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Szalus K, Zysk W, Gleń J, Zabłotna M, Nowicki RJ, Trzeciak M. The Associations of Single Nucleotide Polymorphisms of the COL3A1, COL6A5, and COL8A1 Genes with Atopic Dermatitis. J Pers Med 2023; 13:jpm13040661. [PMID: 37109047 PMCID: PMC10146150 DOI: 10.3390/jpm13040661] [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: 03/20/2023] [Revised: 04/06/2023] [Accepted: 04/10/2023] [Indexed: 04/29/2023] Open
Abstract
The pathophysiology of atopic dermatitis (AD) is complex, multifactorial, and not fully understood. Genes encoding collagens, the most abundant proteins in the extracellular matrix (ECM), may play a potential role in the pathogenesis of AD. Our study aimed to estimate the associations between Col3A1/rs1800255, Col6A5 /29rs12488457, and Col8A1/rs13081855 polymorphisms and the occurrence, course, and features of AD in the Polish population. Blood samples were collected from 157 patients with AD and 111 healthy volunteers. The genotype distribution of the investigated collagens genes did not differ significantly between the AD and control subjects (p > 0.05). The AA genotype of Col3A1/rs1800255 was significantly associated with the occurrence of mild SCORAD (OR = 0.16; 95% Cl: 0.03-0.78; p = 0.02) and mild pruritus (OR = 18.5; 95% Cl: 3.48-98.40; p = 0.0006), while the GG genotype was significantly associated with severe SCORAD (OR = 6.6; 95% Cl: 1.23-32.35; p = 0.03). Regarding Col6A5/29rs12488457 polymorphism, the average SCORAD score was significantly lower in the group of patients with genotype AA than in patients with the AC genotype (39.8 vs. 53.4; p = 0.04). Nevertheless, both average SCORAD scores were high, and represent the moderate and severe grades of the diseases, respectively. The single nucleotide polymorphisms (SNPs) of COL3A1/ rs1800255 and Col6A5/29rs12488457 seem to be associated with AD courses and symptoms, suggesting new disease biomarkers. The modulation of collagens, the major component of the ECM, may serve as a therapeutic target of AD in the future.
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Affiliation(s)
- Krzysztof Szalus
- Department of Dermatology, Venereology and Allergology, Faculty of Medicine, Medical University of Gdansk, 80-214 Gdańsk, Poland
| | - Weronika Zysk
- Dermatological Students Scientific Association, Department of Dermatology, Venereology and Allergology, Faculty of Medicine, Medical University of Gdansk, 80-214 Gdańsk, Poland
| | - Jolanta Gleń
- Department of Dermatology, Venereology and Allergology, Faculty of Medicine, Medical University of Gdansk, 80-214 Gdańsk, Poland
| | - Monika Zabłotna
- Department of Dermatology, Venereology and Allergology, Faculty of Medicine, Medical University of Gdansk, 80-214 Gdańsk, Poland
| | - Roman J Nowicki
- Department of Dermatology, Venereology and Allergology, Faculty of Medicine, Medical University of Gdansk, 80-214 Gdańsk, Poland
| | - Magdalena Trzeciak
- Department of Dermatology, Venereology and Allergology, Faculty of Medicine, Medical University of Gdansk, 80-214 Gdańsk, Poland
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Kozlik-Siwiec P, Buregwa-Czuma S, Zawlik I, Dziedzina S, Myszka A, Zuk-Kuwik J, Siwiec-Kozlik A, Zarychta J, Okon K, Zareba L, Soja J, Jakiela B, Kepski M, Bazan JG, Bazan-Socha S. Co-Expression Analysis of Airway Epithelial Transcriptome in Asthma Patients with Eosinophilic vs. Non-Eosinophilic Airway Infiltration. Int J Mol Sci 2023; 24:3789. [PMID: 36835202 PMCID: PMC9959255 DOI: 10.3390/ijms24043789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/27/2023] [Accepted: 02/07/2023] [Indexed: 02/16/2023] Open
Abstract
Asthma heterogeneity complicates the search for targeted treatment against airway inflammation and remodeling. We sought to investigate relations between eosinophilic inflammation, a phenotypic feature frequent in severe asthma, bronchial epithelial transcriptome, and functional and structural measures of airway remodeling. We compared epithelial gene expression, spirometry, airway cross-sectional geometry (computed tomography), reticular basement membrane thickness (histology), and blood and bronchoalveolar lavage (BAL) cytokines of n = 40 moderate to severe eosinophilic (EA) and non-eosinophilic asthma (NEA) patients distinguished by BAL eosinophilia. EA patients showed a similar extent of airway remodeling as NEA but had an increased expression of genes involved in the immune response and inflammation (e.g., KIR3DS1), reactive oxygen species generation (GYS2, ATPIF1), cell activation and proliferation (ANK3), cargo transporting (RAB4B, CPLX2), and tissue remodeling (FBLN1, SOX14, GSN), and a lower expression of genes involved in epithelial integrity (e.g., GJB1) and histone acetylation (SIN3A). Genes co-expressed in EA were involved in antiviral responses (e.g., ATP1B1), cell migration (EPS8L1, STOML3), cell adhesion (RAPH1), epithelial-mesenchymal transition (ASB3), and airway hyperreactivity and remodeling (FBN3, RECK), and several were linked to asthma in genome- (e.g., MRPL14, ASB3) or epigenome-wide association studies (CLC, GPI, SSCRB4, STRN4). Signaling pathways inferred from the co-expression pattern were associated with airway remodeling (e.g., TGF-β/Smad2/3, E2F/Rb, and Wnt/β-catenin).
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Affiliation(s)
- Pawel Kozlik-Siwiec
- Department of Internal Medicine, Jagiellonian University Medical College, 31-066 Krakow, Poland
- Haematology Clinical Department, University Hospital, 31-501 Krakow, Poland
| | - Sylwia Buregwa-Czuma
- College of Natural Sciences, Institute of Computer Science, University of Rzeszow, Pigonia 1, 35-310 Rzeszow, Poland
| | - Izabela Zawlik
- Centre for Innovative Research in Medical and Natural Sciences, Institute of Medical Sciences, Medical College, University of Rzeszow, Kopisto 2a, 35-959 Rzeszow, Poland
| | - Sylwia Dziedzina
- Department of Internal Medicine, Jagiellonian University Medical College, 31-066 Krakow, Poland
| | - Aleksander Myszka
- Institute of Medical Sciences, Medical College, University of Rzeszow, Kopisto 2a, 35-959 Rzeszow, Poland
| | - Joanna Zuk-Kuwik
- Haematology Clinical Department, University Hospital, 31-501 Krakow, Poland
- Haematology Department, Jagiellonian University Medical College, 31-501 Krakow, Poland
| | | | - Jacek Zarychta
- Department of Internal Medicine, Jagiellonian University Medical College, 31-066 Krakow, Poland
- Pulmonary Hospital, 34-736 Zakopane, Poland
| | - Krzysztof Okon
- Department of Pathology, Jagiellonian University Medical College, 33-332 Krakow, Poland
| | - Lech Zareba
- College of Natural Sciences, Institute of Computer Science, University of Rzeszow, Pigonia 1, 35-310 Rzeszow, Poland
| | - Jerzy Soja
- Department of Internal Medicine, Jagiellonian University Medical College, 31-066 Krakow, Poland
| | - Bogdan Jakiela
- Department of Internal Medicine, Jagiellonian University Medical College, 31-066 Krakow, Poland
| | - Michał Kepski
- College of Natural Sciences, Institute of Computer Science, University of Rzeszow, Pigonia 1, 35-310 Rzeszow, Poland
| | - Jan G. Bazan
- College of Natural Sciences, Institute of Computer Science, University of Rzeszow, Pigonia 1, 35-310 Rzeszow, Poland
| | - Stanislawa Bazan-Socha
- Department of Internal Medicine, Jagiellonian University Medical College, 31-066 Krakow, Poland
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3
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Du S, Zhu C, Ren X, Chen X, Cui X, Guan S. Regulation of secretory pathway kinase or kinase-like proteins in human cancers. Front Immunol 2023; 14:942849. [PMID: 36825005 PMCID: PMC9941534 DOI: 10.3389/fimmu.2023.942849] [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: 05/13/2022] [Accepted: 01/24/2023] [Indexed: 02/09/2023] Open
Abstract
Secretory pathway kinase or kinase-like proteins (SPKKPs) are effective in the lumen of the endoplasmic reticulum (ER), Golgi apparatus (GA), and extracellular space. These proteins are involved in secretory signaling pathways and are distinctive from typical protein kinases. Various reports have shown that SPKKPs regulate the tumorigenesis and progression of human cancer via the phosphorylation of various substrates, which is essential in physiological and pathological processes. Emerging evidence has revealed that the expression of SPKKPs in human cancers is regulated by multiple factors. This review summarizes the current understanding of the contribution of SPKKPs in tumorigenesis and the progression of immunity. With the epidemic trend of immunotherapy, targeting SPKKPs may be a novel approach to anticancer therapy. This study briefly discusses the recent advances regarding SPKKPs.
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Affiliation(s)
- Shaonan Du
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Chen Zhu
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, China
| | - Xiaolin Ren
- Department of Neurosurgery, Shenyang Red Cross Hospital, Shenyang, China
| | - Xin Chen
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xiao Cui
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, China
| | - Shu Guan
- Department of Surgical Oncology and Breast Surgery, The First Hospital of China Medical University, Shenyang, China
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Zhu T, Zhang X, Chen X, Brown AP, Weirauch MT, Guilbert TW, Khurana Hershey GK, Biagini JM, Ji H. Nasal DNA methylation differentiates severe from non-severe asthma in African-American children. Allergy 2021; 76:1836-1845. [PMID: 33175399 PMCID: PMC8110596 DOI: 10.1111/all.14655] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 10/12/2020] [Accepted: 10/16/2020] [Indexed: 12/15/2022]
Abstract
BACKGROUND Asthma is highly heterogeneous, and severity evaluation is key to asthma management. DNA methylation (DNAm) contributes to asthma pathogenesis. This study aimed to identify nasal epithelial DNAm differences between severe and nonsevere asthmatic children and evaluate the impact of environmental exposures. METHODS Thirty-three nonsevere and 22 severe asthmatic African American children were included in an epigenome-wide association study. Genome-wide nasal epithelial DNAm and gene expression were measured. CpG sites associated with asthma severity and environmental exposures and predictive of severe asthma were identified. DNAm was correlated with gene expression. Enrichment for transcription factor (TF) binding sites or histone modifications surrounding DNAm differences were determined. RESULTS We identified 816 differentially methylated CpG positions (DMPs) and 10 differentially methylated regions (DMRs) associated with asthma severity. Three DMPs exhibited discriminatory ability for severe asthma. Intriguingly, six DMPs were simultaneously associated with asthma, allergic asthma, total IgE, environmental IgE, and FeNO in an independent cohort of children. Twenty-seven DMPs were associated with traffic-related air pollution or secondhand smoke. DNAm at 22 DMPs was altered by diesel particles or allergen in human bronchial epithelial cells. DNAm levels at 39 DMPs were correlated with mRNA expression. Proximal to 816 DMPs, three histone marks and several TFs involved in asthma pathogenesis were enriched. CONCLUSIONS Significant differences in nasal epithelial DNAm were observed between nonsevere and severe asthma in African American children, a subset of which may be useful to predict disease severity. These CpG sites are subjected to the influences of environmental exposures and may regulate gene expression.
