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Smulders T, Van Der Schee MP, Maitland-Van Der Zee AH, Dikkers FG, Van Drunen CM. Influence of the gut and airway microbiome on asthma development and disease. Pediatr Allergy Immunol 2024; 35:e14095. [PMID: 38451070 DOI: 10.1111/pai.14095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 02/07/2024] [Indexed: 03/08/2024]
Abstract
There are ample data to suggest that early-life dysbiosis of both the gut and/or airway microbiome can predispose a child to develop along a trajectory toward asthma. Although individual studies show clear associations between dysbiosis and asthma development, it is less clear what (collection of) bacterial species is mechanistically responsible for the observed effects. This is partly due to issues related to the asthma diagnosis and the broad spectrum of anatomical sites, sample techniques, and analysis protocols that are used in different studies. Moreover, there is limited attention for potential differences in the genetics of individuals that would affect the outcome of the interaction between the environment and that individual. Despite these challenges, the first bacterial components were identified that are able to affect the transcriptional state of human cells, ergo the immune system. Such molecules could in the future be the basis for intervention studies that are now (necessarily) restricted to a limited number of bacterial species. For this transition, it might be prudent to develop an ex vivo human model of a local mucosal immune system to better and safer explore the impact of such molecules. With this approach, we might move beyond association toward understanding of causality.
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Affiliation(s)
- Tamar Smulders
- Department of Otorhinolaryngology/Head and Neck Surgery, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, Netherlands
- Department of Paediatric Pulmonary Medicine, Amsterdam UMC location University of Amsterdam, Amsterdam, Netherlands
| | - Marc P Van Der Schee
- Department of Paediatric Pulmonary Medicine, Amsterdam UMC location University of Amsterdam, Amsterdam, Netherlands
| | - Anke H Maitland-Van Der Zee
- Department of Paediatric Pulmonary Medicine, Amsterdam UMC location University of Amsterdam, Amsterdam, Netherlands
- Department of Pulmonary Medicine, Amsterdam UMC location University of Amsterdam, Amsterdam, Netherlands
| | - Frederik G Dikkers
- Department of Otorhinolaryngology/Head and Neck Surgery, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Cornelis M Van Drunen
- Department of Otorhinolaryngology/Head and Neck Surgery, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, Netherlands
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2
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Kimura S, Yokoyama S, Pilon AL, Kurotani R. Emerging role of an immunomodulatory protein secretoglobin 3A2 in human diseases. Pharmacol Ther 2022; 236:108112. [PMID: 35016921 PMCID: PMC9271138 DOI: 10.1016/j.pharmthera.2022.108112] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/30/2021] [Accepted: 01/06/2022] [Indexed: 12/27/2022]
Abstract
Secretoglobin (SCGB) 3A2 was first identified in 2001 as a protein exhibiting similarities in amino acid sequence and gene structure to SCGB1A1, a multi-functional cytokine-like molecule highly expressed in airway epithelial Club cells that was the first identified and extensively studied member of the SCGB gene superfamily. SCGB3A2 is a small secretory protein of ~10 kDa that forms a dimer and a tetramer. SCGB3A2 is predominantly expressed in airway epithelial Club cells, and has anti-inflammatory, growth factor, anti-fibrotic, and anti-cancer activities that influence various lung diseases. This review summarizes the current understanding of SCGB3A2 biological functions and its role in human diseases with emphasis on its mechanisms of actions and signaling pathway.
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Affiliation(s)
- Shioko Kimura
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Shigetoshi Yokoyama
- Center for Molecular Toxicology and Carcinogenesis, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | | | - Reiko Kurotani
- Biochemical Engineering, Graduate School of Science and Engineering, Yamagata University, Yonezawa, Yamagata 992-8510, Japan
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3
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Behairy OGA, Mohammad OI, Salim RF, Sobeih AA. A study of nasal epithelial cell gene expression in a sample of mild to severe asthmatic children and healthy controls. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2022. [DOI: 10.1186/s43042-022-00244-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Airway epithelium contributes to the natural history of bronchial asthma through the production of various cytokines and chemokines. The purpose of this study was to assess nasal epithelial cell genes (TMEM178, FKBP5, CLCA1, SERPINB2 and periostin) in childhood asthma and their utility in predicting asthma severity, and atopic status. Seventy asthmatic children were included and further subdivided into mild, moderate and severe persistent asthma together with 30 apparently healthy children as a control group. All children were subjected to medical history taking, clinical examination. Nasal epithelial samples were collected for detection of epithelial cell genes (TMEM178, FKBP5, CLCA1, SERPINB2 and periostin) by real-time PCR.
Results
TMEM178 showed significant down-regulation in asthmatic children and its expression levels decreased significantly with the progression of asthma severity. CLCA1, SERPINB2 and periostin showed statistically significant up-regulation in asthmatic children, whereas FKBP5 was increased in asthmatic children but with non-significant up-regulation when compared with the control group. Regarding atopic status, relative gene expression levels of CLCA1, SERPINB2 and periostin were significantly up-regulated in atopic asthma.
Conclusion
Our findings suggest the role of nasal airways epithelial cells in predicting asthma severity and atopic status, as TMEM178 expression gained attention as a predictor of asthma severity. CLCA1, SERPINB2 and periostin expression were up-regulated not only in asthmatic children, but also in atopic asthma.
