1
|
The Vista of Application of Specific Anaphylaxis Accurate Diagnosis Based on DNA Single-Nucleotide Methylation Sites. CONTRAST MEDIA & MOLECULAR IMAGING 2021; 2021:8202068. [PMID: 34908915 PMCID: PMC8635942 DOI: 10.1155/2021/8202068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/21/2021] [Accepted: 10/29/2021] [Indexed: 11/29/2022]
Abstract
Anaphylaxis has rapidly spread around the world in the last several decades. Environmental factors seem to play a major role, and epigenetic marks, especially DNA methylation, get more attention. We discussed several GEO opening data classifications with TOP 100 specific methylation region values (normalized M-values on line) by machine learning, which are remarkable to classify specific anaphylaxis after monoallergen exposure. Then, we sequenced the whole-genome DNA methylation of six people (3 wormwood monoallergen atopic rhinitis patients and 3 normal-immune people) during the pollen season and analyzed the difference of the single nucleotide and DNA region. The results' divergences were obvious (the differential single nucleotides were mostly distributed in nongene regions but the differential DNA regions of GWAS, on the other hand), which may have caused most single nucleotides to be concealed in the regions' sequences. Therefore, we suggest that we should conduct more “pragmatic” and directly find special single-nucleotide changes after exposure to atopic allergens instead of complex correlativity. It is possible to try to use DNA methylation marks to accurately diagnose anaphylaxis and form a machine learning classification based on the single methylated CpGs.
Collapse
|
2
|
Suarez-Pajes E, Díaz-García C, Rodríguez-Pérez H, Lorenzo-Salazar JM, Marcelino-Rodríguez I, Corrales A, Zheng X, Callero A, Perez-Rodriguez E, Garcia-Robaina JC, González-Montelongo R, Flores C, Guillen-Guio B. Targeted analysis of genomic regions enriched in African ancestry reveals novel classical HLA alleles associated with asthma in Southwestern Europeans. Sci Rep 2021; 11:23686. [PMID: 34880287 PMCID: PMC8654850 DOI: 10.1038/s41598-021-02893-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 11/24/2021] [Indexed: 12/30/2022] Open
Abstract
Despite asthma has a considerable genetic component, an important proportion of genetic risks remain unknown, especially for non-European populations. Canary Islanders have the largest African genetic ancestry observed among Southwestern Europeans and the highest asthma prevalence in Spain. Here we examined broad chromosomal regions previously associated with an excess of African genetic ancestry in Canary Islanders, with the aim of identifying novel risk variants associated with asthma susceptibility. In a two-stage cases-control study, we revealed a variant within HLA-DQB1 significantly associated with asthma risk (rs1049213, meta-analysis p = 1.30 × 10–7, OR [95% CI] = 1.74 [1.41–2.13]) previously associated with asthma and broad allergic phenotype. Subsequent fine-mapping analyses of classical HLA alleles revealed a novel allele significantly associated with asthma protection (HLA-DQA1*01:02, meta-analysis p = 3.98 × 10–4, OR [95% CI] = 0.64 [0.50–0.82]) that had been linked to infectious and autoimmune diseases, and peanut allergy. HLA haplotype analyses revealed a novel haplotype DQA1*01:02-DQB1*06:04 conferring asthma protection (meta-analysis p = 4.71 × 10–4, OR [95% CI] = 0.47 [0.29– 0.73]).
Collapse
Affiliation(s)
- Eva Suarez-Pajes
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Claudio Díaz-García
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Héctor Rodríguez-Pérez
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Jose M Lorenzo-Salazar
- Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Itahisa Marcelino-Rodríguez
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Almudena Corrales
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Xiuwen Zheng
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Ariel Callero
- Allergy Unit, Hospital Universitario N.S. de Candelaria, Santa Cruz de Tenerife, Spain
| | - Eva Perez-Rodriguez
- Allergy Unit, Hospital Universitario N.S. de Candelaria, Santa Cruz de Tenerife, Spain
| | - Jose C Garcia-Robaina
- Allergy Unit, Hospital Universitario N.S. de Candelaria, Santa Cruz de Tenerife, Spain
| | | | - Carlos Flores
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain. .,Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain. .,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.
| | - Beatriz Guillen-Guio
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain. .,Department of Health Sciences, University of Leicester, Leicester, UK.
| |
Collapse
|
3
|
Ackland J, Watson A, Wilkinson TMA, Staples KJ. Interrupting the Conversation: Implications for Crosstalk Between Viral and Bacterial Infections in the Asthmatic Airway. FRONTIERS IN ALLERGY 2021; 2:738987. [PMID: 35386999 PMCID: PMC8974750 DOI: 10.3389/falgy.2021.738987] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 09/20/2021] [Indexed: 12/20/2022] Open
Abstract
Asthma is a heterogeneous, chronic respiratory disease affecting 300 million people and is thought to be driven by different inflammatory endotypes influenced by a myriad of genetic and environmental factors. The complexity of asthma has rendered it challenging to develop preventative and disease modifying therapies and it remains an unmet clinical need. Whilst many factors have been implicated in asthma pathogenesis and exacerbations, evidence indicates a prominent role for respiratory viruses. However, advances in culture-independent detection methods and extensive microbial profiling of the lung, have also demonstrated a role for respiratory bacteria in asthma. In particular, airway colonization by the Proteobacteria species Nontypeable Haemophilus influenzae (NTHi) and Moraxella catarrhalis (Mcat) is associated with increased risk of developing recurrent wheeze and asthma in early life, poor clinical outcomes in established adult asthma and the development of more severe inflammatory phenotypes. Furthermore, emerging evidence indicates that bacterial-viral interactions may influence exacerbation risk and disease severity, highlighting the need to consider the impact chronic airway colonization by respiratory bacteria has on influencing host responses to viral infection. In this review, we first outline the currently understood role of viral and bacterial infections in precipitating asthma exacerbations and discuss the underappreciated potential impact of bacteria-virus crosstalk in modulating host responses. We discuss the mechanisms by which early life infection may predispose to asthma development. Finally, we consider how infection and persistent airway colonization may drive different asthma phenotypes, with a view to identifying pathophysiological mechanisms that may prove tractable to new treatment modalities.