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Affiliation(s)
- Tao Zhu
- California National Primate Research Center, Davis, CA
| | - Xue Zhang
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Xiaoting Chen
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | | | - Matthew T. Weirauch
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
- Divisions of Biomedical Informatics and Developmental Biology, Cincinnati, Ohio
- Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio
| | - Theresa W. Guilbert
- Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio
- Division of Pulmonary Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Gurjit K. Khurana Hershey
- Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio
- Divison of Asthma Research, Cincinnati Children’s Hospital Medical Center, Davis, CA
| | - Jocelyn M. Biagini
- Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio
- Divison of Asthma Research, Cincinnati Children’s Hospital Medical Center, Davis, CA
| | - Hong Ji
- California National Primate Research Center, Davis, CA
- Department of Anatomy, Physiology and Cell biology, School of Veterinary Medicine, University of California, Davis, CA
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Canut MI, Villa O, Kudsieh B, Mattlin H, Banchs I, González JR, Armengol L, Casaroli-Marano RP. MLIP genotype as a predictor of pharmacological response in primary open-angle glaucoma and ocular hypertension. Sci Rep 2021; 11:1583. [PMID: 33452295 PMCID: PMC7810753 DOI: 10.1038/s41598-020-80954-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 12/24/2020] [Indexed: 11/20/2022] Open
Abstract
Predicting the therapeutic response to ocular hypotensive drugs is crucial for the clinical treatment and management of glaucoma. Our aim was to identify a possible genetic contribution to the response to current pharmacological treatments of choice in a white Mediterranean population with primary open-angle glaucoma (POAG) or ocular hypertension (OH). We conducted a prospective, controlled, randomized, partial crossover study that included 151 patients of both genders, aged 18 years and older, diagnosed with and requiring pharmacological treatment for POAG or OH in one or both eyes. We sought to identify copy number variants (CNVs) associated with differences in pharmacological response, using a DNA pooling strategy of carefully phenotyped treatment responders and non-responders, treated for a minimum of 6 weeks with a beta-blocker (timolol maleate) and/or prostaglandin analog (latanoprost). Diurnal intraocular pressure reduction and comparative genome wide CNVs were analyzed. Our finding that copy number alleles of an intronic portion of the MLIP gene is a predictor of pharmacological response to beta blockers and prostaglandin analogs could be used as a biomarker to guide first-tier POAG and OH treatment. Our finding improves understanding of the genetic factors modulating pharmacological response in POAG and OH, and represents an important contribution to the establishment of a personalized approach to the treatment of glaucoma.
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Affiliation(s)
- María I Canut
- Centro de Oftalmología Barraquer, Instituto Universitario Barraquer (UAB), Barcelona, Spain
| | - Olaya Villa
- Quantitative Genomic Medicine Laboratories (qGenomics), Esplugues del Llobregat, Spain
| | | | - Heidi Mattlin
- Quantitative Genomic Medicine Laboratories (qGenomics), Esplugues del Llobregat, Spain
| | - Isabel Banchs
- Quantitative Genomic Medicine Laboratories (qGenomics), Esplugues del Llobregat, Spain
| | - Juan R González
- Barcelona Institute for Global Health (ISGlobal) and Centro de Investigación Biomédica en Red en Epidemiologia Y Salud Pública (CIBERESP), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Lluís Armengol
- Quantitative Genomic Medicine Laboratories (qGenomics), Esplugues del Llobregat, Spain.
| | - Ricardo P Casaroli-Marano
- Department of Surgery, School of Medicine and Health Sciences and Hospital Clinic de Barcelona (IDIBAPS), University of Barcelona, Calle Sabino de Arana 1 (2nd floor, Ophthalmology), 08028, Barcelona, Spain. .,Institute of Biomedical Research Sant Pau (IIB-Sant Pau, SGR1113) and Barcelona Tissue Bank (BST), Barcelona, Spain.
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6
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Herrera-Luis E, Espuela-Ortiz A, Lorenzo-Diaz F, Keys KL, Mak ACY, Eng C, Huntsman S, Villar J, Rodriguez-Santana JR, Burchard EG, Pino-Yanes M. Genome-wide association study reveals a novel locus for asthma with severe exacerbations in diverse populations. Pediatr Allergy Immunol 2021; 32:106-115. [PMID: 32841424 PMCID: PMC7886969 DOI: 10.1111/pai.13337] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/08/2020] [Accepted: 08/11/2020] [Indexed: 12/18/2022]
Abstract
BACKGROUND Severe asthma exacerbations are a major cause of asthma morbidity and increased healthcare costs. Several studies have shown racial and ethnic differences in asthma exacerbation rates. We aimed to identify genetic variants associated with severe exacerbations in two high-risk populations for asthma. METHODS A genome-wide association study of asthma in children and youth with severe exacerbations was performed in 1283 exacerbators and 2027 controls without asthma of Latino ancestry. Independent suggestive variants (P ≤ 5 × 10-6 ) were selected for replication in 448 African Americans exacerbators and 595 controls. Case-only analyses were performed comparing the exacerbators with additional 898 Latinos and 524 African Americans asthma patients without exacerbations, while adjusting by treatment category as a proxy of asthma severity. We analyzed the functionality of associated variants with in silico methods and by correlating genotypes with methylation levels in whole blood in a subset of 473 Latinos. RESULTS We identified two genome-wide significant associations for susceptibility to asthma with severe exacerbations, including a novel locus located at chromosome 2p21 (rs4952375, odds ratio = 1.39, P = 3.8 × 10-8 ), which was also associated with asthma exacerbations in a case-only analysis (odds ratio = 1.25, P = 1.95 × 10-3 ). This polymorphism is an expression quantitative trait locus of the long intergenic non-protein coding RNA 1913 (LINC01913) in lung tissues (P = 1.3 × 10-7 ) and influences methylation levels of the protein kinase domain-containing cytoplasmic (PKDCC) gene in whole-blood cells (P = 9.8 × 10-5 ). CONCLUSION We identified a novel susceptibility locus for severe asthma exacerbations in Hispanic/Latino and African American youths with functional effects in gene expression and methylation status of neighboring genes.
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Affiliation(s)
- Esther Herrera-Luis
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Tenerife, Spain
| | - Antonio Espuela-Ortiz
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Tenerife, Spain
| | - Fabian Lorenzo-Diaz
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Tenerife, Spain
| | - Kevin L. Keys
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Berkeley Institute for Data Science, University of California Berkeley, Berkeley, CA, USA
| | - Angel C. Y. Mak
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Celeste Eng
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Scott Huntsman
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - 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
- Keenan Research Center for Biomedical Science at the Li Ka Shing Knowledge Institute, St Michael’s Hospital, Toronto, ON, Canada
| | | | - Esteban G. Burchard
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Maria Pino-Yanes
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Instituto de Tecnologías Biomédicas (ITB), Universidad de La Laguna, San Cristóbal de La Laguna, Santa Cruz de Tenerife, Spain
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7
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Cheng Y, Jiao L, Li W, Wang J, Lin Z, Lai H, Ying B. Collagen type XVIII alpha 1 chain (COL18A1) variants affect the risk of anti-tuberculosis drug-induced hepatotoxicity: A prospective study. J Clin Lab Anal 2020; 35:e23630. [PMID: 33296124 PMCID: PMC7891502 DOI: 10.1002/jcla.23630] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 09/16/2020] [Accepted: 09/24/2020] [Indexed: 02/05/2023] Open
Abstract
Background The role of collagen type XVIII alpha 1 chain (COL18A1) in anti‐tuberculosis drug‐induced hepatotoxicity (ATDH) has not been reported. This study aimed to explore the association between of COL18A1 variants and ATDH susceptibility. Methods A total of 746 patients were enrolled in our study from December 2016 to April 2018, and all subjects in the study signed an informed consent form. The custom‐by‐design 2x48‐Plex SNPscanTM kit was used to genotype all selected 11 SNPs. Categorical variables were compared by chi‐square (χ2) or Fisher's exact test, while continuous variables were compared by Mann‐Whitney's U test. Plink was utilized to analyze allelic and genotypic frequencies, and genetic models. Multivariate logistic regression analyses were used to adjust potential factors. The odds ratios (ORs) with corresponding 95% confidence intervals (CIs) were also calculated. Results Among patients with successfully genotyping, there were 114 cases and 612 controls. The mutant A allele of rs12483377 conferred the decreased risk of ATDH (OR = 0.13, 95%CI: 0.02–0.98, P = 0.020), and this significance still existed after adjusting age and gender (P = 0.024). The mutant homozygote AA genotype of rs12483377 was associated with decreased total protein levels (P = 0.018). Conclusion Our study first revealed that the A allele of COL18A1 rs12483377 was associated with the decreased risk of ATDH in the Western Chinese Han population, providing new perspective for the molecular prediction, precise diagnosis, and individual treatment of ATDH.
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Affiliation(s)
- Yuhui Cheng
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Lin Jiao
- West China School of Medicine, Sichuan University, Chengdu, China.,Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Weixiu Li
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Jialing Wang
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Zhangyu Lin
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Hongli Lai
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Binwu Ying
- West China School of Medicine, Sichuan University, Chengdu, China.,Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
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8
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Caputo V, Strafella C, Termine A, Dattola A, Mazzilli S, Lanna C, Cosio T, Campione E, Novelli G, Giardina E, Cascella R. Overview of the molecular determinants contributing to the expression of Psoriasis and Psoriatic Arthritis phenotypes. J Cell Mol Med 2020; 24:13554-13563. [PMID: 33128843 PMCID: PMC7754002 DOI: 10.1111/jcmm.15742] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 07/07/2020] [Accepted: 07/30/2020] [Indexed: 12/17/2022] Open
Abstract
Psoriasis and psoriatic arthritis are multifactorial chronic disorders whose etiopathogenesis essentially derives from the alteration of several signalling pathways and the co-occurrence of genetic, epigenetic and non-genetic susceptibility factors that altogether affect the functional and structural property of the skin. Although shared and differential susceptibility genes and molecular pathways are known to contribute to the onset of pathological phenotypes, further research is needed to dissect the molecular causes of psoriatic disease and its progression towards Psoriatic Arthritis. This review will therefore be addressed to explore differences and similarities in the etiopathogenesis and progression of both disorders, with a particular focus on genes involved in the maintenance of the skin structure and integrity (keratins and collagens), modulation of patterns of recognition (through Toll-like receptors and dectin-1) and immuno-inflammatory response (by NLRP3-dependent inflammasome) to microbial pathogens. In addition, special emphasis will be given to the contribution of epigenetic elements (methylation pattern, non-coding RNAs, chromatin modifiers and 3D genome organization) to the etiopathogenesis and progression of psoriasis and psoriatic arthritis. The evidence discussed in this review highlights how the knowledge of patients' clinical and (epi)genomic make-up could be helpful for improving the available therapeutic strategies for psoriasis and psoriatic arthritis treatment.