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4
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Wang R, Wang Y, Liao G, Chen B, Panettieri RA, Penn RB, Tang DD. Abi1 mediates airway smooth muscle cell proliferation and airway remodeling via Jak2/STAT3 signaling. iScience 2022; 25:103833. [PMID: 35198891 PMCID: PMC8851273 DOI: 10.1016/j.isci.2022.103833] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 12/10/2021] [Accepted: 01/21/2022] [Indexed: 11/05/2022] Open
Abstract
Asthma is a complex pulmonary disorder with multiple pathological mechanisms. A key pathological feature of chronic asthma is airway remodeling, which is largely attributed to airway smooth muscle (ASM) hyperplasia that contributes to thickening of the airway wall and further drives asthma pathology. The cellular processes that mediate ASM cell proliferation are not completely elucidated. Using multiple approaches, we demonstrate that the adapter protein Abi1 (Abelson interactor 1) is upregulated in ∼50% of ASM cell cultures derived from patients with asthma. Loss-of-function studies demonstrate that Abi1 regulates the activation of Jak2 (Janus kinase 2) and STAT3 (signal transducers and activators of transcription 3) as well as the proliferation of both nonasthmatic and asthmatic human ASM cell cultures. These findings identify Abi1 as a molecular switch that activates Jak2 kinase and STAT3 in ASM cells and demonstrate that a dysfunctional Abi1-associated pathway contributes to the progression of asthma.
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Affiliation(s)
- Ruping Wang
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY 12208, USA
| | - Yinna Wang
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY 12208, USA
| | - Guoning Liao
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY 12208, USA
| | - Bohao Chen
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Reynold A. Panettieri
- Department of Medicine, Rutgers Institute for Translational Medicine and Science, Robert Wood Johnson School of Medicine, New Brunswick, NJ 08901, USA
| | - Raymond B. Penn
- Department of Medicine, Center for Translational Medicine, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Dale D. Tang
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY 12208, USA
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5
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Suarez-Pajes E, Díaz-García C, Rodríguez-Pérez H, Lorenzo-Salazar JM, Marcelino-Rodríguez I, Corrales A, Zheng X, Callero A, Perez-Rodriguez E, Garcia-Robaina JC, González-Montelongo R, Flores C, Guillen-Guio B. Targeted analysis of genomic regions enriched in African ancestry reveals novel classical HLA alleles associated with asthma in Southwestern Europeans. Sci Rep 2021; 11:23686. [PMID: 34880287 PMCID: PMC8654850 DOI: 10.1038/s41598-021-02893-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 11/24/2021] [Indexed: 12/30/2022] Open
Abstract
Despite asthma has a considerable genetic component, an important proportion of genetic risks remain unknown, especially for non-European populations. Canary Islanders have the largest African genetic ancestry observed among Southwestern Europeans and the highest asthma prevalence in Spain. Here we examined broad chromosomal regions previously associated with an excess of African genetic ancestry in Canary Islanders, with the aim of identifying novel risk variants associated with asthma susceptibility. In a two-stage cases-control study, we revealed a variant within HLA-DQB1 significantly associated with asthma risk (rs1049213, meta-analysis p = 1.30 × 10–7, OR [95% CI] = 1.74 [1.41–2.13]) previously associated with asthma and broad allergic phenotype. Subsequent fine-mapping analyses of classical HLA alleles revealed a novel allele significantly associated with asthma protection (HLA-DQA1*01:02, meta-analysis p = 3.98 × 10–4, OR [95% CI] = 0.64 [0.50–0.82]) that had been linked to infectious and autoimmune diseases, and peanut allergy. HLA haplotype analyses revealed a novel haplotype DQA1*01:02-DQB1*06:04 conferring asthma protection (meta-analysis p = 4.71 × 10–4, OR [95% CI] = 0.47 [0.29– 0.73]).
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Affiliation(s)
- Eva Suarez-Pajes
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Claudio Díaz-García
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Héctor Rodríguez-Pérez
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Jose M Lorenzo-Salazar
- Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Itahisa Marcelino-Rodríguez
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Almudena Corrales
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Xiuwen Zheng
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Ariel Callero
- Allergy Unit, Hospital Universitario N.S. de Candelaria, Santa Cruz de Tenerife, Spain
| | - Eva Perez-Rodriguez
- Allergy Unit, Hospital Universitario N.S. de Candelaria, Santa Cruz de Tenerife, Spain
| | - Jose C Garcia-Robaina
- Allergy Unit, Hospital Universitario N.S. de Candelaria, Santa Cruz de Tenerife, Spain
| | | | - Carlos Flores
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain. .,Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain. .,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.
| | - Beatriz Guillen-Guio
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain. .,Department of Health Sciences, University of Leicester, Leicester, UK.