Collapse
Affiliation(s)
- Jodie Ackland
- Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, Southampton, United Kingdom
| | - Alastair Watson
- Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, Southampton, United Kingdom
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
- College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Tom M. A. Wilkinson
- Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, Southampton, United Kingdom
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
- Wessex Investigational Sciences Hub, University of Southampton Faculty of Medicine, Southampton General Hospital, Southampton, United Kingdom
| | - Karl J. Staples
- Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, Southampton, United Kingdom
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
- Wessex Investigational Sciences Hub, University of Southampton Faculty of Medicine, Southampton General Hospital, Southampton, United Kingdom
- *Correspondence: Karl J. Staples
| |
Collapse
|
4
|
Pang L, Yu P, Liu X, Fan Y, Shi Y, Zou S. Fine particulate matter induces airway inflammation by disturbing the balance between Th1/Th2 and regulation of GATA3 and Runx3 expression in BALB/c mice. Mol Med Rep 2021; 23:378. [PMID: 33760131 PMCID: PMC7986036 DOI: 10.3892/mmr.2021.12017] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 01/27/2021] [Indexed: 12/24/2022] Open
Abstract
The present study aimed to examine the effects of 2.5 µm particulate matter (PM2.5) on airway inflammation and to investigate the possible underlying mechanism. Specifically, the focus was on the imbalance of T helper (Th)1/Th2 cells and the dysregulated expression of transcription factors, including trans-acting T cell-specific transcription factor 3 (GATA3), runt-related transcription factor 3 (Runx3) and T-box transcription factor TBX21 (T-bet). In this study, ambient PM2.5 was collected and analyzed, male BALB/c mice were sensitized and treated with PBS, ovalbumin (OVA), PM2.5 or OVA + PM2.5. The effects of PM2.5 alone or PM2.5 + OVA on immunopathological changes, the expression of transcription factors GATA3, Runx3 and T-bet, and the imbalance of Th1/Th2 were investigated. It was found that PM2.5 + OVA co-exposure significantly enhanced inflammatory cell infiltration, increased higher tracheal secretions in lung tissue and upregulated respiratory resistance response to acetylcholine compared with PM2.5 or OVA single exposure and control groups. In addition, higher protein and mRNA expression levels of Th2 inflammatory mediators interleukin (IL)-4, IL-5 and IL-13 in bronchoalveolar lavage fluid were observed in PM2.5 + OVA treated mice, whereas the expression levels of GATA3 and STAT6 were exhibited in mice exposed to OVA + PM2.5 compared with the OVA and PM2.5 groups. By contrast, PM2.5 exposure decreased the protein and mRNA expression levels of Th1 cytokine interferon-γ and transcription factors Runx3 and T-bet, especially among asthmatic mice, different from OVA group, PM2.5 exposure only failed to influence the expression of T-bet. To conclude, PM2.5 exposure evoked the allergic airway inflammation response, especially in the asthmatic mouse model and led to Th1/Th2 imbalance. These effects worked mainly by upregulating GATA3 and downregulating Runx3. These data suggested that Runx3 may play an important role in PM2.5-aggravated asthma in BALB/c mice.
Collapse
Affiliation(s)
- Lingling Pang
- Shandong University, Jinan, Shandong 250100, P.R. China
| | - Pengfei Yu
- Shandong University, Jinan, Shandong 250100, P.R. China
| | - Xueping Liu
- Department of Respiratory Medicine, Yantai Yuhuangding Hospital, Yantai, Shandong 264000, P.R. China
| | - Yingqi Fan
- Department of Respiratory Medicine, Yantai Yuhuangding Hospital, Yantai, Shandong 264000, P.R. China
| | - Ying Shi
- Department of Respiratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu 210006, P.R. China
| | - Shenchun Zou
- Department of Respiratory Medicine, Yantai Yuhuangding Hospital, Yantai, Shandong 264000, P.R. China
| |
Collapse
|
5
|
Abstract
BACKGROUND During the last decade, a number of studies have evaluated the potential association between some genetic polymorphisms and childhood asthma risk, however, the results of published studies appear conflicts. The aim of the present study was to investigate association between genetic polymorphisms and pediatric asthma. METHODS Relevant studies were searched in PubMed, Embase, Web of Science, CNKI (China National Knowledge Infrastructure), Wanfang, and Weipu database. Pooled odds ratios (OR) with 95% confidence interval (CI) were calculated to evaluate the strength of the associations. RESULTS Fifty five case-control studies were finally included in this meta-analysis, including 17,971 pediatric asthma cases and 17,500 controls. Eighteen polymorphisms were identified, of which, 9 polymorphisms were found to be associated with asthma risk in overall populations: IL-13 +2044G/A, IL-4 -590C/T, ADAM33 F+1, ADAM33 T2, ADAM33 T1, ADAM33 ST+4,ORMDL3 rs7216389, VDR FokI, VDR TaqI. Furthermore, IL-13 +2044G/A, IL-4 -590C/T, ADAM33 T2, ADAM33 T1, VDR BsmI polymorphisms may cause an increased risk of asthma among Chinese children. CONCLUSIONS This meta-analysis found that IL-13 +2044G/A, IL-4 -590C/T, ADAM33 F+1, ADAM33 T2, ADAM33 T1, ADAM33 ST+4,ORMDL3 rs7216389, VDR FokI, and VDR TaqI polymorphisms might be risk factors for childhood asthma. Further study with large population and more ethnicities is needed to estimate these associations.
Collapse
Affiliation(s)
- Zhen Ruan
- Shaanxi University of Chinese Medicine
| | - Zhaoling Shi
- Children's Hospital the Second Affiliated Hospital of Shaanxi University of Chinese Medicine
| | - Guocheng Zhang
- Children's Hospital the Second Affiliated Hospital of Shaanxi University of Chinese Medicine
| | - Jiushe Kou
- The Second Affiliated Hospital of Shaanxi University of Chinese Medicine, Xianyang, China
| | - Hui Ding
- Children's Hospital the Second Affiliated Hospital of Shaanxi University of Chinese Medicine
| |
Collapse
|
6
|
Zhu S, Guo T, Zhao H, Qiao G, Han M, Liu J, Yuan C, Wang T, Li F, Yue Y, Yang B. Genome-Wide Association Study Using Individual Single-Nucleotide Polymorphisms and Haplotypes for Erythrocyte Traits in Alpine Merino Sheep. Front Genet 2020; 11:848. [PMID: 32849829 PMCID: PMC7411260 DOI: 10.3389/fgene.2020.00848] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 07/13/2020] [Indexed: 11/13/2022] Open
Abstract
Adaptation to high-altitude hypoxia is essential for domestic animals, such as yak, Tibetan chicken, and Tibetan sheep, living on high plateaus, as it ensures efficient oxygen absorption and utilization. Red blood cells are the primary medium for transporting oxygen in the blood. However, little is known about the genetic mechanism of erythrocyte traits. Genome-wide association studies (GWASs) based on single markers or haplotypes have identified potential mechanisms for genetic variation and quantitative traits. To identify loci associated with erythrocyte traits, we performed a GWAS based on the method of the single marker and haplotype in 498 Alpine Merino sheep for six erythrocyte traits: red blood cell count (RBC), hemoglobin (HGB), hematocrit (HCT), mean corpuscular hemoglobin (MCH), mean corpuscular hemoglobin concentration (MCHC), and RBC volume distribution width coefficient of variation (RWD_CV). Forty-two significant single-nucleotide polymorphisms (SNPs) associated with the six erythrocyte traits were detected by means of a single-marker GWAS, and 34 significant haplotypes associated with five erythrocyte traits were detected by means of haplotype analysis. We identified six genes (DHCR24, SPATA9, FLI1, PLCB1, EFNB2, and SH2B3) as potential genes of interest via gene function annotations, location, and expression variation. In particular, FLI1 and PLCB1 were associated with hematopoiesis and erythropoiesis, respectively. These results provide a theoretical basis for analyzing erythrocyte traits and high-altitude hypoxia adaptation in Alpine Merino sheep and will be a useful reference for future studies of plateau-dwelling livestock.