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Affiliation(s)
- Valerio Caputo
- Medical Genetics LaboratoryDepartment of Biomedicine and PreventionTor Vergata UniversityRomeItaly
- Genomic Medicine Laboratory UILDMIRCCS Santa Lucia FoundationRomeItaly
| | - Claudia Strafella
- Medical Genetics LaboratoryDepartment of Biomedicine and PreventionTor Vergata UniversityRomeItaly
- Genomic Medicine Laboratory UILDMIRCCS Santa Lucia FoundationRomeItaly
| | - Andrea Termine
- Genomic Medicine Laboratory UILDMIRCCS Santa Lucia FoundationRomeItaly
| | - Annunziata Dattola
- Dermatologic ClinicDepartment of Systems MedicineTor Vergata UniversityRomeItaly
| | - Sara Mazzilli
- Dermatologic ClinicDepartment of Systems MedicineTor Vergata UniversityRomeItaly
| | - Caterina Lanna
- Dermatologic ClinicDepartment of Systems MedicineTor Vergata UniversityRomeItaly
| | - Terenzio Cosio
- Dermatologic ClinicDepartment of Systems MedicineTor Vergata UniversityRomeItaly
| | - Elena Campione
- Dermatologic ClinicDepartment of Systems MedicineTor Vergata UniversityRomeItaly
| | - Giuseppe Novelli
- Medical Genetics LaboratoryDepartment of Biomedicine and PreventionTor Vergata UniversityRomeItaly
- Neuromed Institute IRCCSPozzilliItaly
| | - Emiliano Giardina
- Genomic Medicine Laboratory UILDMIRCCS Santa Lucia FoundationRomeItaly
- Department of Biomedicine and PreventionUILDM Lazio Onlus FoundationTor Vergata UniversityRomeItaly
| | - Raffaella Cascella
- Medical Genetics LaboratoryDepartment of Biomedicine and PreventionTor Vergata UniversityRomeItaly
- Department of Biomedical SciencesCatholic University Our Lady of Good CounselTiranaAlbania
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He H, Suryawanshi H, Morozov P, Gay-Mimbrera J, Del Duca E, Kim HJ, Kameyama N, Estrada Y, Der E, Krueger JG, Ruano J, Tuschl T, Guttman-Yassky E. Single-cell transcriptome analysis of human skin identifies novel fibroblast subpopulation and enrichment of immune subsets in atopic dermatitis. J Allergy Clin Immunol 2020; 145:1615-1628. [DOI: 10.1016/j.jaci.2020.01.042] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 01/15/2020] [Accepted: 01/21/2020] [Indexed: 12/18/2022]
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10
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Duan Y, Liu G, Sun Y, Wu J, Xiong Z, Jin T, Chen M. Collagen type VI α5 gene variations may predict the risk of lung cancer development in Chinese Han population. Sci Rep 2020; 10:5010. [PMID: 32193401 PMCID: PMC7081318 DOI: 10.1038/s41598-020-61614-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 02/17/2020] [Indexed: 12/24/2022] Open
Abstract
The abundant expression of collagen type VI α5 (COL6A5) exists in lung tissue, and its role in lung cancer is still unknown. We performed a genetic association study with an attempt to detect the relationships between single nucleotide polymorphisms (SNPs) in COL6A5 and lung cancer predisposition in Chinese Han population. We finally selected six tag-SNPs to determine their genotypes among 510 lung cancer patients and 495 healthy controls with the MassARRAY platform. The associations of SNPs and lung cancer risk were estimated by logistic regression method with adjustment for confounding factors. Two available databases were used for gene expression and prognosis analysis. COL6A5 rs13062453, rs1497305, and rs77123808 were significantly associated with the risk of lung cancer in the whole population or stratified subgroups (p < 0.05). Among them, COL6A5 rs13062453 and rs1497305 were also linked to the susceptibility of lung adenocarcinoma. Additionally, rs1497305 was found to be strongly related to the TNM staging under five genetic models (p < 0.05). Results from databases suggested the important role of COL6A5 in lung cancer development. COL6A5 polymorphisms rs13062453, rs1497305 and rs77123808 were associated with lung cancer risk in Chinese Han population. These findings first yield new insight of COL6A5 in lung cancer.
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Affiliation(s)
- Ying Duan
- Department of Respiratory Medicine, The First Affiliated Hospital of School of Medicine of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Gaowen Liu
- Xianyang Central hospital, Xianyang, Shaanxi, 712000, China
| | - Yao Sun
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education. School of Medicine, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Jiamin Wu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education. School of Medicine, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Zichao Xiong
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education. School of Medicine, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Tianbo Jin
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education. School of Medicine, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Mingwei Chen
- Department of Respiratory Medicine, The First Affiliated Hospital of School of Medicine of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China.
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11
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Schofield JPR, Burg D, Nicholas B, Strazzeri F, Brandsma J, Staykova D, Folisi C, Bansal AT, Xian Y, Guo Y, Rowe A, Corfield J, Wilson S, Ward J, Lutter R, Shaw DE, Bakke PS, Caruso M, Dahlen SE, Fowler SJ, Horváth I, Howarth P, Krug N, Montuschi P, Sanak M, Sandström T, Sun K, Pandis I, Riley J, Auffray C, De Meulder B, Lefaudeux D, Sousa AR, Adcock IM, Chung KF, Sterk PJ, Skipp PJ, Djukanović R. Stratification of asthma phenotypes by airway proteomic signatures. J Allergy Clin Immunol 2019; 144:70-82. [PMID: 30928653 DOI: 10.1016/j.jaci.2019.03.013] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 02/14/2019] [Accepted: 03/08/2019] [Indexed: 12/22/2022]
Abstract
BACKGROUND Stratification by eosinophil and neutrophil counts increases our understanding of asthma and helps target therapy, but there is room for improvement in our accuracy in prediction of treatment responses and a need for better understanding of the underlying mechanisms. OBJECTIVE We sought to identify molecular subphenotypes of asthma defined by proteomic signatures for improved stratification. METHODS Unbiased label-free quantitative mass spectrometry and topological data analysis were used to analyze the proteomes of sputum supernatants from 246 participants (206 asthmatic patients) as a novel means of asthma stratification. Microarray analysis of sputum cells provided transcriptomics data additionally to inform on underlying mechanisms. RESULTS Analysis of the sputum proteome resulted in 10 clusters (ie, proteotypes) based on similarity in proteomic features, representing discrete molecular subphenotypes of asthma. Overlaying granulocyte counts onto the 10 clusters as metadata further defined 3 of these as highly eosinophilic, 3 as highly neutrophilic, and 2 as highly atopic with relatively low granulocytic inflammation. For each of these 3 phenotypes, logistic regression analysis identified candidate protein biomarkers, and matched transcriptomic data pointed to differentially activated underlying mechanisms. CONCLUSION This study provides further stratification of asthma currently classified based on quantification of granulocytic inflammation and provided additional insight into their underlying mechanisms, which could become targets for novel therapies.
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Affiliation(s)
- James P R Schofield
- Centre for Proteomic Research, Biological Sciences, University of Southampton, Southampton, United Kingdom; NIHR Southampton Biomedical Research Centre, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Dominic Burg
- Centre for Proteomic Research, Biological Sciences, University of Southampton, Southampton, United Kingdom; NIHR Southampton Biomedical Research Centre, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Ben Nicholas
- NIHR Southampton Biomedical Research Centre, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Fabio Strazzeri
- Centre for Proteomic Research, Biological Sciences, University of Southampton, Southampton, United Kingdom; Mathematical Sciences, University of Southampton, Southampton, United Kingdom
| | - Joost Brandsma
- NIHR Southampton Biomedical Research Centre, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Doroteya Staykova
- Centre for Proteomic Research, Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Caterina Folisi
- Centre for Proteomic Research, Biological Sciences, University of Southampton, Southampton, United Kingdom
| | | | - Yang Xian
- Data Science Institute, Imperial College, London, United Kingdom
| | - Yike Guo
- Data Science Institute, Imperial College, London, United Kingdom
| | - Anthony Rowe
- Janssen Research & Development, High Wycombe, United Kingdom
| | | | - Susan Wilson
- NIHR Southampton Biomedical Research Centre, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Jonathan Ward
- NIHR Southampton Biomedical Research Centre, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Rene Lutter
- AMC, Department of Experimental Immunology, University of Amsterdam, Amsterdam, The Netherlands; Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Dominick E Shaw
- Respiratory Research Unit, University of Nottingham, Nottingham, United Kingdom
| | - Per S Bakke
- Institute of Medicine, University of Bergen, Bergen, Norway
| | - Massimo Caruso
- Department of Clinical and Experimental Medicine Hospital University, University of Catania, Catania, Italy
| | - Sven-Erik Dahlen
- Centre for Allergy Research, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Stephen J Fowler
- Respiratory and Allergy Research Group, University of Manchester, Manchester, United Kingdom
| | - Ildikó Horváth
- Department of Pulmonology, Semmelweis University, Budapest, Hungary
| | - Peter Howarth
- NIHR Southampton Biomedical Research Centre, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Norbert Krug
- Fraunhofer Institute for Toxicology and Experimental Medicine Hannover, Hannover, Germany
| | - Paolo Montuschi
- Faculty of Medicine, Catholic University of the Sacred Heart, Rome, Italy
| | - Marek Sanak
- Laboratory of Molecular Biology and Clinical Genetics, Medical College, Jagiellonian University, Krakow, Poland
| | - Thomas Sandström
- Department of Medicine, Department of Public Health and Clinical Medicine Respiratory Medicine Unit, Umeå University, Umeå, Sweden
| | - Kai Sun
- Data Science Institute, Imperial College, London, United Kingdom
| | - Ioannis Pandis
- Data Science Institute, Imperial College, London, United Kingdom
| | - John Riley
- Respiratory Therapeutic Unit, GlaxoSmithKline, Stockley Park, United Kingdom
| | - Charles Auffray
- European Institute for Systems Biology and Medicine, CNRS-ENS-UCBL-INSERM, Université de Lyon, Lyon, France
| | - Bertrand De Meulder
- European Institute for Systems Biology and Medicine, CNRS-ENS-UCBL-INSERM, Université de Lyon, Lyon, France
| | - Diane Lefaudeux
- European Institute for Systems Biology and Medicine, CNRS-ENS-UCBL-INSERM, Université de Lyon, Lyon, France
| | - Ana R Sousa
- Respiratory Therapeutic Unit, GlaxoSmithKline, Stockley Park, United Kingdom
| | - Ian M Adcock
- Cell and Molecular Biology Group, Airways Disease Section, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Kian Fan Chung
- Cell and Molecular Biology Group, Airways Disease Section, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Peter J Sterk
- Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Paul J Skipp
- Centre for Proteomic Research, Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Ratko Djukanović
- NIHR Southampton Biomedical Research Centre, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom.
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12
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Ziyab AH, Hankinson J, Ewart S, Schauberger E, Kopec-Harding K, Zhang H, Custovic A, Arshad H, Simpson A, Karmaus WJ. Epistasis between FLG and IL4R Genes on the Risk of Allergic Sensitization: Results from Two Population-Based Birth Cohort Studies. Sci Rep 2018; 8:3221. [PMID: 29459738 PMCID: PMC5818621 DOI: 10.1038/s41598-018-21459-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 02/05/2018] [Indexed: 11/12/2022] Open
Abstract
Immune-specific genes as well as genes responsible for the formation and integrity of the epidermal barrier have been implicated in the pathogeneses of allergic sensitization. This study sought to determine whether an epistatic effect (gene-gene interaction) between genetic variants within interleukin 4 receptor (IL4R) and filaggrin (FLG) genes predispose to the development of allergic sensitization. Data from two birth cohort studies were analyzed, namely the Isle of Wight (IOW; n = 1,456) and the Manchester Asthma and Allergy Study (MAAS; n = 1,058). In the IOW study, one interaction term (IL4R rs3024676 × FLG variants) showed statistical significance (interaction term: P = 0.003). To illustrate the observed epistasis, stratified analyses were performed, which showed that FLG variants were associated with allergic sensitization only among IL4R rs3024676 homozygotes (OR, 1.97; 95% CI, 1.27–3.05; P = 0.003). In contrast, FLG variants effect was masked among IL4R rs3024676 heterozygotes (OR, 0.53; 95% CI, 0.22–1.32; P = 0.175). Similar results were demonstrated in the MAAS study. Epistasis between immune (IL4R) and skin (FLG) regulatory genes exist in the pathogenesis of allergic sensitization. Hence, genetic susceptibility towards defective epidermal barrier and deviated immune responses could work together in the development of allergic sensitization.