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6
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Aslam R, Shahid M, Bano I, Ayoub M, Sabar MF, Altaf S, Kousar S, Ghani MU, Husnain T, Shahid AA. Major histocompatibility complex class II polymorphic variants are associated with asthma predisposition in the Punjabi population of Lahore, Pakistan. THE CLINICAL RESPIRATORY JOURNAL 2021; 15:374-381. [PMID: 33211378 DOI: 10.1111/crj.13309] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 10/09/2020] [Accepted: 11/13/2020] [Indexed: 02/05/2023]
Abstract
INTRODUCTION Various genome wide association studies have manifested that Major Histocompatibility Complex (MHC) region on chromosome 6p21 houses many potential candidate genes for asthma. OBJECTIVE This Case-Control association study was planned to determine the association of 10 Single Nucleotide Polymorphisms (SNPs), residing within and around MHC genes' region on chromosome 6p21, with Asthma in Punjabi population of Lahore, Pakistan. METHODS A total of 161 subjects, 61 physician-diagnosed asthma patients and 100 age-matched healthy controls, were recruited from Lahore, a city in Punjab. Ten single nucleotide polymorphisms (SNPs) (rs9378249, rs2070600, rs404860, rs6689, rs1049124, rs1063355, rs1049225, rs1049219, rs7773955 and rs928976) located within or near AGER, NOTCH and HLA genes in MHC region, were genotyped in both patients and controls using single base extension reaction and capillary electrophoresis-based genetic analyser. Statistical models were applied using SHEsis Plus. Results were adjusted for various cofactors (age, gender and environment) and by applying multiple corrections. Haplotype and linkage disequilibrium analyses were performed on Haploview software v4.1. RESULTS Three of the studied SNPs rs1049124, rs1049219 and rs7773955 show independent significant association with asthma under allelic and genotypic models. Two of the haplotypes, H7 and H13, "CTAATTT" and "CCACTAT", respectively, for rs2070600, rs404860, rs6689, rs1049124, rs1063355, rs1049219 and rs7773955, are found to be significantly associated with the disease. CONCLUSION This study reports association of SNP variants residing on HLA-DQB1 and HLA-DQA2 genes and haplotypes H7 and H13 on genomic region 6p21 with Asthma in the Punjabi population of Lahore, Pakistan.
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Affiliation(s)
- Raheela Aslam
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Mariam Shahid
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Iqbal Bano
- The Children's Hospital and The Institute of Child Health, Pediatric Pulmonology, Lahore, Pakistan
| | - Muhammad Ayoub
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | | | - Saba Altaf
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Samra Kousar
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Muhammad Usman Ghani
- Centre for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Tayyab Husnain
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Ahmad Ali Shahid
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
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7
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Aslam R, Shahid M, Bano I, Ayoub M, Sabar MF, Altaf S, Kousar S, Ghani MU, Husnain T, Shahid AA. Major histocompatibility complex class II polymorphic variants are associated with asthma predisposition in the Punjabi population of Lahore, Pakistan. THE CLINICAL RESPIRATORY JOURNAL 2021. [DOI: https:/doi.org/10.1111/crj.13309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Raheela Aslam
- Centre of Excellence in Molecular Biology University of the Punjab Lahore Pakistan
| | - Mariam Shahid
- Centre of Excellence in Molecular Biology University of the Punjab Lahore Pakistan
| | - Iqbal Bano
- The Children’s Hospital and The Institute of Child Health, Pediatric Pulmonology Lahore Pakistan
| | - Muhammad Ayoub
- Centre of Excellence in Molecular Biology University of the Punjab Lahore Pakistan
| | | | - Saba Altaf
- Centre of Excellence in Molecular Biology University of the Punjab Lahore Pakistan
| | - Samra Kousar
- Centre of Excellence in Molecular Biology University of the Punjab Lahore Pakistan
| | | | - Tayyab Husnain
- Centre of Excellence in Molecular Biology University of the Punjab Lahore Pakistan
| | - Ahmad Ali Shahid
- Centre of Excellence in Molecular Biology University of the Punjab Lahore Pakistan
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Chen YC, Tsai YH, Wang CC, Liu SF, Chen TW, Fang WF, Lee CP, Hsu PY, Chao TY, Wu CC, Wei YF, Chang HC, Tsen CC, Chang YP, Lin MC. Epigenome-wide association study on asthma and chronic obstructive pulmonary disease overlap reveals aberrant DNA methylations related to clinical phenotypes. Sci Rep 2021; 11:5022. [PMID: 33658578 PMCID: PMC7930096 DOI: 10.1038/s41598-021-83185-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 01/06/2021] [Indexed: 12/15/2022] Open
Abstract
We hypothesized that epigenetics is a link between smoking/allergen exposures and the development of Asthma and chronic obstructive pulmonary disease (ACO). A total of 75 of 228 COPD patients were identified as ACO, which was independently associated with increased exacerbations. Microarray analysis identified 404 differentially methylated loci (DML) in ACO patients, and 6575 DML in those with rapid lung function decline in a discovery cohort. In the validation cohort, ACO patients had hypermethylated PDE9A (+ 30,088)/ZNF323 (− 296), and hypomethylated SEPT8 (− 47) genes as compared with either pure COPD patients or healthy non-smokers. Hypermethylated TIGIT (− 173) gene and hypomethylated CYSLTR1 (+ 348)/CCDC88C (+ 125,722)/ADORA2B (+ 1339) were associated with severe airflow limitation, while hypomethylated IFRD1 (− 515) gene with frequent exacerbation in all the COPD patients. Hypermethylated ZNF323 (− 296) / MPV17L (+ 194) and hypomethylated PTPRN2 (+ 10,000) genes were associated with rapid lung function decline. In vitro cigarette smoke extract and ovalbumin concurrent exposure resulted in specific DNA methylation changes of the MPV17L / ZNF323 genes, while 5-aza-2′-deoxycytidine treatment reversed promoter hypermethylation-mediated MPV17L under-expression accompanied with reduced apoptosis and decreased generation of reactive oxygen species. Aberrant DNA methylations may constitute a determinant for ACO, and provide a biomarker of airflow limitation, exacerbation, and lung function decline.