Collapse
Affiliation(s)
- Shaohua Zhu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Sheep Breeding Engineering Technology Center, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Tingting Guo
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Sheep Breeding Engineering Technology Center, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Hongchang Zhao
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Sheep Breeding Engineering Technology Center, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Guoyan Qiao
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Sheep Breeding Engineering Technology Center, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Mei Han
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Sheep Breeding Engineering Technology Center, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Jianbin Liu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Sheep Breeding Engineering Technology Center, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Chao Yuan
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Sheep Breeding Engineering Technology Center, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Tianxiang Wang
- Gansu Provincial Sheep Breeding Technology Extension Station, Sunan, China
| | - Fanwen Li
- Gansu Provincial Sheep Breeding Technology Extension Station, Sunan, China
| | - Yaojing Yue
- Sheep Breeding Engineering Technology Center, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Bohui Yang
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| |
Collapse
|
7
|
Ivanova O, Richards LB, Vijverberg SJ, Neerincx AH, Sinha A, Sterk PJ, Maitland‐van der Zee AH. What did we learn from multiple omics studies in asthma? Allergy 2019; 74:2129-2145. [PMID: 31004501 DOI: 10.1111/all.13833] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 03/25/2019] [Accepted: 04/12/2019] [Indexed: 12/13/2022]
Abstract
More than a decade has passed since the finalization of the Human Genome Project. Omics technologies made a huge leap from trendy and very expensive to routinely executed and relatively cheap assays. Simultaneously, we understood that omics is not a panacea for every problem in the area of human health and personalized medicine. Whilst in some areas of research omics showed immediate results, in other fields, including asthma, it only allowed us to identify the incredibly complicated molecular processes. Along with their possibilities, omics technologies also bring many issues connected to sample collection, analyses and interpretation. It is often impossible to separate the intrinsic imperfection of omics from asthma heterogeneity. Still, many insights and directions from applied omics were acquired-presumable phenotypic clusters of patients, plausible biomarkers and potential pathways involved. Omics technologies develop rapidly, bringing improvements also to asthma research. These improvements, together with our growing understanding of asthma subphenotypes and underlying cellular processes, will likely play a role in asthma management strategies.
Collapse
Affiliation(s)
- Olga Ivanova
- Department of Respiratory Medicine, Amsterdam University Medical Centres (AUMC) University of Amsterdam Amsterdam the Netherlands
| | - Levi B. Richards
- Department of Respiratory Medicine, Amsterdam University Medical Centres (AUMC) University of Amsterdam Amsterdam the Netherlands
| | - Susanne J. Vijverberg
- Department of Respiratory Medicine, Amsterdam University Medical Centres (AUMC) University of Amsterdam Amsterdam the Netherlands
| | - Anne H. Neerincx
- Department of Respiratory Medicine, Amsterdam University Medical Centres (AUMC) University of Amsterdam Amsterdam the Netherlands
| | - Anirban Sinha
- Department of Respiratory Medicine, Amsterdam University Medical Centres (AUMC) University of Amsterdam Amsterdam the Netherlands
| | - Peter J. Sterk
- Department of Respiratory Medicine, Amsterdam University Medical Centres (AUMC) University of Amsterdam Amsterdam the Netherlands
| | - Anke H. Maitland‐van der Zee
- Department of Respiratory Medicine, Amsterdam University Medical Centres (AUMC) University of Amsterdam Amsterdam the Netherlands
- Department of Paediatric Pulmonology Amsterdam UMC/ Emma Children's Hospital Amsterdam the Netherlands
| |
Collapse
|
8
|
Abstract
Asthma has been the most common chronic disease in children that places a major burden for affected people and their families.An integrated analysis of microarrays studies was performed to identify differentially expressed genes (DEGs) in childhood asthma compared with normal control. We also obtained the differentially methylated genes (DMGs) in childhood asthma according to GEO. The genes that were both differentially expressed and differentially methylated were identified. Functional annotation and protein-protein interaction network construction were performed to interpret biological functions of DEGs. We performed q-RT-PCR to verify the expression of selected DEGs.One DNA methylation and 3 gene expression datasets were obtained. Four hundred forty-one DEGs and 1209 DMGs in childhood asthma were identified. Among which, 16 genes were both differentially expressed and differentially methylated in childhood asthma. Natural killer cell mediated cytotoxicity pathway, Jak-STAT signaling pathway, and Wnt signaling pathway were 3 significantly enriched pathways in childhood asthma according to our KEGG enrichment analysis. The PPI network of top 20 up- and downregulated DEGs consisted of 822 nodes and 904 edges and 2 hub proteins (UBQLN4 and MID2) were identified. The expression of 8 DEGs (GZMB, FGFBP2, CLC, TBX21, ALOX15, IL12RB2, UBQLN4) was verified by qRT-PCR and only the expression of GZMB and FGFBP2 was inconsistent with our integrated analysis.Our finding was helpful to elucidate the underlying mechanism of childhood asthma and develop new potential diagnostic biomarker and provide clues for drug design.
Collapse
Affiliation(s)
| | | | - Yu-Hua Mu
- Department of General Surgery, Rizhao People's Hospital, Rizhao, China
| | | |
Collapse
|
9
|
Zhang X, Biagini Myers JM, Burleson JD, Ulm A, Bryan KS, Chen X, Weirauch MT, Baker TA, Butsch Kovacic MS, Ji H. Nasal DNA methylation is associated with childhood asthma. Epigenomics 2018; 10:629-641. [PMID: 29692198 DOI: 10.2217/epi-2017-0127] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
AIM We aim to study DNA methylation (DNAm) variations associated with childhood asthma. METHODS Nasal DNAm was compared between sibling pairs discordant for asthma, 29 sib pairs for genome-wide association studies and 54 sib pairs for verification by pyrosequencing. Associations of methylation with asthma symptoms, allergy and environmental exposures were evaluated. In vitro experiments and functional genomic analyses were performed to explore biologic relevance. RESULTS Three CpGs were associated with asthma. cg14830002 was associated with allergies in nonasthmatics. cg23602092 was associated with asthma symptoms. cg14830002 and cg23602092 were associated with traffic-related air pollution exposure. Nearby genes were transcriptionally regulated by diesel exhaust, house dust mite and 5-aza-2'-deoxycytidine. Active chromatin marks and transcription factor binding were found around these sites. CONCLUSION We identified novel DNAm variations associated with childhood asthma and suggested new disease-contributing epigenetic mechanisms.