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Affiliation(s)
- Ali H Ziyab
- Department of Community Medicine and Behavioral Sciences, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait.
| | - Jenny Hankinson
- Division of Infection, Immunity and Respiratory Medicine, Manchester Academic Health Science Centre, The University of Manchester, Manchester University NHS Foundation Trust, Manchester, UK
| | - Susan Ewart
- College of Veterinary Medicine, Michigan State University, East Lansing, Michigan, USA
| | - Eric Schauberger
- Division of Allergy and Immunology, Cincinnati Children's Hospital, Cincinnati, OH, USA
| | - Kamilla Kopec-Harding
- Centre for Respiratory Medicine and Allergy, Institute of Inflammation and Repair, University of Manchester, University Hospital of South Manchester NHS Foundation Trust, Manchester, UK
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Adnan Custovic
- Department of Paediatrics, Imperial College London, London, UK
| | - Hasan Arshad
- David Hide Asthma and Allergy Research Centre, St Mary's Hospital, Isle of Wight, UK.,Clinical and Experimental Sciences Academic Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Angela Simpson
- Division of Infection, Immunity and Respiratory Medicine, Manchester Academic Health Science Centre, The University of Manchester, Manchester University NHS Foundation Trust, Manchester, UK
| | - Wilfried J Karmaus
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
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13
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Sugier PE, Brossard M, Sarnowski C, Vaysse A, Morin A, Pain L, Margaritte-Jeannin P, Dizier MH, Cookson WOCM, Lathrop M, Moffatt MF, Laprise C, Demenais F, Bouzigon E. A novel role for ciliary function in atopy: ADGRV1 and DNAH5 interactions. J Allergy Clin Immunol 2017; 141:1659-1667.e11. [PMID: 28927820 DOI: 10.1016/j.jaci.2017.06.050] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 05/30/2017] [Accepted: 06/21/2017] [Indexed: 12/30/2022]
Abstract
BACKGROUND Atopy, an endotype underlying allergic diseases, has a substantial genetic component. OBJECTIVE Our goal was to identify novel genes associated with atopy in asthma-ascertained families. METHODS We implemented a 3-step analysis strategy in 3 data sets: the Epidemiological Study on the Genetics and Environment of Asthma (EGEA) data set (1660 subjects), the Saguenay-Lac-Saint-Jean study data set (1138 subjects), and the Medical Research Council (MRC) data set (446 subjects). This strategy included a single nucleotide polymorphism (SNP) genome-wide association study (GWAS), the selection of related gene pairs based on statistical filtering of GWAS results, and text-mining filtering using Gene Relationships Across Implicated Loci and SNP-SNP interaction analysis of selected gene pairs. RESULTS We identified the 5q14 locus, harboring the adhesion G protein-coupled receptor V1 (ADGRV1) gene, which showed genome-wide significant association with atopy (rs4916831, meta-analysis P value = 6.8 × 10-9). Statistical filtering of GWAS results followed by text-mining filtering revealed relationships between ADGRV1 and 3 genes showing suggestive association with atopy (P ≤ 10-4). SNP-SNP interaction analysis between ADGRV1 and these 3 genes showed significant interaction between ADGRV1 rs17554723 and 2 correlated SNPs (rs2134256 and rs1354187) within the dynein axonemal heavy chain 5 (DNAH5) gene (Pmeta-int = 3.6 × 10-5 and 6.1 × 10-5, which met the multiple-testing corrected threshold of 7.3 × 10-5). Further conditional analysis indicated that rs2134256 alone accounted for the interaction signal with rs17554723. CONCLUSION Because both DNAH5 and ADGRV1 contribute to ciliary function, this study suggests that ciliary dysfunction might represent a novel mechanism underlying atopy. Combining GWAS and epistasis analysis driven by statistical and knowledge-based evidence represents a promising approach for identifying new genes involved in complex traits.
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Affiliation(s)
- Pierre-Emmanuel Sugier
- Genetic Variation and Human Diseases Unit, INSERM, Université Paris Diderot, Université Sorbonne Paris Cité, Paris, France; Université Pierre et Marie Curie, Paris, France
| | - Myriam Brossard
- Genetic Variation and Human Diseases Unit, INSERM, Université Paris Diderot, Université Sorbonne Paris Cité, Paris, France
| | - Chloé Sarnowski
- Genetic Variation and Human Diseases Unit, INSERM, Université Paris Diderot, Université Sorbonne Paris Cité, Paris, France
| | - Amaury Vaysse
- Genetic Variation and Human Diseases Unit, INSERM, Université Paris Diderot, Université Sorbonne Paris Cité, Paris, France
| | - Andréanne Morin
- McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada; Département des Sciences Fondamentales, Université du Québec à Chicoutimi, Chicoutimi, Quebec, Canada
| | - Lucile Pain
- Département des Sciences Fondamentales, Université du Québec à Chicoutimi, Chicoutimi, Quebec, Canada
| | - Patricia Margaritte-Jeannin
- Genetic Variation and Human Diseases Unit, INSERM, Université Paris Diderot, Université Sorbonne Paris Cité, Paris, France
| | - Marie-Hélène Dizier
- Genetic Variation and Human Diseases Unit, INSERM, Université Paris Diderot, Université Sorbonne Paris Cité, Paris, France
| | - William O C M Cookson
- Section of Genomic Medicine, National Heart and Lung Institute, London, United Kingdom
| | - Mark Lathrop
- McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada
| | - Miriam F Moffatt
- Section of Genomic Medicine, National Heart and Lung Institute, London, United Kingdom
| | - Catherine Laprise
- Département des Sciences Fondamentales, Université du Québec à Chicoutimi, Chicoutimi, Quebec, Canada
| | - Florence Demenais
- Genetic Variation and Human Diseases Unit, INSERM, Université Paris Diderot, Université Sorbonne Paris Cité, Paris, France.
| | - Emmanuelle Bouzigon
- Genetic Variation and Human Diseases Unit, INSERM, Université Paris Diderot, Université Sorbonne Paris Cité, Paris, France
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14
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Danielewicz H. Hits and defeats of genome-wide association studies of atopy and asthma. J Appl Biomed 2017. [DOI: 10.1016/j.jab.2017.03.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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15
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Sánchez-Borges M, Fernandez-Caldas E, Thomas WR, Chapman MD, Lee BW, Caraballo L, Acevedo N, Chew FT, Ansotegui IJ, Behrooz L, Phipatanakul W, Gerth van Wijk R, Pascal D, Rosario N, Ebisawa M, Geller M, Quirce S, Vrtala S, Valenta R, Ollert M, Canonica GW, Calderón MA, Barnes CS, Custovic A, Benjaponpitak S, Capriles-Hulett A. International consensus (ICON) on: clinical consequences of mite hypersensitivity, a global problem. World Allergy Organ J 2017; 10:14. [PMID: 28451053 PMCID: PMC5394630 DOI: 10.1186/s40413-017-0145-4] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 02/27/2017] [Indexed: 01/09/2023] Open
Abstract
Since mite allergens are the most relevant inducers of allergic diseases worldwide, resulting in significant morbidity and increased burden on health services, the International Collaboration in Asthma, Allergy and Immunology (iCAALL), formed by the American Academy of Allergy, Asthma and Immunology (AAAAI), the American College of Allergy, Asthma and Immunology (ACAAI), the European Academy of Allergy and Clinical Immunology (EAACI), and the World Allergy Organization (WAO), has proposed to issue an International Consensus (ICON) on the clinical consequences of mite hypersensitivity. The objectives of this document are to highlight aspects of mite biology that are clinically relevant, to update the current knowledge on mite allergens, routes of sensitization, the genetics of IgE responses to mites, the epidemiologic aspects of mite hypersensitivity, the clinical pictures induced by mites, the diagnosis, specific immunotherapeutic approaches, and prevention.
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Affiliation(s)
- Mario Sánchez-Borges
- Allergy and Clinical Immunology Department, Centro Médico Docente La Trinidad, Caracas, Venezuela
- Clínica El Avila, 6ª transversal Urb. Altamira, Piso 8, Consultoria 803, Caracas, 1060 Venezuela
| | - Enrique Fernandez-Caldas
- Inmunotek S.L., Madrid, Spain and Division of Allergy and Immunology, University of South Florida College of Medicine, Tampa, FL USA
| | - Wayne R. Thomas
- Telethon Kids Institute, University of Western Australia, Crawley, WA Australia
| | | | - Bee Wah Lee
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Luis Caraballo
- Institute for Immunological Research, University of Cartagena, Cartagena, Colombia
| | | | - Fook Tim Chew
- Department of Biological Sciences, Allergy and Molecular Immunology Laboratory, Functional Genomics Laboratories, National University of Singapore, Singapore, Singapore
| | | | - Leili Behrooz
- Division of Immunology and Allergy, Boston Cshildren’s Hospital, Harvard Medical School, Boston, MA USA
| | - Wanda Phipatanakul
- Division of Immunology and Allergy, Boston Cshildren’s Hospital, Harvard Medical School, Boston, MA USA
| | - Roy Gerth van Wijk
- Department of Internal Medicine, Allergology, Erasmus MC, Rotterdam, the Netherlands
| | - Demoly Pascal
- Division of Allergy, Department of Pulmonology, University Hospital of Montpellier, Paris, France
- Montpellier and Pierre Louis Institute of Epidemiology and Public Health, Sorbonne Universités, Paris, France
| | - Nelson Rosario
- Federal University of Parana, Rua General Carneiro, Curitiba, Brazil
| | - Motohiro Ebisawa
- Department of Allergy, Clinical Research Center for Allergology and Rheumatology, Sagamihara National Hospital, Sagamihara, Kanagawa Japan
| | - Mario Geller
- Division of Medicine, Academy of Medicine of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Santiago Quirce
- Department of Allergy, Hospital La Paz Institute for Health Research and CIBER of Respiratory Diseases (CIBERES), Madrid, Spain
| | - Susanne Vrtala
- Division of Immunopathology, Department of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Rudolf Valenta
- Division of Immunopathology, Department of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Markus Ollert
- Department of Infection & Immunity, Laboratory of Immunogenetics and Allergology, Luxembourg Institute of Health, Luxembourg, UK
| | - Giorgio Walter Canonica
- Allergy & Respiratory Diseases Clinic, University of Genoa, IRCCS AOU San Martino-IST, Genoa, Italy
| | - Moises A. Calderón
- Section of Allergy and Clinical Immunology, Imperial College London – NHLI, London, United Kingdom
| | - Charles S. Barnes
- Division of Allergy/Immunology, Children’s Mercy Hospital, Kansas City, MO USA
| | - Adnan Custovic
- Department of Paediatrics, Imperial College London, London, United Kingdom
| | - Suwat Benjaponpitak
- Division of Pediatric Allergy/Immunology/Rheumatology, Department of Pediatrics, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Arnaldo Capriles-Hulett
- Allergy and Clinical Immunology Department, Centro Médico Docente La Trinidad, Caracas, Venezuela
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16
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Pouladi N, Bime C, Garcia JGN, Lussier YA. Complex genetics of pulmonary diseases: lessons from genome-wide association studies and next-generation sequencing. Transl Res 2016; 168:22-39. [PMID: 26006746 PMCID: PMC4658294 DOI: 10.1016/j.trsl.2015.04.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 04/27/2015] [Accepted: 04/29/2015] [Indexed: 12/16/2022]
Abstract
The advent of high-throughput technologies has provided exceptional assistance for lung scientists to discover novel genetic variants underlying the development and progression of complex lung diseases. However, the discovered variants thus far do not explain much of the estimated heritability of complex lung diseases. Here, we review the literature of successfully used genome-wide association studies (GWASs) and identified the polymorphisms that reproducibly underpin the susceptibility to various noncancerous complex lung diseases or affect therapeutic responses. We also discuss the inherent limitations of GWAS approaches and how the use of next-generation sequencing technologies has furthered our understanding about the genetic determinants of these diseases. Next, we describe the contribution of the metagenomics to understand the interactions of the airways microbiome with lung diseases. We then highlight the urgent need for new integrative genomics-phenomics methods to more effectively interrogate and understand multiple downstream "omics" (eg, chromatin modification patterns). Finally, we address the scarcity of genetic studies addressing under-represented populations such as African Americans and Hispanics.