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Affiliation(s)
- Yung-Che Chen
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Niao-Sung District, 123, Ta-Pei Rd, Kaohsiung, 83301, Taiwan. .,Medical Department, College of Medicine, Chang Gung University, Taoyuan, Taiwan.
| | - Ying-Huang Tsai
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Niao-Sung District, 123, Ta-Pei Rd, Kaohsiung, 83301, Taiwan
| | - Chin-Chou Wang
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Niao-Sung District, 123, Ta-Pei Rd, Kaohsiung, 83301, Taiwan.,Chang Gung University of Science and Technology, Chia-Yi, Taiwan
| | - Shih-Feng Liu
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Niao-Sung District, 123, Ta-Pei Rd, Kaohsiung, 83301, Taiwan.,Department of Respiratory Therapy, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Ting-Wen Chen
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Bioinformatics Center, Chang Gung University, Taoyuan, Taiwan.,Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 30068, Taiwan
| | - Wen-Feng Fang
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Niao-Sung District, 123, Ta-Pei Rd, Kaohsiung, 83301, Taiwan.,Chang Gung University of Science and Technology, Chia-Yi, Taiwan
| | - Chiu-Ping Lee
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Niao-Sung District, 123, Ta-Pei Rd, Kaohsiung, 83301, Taiwan
| | - Po-Yuan Hsu
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Niao-Sung District, 123, Ta-Pei Rd, Kaohsiung, 83301, Taiwan
| | - Tung-Ying Chao
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Niao-Sung District, 123, Ta-Pei Rd, Kaohsiung, 83301, Taiwan
| | - Chao-Chien Wu
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Niao-Sung District, 123, Ta-Pei Rd, Kaohsiung, 83301, Taiwan
| | - Yu-Feng Wei
- Department of Internal Medicine, E-Da Hospital, I-Shou University, Kaohsiung, Taiwan
| | - Huang-Chih Chang
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Niao-Sung District, 123, Ta-Pei Rd, Kaohsiung, 83301, Taiwan
| | - Chia-Cheng Tsen
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Niao-Sung District, 123, Ta-Pei Rd, Kaohsiung, 83301, Taiwan
| | - Yu-Ping Chang
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Niao-Sung District, 123, Ta-Pei Rd, Kaohsiung, 83301, Taiwan
| | - Meng-Chih Lin
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Niao-Sung District, 123, Ta-Pei Rd, Kaohsiung, 83301, Taiwan. .,Medical Department, College of Medicine, Chang Gung University, Taoyuan, Taiwan.
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9
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Aslam R, Shahid M, Bano I, Ayoub M, Sabar MF, Altaf S, Kousar S, Ghani MU, Husnain T, Shahid AA. Major histocompatibility complex class II polymorphic variants are associated with asthma predisposition in the Punjabi population of Lahore, Pakistan. THE CLINICAL RESPIRATORY JOURNAL 2020. [DOI: https://doi.org/10.1111/crj.13309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Raheela Aslam
- Centre of Excellence in Molecular Biology University of the Punjab Lahore Pakistan
| | - Mariam Shahid
- Centre of Excellence in Molecular Biology University of the Punjab Lahore Pakistan
| | - Iqbal Bano
- The Children’s Hospital and The Institute of Child Health, Pediatric Pulmonology Lahore Pakistan
| | - Muhammad Ayoub
- Centre of Excellence in Molecular Biology University of the Punjab Lahore Pakistan
| | | | - Saba Altaf
- Centre of Excellence in Molecular Biology University of the Punjab Lahore Pakistan
| | - Samra Kousar
- Centre of Excellence in Molecular Biology University of the Punjab Lahore Pakistan
| | | | - Tayyab Husnain
- Centre of Excellence in Molecular Biology University of the Punjab Lahore Pakistan
| | - Ahmad Ali Shahid
- Centre of Excellence in Molecular Biology University of the Punjab Lahore Pakistan
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10
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Understanding the genetics of asthma and implications for clinical practice. J Am Assoc Nurse Pract 2020; 31:384-387. [PMID: 31290808 DOI: 10.1097/jxx.0000000000000246] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Asthma is one of the most common heritable diseases globally, with variable clinical expression and response to treatment that is attributed to underlying genetic differences. Hundreds of loci on multiple chromosomes are associated with asthma. Although routine genetic screening is not recommended, testing for medication responsiveness might soon play a role in clinical management. Pharmacogenetic research remains early stage but has demonstrated potential for both clinical and cost effectiveness. Furthermore, recognition of clinically apparent asthma phenotypes, the result of genetic and environmental interactions, can help to inform treatment decisions. Phenotypes are divided into two broad categories of atopic and nonatopic disease, with further subdivisions that are associated with clinical presentation patterns and responsiveness to treatment. In general, earlier onset and allergic disease will respond well to traditional therapy with inhaled corticosteroids (ICSs) and leukotrienes because these medications target inflammatory pathways for allergic disease. However, patients with late-onset, symptom predominant (lacking inflammation), and obese asthma might be resistant to standard therapy and may require treatment modification. These patients are at risk for overuse of ICSs with poor response and may benefit more by use of long-acting beta agonists, long-acting muscarinic agonists, weight reduction, and exercise.