Collapse
Affiliation(s)
- Xue Zhang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Pyrosequencing Lab for Genomic & Epigenomic Research, Cincinnati, Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Jocelyn M Biagini Myers
- Division of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Pediatrics, University of Cincinnati, Cincinnati, OH 45229, USA
| | - J D Burleson
- Division of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Ashley Ulm
- Pyrosequencing Lab for Genomic & Epigenomic Research, Cincinnati, Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Division of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Kelly S Bryan
- Division of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Xiaoting Chen
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Matthew T Weirauch
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH 45229, USA.,Center for Autoimmune Genomics & Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Divisions of Biomedical Informatics & Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Theresa A Baker
- Division of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Melinda S Butsch Kovacic
- Division of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Pediatrics, University of Cincinnati, Cincinnati, OH 45229, USA.,Division of Biostatistics & Epidemiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Hong Ji
- Pyrosequencing Lab for Genomic & Epigenomic Research, Cincinnati, Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Division of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Pediatrics, University of Cincinnati, Cincinnati, OH 45229, USA
| |
Collapse
|
10
|
Yang IV, Richards A, Davidson EJ, Stevens AD, Kolakowski CA, Martin RJ, Schwartz DA. The Nasal Methylome: A Key to Understanding Allergic Asthma. Am J Respir Crit Care Med 2017; 195:829-831. [PMID: 28294656 DOI: 10.1164/rccm.201608-1558le] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Ivana V Yang
- 1 University of Colorado School of Medicine Aurora, Colorado and.,2 National Jewish Health Denver, Colorado
| | - Adam Richards
- 1 University of Colorado School of Medicine Aurora, Colorado and
| | | | | | | | - Richard J Martin
- 1 University of Colorado School of Medicine Aurora, Colorado and.,2 National Jewish Health Denver, Colorado
| | - David A Schwartz
- 1 University of Colorado School of Medicine Aurora, Colorado and.,2 National Jewish Health Denver, Colorado
| |
Collapse
|
11
|
Yang IV, Pedersen BS, Liu AH, O'Connor GT, Pillai D, Kattan M, Misiak RT, Gruchalla R, Szefler SJ, Khurana Hershey GK, Kercsmar C, Richards A, Stevens AD, Kolakowski CA, Makhija M, Sorkness CA, Krouse RZ, Visness C, Davidson EJ, Hennessy CE, Martin RJ, Togias A, Busse WW, Schwartz DA. The nasal methylome and childhood atopic asthma. J Allergy Clin Immunol 2016; 139:1478-1488. [PMID: 27745942 DOI: 10.1016/j.jaci.2016.07.036] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Revised: 06/24/2016] [Accepted: 07/14/2016] [Indexed: 12/13/2022]
Abstract
BACKGROUND Given the strong environmental influence on both epigenetic marks and allergic asthma in children, the epigenetic alterations in respiratory epithelia might provide insight into allergic asthma. OBJECTIVE We sought to identify DNA methylation and gene expression changes associated with childhood allergic persistent asthma. METHODS We compared genomic DNA methylation patterns and gene expression in African American children with persistent atopic asthma (n = 36) versus healthy control subjects (n = 36). Results were validated in an independent population of asthmatic children (n = 30) by using a shared healthy control population (n = 36) and in an independent population of white adult atopic asthmatic patients (n = 12) and control subjects (n = 12). RESULTS We identified 186 genes with significant methylation changes, differentially methylated regions or differentially methylated probes, after adjustment for age, sex, race/ethnicity, batch effects, inflation, and multiple comparisons. Genes differentially methylated included those with established roles in asthma and atopy and genes related to extracellular matrix, immunity, cell adhesion, epigenetic regulation, and airflow obstruction. The methylation changes were substantial (median, 9.5%; range, 2.6% to 29.5%). Hypomethylated and hypermethylated genes were associated with increased and decreased gene expression, respectively (P < 2.8 × 10-6 for differentially methylated regions and P < 7.8 × 10-10 for differentially methylated probes). Quantitative analysis in 53 differentially expressed genes demonstrated that 32 (60%) have significant methylation-expression relationships within 5 kb of the gene. Ten loci selected based on the relevance to asthma, magnitude of methylation change, and methylation-expression relationships were validated in an independent cohort of children with atopic asthma. Sixty-seven of 186 genes also have significant asthma-associated methylation changes in nasal epithelia of adult white asthmatic patients. CONCLUSIONS Epigenetic marks in respiratory epithelia are associated with allergic asthma and gene expression changes in inner-city children.
Collapse
Affiliation(s)
- Ivana V Yang
- Department of Medicine and University of Colorado, School of Medicine, Aurora, Colo; National Jewish Health, Denver, Colo; Department of Epidemiology, Colorado School of Public Health, Aurora, Colo.
| | - Brent S Pedersen
- Department of Medicine and University of Colorado, School of Medicine, Aurora, Colo
| | | | - George T O'Connor
- Department of Medicine, Boston University School of Medicine, Boston, Mass
| | | | - Meyer Kattan
- Columbia University Medical Center, New York, NY
| | | | | | - Stanley J Szefler
- Department of Pediatrics, Children's Hospital Colorado and University of Colorado, School of Medicine, Aurora, Colo
| | | | | | - Adam Richards
- Department of Medicine and University of Colorado, School of Medicine, Aurora, Colo
| | | | | | | | - Christine A Sorkness
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wis
| | | | | | - Elizabeth J Davidson
- Department of Medicine and University of Colorado, School of Medicine, Aurora, Colo
| | - Corinne E Hennessy
- Department of Medicine and University of Colorado, School of Medicine, Aurora, Colo
| | | | - Alkis Togias
- National Institute of Allergy and Infectious Diseases, Bethesda, Md; and University of Colorado, Aurora, CO
| | - William W Busse
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wis
| | - David A Schwartz
- Department of Medicine and University of Colorado, School of Medicine, Aurora, Colo; National Jewish Health, Denver, Colo; Department of Immunology, University of Colorado, Aurora, Colo.
| |
Collapse
|
12
|
Lockett GA, Soto-Ramírez N, Ray MA, Everson TM, Xu CJ, Patil VK, Terry W, Kaushal A, Rezwan FI, Ewart SL, Gehring U, Postma DS, Koppelman GH, Arshad SH, Zhang H, Karmaus W, Holloway JW. Association of season of birth with DNA methylation and allergic disease. Allergy 2016; 71:1314-24. [PMID: 26973132 PMCID: PMC5639882 DOI: 10.1111/all.12882] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/08/2016] [Indexed: 12/31/2022]
Abstract
BACKGROUND Season of birth influences allergy risk; however, the biological mechanisms underlying this observation are unclear. The environment affects DNA methylation, with potentially long-lasting effects on gene expression and disease. This study examined whether DNA methylation could underlie the association between season of birth and allergy. METHODS In a subset of 18-year-old participants from the Isle of Wight (IoW) birth cohort (n = 367), the risks of birth season on allergic outcomes were estimated. Whole blood epigenome-wide DNA methylation was measured, and season-associated CpGs detected using a training-and-testing-based technique. Validation method examined the 8-year-old Prevention and Incidence of Asthma and Mite Allergy (PIAMA) cohort. The relationships between DNA methylation, season of birth and allergy were examined. CpGs were analysed in IoW third-generation cohort newborns. RESULTS Autumn birth increased risk of eczema, relative to spring birth. Methylation at 92 CpGs showed association with season of birth in the epigenome-wide association study. In validation, significantly more CpGs had the same directionality than expected by chance, and four were statistically significant. Season-associated methylation was enriched among networks relating to development, the cell cycle and apoptosis. Twenty CpGs were nominally associated with allergic outcomes. Two CpGs were marginally on the causal pathway to allergy. Season-associated methylation was largely absent in newborns, suggesting it arises post-natally. CONCLUSIONS This study demonstrates that DNA methylation in adulthood is associated with season of birth, supporting the hypothesis that DNA methylation could mechanistically underlie the effect of season of birth on allergy, although other mechanisms are also likely to be involved.