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Affiliation(s)
- Nima Pouladi
- Department of Medicine, University of Arizona, Tucson, Ariz; Center for Biomedical Informatics and Biostatistics, University of Arizona, Tucson, Ariz; BIO5 Institute, University of Arizona, Tucson, Ariz
| | - Christian Bime
- University of Arizona Health Sciences Center, University of Arizona, Tucson, Ariz; Arizona Respiratory Center, University of Arizona, Tucson, Ariz
| | - Joe G N Garcia
- University of Arizona Health Sciences Center, University of Arizona, Tucson, Ariz; Arizona Respiratory Center, University of Arizona, Tucson, Ariz
| | - Yves A Lussier
- Department of Medicine, University of Arizona, Tucson, Ariz; Center for Biomedical Informatics and Biostatistics, University of Arizona, Tucson, Ariz; BIO5 Institute, University of Arizona, Tucson, Ariz; University of Arizona Health Sciences Center, University of Arizona, Tucson, Ariz; Institute for Genomics and Systems Biology, Argonne National Laboratory and University of Chicago, Chicago, Ill.
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17
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Abrantes P, Santos MM, Sousa I, Xavier JM, Francisco V, Krug T, Sobral J, Matos M, Martins M, Jacinto A, Coiteiro D, Oliveira SA. Genetic Variants Underlying Risk of Intracranial Aneurysms: Insights from a GWAS in Portugal. PLoS One 2015; 10:e0133422. [PMID: 26186006 PMCID: PMC4505843 DOI: 10.1371/journal.pone.0133422] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 06/26/2015] [Indexed: 12/03/2022] Open
Abstract
Subarachnoid hemorrhage (SAH) is a life-threatening event that most frequently leads to severe disability and death. Its most frequent cause is the rupture of a saccular intracranial aneurysm (IA), which is a blood vessel dilation caused by disease or weakening of the vessel wall. Although the genetic contribution to IA is well established, to date no single gene has been unequivocally identified as responsible for IA formation or rupture. We aimed to identify IA susceptibility genes in the Portuguese population through a pool-based multistage genome-wide association study. Replicate pools were allelotyped in triplicate in a discovery dataset (100 IA cases and 92 gender-matched controls) using the Affymetrix Human SNP Array 6.0. Top SNPs (absolute value of the relative allele score difference between cases and controls |RASdiff|≥13.0%) were selected for technical validation by individual genotyping in the discovery dataset. From the 101 SNPs successfully genotyped, 99 SNPs were nominally associated with IA. Replication of technically validated SNPs was conducted in an independent replication dataset (100 Portuguese IA cases and 407 controls). rs4667622 (between UBR3 and MYO3B), rs6599001 (between SCN11A and WDR48), rs3932338 (214 kilobases downstream of PRDM9), and rs10943471 (96 kilobases upstream of HTR1B) were associated with IA (unadjusted allelic chi-square tests) in the datasets tested (discovery: 6.84E-04≤P≤1.92E-02, replication: 2.66E-04≤P≤2.28E-02, and combined datasets: 6.05E-05≤P≤5.50E-04). Additionally, we confirmed the known association with IA of rs1333040 at the 9p21.3 genomic region, thus validating our dataset. These novel findings in the Portuguese population warrant further replication in additional independent studies, and provide additional candidates to more comprehensively understand IA etiopathogenesis.
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Affiliation(s)
- Patrícia Abrantes
- Instituto Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Maria M. Santos
- Serviço de Neurocirurgia, Hospital de Santa Maria, Lisboa, Portugal
| | - Inês Sousa
- Instituto Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Joana M. Xavier
- Instituto Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Vânia Francisco
- Instituto Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Tiago Krug
- Instituto Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - João Sobral
- Instituto Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Mafalda Matos
- Instituto Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Madalena Martins
- Instituto Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - António Jacinto
- Centro de Estudos de Doenças Crónicas (CEDOC), Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisboa, Portugal
| | | | - Sofia A. Oliveira
- Instituto Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- * E-mail:
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18
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Tunesi S, Ferrante D, Mirabelli D, Andorno S, Betti M, Fiorito G, Guarrera S, Casalone E, Neri M, Ugolini D, Bonassi S, Matullo G, Dianzani I, Magnani C. Gene–asbestos interaction in malignant pleural mesothelioma susceptibility. Carcinogenesis 2015; 36:1129-35. [DOI: 10.1093/carcin/bgv097] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 06/26/2015] [Indexed: 12/27/2022] Open
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19
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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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20
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van der Valk RJ, Duijts L, Timpson NJ, Salam MT, Standl M, Curtin JA, Genuneit J, Kerhof M, Kreiner-Møller E, Cáceres A, Gref A, Liang LL, Taal HR, Bouzigon E, Demenais F, Nadif R, Ober C, Thompson EE, Estrada K, Hofman A, Uitterlinden AG, van Duijn C, Rivadeneira F, Li X, Eckel SP, Berhane K, Gauderman WJ, Granell R, Evans DM, St Pourcain B, McArdle W, Kemp JP, Smith GD, Tiesler CM, Flexeder C, Simpson A, Murray CS, Fuchs O, Postma DS, Bønnelykke K, Torrent M, Andersson M, Sleiman P, Hakonarson H, Cookson WO, Moffatt MF, Paternoster L, Melén E, Sunyer J, Bisgaard H, Koppelman GH, Ege M, Custovic A, Heinrich J, Gilliland FD, Henderson AJ, Jaddoe VW, de Jongste JC. Fraction of exhaled nitric oxide values in childhood are associated with 17q11.2-q12 and 17q12-q21 variants. J Allergy Clin Immunol 2014; 134:46-55. [PMID: 24315451 PMCID: PMC4334587 DOI: 10.1016/j.jaci.2013.08.053] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 06/21/2013] [Accepted: 08/28/2013] [Indexed: 11/30/2022]
Abstract
BACKGROUND The fraction of exhaled nitric oxide (Feno) value is a biomarker of eosinophilic airway inflammation and is associated with childhood asthma. Identification of common genetic variants associated with childhood Feno values might help to define biological mechanisms related to specific asthma phenotypes. OBJECTIVE We sought to identify the genetic variants associated with childhood Feno values and their relation with asthma. METHODS Feno values were measured in children age 5 to 15 years. In 14 genome-wide association studies (N = 8,858), we examined the associations of approximately 2.5 million single nucleotide polymorphisms (SNPs) with Feno values. Subsequently, we assessed whether significant SNPs were expression quantitative trait loci in genome-wide expression data sets of lymphoblastoid cell lines (n = 1,830) and were related to asthma in a previously published genome-wide association data set (cases, n = 10,365; control subjects: n = 16,110). RESULTS We identified 3 SNPs associated with Feno values: rs3751972 in LYR motif containing 9 (LYRM9; P = 1.97 × 10(-10)) and rs944722 in inducible nitric oxide synthase 2 (NOS2; P = 1.28 × 10(-9)), both of which are located at 17q11.2-q12, and rs8069176 near gasdermin B (GSDMB; P = 1.88 × 10(-8)) at 17q12-q21. We found a cis expression quantitative trait locus for the transcript soluble galactoside-binding lectin 9 (LGALS9) that is in linkage disequilibrium with rs944722. rs8069176 was associated with GSDMB and ORM1-like 3 (ORMDL3) expression. rs8069176 at 17q12-q21, but not rs3751972 and rs944722 at 17q11.2-q12, were associated with physician-diagnosed asthma. CONCLUSION This study identified 3 variants associated with Feno values, explaining 0.95% of the variance. Identification of functional SNPs and haplotypes in these regions might provide novel insight into the regulation of Feno values. This study highlights that both shared and distinct genetic factors affect Feno values and childhood asthma.