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11
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Zhorina Y, Abramovskikh S, Ignatova G, Ploshchanskay O. Analysis of associations of polymorphisms in the genes coding for L4, IL10, IL13 with the development of atopic bronchial asthma and its remission. BULLETIN OF RUSSIAN STATE MEDICAL UNIVERSITY 2019. [DOI: 10.24075/brsmu.2019.067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Bronchial asthma is a multifactorial disease underpinned by chronic inflammation. The atopic phenotype of BA implies the presence of similar molecular mechanisms of pathogenesis between the patients. The aim of this study was to analyze the associations between the development of atopic BA/its remission and the following polymorphisms of interleukin genes: IL4 (rs2243250; C-589T), IL10 (rs1800896; G-1082A; rs1800872; C-592A), and IL13 (rs20541; Arg130Gln). Using allele-specific polymerase chain reaction (PCR), we studied the listed SNPs in the mixed urban sample of patients with BA (n = 53) and the controls (n = 30) residing in South Ural. The analysis revealed that genotype АА of IL10 (rs1800872) occurred more frequently in the control group (23.3%) than in the patients with atopic BA (5.7%) (OR = 0.197; 95% CI [0.047–0.832]; р = 0.031). No differences in genotype frequencies were observed between the patients with atopic BA and the controls for other studied polymorphisms. Our study failed to demonstrate the association of the listed polymorphisms and BA remission.
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Affiliation(s)
- Yu.V. Zhorina
- South Ural State Medical University, Chelyabinsk, Russia
| | | | - G.L. Ignatova
- South Ural State Medical University, Chelyabinsk, Russia
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12
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Akhavanakbari G, Babapour B, Alipour MR, Keyhanmanesh R, Ahmadi M, Aslani MR. Effect of high fat diet on NF-кB microRNA146a negative feedback loop in ovalbumin-sensitized rats. Biofactors 2019; 45:75-84. [PMID: 30521085 DOI: 10.1002/biof.1466] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Revised: 08/23/2018] [Accepted: 09/10/2018] [Indexed: 02/01/2023]
Abstract
The present study aimed to investigate the role of microRNA-146a and its adapter proteins [interleukin-1 receptor-associated kinase 1 (IRAK1) and tumor necrosis factor (TNF) receptor-associated factor 6 (TRAF6)] in the pathogenesis of ovalbumin (OVA)-sensitized rats in association with the diet-induced obesity condition. Twenty male Wistar rats were divided into four groups: control with normal diet (ND), OVA-sensitized with normal diet (S + ND), high-fat diet (HFD), and OVA-sensitized with high-fat diet (S + HFD). All the animals were fed for 8 weeks with standard pelts or high-fat diet, and were then sensitized and challenged with OVA or saline for another 4 weeks. The tracheal responsiveness to methacholine, serum protein levels, and lipid profile levels was measured by the ELISA method. Moreover, the gene expression level of microRNA-146a (miR-146a) was measured in the lung tissue of the rats using the real-time PCR method. Maximum response to methacholin increased in the S + HFD group in compared with ND, S + ND, and HFD groups (P < 0.05 to P < 0.001). Moreover, in the S + HFD group the mRNA expression levels of miRNA-146a increased in the lung tissue (P < 0.001). In addition, the protein analysis results showed that IRAK1, TRAF6, NF-kB, and IL-1β protein levels were high in the S + HFD group compared to the ND and HFD groups; however, in compared with the S + ND group, only the IL-1β protein level was higher in the S + HFD group (P < 0.05). These results suggest that a defect in the NF-kB-miR-146a negative feedback loop may be involved in the pathogenesis of obesity associated with OVA-sensitized condition. © 2018 BioFactors, 45(1):75-84, 2019.
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Affiliation(s)
- Godrat Akhavanakbari
- Department of Anesthesiology, Faculty of Medicine, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Behzad Babapour
- Department of Cardiology, Faculty of Medicine, Ardabil University of Medical Sciences, Ardabil, Iran
| | | | - Rana Keyhanmanesh
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mahdi Ahmadi
- Faculty of Medicine, Department of Physiology, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Reza Aslani
- Lung Inflammatory Diseases Research Center, Department of Physiology, Ardabil University of Medical Sciences, Ardabil, Iran
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13
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Pandey G, Pandey OP, Rogers AJ, Ahsen ME, Hoffman GE, Raby BA, Weiss ST, Schadt EE, Bunyavanich S. A Nasal Brush-based Classifier of Asthma Identified by Machine Learning Analysis of Nasal RNA Sequence Data. Sci Rep 2018; 8:8826. [PMID: 29891868 PMCID: PMC5995932 DOI: 10.1038/s41598-018-27189-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 05/25/2018] [Indexed: 12/31/2022] Open
Abstract
Asthma is a common, under-diagnosed disease affecting all ages. We sought to identify a nasal brush-based classifier of mild/moderate asthma. 190 subjects with mild/moderate asthma and controls underwent nasal brushing and RNA sequencing of nasal samples. A machine learning-based pipeline identified an asthma classifier consisting of 90 genes interpreted via an L2-regularized logistic regression classification model. This classifier performed with strong predictive value and sensitivity across eight test sets, including (1) a test set of independent asthmatic and control subjects profiled by RNA sequencing (positive and negative predictive values of 1.00 and 0.96, respectively; AUC of 0.994), (2) two independent case-control cohorts of asthma profiled by microarray, and (3) five cohorts with other respiratory conditions (allergic rhinitis, upper respiratory infection, cystic fibrosis, smoking), where the classifier had a low to zero misclassification rate. Following validation in large, prospective cohorts, this classifier could be developed into a nasal biomarker of asthma.
