinants have been suggested for asthma pathogenesis by a new technology termed omics, including genomics, transcriptomics, proteomics, and metabolomics. In particular, the systematic analysis of all metabolites in a biological system, such as carbohydrates, amino acids, and lipids, has helped identify a novel pathway related to complex diseases. These metabolites are involved in the regulation of hypermethylation, response to hypoxia, and immune reactions in the pathogenesis of asthma. Among them, lipid metabolism has been suggested to be related to lung dysfunction in mild-to-moderate asthma. Sphingolipid metabolites are an important mediator contributing to airway inflammation in obese asthma and aspirin-exacerbated respiratory disease. Although how these molecular variants impact the disease has not been completely determined, identification of new causative factors may possibly lead to more-personalized and precise pathway-specific approaches for better diagnosis and treatment of asthma. In this review, perspectives of metabolites related to asthma and clinical implications have been highlighted according to various phenotypes.
Collapse
Affiliation(s)
| | | | - Hae-Sim Park
- Correspondence: ; Tel.: +82-31-219-5196; Fax: +82-31-219-5154
| |
Collapse
|