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Affiliation(s)
- Ralf Jp van der Valk
- The Generation R Study Group, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Liesbeth Duijts
- Department of Pediatrics, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- School of Social and Community Medicine, University of Bristol, Uk
| | - Nicolas J Timpson
- School of Social and Community Medicine, University of Bristol, Uk
- MRC Centre for Causal Analyses in Translational Epidemiology, University of Bristol, UK
| | - Muhammad T Salam
- Department of Preventive Medicine, University of Southern California Keck School of Medicine, Los Angeles, USA
| | - Marie Standl
- Institute of Epidemiology I, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - John A Curtin
- University of Manchester, Manchester Academic Health Science Centre, University Hospital of South Manchester NHS Foundation Trust, Manchester, United Kingdom
| | - Jon Genuneit
- Institute of Epidemiology and Medical Biometry, Ulm University, Ulm, Germany
| | - Marjan Kerhof
- University Medical Center Groningen, University of Groningen, Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital
| | - Eskil Kreiner-Møller
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, The Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- The Danish Pediatric Asthma Center, Copenhagen University Hospital, Gentofte, Copenhagen, Denmark
| | - Alejandro Cáceres
- Center for Research in Environmental Epidemiology (CREAL), Barcelona, Catalonia, Spain
- Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Catalonia, Spain
- Spanish consortium for Research on Epidemiology and Public Health (CIBERESP), Spain
| | - Anna Gref
- Institute of Environmental Medicine and Centre for Allergy Research, Karolinska Institutet, Stockholm, Sweden
| | - Liming L Liang
- Department of Epidemiology, Harvard School of Public Health, Boston, USA
- Department of Biostatistics, Harvard School of Public Health, Boston, USA
| | - H Rob Taal
- The Generation R Study Group, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Emmanuelle Bouzigon
- Inserm, UMR 946, Genetic Variation and Human Diseases Unit, F-75010, Paris, France
- Univ Paris Diderot, Sorbonne Paris Cité, Institut Universitaire d'Hématologie, F- 75007, Paris, France
| | - Florence Demenais
- Inserm, UMR 946, Genetic Variation and Human Diseases Unit, F-75010, Paris, France
- Univ Paris Diderot, Sorbonne Paris Cité, Institut Universitaire d'Hématologie, F- 75007, Paris, France
| | - Rachel Nadif
- Inserm, Centre for research in Epidemiology and Population Health (CEPH), U1018, Respiratory and Environmental Epidemiology Team, F-94807, Villejuif, France
- Univ Paris-Sud, UMRS 1018, F-94807, Villejuif, France
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, IL 60637
| | - Emma E Thompson
- Department of Human Genetics, University of Chicago, Chicago, IL 60637
| | - Karol Estrada
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - André G Uitterlinden
- The Generation R Study Group, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Cornélia van Duijn
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Xia Li
- Department of Preventive Medicine, University of Southern California Keck School of Medicine, Los Angeles, USA
| | - Sandrah P Eckel
- Department of Preventive Medicine, University of Southern California Keck School of Medicine, Los Angeles, USA
| | - Kiros Berhane
- Department of Preventive Medicine, University of Southern California Keck School of Medicine, Los Angeles, USA
| | - W James Gauderman
- Department of Preventive Medicine, University of Southern California Keck School of Medicine, Los Angeles, USA
| | - Raquel Granell
- School of Social and Community Medicine, University of Bristol, Uk
| | - David M Evans
- School of Social and Community Medicine, University of Bristol, Uk
- MRC Centre for Causal Analyses in Translational Epidemiology, University of Bristol, UK
| | | | - Wendy McArdle
- School of Social and Community Medicine, University of Bristol, Uk
| | - John P Kemp
- School of Social and Community Medicine, University of Bristol, Uk
- MRC Centre for Causal Analyses in Translational Epidemiology, University of Bristol, UK
| | - George Davey Smith
- School of Social and Community Medicine, University of Bristol, Uk
- MRC Centre for Causal Analyses in Translational Epidemiology, University of Bristol, UK
| | - Carla Mt Tiesler
- Institute of Epidemiology I, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Claudia Flexeder
- Institute of Epidemiology I, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Angela Simpson
- University of Manchester, Manchester Academic Health Science Centre, University Hospital of South Manchester NHS Foundation Trust, Manchester, United Kingdom
| | - Clare S Murray
- University of Manchester, Manchester Academic Health Science Centre, University Hospital of South Manchester NHS Foundation Trust, Manchester, United Kingdom
| | - Oliver Fuchs
- Inselspital, Universitätsspital, Bern, Universitätklinik für Kinderheilkunde, Bern, Switzerland
- Dr. von Hauner Children's Hospital, Ludwig Maximilian University, Munich, Germany
| | - Dirkje S Postma
- University of Groningen, University Medical Center Groningen, Department of Pulmonology, Groningen, The Netherlands
- Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Klaus Bønnelykke
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, The Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- The Danish Pediatric Asthma Center, Copenhagen University Hospital, Gentofte, Copenhagen, Denmark
| | - Maties Torrent
- Spanish consortium for Research on Epidemiology and Public Health (CIBERESP), Spain
- ib-salut, Area de Salut de Menorca, Balearic Islands, Spain
| | - Martin Andersson
- Department of Public Health Sciences, Karolinska Institutet, Stockholm, Sweden
- Department of Physiology, South Central Hospital, Stockholm, Sweden
| | - Patrick Sleiman
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - William O Cookson
- National Heart and Lung Institute, Imperial College London, London SW3 6LY
| | - Miriam F Moffatt
- National Heart and Lung Institute, Imperial College London, London SW3 6LY
| | - Lavinia Paternoster
- School of Social and Community Medicine, University of Bristol, Uk
- MRC Centre for Causal Analyses in Translational Epidemiology, University of Bristol, UK
| | - Erik Melén
- Institute of Environmental Medicine and Centre for Allergy Research, Karolinska Institutet, Stockholm, Sweden
- Sach's Children's Hospital, Stockholm, Sweden
| | - Jordi Sunyer
- Center for Research in Environmental Epidemiology (CREAL), Barcelona, Catalonia, Spain
- Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Catalonia, Spain
- Spanish consortium for Research on Epidemiology and Public Health (CIBERESP), Spain
- Pompeu Fabra University (UPF), Barcelona, Catalonia, Spain
| | - Hans Bisgaard
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, The Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- The Danish Pediatric Asthma Center, Copenhagen University Hospital, Gentofte, Copenhagen, Denmark
| | - Gerard H Koppelman
- University Medical Center Groningen, University of Groningen, Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital
- University of Groningen, University Medical Center Groningen, Department of Pulmonology, Groningen, The Netherlands
- Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Markus Ege
- Dr. von Hauner Children's Hospital, Ludwig Maximilian University, Munich, Germany
| | - Adnan Custovic
- University of Manchester, Manchester Academic Health Science Centre, University Hospital of South Manchester NHS Foundation Trust, Manchester, United Kingdom
| | - Joachim Heinrich
- Institute of Epidemiology I, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Frank D Gilliland
- Department of Preventive Medicine, University of Southern California Keck School of Medicine, Los Angeles, USA
| | | | - Vincent Wv Jaddoe
- The Generation R Study Group, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Johan C de Jongste
- Department of Pediatrics, Erasmus Medical Center, Rotterdam, The Netherlands
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21
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González JR, Cáceres A, Esko T, Cuscó I, Puig M, Esnaola M, Reina J, Siroux V, Bouzigon E, Nadif R, Reinmaa E, Milani L, Bustamante M, Jarvis D, Antó JM, Sunyer J, Demenais F, Kogevinas M, Metspalu A, Cáceres M, Pérez-Jurado LA. A common 16p11.2 inversion underlies the joint susceptibility to asthma and obesity. Am J Hum Genet 2014; 94:361-72. [PMID: 24560518 PMCID: PMC3951940 DOI: 10.1016/j.ajhg.2014.01.015] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2013] [Accepted: 01/28/2014] [Indexed: 12/21/2022] Open
Abstract
The prevalence of asthma and obesity is increasing worldwide, and obesity is a well-documented risk factor for asthma. The mechanisms underlying this association and parallel time trends remain largely unknown but genetic factors may be involved. Here, we report on a common ~0.45 Mb genomic inversion at 16p11.2 that can be accurately genotyped via SNP array data. We show that the inversion allele protects against the joint occurrence of asthma and obesity in five large independent studies (combined sample size of 317 cases and 543 controls drawn from a total of 5,809 samples; combined OR = 0.48, p = 5.5 × 10(-6)). Allele frequencies show remarkable worldwide population stratification, ranging from 10% in East Africa to 49% in Northern Europe, consistent with discordant and extreme genetic drifts or adaptive selections after human migration out of Africa. Inversion alleles strongly correlate with expression levels of neighboring genes, especially TUFM (p = 3.0 × 10(-40)) that encodes a mitochondrial protein regulator of energy balance and inhibitor of type 1 interferon, and other candidates for asthma (IL27) and obesity (APOB48R and SH2B1). Therefore, by affecting gene expression, the ~0.45 Mb 16p11.2 inversion provides a genetic basis for the joint susceptibility to asthma and obesity, with a population attributable risk of 39.7%. Differential mitochondrial function and basal energy balance of inversion alleles might also underlie the potential selection signature that led to their uneven distribution in world populations.
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Affiliation(s)
- Juan R González
- Center for Research in Environmental Epidemiology (CREAL), Barcelona 08003, Spain; Hospital del Mar Research Institute (IMIM), Barcelona 08003, Spain; Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Barcelona 08003, Spain; Department of Mathematics, Universitat Autònoma de Barcelona, Bellaterra (Barcelona) 08193, Spain.
| | - Alejandro Cáceres
- Center for Research in Environmental Epidemiology (CREAL), Barcelona 08003, Spain; Hospital del Mar Research Institute (IMIM), Barcelona 08003, Spain
| | - Tonu Esko
- Estonian Genome Center, University of Tartu, Tartu 50090, Estonia; Institute of Molecular and Cell Biology, University of Tartu, Tartu 50090, Estonia
| | - Ivon Cuscó
- Hospital del Mar Research Institute (IMIM), Barcelona 08003, Spain; Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona 08003, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona 08003, Spain
| | - Marta Puig
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona) 08193, Spain
| | - Mikel Esnaola
- Center for Research in Environmental Epidemiology (CREAL), Barcelona 08003, Spain; Hospital del Mar Research Institute (IMIM), Barcelona 08003, Spain; Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Barcelona 08003, Spain
| | - Judith Reina
- Hospital del Mar Research Institute (IMIM), Barcelona 08003, Spain; Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona 08003, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona 08003, Spain
| | - Valerie Siroux
- INSERM-UJF, U823, Institut Albert Bonniot, 38042 Grenoble, France; Université Joseph Fourier - BP 53, 38041 Grenoble, France
| | - Emmanuelle Bouzigon
- INSERM, UMRS-946, Genetic Variation of Human Diseases Unit, 75010 Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Institut Universitaire d'Hématologie, 75010 Paris, France
| | - Rachel Nadif
- INSERM, U1018, CESP Centre for Research in Epidemiology and Population Health, Respiratory and Environmental Epidemiology Team, 94807 Villejuif, France; Université Paris-Sud 11, UMRS 1018, 94807 Villejuif, France
| | - Eva Reinmaa
- Estonian Genome Center, University of Tartu, Tartu 50090, Estonia
| | - Lili Milani
- Estonian Genome Center, University of Tartu, Tartu 50090, Estonia
| | - Mariona Bustamante
- Center for Research in Environmental Epidemiology (CREAL), Barcelona 08003, Spain; Hospital del Mar Research Institute (IMIM), Barcelona 08003, Spain; Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Barcelona 08003, Spain; Genes and Disease Group, Centre for Genomic Regulation (CRG), Barcelona 08003, Spain
| | - Deborah Jarvis
- National Heart and Lung Institute, Imperial College, London SW7 2AZ, UK
| | - Josep M Antó
- Center for Research in Environmental Epidemiology (CREAL), Barcelona 08003, Spain; Hospital del Mar Research Institute (IMIM), Barcelona 08003, Spain; Department of Mathematics, Universitat Autònoma de Barcelona, Bellaterra (Barcelona) 08193, Spain; Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Jordi Sunyer
- Center for Research in Environmental Epidemiology (CREAL), Barcelona 08003, Spain; Hospital del Mar Research Institute (IMIM), Barcelona 08003, Spain; Department of Mathematics, Universitat Autònoma de Barcelona, Bellaterra (Barcelona) 08193, Spain; Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Florence Demenais
- INSERM, UMRS-946, Genetic Variation of Human Diseases Unit, 75010 Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Institut Universitaire d'Hématologie, 75010 Paris, France
| | - Manolis Kogevinas
- Center for Research in Environmental Epidemiology (CREAL), Barcelona 08003, Spain; Hospital del Mar Research Institute (IMIM), Barcelona 08003, Spain; Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Barcelona 08003, Spain; National School of Public Health, Athens 115 21, Greece
| | - Andres Metspalu
- Estonian Genome Center, University of Tartu, Tartu 50090, Estonia; Institute of Molecular and Cell Biology, University of Tartu, Tartu 50090, Estonia
| | - Mario Cáceres
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona) 08193, Spain; Institució Catalana de Recerca i Estudis Avancats (ICREA), Barcelona 08010, Spain
| | - Luis A Pérez-Jurado
- Hospital del Mar Research Institute (IMIM), Barcelona 08003, Spain; Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona 08003, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona 08003, Spain.