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Affiliation(s)
- Gaurav Pandey
- Icahn Institute for Genomics and Multiscale Biology and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Om P Pandey
- Icahn Institute for Genomics and Multiscale Biology and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Angela J Rogers
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Mehmet E Ahsen
- Icahn Institute for Genomics and Multiscale Biology and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gabriel E Hoffman
- Icahn Institute for Genomics and Multiscale Biology and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Benjamin A Raby
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham & Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Scott T Weiss
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham & Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Eric E Schadt
- Icahn Institute for Genomics and Multiscale Biology and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Supinda Bunyavanich
- Icahn Institute for Genomics and Multiscale Biology and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Division of Allergy & Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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14
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Licari A, Castagnoli R, Brambilla I, Marseglia A, Tosca MA, Marseglia GL, Ciprandi G. Asthma Endotyping and Biomarkers in Childhood Asthma. PEDIATRIC ALLERGY IMMUNOLOGY AND PULMONOLOGY 2018; 31:44-55. [PMID: 30069422 PMCID: PMC6069590 DOI: 10.1089/ped.2018.0886] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 03/23/2018] [Indexed: 12/17/2022]
Abstract
Childhood asthma represents a heterogeneous challenging disease, in particular in its severe forms. The identification of different asthma phenotypes has stimulated research in underlying molecular mechanisms, such as the endotypes, and paved the way to the search for related specific biomarkers, which may guide diagnosis, management, and predict response to treatment. A limited number of biomarkers are currently available in clinical practice in the pediatric population, mostly reflecting type 2-high airway inflammation. The identification of biomarkers of childhood asthma is an active area of research that holds a potential great clinical utility and may represent a step forward toward tailored management and therapy: the so-called Precision Medicine. The aim of the present review is to provide an updated overview of asthma endotyping, mostly focusing on novel noninvasive biomarkers in childhood asthma.
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Affiliation(s)
- Amelia Licari
- Pediatric Clinic, Fondazione IRCCS San Matteo, Pavia, Italy
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15
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Cai X, Lin M, Cao S, Liu Y, Lin N. The association of RAR-related orphan receptor A (RORA) gene polymorphisms with the risk of asthma. Ann Hum Genet 2017; 82:158-164. [PMID: 29282706 DOI: 10.1111/ahg.12238] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 11/03/2017] [Accepted: 11/20/2017] [Indexed: 12/29/2022]
Abstract
Asthma is a common, heterogeneous chronic respiratory disease characterized by chronic inflammation of the airway, airway hyperreactivity, and airway remodeling. The RAR-related orphan receptor A (RORA) gene has been identified for the pathogenesis of asthma. The purpose of this research was to investigate the relationship between RORA gene polymorphisms and asthma susceptibility in the Chinese Zhuang population. This was a case-control study including 231 children with asthma and 343 healthy controls. The RORA gene polymorphisms were measured by the polymerase chain reaction-ligase detection reaction genotyping assays and confirmed by sequencing. The distribution of the genotype frequencies of the RORA rs11071559 C>T was significantly different in the group of cases and the healthy children (P < 0.05). By haplotype analyses, the haplotype TT (rs7164773/rs11071559) was statistically significant between asthmatics and nonasthmatics, but the association was not significant after correction for multiple comparisons. Our results provided evidence that the RORA rs11071559C>T polymorphism was associated with an elevated susceptibility to pediatric asthma in the Chinese Zhuang population.
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Affiliation(s)
- Xulong Cai
- Youjiang Medical University for Nationalities, Baise, China
| | - Mali Lin
- Youjiang Medical University for Nationalities, Baise, China
| | - Shan Cao
- Youjiang Medical University for Nationalities, Baise, China
| | - Yunguang Liu
- Department of Pediatrics, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Na Lin
- Department of Pediatrics, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
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16
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Gupta J, Johansson E, Bernstein JA, Chakraborty R, Khurana Hershey GK, Rothenberg ME, Mersha TB. Resolving the etiology of atopic disorders by using genetic analysis of racial ancestry. J Allergy Clin Immunol 2016; 138:676-699. [PMID: 27297995 PMCID: PMC5014679 DOI: 10.1016/j.jaci.2016.02.045] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 02/09/2016] [Accepted: 02/25/2016] [Indexed: 12/23/2022]
Abstract
Atopic dermatitis (AD), food allergy, allergic rhinitis, and asthma are common atopic disorders of complex etiology. The frequently observed atopic march from early AD to asthma, allergic rhinitis, or both later in life and the extensive comorbidity of atopic disorders suggest common causal mechanisms in addition to distinct ones. Indeed, both disease-specific and shared genomic regions exist for atopic disorders. Their prevalence also varies among races; for example, AD and asthma have a higher prevalence in African Americans when compared with European Americans. Whether this disparity stems from true genetic or race-specific environmental risk factors or both is unknown. Thus far, the majority of the genetic studies on atopic diseases have used populations of European ancestry, limiting their generalizability. Large-cohort initiatives and new analytic methods, such as admixture mapping, are currently being used to address this knowledge gap. Here we discuss the unique and shared genetic risk factors for atopic disorders in the context of ancestry variations and the promise of high-throughput "-omics"-based systems biology approach in providing greater insight to deconstruct their genetic and nongenetic etiologies. Future research will also focus on deep phenotyping and genotyping of diverse racial ancestry, gene-environment, and gene-gene interactions.