Collapse
Affiliation(s)
- Gabrielle A. Lockett
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Nelís Soto-Ramírez
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Meredith A. Ray
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Todd M. Everson
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
| | - Cheng-Jian Xu
- Department of Pulmonology, GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Genetics, GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Veeresh K. Patil
- The David Hide Asthma and Allergy Research Centre, Isle of Wight, UK
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - William Terry
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Akhilesh Kaushal
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Faisal I. Rezwan
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Susan L. Ewart
- Department of Large Animal Clinical Sciences, Michigan State University, East Lansing, MI, USA
| | - Ulrike Gehring
- Institute for Risk Assessment Sciences, Division of Environmental Epidemiology, Utrecht University, The Netherlands
| | - Dirkje S. Postma
- Department of Pulmonary Medicine and Tuberculosis, GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Gerard H. Koppelman
- Department of Pediatric Pulmonology and Pediatric Allergology, GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Beatrix Children’s Hospital, Groningen, The Netherlands
| | - S. Hasan Arshad
- The David Hide Asthma and Allergy Research Centre, Isle of Wight, UK
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - John W. Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| |
Collapse
|
13
|
Cho SH, Min JY, Kim DY, Oh SS, Torgerson DR, Pino-Yanes M, Hu D, Sen S, Huntsman S, Eng C, Farber HJ, Rodriguez-Cintron W, Rodriguez-Santana JR, Serebrisky D, Thyne SM, Borrell LN, Williams LK, DuPont W, Seibold MA, Burchard EG, Avila PC, Kumar R. Association of a PAI-1 Gene Polymorphism and Early Life Infections with Asthma Risk, Exacerbations, and Reduced Lung Function. PLoS One 2016; 11:e0157848. [PMID: 27556405 PMCID: PMC4996454 DOI: 10.1371/journal.pone.0157848] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 06/06/2016] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Plasminogen activator inhibitor-1 (PAI-1) is induced in airways by virus and may mediate asthmatic airway remodeling. We sought to evaluate if genetic variants and early life lower respiratory infections jointly affect asthma risk. METHODS We included Latino children, adolescents, and young adults aged 8-21 years (1736 subjects with physician-diagnosed asthma and 1747 healthy controls) from five U.S. centers and Puerto Rico after excluding subjects with incomplete clinical or genetic data. We evaluated the independent and joint effects of a PAI-1 gain of function polymorphism and bronchiolitis / Respiratory Syncytial Virus (RSV) or other lower respiratory infections (LRI) within the first 2 years of life on asthma risk, asthma exacerbations and lung function. RESULTS RSV infection (OR 9.9, 95%CI 4.9-20.2) and other LRI (OR 9.1, 95%CI 7.2-11.5) were independently associated with asthma, but PAI-1 genotype was not. There were joint effects on asthma risk for both genotype-RSV (OR 17.7, 95% CI 6.3-50.2) and genotype-LRI (OR 11.7, 95% CI 8.8-16.4). A joint effect of genotype-RSV resulted in a 3.1-fold increased risk for recurrent asthma hospitalizations. In genotype-respiratory infection joint effect analysis, FEV1% predicted and FEV1/FVC % predicted were further reduced in the genotype-LRI group (β -2.1, 95% CI -4.0 to -0.2; β -2.0, 95% CI -3.1 to -0.8 respectively). Similarly, lower FEV1% predicted was noted in genotype-RSV group (β -3.1, 95% CI -6.1 to -0.2) with a trend for lower FEV1/FVC % predicted. CONCLUSIONS A genetic variant of PAI-1 together with early life LRI such as RSV bronchiolitis is associated with an increased risk of asthma, morbidity, and reduced lung function in this Latino population.
Collapse
Affiliation(s)
- Seong H. Cho
- Division of Allergy-Immunology, Department of Medicine, Northwestern University, Chicago, Illinois, United States of America
- Division of Allergy-Immunology, Department of Internal Medicine, University of South Florida, Tampa, Florida, United States of America
| | - Jin-Young Min
- Department of Otolaryngology, Northwestern University, Chicago, Illinois, United States of America
| | - Dong Young Kim
- Division of Allergy-Immunology, Department of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Sam S. Oh
- Department of Medicine, University of California, San Francisco, California, United States of America
| | - Dara R. Torgerson
- Department of Medicine, University of California, San Francisco, California, United States of America
| | - Maria Pino-Yanes
- Department of Medicine, University of California, San Francisco, California, United States of America
| | - Donglei Hu
- Department of Medicine, University of California, San Francisco, California, United States of America
| | - Saunak Sen
- Division of Biostatistics, Department of Preventive Medicine, UTHSC, Memphis, Tennessee, United States of America
| | - Scott Huntsman
- Department of Medicine, University of California, San Francisco, California, United States of America
| | - Celeste Eng
- Department of Medicine, University of California, San Francisco, California, United States of America
| | - Harold J. Farber
- Department of Pediatrics, Section of Pulmonology, Baylor College of Medicine, Texas Children's Hospital, Houston, Texas, United States of America
| | | | | | - Denise Serebrisky
- Pediatric Pulmonary Division, Jacobi Medical Center, Bronx, New York, United States of America
| | - Shannon M. Thyne
- Department of Pediatrics, University of California, San Francisco, California, United States of America
| | - Luisa N. Borrell
- Department of Health Sciences, Lehman College, CUNY, New York, New York, United States of America
| | - L. Keoki Williams
- Department of Internal Medicine, Henry Ford Health System, Detroit, Michigan, United States of America
- Center for Health Policy and Health Services Research, Henry Ford Health System, Detroit, Michigan, United States of America
| | - William DuPont
- Department of Biostatistics, Vanderbilt University Medical School, Nashville, Tennessee, United States of America
| | - Max A. Seibold
- Center for Genes, Environment and Health, National Jewish Health, Denver, Colorado, United States of America
| | - Esteban G. Burchard
- Department of Medicine, University of California, San Francisco, California, United States of America
| | - Pedro C. Avila
- Division of Allergy-Immunology, Department of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Rajesh Kumar
- Division of Allergy-Immunology, Department of Pediatrics, Northwestern University, Chicago, Illinois, United States of America
- The Ann and Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, United States of America
- * E-mail:
| |
Collapse
|
14
|
Identification of Susceptibility Genes of Adult Asthma in French Canadian Women. Can Respir J 2016; 2016:3564341. [PMID: 27445529 PMCID: PMC4904514 DOI: 10.1155/2016/3564341] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 12/05/2015] [Indexed: 11/18/2022] Open
Abstract
Susceptibility genes of asthma may be more successfully identified by studying subgroups of phenotypically similar asthma patients. This study aims to identify single nucleotide polymorphisms (SNPs) associated with asthma in French Canadian adult women. A pooling-based genome-wide association study was performed in 240 allergic asthmatic and 120 allergic nonasthmatic women. The top associated SNPs were selected for individual genotyping in an extended cohort of 349 asthmatic and 261 nonasthmatic women. The functional impact of asthma-associated SNPs was investigated in a lung expression quantitative trait loci (eQTL) mapping study (n = 1035). Twenty-one of the 38 SNPs tested by individual genotyping showed P values lower than 0.05 for association with asthma. Cis-eQTL analyses supported the functional contribution of rs17801353 associated with C3AR1 (P = 7.90E - 10). The asthma risk allele for rs17801353 is associated with higher mRNA expression levels of C3AR1 in lung tissue. In silico functional characterization of the asthma-associated SNPs also supported the contribution of C3AR1 and additional genes including SYNE1, LINGO2, and IFNG-AS1. This pooling-based GWAS in French Canadian adult women followed by lung eQTL mapping suggested C3AR1 as a functional locus associated with asthma. Additional susceptibility genes were suggested in this homogenous subgroup of asthma patients.