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22
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Perin P, Potočnik U. Polymorphisms in recent GWA identified asthma genes CA10, SGK493, and CTNNA3 are associated with disease severity and treatment response in childhood asthma. Immunogenetics 2014; 66:143-51. [PMID: 24407380 DOI: 10.1007/s00251-013-0755-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 12/24/2013] [Indexed: 01/15/2023]
Abstract
Recent genome-wide association studies (GWAs) have identified several new genetic risk factors for asthma; however, their influence on disease behavior and treatment response is still unclear. The aim of our study was the association analysis of the most significant single nucleotide polymorphisms (SNPs) recently reported by GWAs in different phenotypes of childhood asthma and analysis of correlation between these SNPs and clinical parameters. We have genotyped 288 children with asthma and 276 healthy controls. We provided here first replication of bivariate associations between CA10 (p = 0.001) and SGK493 (p = 0.011) with asthma. In addition, we have identified new correlation between SNPs in CA10, SGK493, and CTNNA3 with asthma behavior and glucocorticoid treatment response. Asthma patients who carried G allele in SNP rs967676 in gene CA10 were associated with more pronounced airway obstruction, higher bronchial hyper-reactivity, and increased inflammation. Higher bronchial hyper-reactivity was also associated with C allele in SNP rs1440095 in gene SGK493 but only in nonatopic asthmatics. In addition, we found that patients who carried at least one T allele in SNP rs1786929 in CTNNA3 (p = 0.022) and atopic patients who carried at least one G allele in SNP rs967676 in gene CA10 (p = 0.034) had higher increase in pulmonary function after glucocorticoid therapy. Our results suggest genetic heterogeneity between atopic and nonatopic asthma. We provided further evidence that treatment response in childhood asthma is genetically predisposed, and we report here two novel SNPs in genes CA10 and CTNNA3 as potential pharmacogenetic biomarkers that could be used in personalized treatment in childhood asthma.
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Affiliation(s)
- Petra Perin
- Faculty of Medicine, Center for Human Molecular Genetics and Pharmacogenomics, University of Maribor, Slomškov trg 15, 2000, Maribor, Slovenia
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23
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Li W, Zhang Y, Gu R, Zhang P, Liang F, Gu J, Zhang X, Zhang H, Zhang H. DNA pooling base genome-wide association study identifies variants at NRXN3 associated with delayed encephalopathy after acute carbon monoxide poisoning. PLoS One 2013; 8:e79159. [PMID: 24265751 PMCID: PMC3827149 DOI: 10.1371/journal.pone.0079159] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Accepted: 09/18/2013] [Indexed: 11/19/2022] Open
Abstract
Delayed encephalopathy after acute carbon monoxide poisoning (DEACMP) is more characteristic of anoxic encephalopathy than of other types of anoxia. Those who have the same poisoning degree and are of similar age and gender have a greater risk of getting DEACMP. This has made it clear that there are obvious personal differences. Genetic factors may play a very important role. The authors performed a genome-wide association study involving pooling of DNA obtained from 175 patients and 244 matched acute carbon monoxide poisoning without delayed encephalopathy controls. The Illumina HumanHap 660 Chip array was used for DNA pools. Allele frequencies of all SNPs were compared between delayed encephalopathy after acute carbon monoxide poisoning and control groups and ranked. A total of 123 SNPs gave an OR >1.4. Of these, 46 mapped in or close to known genes. Forty-eight SNPs located in 19 genes were associated with DEACMP after correction for 5% FDR in the genome-wide association of pooled DNA. Two SNPs (rs11845632 and rs2196447) locate in the Neurexin 3 gene were selected for individual genotyping in all samples and another cohort consisted of 234 and 271 controls. There were significant differences in the genotype and allele frequencies of rs11845632 and rs2196447 between the DEACMP group and controls group (all P-values <0.05). This study describes a positive association between Neurexin 3 and controls in the Han Chinese population, and provides genetic evidence to support the susceptibility of DEACMP, which may be the resulting interaction of environmental and genetic factors.
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Affiliation(s)
- Wenqiang Li
- Department of Neurology, the Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
- Henan Key Lab of Biological Psychiatry, Xinxiang Medical University, Xinxiang, China
- * E-mail: (WL); (RG)
| | - Yanxia Zhang
- Department of Neurology, the Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
- Tongzhou Hospital for Matenal and Child Health Care, Beijing, China
| | - Renjun Gu
- Department of Neurology, the Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
- Henan Key Lab of Biological Psychiatry, Xinxiang Medical University, Xinxiang, China
- * E-mail: (WL); (RG)
| | - Ping Zhang
- Department of Neurology, the Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
| | - Fei Liang
- Health Team of the 93123 Unit, The Chinese People’s Liberation Army, Dalian, China
| | - Jiapeng Gu
- Department of Neurology, the Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
| | - Xuemin Zhang
- Department of Neurology, the Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
| | - Hongya Zhang
- Yang Pu District Center for Disease Control and Prevention, Shanghai, China
| | - Hongxing Zhang
- Henan Key Lab of Biological Psychiatry, Xinxiang Medical University, Xinxiang, China
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24
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Kim YJ, Park SW, Kim TH, Park JS, Cheong HS, Shin HD, Park CS. Genome-wide methylation profiling of the bronchial mucosa of asthmatics: relationship to atopy. BMC MEDICAL GENETICS 2013; 14:39. [PMID: 23521807 PMCID: PMC3616917 DOI: 10.1186/1471-2350-14-39] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 03/14/2013] [Indexed: 01/26/2023]
Abstract
Background Asthma is a common respiratory disease that is characterized by bronchial hyperresponsiveness and airway obstruction due to chronic airway inflammation. Atopic asthma is a typical IgE-mediated disease in which the enhanced production of IgE is driven by the activation of Th2 cells, which release a distinct pattern of cytokines, including interleukin 4 (IL4) and IL3, in response to specific antigen presentation. To evaluate the methylation status of the whole genomes of bronchial mucosa tissues from subjects who lacked or had sensitization to Dermatophagoides farina (Df) and Dermatophagoides pteronyssinus (Dp). Methods The genome-wide DNA methylation levels in the bronchial mucosa tissues of atopic asthmatics (N = 10), non-atopic asthmatics (N = 7), and normal controls (N = 7) were examined using microarrays. Results In the bronchial mucosa of atopic asthmatics, hypermethylation was detected at 6 loci in 6 genes, while hypomethylation was detected at 49 loci in 48 genes compared to those of non-atopic asthmatics. Genes that were assigned the ontologies of multicellular organismal process, response to organic substance, hormone metabolic process, and growth factor receptor binding were hypomethylated. The methylation levels in the mucosa of asthmatics and normal controls were similar. Conclusions The bronchial mucosa of asthmatics who are atopic to Df or Dp have characteristic methylation patterns for 52 genes. The genes and pathways identified in the present study may be associated with the presence of atopy in asthmatics and therefore represent attractive targets for future research.
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Affiliation(s)
- Yoon-Jeong Kim
- Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, 1174, Jung Dong, Wonmi-Gu, Bucheon, Gyeonggi Do 420-021, Korea
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Gerasimova A, Chavez L, Li B, Seumois G, Greenbaum J, Rao A, Vijayanand P, Peters B. Predicting cell types and genetic variations contributing to disease by combining GWAS and epigenetic data. PLoS One 2013; 8:e54359. [PMID: 23382893 PMCID: PMC3559682 DOI: 10.1371/journal.pone.0054359] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 12/11/2012] [Indexed: 12/22/2022] Open
Abstract
Genome-wide association studies (GWASs) identify single nucleotide polymorphisms (SNPs) that are enriched in individuals suffering from a given disease. Most disease-associated SNPs fall into non-coding regions, so that it is not straightforward to infer phenotype or function; moreover, many SNPs are in tight genetic linkage, so that a SNP identified as associated with a particular disease may not itself be causal, but rather signify the presence of a linked SNP that is functionally relevant to disease pathogenesis. Here, we present an analysis method that takes advantage of the recent rapid accumulation of epigenomics data to address these problems for some SNPs. Using asthma as a prototypic example; we show that non-coding disease-associated SNPs are enriched in genomic regions that function as regulators of transcription, such as enhancers and promoters. Identifying enhancers based on the presence of the histone modification marks such as H3K4me1 in different cell types, we show that the location of enhancers is highly cell-type specific. We use these findings to predict which SNPs are likely to be directly contributing to disease based on their presence in regulatory regions, and in which cell types their effect is expected to be detectable. Moreover, we can also predict which cell types contribute to a disease based on overlap of the disease-associated SNPs with the locations of enhancers present in a given cell type. Finally, we suggest that it will be possible to re-analyze GWAS studies with much higher power by limiting the SNPs considered to those in coding or regulatory regions of cell types relevant to a given disease.
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Affiliation(s)
- Anna Gerasimova
- La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America.
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Potaczek DP, Kabesch M. Current concepts of IgE regulation and impact of genetic determinants. Clin Exp Allergy 2013; 42:852-71. [PMID: 22909159 DOI: 10.1111/j.1365-2222.2011.03953.x] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Immunoglobulin E (IgE) mediated immune responses seem to be directed against parasites and neoplasms, but are best known for their involvement in allergies. The IgE network is tightly controlled at different levels as outlined in this review. Genetic determinants were suspected to influence IgE regulation and IgE levels considerably for many years. Linkage and candidate gene studies suggested a number of loci and genes to correlate with total serum IgE levels, and recently genome-wide association studies (GWAS) provided the power to identify genetic determinants for total serum IgE levels: 1q23 (FCER1A), 5q31 (RAD50, IL13, IL4), 12q13 (STAT6), 6p21.3 (HLA-DRB1) and 16p12 (IL4R, IL21R). In this review, we analyse the potential role of these GWAS hits in the IgE network and suggest mechanisms of how genes and genetic variants in these loci may influence IgE regulation.
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Affiliation(s)
- D P Potaczek
- Department of Pediatric Pneumology, Allergy and Neonatology, Hannover Medical School, Hannover, Germany
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Yoon D, Ban HJ, Kim YJ, Kim EJ, Kim HC, Han BG, Park JW, Hong SJ, Cho SH, Park K, Lee JS. Replication of genome-wide association studies on asthma and allergic diseases in Korean adult population. BMB Rep 2012; 45:305-10. [PMID: 22617455 DOI: 10.5483/bmbrep.2012.45.5.305] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Allergic diseases such as asthma, allergic rhinitis, and atopic dermatitis are heterogeneous diseases characterized by multiple symptoms and phenotypes. Recent advancements in genetic study enabled us to identify disease associated genetic factors. Numerous genome-wide association studies (GWAS) have revealed multiple associated loci for allergic diseases. However, the majority of previous studies have been conducted in populations of European ancestry. Moreover, the associations of single nucleotide polymorphisms (SNPs) with allergic diseases have not been studied amongst the large-scale general Korean population. Herein, we performed the replication study to validate the previous variants, known to be associated with allergic diseases, in the Korean population. In this study, we categorized three allergic related phenotypes, one allergy and two asthma related phenotypes, based on self-reports of physician diagnosis and their symptoms from 8,842 samples. As a result, we found nominally significant associations of 6 SNPs with at least one allergic related phenotype in the Korean population.