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Affiliation(s)
- Jayanta Gupta
- Division of Asthma Research, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio
| | - Elisabet Johansson
- Division of Asthma Research, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio
| | - Jonathan A Bernstein
- Division of Immunology/Allergy Section, Department of Internal Medicine, University of Cincinnati, Cincinnati, Ohio
| | - Ranajit Chakraborty
- Center for Computational Genomics, Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, Fort Worth, Tex
| | - Gurjit K Khurana Hershey
- Division of Asthma Research, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio
| | - Marc E Rothenberg
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio
| | - Tesfaye B Mersha
- Division of Asthma Research, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio.
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17
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Mersha TB. Mapping asthma-associated variants in admixed populations. Front Genet 2015; 6:292. [PMID: 26483834 PMCID: PMC4586512 DOI: 10.3389/fgene.2015.00292] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 09/03/2015] [Indexed: 12/19/2022] Open
Abstract
Admixed populations arise when two or more previously isolated populations interbreed. Mapping asthma susceptibility loci in an admixed population using admixture mapping (AM) involves screening the genome of individuals of mixed ancestry for chromosomal regions that have a higher frequency of alleles from a parental population with higher asthma risk as compared with parental population with lower asthma risk. AM takes advantage of the admixture created in populations of mixed ancestry to identify genomic regions where an association exists between genetic ancestry and asthma (in contrast to between the genotype of the marker and asthma). The theory behind AM is that chromosomal segments of affected individuals contain a significantly higher-than-average proportion of alleles from the high-risk parental population and thus are more likely to harbor disease-associated loci. Criteria to evaluate the applicability of AM as a gene mapping approach include: (1) the prevalence of the disease differences in ancestral populations from which the admixed population was formed; (2) a measurable difference in disease-causing alleles between the parental populations; (3) reduced linkage disequilibrium (LD) between unlinked loci across chromosomes and strong LD between neighboring loci; (4) a set of markers with noticeable allele-frequency differences between parental populations that contributes to the admixed population (single nucleotide polymorphisms (SNPs) are the markers of choice because they are abundant, stable, relatively cheap to genotype, and informative with regard to the LD structure of chromosomal segments); and (5) there is an understanding of the extent of segmental chromosomal admixtures and their interactions with environmental factors. Although genome-wide association studies have contributed greatly to our understanding of the genetic components of asthma, the large and increasing degree of admixture in populations across the world create many challenges for further efforts to map disease-causing genes. This review, summarizes the historical context of admixed populations and AM, and considers current opportunities to use AM to map asthma genes. In addition, we provide an overview of the potential limitations and future directions of AM in biomedical research, including joint admixture and association mapping for asthma and asthma-related disorders.
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Affiliation(s)
- Tesfaye B Mersha
- Division of Asthma Research, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati Cincinnati, OH, USA
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18
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Larkin EK, Hartert TV. Genes associated with RSV lower respiratory tract infection and asthma: the application of genetic epidemiological methods to understand causality. Future Virol 2015; 10:883-897. [PMID: 26478738 DOI: 10.2217/fvl.15.55] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Infants with respiratory syncytial virus (RSV) lower respiratory tract infections (LRIs) are at increased risk for childhood asthma. The objectives of this article are to review the genes associated with both RSV LRI and asthma, review analytic approaches to assessing shared genetic risk and propose a future perspective on how these approaches can help us to understand the role of infant RSV infection as both an important risk factor for asthma and marker of shared genetic etiology between the two conditions. The review of shared genes and thus pathways associated with severity of response to RSV infection and asthma risk can help us to understand mechanisms of disease and ultimately propose new and novel targets for primary prevention of both diseases.
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Affiliation(s)
- Emma K Larkin
- Department of Medicine, Division of Allergy, Pulmonary & Critical Care Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Tina V Hartert
- Department of Medicine, Division of Allergy, Pulmonary & Critical Care Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
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19
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Guibas GV, Megremis S, West P, Papadopoulos NG. Contributing factors to the development of childhood asthma: working toward risk minimization. Expert Rev Clin Immunol 2015; 11:721-35. [PMID: 25873298 DOI: 10.1586/1744666x.2015.1035649] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Asthma is the most common chronic disease in childhood, and considerable research has been undertaken to find ways to prevent its development and reduce its prevalence. For such interventions to be successful, risk factors for asthma emergence should be identified and clearly defined. Data are robust for some of them, including atopy, viral infections and exposure to airborne irritants, whereas it is less conclusive for others, such as aeroallergen exposure and bacterial infections. Several interventions for asthma prevention, including avoidance and pharmacotherapy, have been attempted. However, most of them have furnished equivocal results. Various issues hinder the establishment of risk factors for asthma development and reduce the effectiveness of interventions, including the complexity of the disease and the fluidity of the developing systems in childhood. In this review, we revisit the evidence on pediatric asthma risk factors and prevention and discuss issues that perplex this field.
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Affiliation(s)
- George V Guibas
- Centre for Pediatrics and Child Health, Institute of Human Development, University of Manchester, Manchester, UK
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20
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Abstract
Genome-wide association studies (GWAS) have been employed in the field of allergic disease, and significant associations have been published for nearly 100 asthma genes/loci. An outcome of GWAS in allergic disease has been the formation of national and international collaborations leading to consortia meta-analyses, and an appreciation for the specificity of genetic associations to sub-phenotypes of allergic disease. Molecular genetics has undergone a technological revolution, leading to next-generation sequencing strategies that are increasingly employed to hone in on the causal variants associated with allergic diseases. Unmet needs include the inclusion of diverse cohorts and strategies for managing big data.