Collapse
|
15
|
Kidd CDA, Thompson PJ, Barrett L, Baltic S. Histone Modifications and Asthma. The Interface of the Epigenetic and Genetic Landscapes. Am J Respir Cell Mol Biol 2016; 54:3-12. [PMID: 26397168 DOI: 10.1165/rcmb.2015-0050tr] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Complex lung diseases, such as asthma, are influenced by both genetic predisposition and environmental stimuli. The epigenetic landscape of such diseases is attracting increasing interest and research. Epigenetics broadly covers the transient and the inheritable changes to gene expression that are not directly due to changes in nucleotide sequences. Epigenetic mechanisms could have significant impact on asthma-related allergic, immune, and regulatory pathways, as well as on the generation of biomarkers and the heritable transmission of asthma phenotypes. Recent technological advances have allowed mapping of the epigenome and analysis of genome-wide epigenetic contributors to disease. As a result, ground-breaking observations regarding histone post-translational modifications in a number of immunological diseases have emerged. In this review, we look beyond the biological information coded by DNA and review the epigenetic modifications made to histones, with evidence suggesting a role for their modification in asthma.
Collapse
Affiliation(s)
- Courtney D A Kidd
- 1 Institute for Respiratory Health, Perth, Western Australia, Australia.,2 Centre for Respiratory Health, School of Medicine and Pharmacology, University of Western Australia, Perth, Western Australia, Australia; and
| | - Philip J Thompson
- 1 Institute for Respiratory Health, Perth, Western Australia, Australia.,2 Centre for Respiratory Health, School of Medicine and Pharmacology, University of Western Australia, Perth, Western Australia, Australia; and.,3 Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Western Australia, Perth, Western Australia, Australia
| | - Lucy Barrett
- 1 Institute for Respiratory Health, Perth, Western Australia, Australia.,2 Centre for Respiratory Health, School of Medicine and Pharmacology, University of Western Australia, Perth, Western Australia, Australia; and
| | - Svetlana Baltic
- 1 Institute for Respiratory Health, Perth, Western Australia, Australia.,2 Centre for Respiratory Health, School of Medicine and Pharmacology, University of Western Australia, Perth, Western Australia, Australia; and
| |
Collapse
|
16
|
Han S, Zhang H, Lockett GA, Mukherjee N, Holloway JW, Karmaus W. Identifying heterogeneous transgenerational DNA methylation sites via clustering in beta regression. Ann Appl Stat 2015. [DOI: 10.1214/15-aoas865] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
17
|
Abstract
Asthma is the most common chronic disease among children. It cannot be prevented but can be controlled. Industrialized countries experience high lifetime asthma prevalence that has increased over recent decades. Asthma has a complex interplay of genetic and environmental triggers. Studies have revealed complex interactions of lung structure and function genes with environmental exposures such as environmental tobacco smoke and vitamin D. Home environmental strategies can reduce asthma morbidity in children but should be tailored to specific allergens. Coupled with education and severity-specific asthma therapy, tailored interventions may be the most effective strategy to manage childhood asthma.
Collapse
Affiliation(s)
- Jessica P Hollenbach
- Department of Pediatrics, Asthma Center, The Children's Center for Community Research, CT Children's Medical Center, University of Connecticut School of Medicine, 282 Washington Street, Hartford, CT 06106, USA
| | - Michelle M Cloutier
- Department of Pediatrics, Asthma Center, The Children's Center for Community Research, Connecticut Children's Medical Center, University of Connecticut Health Center, 282 Washington Street, Hartford, CT 06106, USA.
| |
Collapse
|
18
|
Abstract
It has been recognized for centuries that allergic disease runs in families, implying a role for genetic factors in determining individual susceptibility. More recently, a range of evidence shows that many of these genetic factors, together with in utero environmental exposures, lead to the development of allergic disease through altered immune and organ development. Environmental exposures during pregnancy including diet, nutrient intake and toxin exposures can alter the epigenome and interact with inherited genetic and epigenetic risk factors to directly and indirectly influence organ development and immune programming. Understanding of these factors will be essential in identifying at-risk individuals and possible development of therapeutic interventions for the primary prevention of allergic disease. In this review, we summarize the evidence that suggests allergic disease begins in utero, together with possible mechanisms for the effect of environmental exposures during pregnancy on allergic disease risk, including epigenetics.
Collapse
Affiliation(s)
- Gabrielle A Lockett
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Johanna Huoman
- Department of Clinical and Experimental Medicine, Division of Neuro and Inflammation Sciences, Unit of Autoimmunity and Immune Regulation, Linköping University, Linköping, Sweden
| | - John W Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK.,Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK.,International Inflammation network (in-FLAME) of the World Universities Network
| |
Collapse
|
19
|
Abstract
BACKGROUND Pediatric Inflammatory Bowel Disease (PIBD) is a chronic condition seen in genetically predisposed individuals. Genome-wide association studies have implicated >160 genomic loci in IBD with many genes coding for proteins in key immune pathways. This study looks at autoimmune disease burden in patients diagnosed with PIBD and interrogates exome data of a subset of patients. METHODS Patients were recruited from the Southampton Genetics of PIBD cohort. Clinical diagnosis of autoimmune disease in these individuals was ascertained from medical records. For a subset of patients with PIBD and concurrent asthma, exome data was interrogated to ascertain the burden of pathogenic variants within genes implicated in asthma. Association testing was conducted between cases and population controls using the SKAT-O test. RESULTS Forty-nine (28.3%) PIBD children (18.49% CD, 8.6% UC, and 21.15% IBDU patients) had a concurrent clinical diagnosis of at least one other autoimmune disorder; asthma was the most prevalent, affecting 16.2% of the PIBD cohort. Rare and common variant association testing revealed 6 significant genes (P < 0.05) before Bonferroni adjustment. Three of these genes were previously implicated in both asthma and IBD (ZPBP2 IL1R1, and IL18R1) and 3 in asthma only (PYHIN1, IL2RB, and GSTP1). CONCLUSIONS One-third of our cohort had a concurrent autoimmune condition. We observed higher incidence of asthma compared with the overall pediatric prevalence. Despite a small sample size, SKAT-O evaluated a significant burden of rare and common mutations in 6 genes. Variant burden suggests that a systemic immune dysregulation rather than organ-specific could underpin immune dysfunction for a subset of patients.