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Affiliation(s)
- Dankyu Yoon
- Research Center for Standardization of Allergic Disease, Korea National Institute of Health, Osong 363-951, Korea
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Anantharaman R, Andiappan AK, Nilkanth PP, Suri BK, Wang DY, Chew FT. Genome-wide association study identifies PERLD1 as asthma candidate gene. BMC MEDICAL GENETICS 2011; 12:170. [PMID: 22188591 PMCID: PMC3268734 DOI: 10.1186/1471-2350-12-170] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Accepted: 12/21/2011] [Indexed: 11/10/2022]
Abstract
Background Recent genome-wide association studies (GWAS) for asthma have been successful in identifying novel associations which have been well replicated. The aim of this study is to identify the genetic variants that influence predisposition towards asthma in an ethnic Chinese population in Singapore using a GWAS approach. Methods A two-stage GWAS was performed in case samples with allergic asthma, and in control samples without asthma and atopy. In the discovery stage, 490 case and 490 control samples were analysed by pooled genotyping. Significant associations from the first stage were evaluated in a replication cohort of 521 case and 524 control samples in the second stage. The same 980 samples used in the discovery phase were also individually genotyped for purposes of a combined analysis. An additional 1445 non-asthmatic atopic control samples were also genotyped. Results 19 promising SNPs which passed our genome-wide P value threshold of 5.52 × 10-8 were individually genotyped. In the combined analysis of 1011 case and 1014 control samples, SNP rs2941504 in PERLD1 on chromosome 17q12 was found to be significantly associated with asthma at the genotypic level (P = 1.48 × 10-6, ORAG = 0.526 (0.369-0.700), ORAA = 0.480 (0.361-0.639)) and at the allelic level (P = 9.56 × 10-6, OR = 0.745 (0.654-0.848)). These findings were found to be replicated in 3 other asthma GWAS studies, thus validating our own results. Analysis against the atopy control samples suggested that the SNP was associated with allergic asthma and not to either the asthma or allergy components. Genotyping of additional SNPs in 100 kb flanking rs2941504 further confirmed that the association was indeed to PERLD1. PERLD1 is involved in the modification of the glycosylphosphatidylinositol anchors for cell surface markers such as CD48 and CD59 which are known to play multiple roles in T-cell activation and proliferation. Conclusions These findings reveal the association of a PERLD1 as a novel asthma candidate gene and reinforce the involvement of genes on the 17q12-21 chromosomal region in the etiology of asthma.
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Affiliation(s)
- Ramani Anantharaman
- Department of Biological Sciences, National University of Singapore, Singapore
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ColVI myopathies: where do we stand, where do we go? Skelet Muscle 2011; 1:30. [PMID: 21943391 PMCID: PMC3189202 DOI: 10.1186/2044-5040-1-30] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Accepted: 09/23/2011] [Indexed: 02/08/2023] Open
Abstract
Collagen VI myopathies, caused by mutations in the genes encoding collagen type VI (ColVI), represent a clinical continuum with Ullrich congenital muscular dystrophy (UCMD) and Bethlem myopathy (BM) at each end of the spectrum, and less well-defined intermediate phenotypes in between. ColVI myopathies also share common features with other disorders associated with prominent muscle contractures, making differential diagnosis difficult. This group of disorders, under-recognized for a long time, has aroused much interest over the past decade, with important advances made in understanding its molecular pathogenesis. Indeed, numerous mutations have now been reported in the COL6A1, COL6A2 and COL6A3 genes, a large proportion of which are de novo and exert dominant-negative effects. Genotype-phenotype correlations have also started to emerge, which reflect the various pathogenic mechanisms at play in these disorders: dominant de novo exon splicing that enables the synthesis and secretion of mutant tetramers and homozygous nonsense mutations that lead to premature termination of translation and complete loss of function are associated with early-onset, severe phenotypes. In this review, we present the current state of diagnosis and research in the field of ColVI myopathies. The past decade has provided significant advances, with the identification of altered cellular functions in animal models of ColVI myopathies and in patient samples. In particular, mitochondrial dysfunction and a defect in the autophagic clearance system of skeletal muscle have recently been reported, thereby opening potential therapeutic avenues.
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Tan THT, Ellis JA, Saffery R, Allen KJ. The role of genetics and environment in the rise of childhood food allergy. Clin Exp Allergy 2011; 42:20-9. [DOI: 10.1111/j.1365-2222.2011.03823.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Freidin MB, Bragina EY, Fedorova OS, Deev IA, Kulikov ES, Ogorodova LM, Puzyrev VP. Genome-wide association study of allergic diseases in Russians of West Siberia. Mol Biol 2011. [DOI: 10.1134/s0026893311020075] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Naumann A, Söderhäll C, Fölster-Holst R, Baurecht H, Harde V, Müller-Wehling K, Rodríguez E, Ruether A, Franke A, Wagenpfeil S, Novak N, Mempel M, Kalali BN, Allgaeuer M, Koch J, Gerhard M, Melén E, Wahlgren CF, Kull I, Stahl C, Pershagen G, Lauener R, Riedler J, Doekes G, Scheynius A, Illig T, von Mutius E, Schreiber S, Kere J, Kabesch M, Weidinger S. A comprehensive analysis of the COL29A1 gene does not support a role in eczema. J Allergy Clin Immunol 2011; 127:1187-94.e7. [DOI: 10.1016/j.jaci.2010.12.1123] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Revised: 12/16/2010] [Accepted: 12/27/2010] [Indexed: 01/09/2023]
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Gara SK, Grumati P, Squarzoni S, Sabatelli P, Urciuolo A, Bonaldo P, Paulsson M, Wagener R. Differential and restricted expression of novel collagen VI chains in mouse. Matrix Biol 2011; 30:248-57. [PMID: 21477648 DOI: 10.1016/j.matbio.2011.03.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Revised: 03/15/2011] [Accepted: 03/29/2011] [Indexed: 12/22/2022]
Abstract
Recently, three novel collagen VI chains, α4, α5 and α6, were identified. These are thought to substitute for the collagen VI α3 chain, probably forming α1α2α4, α1α2α5 or α1α2α6 heterotrimers. The expression pattern of the novel chains is so far largely unknown. In the present study, we compared the tissue distribution of the novel collagen VI chains in mouse with that of the α3 chain by immunohistochemistry, immunoelectron microscopy and immunoblots. In contrast to the widely expressed α3 chain, the novel chains show a highly differential, restricted and often complementary expression. The α4 chain is strongly expressed in the intestinal smooth muscle, surrounding the follicles in ovary, and in testis. The α5 chain is present in perimysium and at the neuromuscular junctions in skeletal muscle, in skin, in the kidney glomerulus, in the interfollicular stroma in ovary and in the tunica albuginea of testis. The α6 chain is most abundant in the endomysium and perimysium of skeletal muscle and in myocard. Immunoelectron microscopy of skeletal muscle localized the α6 chain to the reticular lamina of muscle fibers. The highly differential and restricted expression points to the possibility of tissue-specific roles of the novel chains in collagen VI assembly and function.
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AKHABIR LOUBNA, SANDFORD ANDREWJ. Genome-wide association studies for discovery of genes involved in asthma. Respirology 2011; 16:396-406. [DOI: 10.1111/j.1440-1843.2011.01939.x] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Genome-wide association studies on IgE regulation: are genetics of IgE also genetics of atopic disease? Curr Opin Allergy Clin Immunol 2011; 10:408-17. [PMID: 20736732 DOI: 10.1097/aci.0b013e32833d7d2d] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW Total IgE levels are considered a useful endophenotype for studying the genetics of atopic diseases. However, the role and significance of genetic factors influencing IgE regulation for atopic diseases as endpoints is unclear. RECENT FINDINGS Recently, genome-wide association studies (GWASs) have been applied to atopic traits with considerable success. A total of seven published GWASs on asthma, one GWAS on eczema, and one GWAS on total IgE have reported 11 new loci. Most of these loci appear to be trait-specific. A notable exception is the Th2 cytokine cluster, where genetic variation seems to be relevant across atopic phenotypes. SUMMARY GWASs have identified several novel asthma and eczema loci as well as novel loci for IgE levels. In this review, we evaluate the interrelation between these loci and summarize to which degree recent findings on IgE reflect genetic vulnerability for atopic disease.
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Miller EK, Dumitrescu L, Cupp C, Dorris S, Taylor S, Sparks R, Fawkes D, Frontiero V, Rezendes AM, Marchant C, Edwards KM, Crawford DC. Atopy history and the genomics of wheezing after influenza vaccination in children 6-59 months of age. Vaccine 2011; 29:3431-7. [PMID: 21396408 DOI: 10.1016/j.vaccine.2011.02.071] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Revised: 02/13/2011] [Accepted: 02/20/2011] [Indexed: 01/13/2023]
Abstract
BACKGROUND A multinational clinical trial compared the safety and efficacy of intranasal trivalent live attenuated influenza vaccine (LAIV) with intramuscular trivalent inactivated vaccine (TIV) in very young children prior to the 2004-5 influenza season [1]. Wheezing was noted more often in recipients of LAIV and laboratory-confirmed influenza infection was noted more often in recipients of TIV. We sought to determine whether epidemiologic or genetic factors were associated with these outcomes. METHODS Atopy surveys and DNA collections were performed in trial participants at two United States sites, Nashville, TN and Boston, MA. DNA samples were genotyped on Illumina Infinium 610 or 660-Quad. Standard allelic tests of association were performed. RESULTS At the Nashville and Boston sites, a total of 99 children completed the trial, 6 (1 TIV, 5 LAIV) developed medically attended wheezing within 42 days following vaccination, and 8 (5 TIV, 3 LAIV) developed laboratory-confirmed influenza during the season. Eighty-one surveys and 70 DNA samples were collected. Family history of asthma (p=0.001) was associated with wheezing after vaccination. Of 468,458 single nucleotide polymorphisms tested in the genome-wide association study (GWAS), none achieved genome-wide significance for either wheezing after vaccination or laboratory-confirmed influenza infection. CONCLUSIONS Family history of asthma appears to be a risk factor for wheezing after influenza vaccination. Given the limitations of the sample size, our pilot study demonstrated the feasibility of performing a GWAS but was not able to determine genetic polymorphisms associated with wheezing after influenza immunization.
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Affiliation(s)
- E Kathryn Miller
- Department of Pediatrics, Vanderbilt University Medical Center, CCC-5323 Medical Center North, Nashville, TN 37232, USA
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Seppinen L, Pihlajaniemi T. The multiple functions of collagen XVIII in development and disease. Matrix Biol 2011; 30:83-92. [DOI: 10.1016/j.matbio.2010.11.001] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2010] [Revised: 11/19/2010] [Accepted: 11/22/2010] [Indexed: 12/11/2022]
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Expression of the Collagen VI α5 and α6 Chains in Normal Human Skin and in Skin of Patients with Collagen VI-Related Myopathies. J Invest Dermatol 2011; 131:99-107. [DOI: 10.1038/jid.2010.284] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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Abstract
Collagens are the most abundant proteins in mammals. The collagen family comprises 28 members that contain at least one triple-helical domain. Collagens are deposited in the extracellular matrix where most of them form supramolecular assemblies. Four collagens are type II membrane proteins that also exist in a soluble form released from the cell surface by shedding. Collagens play structural roles and contribute to mechanical properties, organization, and shape of tissues. They interact with cells via several receptor families and regulate their proliferation, migration, and differentiation. Some collagens have a restricted tissue distribution and hence specific biological functions.
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Affiliation(s)
- Sylvie Ricard-Blum
- Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS, Université Lyon 1, Lyon, 69367, France.
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Madore AM, Laprise C. Immunological and genetic aspects of asthma and allergy. J Asthma Allergy 2010; 3:107-21. [PMID: 21437045 PMCID: PMC3047903 DOI: 10.2147/jaa.s8970] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2010] [Indexed: 12/21/2022] Open
Abstract
Prevalence of allergy and allergic asthma are increasing worldwide. More than half of the US population has a positive skin prick test and approximately 10% are asthmatics. Many studies have been conducted to define immunological pathways underlying allergy and asthma development and to identify the main genetic determinants. In the effort to find missing pieces of the puzzle, new genomic approaches and more standardized ones, such as the candidate gene approach, have been used collectively. This article proposes an overview of the actual knowledge about immunological and genetic aspects of allergy and asthma. Special attention has been drawn to the challenges linked to genetic research in complex traits such as asthma and to the contribution of new genomic approaches.
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Affiliation(s)
- Anne-Marie Madore
- Université du Québec à Chicoutimi, Département des sciences fondamentales, Saguenay, Canada
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