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Affiliation(s)
- Romina A Ortiz
- Department of Medicine, The Johns Hopkins Asthma and Allergy Center, 5501 Hopkins Bayview Circle, Room 3A.62, Baltimore, MD 21224, USA
| | - Kathleen C Barnes
- Department of Medicine, The Johns Hopkins Asthma and Allergy Center, 5501 Hopkins Bayview Circle, Room 3A.62, Baltimore, MD 21224, USA.
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21
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Systems biology of asthma and allergic diseases: a multiscale approach. J Allergy Clin Immunol 2014; 135:31-42. [PMID: 25468194 DOI: 10.1016/j.jaci.2014.10.015] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 10/10/2014] [Accepted: 10/15/2014] [Indexed: 01/15/2023]
Abstract
Systems biology is an approach to understanding living systems that focuses on modeling diverse types of high-dimensional interactions to develop a more comprehensive understanding of complex phenotypes manifested by the system. High-throughput molecular, cellular, and physiologic profiling of populations is coupled with bioinformatic and computational techniques to identify new functional roles for genes, regulatory elements, and metabolites in the context of the molecular networks that define biological processes associated with system physiology. Given the complexity and heterogeneity of asthma and allergic diseases, a systems biology approach is attractive, as it has the potential to model the myriad connections and interdependencies between genetic predisposition, environmental perturbations, regulatory intermediaries, and molecular sequelae that ultimately lead to diverse disease phenotypes and treatment responses across individuals. The increasing availability of high-throughput technologies has enabled system-wide profiling of the genome, transcriptome, epigenome, microbiome, and metabolome, providing fodder for systems biology approaches to examine asthma and allergy at a more holistic level. In this article we review the technologies and approaches for system-wide profiling, as well as their more recent applications to asthma and allergy. We discuss approaches for integrating multiscale data through network analyses and provide perspective on how individually captured health profiles will contribute to more accurate systems biology views of asthma and allergy.
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22
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Zhao YF, Luo YM, Xiong W, Wu XL. Genetic variation in ORMDL3 gene may contribute to the risk of asthma: a meta-analysis. Hum Immunol 2014; 75:960-7. [PMID: 25167772 DOI: 10.1016/j.humimm.2014.08.202] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 08/18/2014] [Accepted: 08/18/2014] [Indexed: 01/11/2023]
Abstract
BACKGROUND Since the first genome-wide association study report of an association between the ORMDL3 rs7216389 polymorphism and asthma, many studies have been carried out to establish its role in asthma susceptibility among different ethnic groups. However, results have not been consistent across all studies, compelling us to conduct the present meta-analysis. METHODS A literature search for eligible studies published before January 20, 2014 was conducted in the MEDLINE, EMBASE, and CNKI databases. The association was assessed using pooled crude odds ratios (ORs) with their corresponding 95% confidence intervals (CIs). RESULTS A total of 18 individual studies in 15 publications (total 7904 asthma patients and 10,874 healthy controls) were included in the meta-analysis. A meta-analysis of all included studies suggested that there was a highly significant risk effect conferred by the rs7216389*T allele on asthma susceptibility. In addition, we performed stratified analyses to evaluate ethnicity-specific and age-specific effects. Our subgroup analyses based on ethnicity and age-of-onset confirmed the role of the ORMDL3 rs7216389 polymorphism in conferring susceptibility to both childhood- and adult-onset asthma, especially in Caucasians and Asians. CONCLUSIONS The results of this meta-analysis firmly established that genetic variation at the rs7216389 locus, which controls the expression of the ORMDL3, may be a major, independent predisposing factor for asthma in ethnically diverse populations. However, further systematic studies are needed to determine the underlying mechanisms of this association.
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Affiliation(s)
- Yun-Feng Zhao
- Department of Respiratory Medicine, Pudong New Area Gongli Hospital, Shanghai, China
| | - Yi-Min Luo
- Diagnostics Teaching and Research Section, Southeast University Medical College, Nanjing 210009, China
| | - Wei Xiong
- Department of Respiratory Medicine, Pudong New Area Gongli Hospital, Shanghai, China
| | - Xue-Ling Wu
- Institute of Respiratory Medicine, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China.
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23
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Antioxidant defense enzyme genes and asthma susceptibility: gender-specific effects and heterogeneity in gene-gene interactions between pathogenetic variants of the disease. BIOMED RESEARCH INTERNATIONAL 2014; 2014:708903. [PMID: 24895604 PMCID: PMC4026955 DOI: 10.1155/2014/708903] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2014] [Revised: 04/05/2014] [Accepted: 04/07/2014] [Indexed: 12/15/2022]
Abstract
Oxidative stress resulting from an increased amount of reactive oxygen species and an imbalance between oxidants and antioxidants plays an important role in the pathogenesis of asthma. The present study tested the hypothesis that genetic susceptibility to allergic and nonallergic variants of asthma is determined by complex interactions between genes encoding antioxidant defense enzymes (ADE). We carried out a comprehensive analysis of the associations between adult asthma and 46 single nucleotide polymorphisms of 34 ADE genes and 12 other candidate genes of asthma in Russian population using set association analysis and multifactor dimensionality reduction approaches. We found for the first time epistatic interactions between ADE genes underlying asthma susceptibility and the genetic heterogeneity between allergic and nonallergic variants of the disease. We identified GSR (glutathione reductase) and PON2 (paraoxonase 2) as novel candidate genes for asthma susceptibility. We observed gender-specific effects of ADE genes on the risk of asthma. The results of the study demonstrate complexity and diversity of interactions between genes involved in oxidative stress underlying susceptibility to allergic and nonallergic asthma.
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