Collapse
|
20
|
Guibas GV, Megremis S, West P, Papadopoulos NG. Contributing factors to the development of childhood asthma: working toward risk minimization. Expert Rev Clin Immunol 2015; 11:721-35. [PMID: 25873298 DOI: 10.1586/1744666x.2015.1035649] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Asthma is the most common chronic disease in childhood, and considerable research has been undertaken to find ways to prevent its development and reduce its prevalence. For such interventions to be successful, risk factors for asthma emergence should be identified and clearly defined. Data are robust for some of them, including atopy, viral infections and exposure to airborne irritants, whereas it is less conclusive for others, such as aeroallergen exposure and bacterial infections. Several interventions for asthma prevention, including avoidance and pharmacotherapy, have been attempted. However, most of them have furnished equivocal results. Various issues hinder the establishment of risk factors for asthma development and reduce the effectiveness of interventions, including the complexity of the disease and the fluidity of the developing systems in childhood. In this review, we revisit the evidence on pediatric asthma risk factors and prevention and discuss issues that perplex this field.
Collapse
Affiliation(s)
- George V Guibas
- Centre for Pediatrics and Child Health, Institute of Human Development, University of Manchester, Manchester, UK
| | | | | | | |
Collapse
|
21
|
Yang IV, Pedersen BS, Liu A, O'Connor GT, Teach SJ, Kattan M, Misiak RT, Gruchalla R, Steinbach SF, Szefler SJ, Gill MA, Calatroni A, David G, Hennessy CE, Davidson EJ, Zhang W, Gergen P, Togias A, Busse WW, Schwartz DA. DNA methylation and childhood asthma in the inner city. J Allergy Clin Immunol 2015; 136:69-80. [PMID: 25769910 DOI: 10.1016/j.jaci.2015.01.025] [Citation(s) in RCA: 156] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 01/21/2015] [Accepted: 01/23/2015] [Indexed: 01/15/2023]
Abstract
BACKGROUND Epigenetic marks are heritable, influenced by the environment, direct the maturation of T lymphocytes, and in mice enhance the development of allergic airway disease. Thus it is important to define epigenetic alterations in asthmatic populations. OBJECTIVE We hypothesize that epigenetic alterations in circulating PBMCs are associated with allergic asthma. METHODS We compared DNA methylation patterns and gene expression in inner-city children with persistent atopic asthma versus healthy control subjects by using DNA and RNA from PBMCs. Results were validated in an independent population of asthmatic patients. RESULTS Comparing asthmatic patients (n = 97) with control subjects (n = 97), we identified 81 regions that were differentially methylated. Several immune genes were hypomethylated in asthma, including IL13, RUNX3, and specific genes relevant to T lymphocytes (TIGIT). Among asthmatic patients, 11 differentially methylated regions were associated with higher serum IgE concentrations, and 16 were associated with percent predicted FEV1. Hypomethylated and hypermethylated regions were associated with increased and decreased gene expression, respectively (P < 6 × 10(-12) for asthma and P < .01 for IgE). We further explored the relationship between DNA methylation and gene expression using an integrative analysis and identified additional candidates relevant to asthma (IL4 and ST2). Methylation marks involved in T-cell maturation (RUNX3), TH2 immunity (IL4), and oxidative stress (catalase) were validated in an independent asthmatic cohort of children living in the inner city. CONCLUSIONS Our results demonstrate that DNA methylation marks in specific gene loci are associated with asthma and suggest that epigenetic changes might play a role in establishing the immune phenotype associated with asthma.
Collapse
Affiliation(s)
- Ivana V Yang
- Department of Medicine, University of Colorado, School of Medicine, Aurora, Colo; Departments of Pediatrics and Medicine, National Jewish Health, Denver, Colo
| | - Brent S Pedersen
- Department of Medicine, University of Colorado, School of Medicine, Aurora, Colo
| | - Andrew Liu
- Departments of Pediatrics and Medicine, National Jewish Health, Denver, Colo
| | - George T O'Connor
- Department of Medicine, Boston University School of Medicine, Boston, Mass
| | | | - Meyer Kattan
- Columbia University Medical Center, New York, NY
| | | | | | | | - Stanley J Szefler
- Department of Pediatrics, Children's Hospital Colorado and University of Colorado, School of Medicine, Aurora, Colo
| | - Michelle A Gill
- University of Texas, Southwestern Medical Center, Dallas, Tex
| | | | | | - Corinne E Hennessy
- Department of Medicine, University of Colorado, School of Medicine, Aurora, Colo
| | - Elizabeth J Davidson
- Department of Medicine, University of Colorado, School of Medicine, Aurora, Colo
| | - Weiming Zhang
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado, Aurora, Colo
| | - Peter Gergen
- National Institute of Allergy and Infectious Diseases, Bethesda, Md
| | - Alkis Togias
- National Institute of Allergy and Infectious Diseases, Bethesda, Md
| | - William W Busse
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wis
| | - David A Schwartz
- Department of Medicine, University of Colorado, School of Medicine, Aurora, Colo; Departments of Pediatrics and Medicine, National Jewish Health, Denver, Colo; Department of Immunology, University of Colorado, Aurora, Colo.
| |
Collapse
|
22
|
Henneman P, Petrus NCM, Venema A, van Sinderen F, van der Lip K, Hennekam RC, Mannens M, Sprikkelman AB. Genetic susceptibility for cow's milk allergy in Dutch children: the start of the allergic march? Clin Transl Allergy 2015; 6:7. [PMID: 26941931 PMCID: PMC4776421 DOI: 10.1186/s13601-016-0096-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 01/18/2016] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Cow's milk allergy (CMA) is the most common allergic disease in infancy. It is not clear, whether infants with CMA have an increased risk of developing other allergic diseases later in life, the so-called "allergic march". We aimed to detect genetic associations of CMA using reported single nucleotide polymorphisms (SNP) in other allergic diseases and genetic mutations within the filaggrin (FLG) gene. Both to investigate possible causes of CMA, which also suggests an "allergic march". METHODS Thirty children from the Dutch EuroPrevall birth cohort study with CMA in infancy and twenty-three healthy controls were studied. Six candidate SNPs were selected (minor allele frequency 10-50 % combined with a large effect) based on the literature. Thirteen FLG candidate mutations were selected spread over repeats 1, 3, 4, 5, 6, 7, 9 and 10 respectively. RESULTS We found two SNP's, rs17616434 (P = 0.002) and rs2069772 (P = 0.038), significantly associated with CMA. One is located near the toll like receptor 6 (TLR6) gene, which functionally interacts with toll-like receptor 2, and is associated with an increased risk of other allergic diseases. One is located at the Interleukin 2 (IL2) locus. Twelve FLG amplicons were analyzed, but showed no significant enrichment. Nevertheless, we did observe more FLG mutations in the CMA-group compared to controls. CONCLUSION We significantly associated two SNPs with CMA, suggesting that variation in the TLR6 and IL2 genes contribute to the expression of CMA. In addition, since TLR6 and IL2 were earlier associated with other later onset allergies, this also favours the "allergic march" hypothesis. We observed more FLG mutations in the CMA-group, albeit we found no statistical significant enrichment of FLG mutations. Further studies are necessary to investigate the role of common variants and FLG or other skin barrier gene mutations in CMA.
Collapse
Affiliation(s)
- Peter Henneman
- Department Clinical Genetics, DNA-diagnostics laboratory, Amsterdam Medical Center, Amsterdam, The Netherlands
| | - Nicole C. M. Petrus
- Department of Paediatric Respiratory Medicine and Allergy, Emma Children’s Hospital, Amsterdam Medical Center, Amsterdam, The Netherlands
| | - Andrea Venema
- Department Clinical Genetics, DNA-diagnostics laboratory, Amsterdam Medical Center, Amsterdam, The Netherlands
| | - Femke van Sinderen
- Department Clinical Genetics, DNA-diagnostics laboratory, Amsterdam Medical Center, Amsterdam, The Netherlands
| | - Karin van der Lip
- Department Clinical Genetics, DNA-diagnostics laboratory, Amsterdam Medical Center, Amsterdam, The Netherlands
| | - Raoul C. Hennekam
- Department Clinical Genetics, DNA-diagnostics laboratory, Amsterdam Medical Center, Amsterdam, The Netherlands
| | - Marcel Mannens
- Department Clinical Genetics, DNA-diagnostics laboratory, Amsterdam Medical Center, Amsterdam, The Netherlands
| | - Aline B. Sprikkelman
- Department of Paediatric Respiratory Medicine and Allergy, Emma Children’s Hospital, Amsterdam Medical Center, Amsterdam, The Netherlands
| |
Collapse
|
23
|
Lockett GA, Patil VK, Soto-Ramírez N, Ziyab AH, Holloway JW, Karmaus W. Epigenomics and allergic disease. Epigenomics 2014; 5:685-99. [PMID: 24283882 DOI: 10.2217/epi.13.68] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Allergic disease development is affected by both genes and the environment, and epigenetic mechanisms are hypothesized to mediate these environmental effects. In this article, we discuss the link between the environment, DNA methylation and allergic disease, as well as questions of causality inherent to analyses of DNA methylation. From the practical side, we describe characteristics of allergic phenotypes and contrast different epidemiologic study designs used in epigenetic research. We examine methodological considerations, how best to conduct preprocessing and analysis of DNA methylation data sets, and the latest methods, technologies and discoveries in this rapidly advancing field. DNA methylation and other epigenetic marks are firmly entwined with allergic disease, a link that may hold the basis for future allergic disease diagnosis and treatment.
Collapse
Affiliation(s)
- Gabrielle A Lockett
- Human Development & Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | | | | | | | | | | |
Collapse
|
24
|
Meyers DA, Bleecker ER, Holloway JW, Holgate ST. Asthma genetics and personalised medicine. THE LANCET. RESPIRATORY MEDICINE 2014; 2:405-15. [PMID: 24794577 PMCID: PMC4768462 DOI: 10.1016/s2213-2600(14)70012-8] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Unbiased genetic approaches, especially genome-wide association studies, have identified novel genetic targets in the pathogenesis of asthma, but so far these targets account for only a small proportion of the heritability of asthma. Recognition of the importance of disease heterogeneity, the need for improved disease phenotyping, and the fact that genes involved in the inception of asthma are likely to be different from those involved in severity widens the scope of asthma genetics. The identification of genes implicated in several causal pathways suggests that genetic scores could be used to capture the effect of genetic variations on individuals. Gene-environment interaction adds another layer of complexity, which is being successfully explored by epigenetic approaches. Pharmacogenetics is one example of how gene-environment interactions are already being taken into account in the identification of drug responders and non-responders, and patients most susceptible to adverse effects. Such applications represent one component of personalised medicine, an approach that places the individual at the centre of health care.
Collapse
Affiliation(s)
- Deborah A Meyers
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Eugene R Bleecker
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - John W Holloway
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Stephen T Holgate
- Human Development and Health, and Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK.
| |
Collapse
|
25
|
The genetics of asthma and allergic diseases: pieces of the puzzle are starting to come together. Curr Opin Allergy Clin Immunol 2014; 13:461-2. [PMID: 23974676 DOI: 10.1097/aci.0b013e328364ebc3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
26
|
Abstract
The question whether eosinophilic esophagitis (EoE) might be an 'asthma of the esophagus' is reasonable. There are a number of similarities between the two diseases: EoE and asthma, as well as other atopic diseases, are frequently associated and have a number of similarities in their pathogenesis. Thus, investigating differences and similarities between the diseases might be a worthwhile endeavor. Both EoE and asthma are chronic immune-mediated conditions characterized by inflammatory changes in the mucosa and submucosa with a characteristic and diagnostic infiltration of eosinophils. They result in organ dysfunction with considerable morbidity and (in the case of asthma) even mortality. Asthma and EoE affect all ages, but frequently start in childhood or adolescence. While asthma has seen a large increase in its prevalence in the past 50 years, EoE was first described in the 1970s. Since then the frequency of the diagnosis of EoE has increased significantly. The prevalence for both diseases seems to be highest in the Western world. In contrast to asthma, where females are more often affected, EoE is more frequent in males. Asthma in children, however, is also more common in boys, but this changes after puberty. EoE is frequently associated with asthma, and up to 80% of patients with EoE are atopic, similar to childhood asthma. Adult-onset asthma is not necessarily associated with atopy (termed intrinsic asthma) and similar observations have been made for EoE. Endoscopically, asthmatic airway mucosa as well as esophageal mucosa in EoE can appear normal, and biopsies are required for diagnosis. Long-standing disease in asthma has been associated with 'remodeling' compared to predominantly reversible inflammatory changes early in the course of the disease. Similar observations have been made in EoE. Toxic proteins derived from eosinophils such as major basic protein, eosinophil-derived neurotoxin and eosinophil cationic protein can be found in the mucosa of both diseases, which are also characterized by a thickening of the lamina propria or basement membrane, respectively. Despite these histologic and immunochemistry findings, asthma as well as EoE remain clinical diagnoses, and diagnosing either condition can be challenging. Therapeutically, both diseases respond well to corticosteroids. Ironically, corticosteroids for inhalation are deliberately swallowed in EoE to reach the esophageal mucosa. Allergen/food avoidance can improve symptoms in asthma and EoE. Taken together, allergic asthma and EoE have a number of common features which make a common pathogenesis manifested in different organs for reasons not yet fully understood likely. Combining allergological research with gastroenterologic and pneumologic expertise with a focus on similarities between these diseases might be a way forward.
Collapse
Affiliation(s)
- J Christian Virchow
- Department of Pneumology, Intensive Care Medicine, Klinikum der Universität Rostock, Rostock, Germany
| |
Collapse
|