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Vasileva D, Greenwood CMT, Daley D. A Review of the Epigenetic Clock: Emerging Biomarkers for Asthma and Allergic Disease. Genes (Basel) 2023; 14:1724. [PMID: 37761864 PMCID: PMC10531327 DOI: 10.3390/genes14091724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023] Open
Abstract
DNA methylation (DNAm) is a dynamic, age-dependent epigenetic modification that can be used to study interactions between genetic and environmental factors. Environmental exposures during critical periods of growth and development may alter DNAm patterns, leading to increased susceptibility to diseases such as asthma and allergies. One method to study the role of DNAm is the epigenetic clock-an algorithm that uses DNAm levels at select age-informative Cytosine-phosphate-Guanine (CpG) dinucleotides to predict epigenetic age (EA). The difference between EA and calendar age (CA) is termed epigenetic age acceleration (EAA) and reveals information about the biological capacity of an individual. Associations between EAA and disease susceptibility have been demonstrated for a variety of age-related conditions and, more recently, phenotypes such as asthma and allergic diseases, which often begin in childhood and progress throughout the lifespan. In this review, we explore different epigenetic clocks and how they have been applied, particularly as related to childhood asthma. We delve into how in utero and early life exposures (e.g., smoking, air pollution, maternal BMI) result in methylation changes. Furthermore, we explore the potential for EAA to be used as a biomarker for asthma and allergic diseases and identify areas for further study.
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Affiliation(s)
- Denitsa Vasileva
- Centre for Heart Lung Innovation, University of British Columbia and Saint Paul’s Hospital, Vancouver, BC V6Z 1Y6, Canada;
| | - Celia M. T. Greenwood
- Lady Davis Institute for Medical Research, Montreal, QC H3T 1E2, Canada;
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC H3A 0G4, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montreal, QC H3A 0G4, Canada
- Department of Human Genetics, McGill University, Montreal, QC H3A 0G4, Canada
| | - Denise Daley
- Centre for Heart Lung Innovation, University of British Columbia and Saint Paul’s Hospital, Vancouver, BC V6Z 1Y6, Canada;
- Department of Medicine, Respiratory Division, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
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2
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Khan T, Ledoux IM, Aziz F, Al Ali F, Chin-Smith E, Ata M, Karim MY, Marr N. Associations between HLA class II alleles and IgE sensitization to allergens in the Qatar Biobank cohort. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. GLOBAL 2023; 2:100117. [PMID: 37779520 PMCID: PMC10509938 DOI: 10.1016/j.jacig.2023.100117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 01/16/2023] [Accepted: 02/05/2023] [Indexed: 10/03/2023]
Abstract
Background Allergic disorders are the consequence of IgE sensitization to allergens. Population studies have shown that certain human leukocyte antigen (HLA) alleles are associated with increased or decreased risk of developing allergy. Objective We aimed to characterize the relationship between HLA class II allelic diversity and IgE sensitization in an understudied Arab population. Methods We explored associations between IgE sensitization to 7 allergen mixes and mesquite (comprising 41 food or aeroallergens) and 45 common classical HLA class II alleles in a well-defined cohort of 797 individuals representing the general adult population of Qatari nationals and long-term residents. To do so, we performed HLA calling from whole genome sequencing data at 2-field resolution using 2 independent algorithms. We then applied 3 different regression models to assess either each allergen mix independently, in the context of IgE sensitization to other allergens tested, or polysensitization. Results More than half (n = 447) of the study participants showed IgE sensitization to at least 1 allergen, most of them (n = 400) to aeroallergens (Phadiatop). We identified statistically significant negative and positive associations with 24 HLA class II alleles. These have been reported to confer risk or protection from variety of diseases; however, only a few have previously been associated with allergy in other populations. Conclusions Our study reveals several new risk and protective genetic markers for allergen-specific IgE sensitization. This is a first and essential step toward a better understanding of the origins of allergic diseases in this understudied population.
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Affiliation(s)
- Taushif Khan
- Department of Human Immunology, Sidra Medicine, Doha, Qatar
- Department of Computational Science, The Jackson Laboratory, Farmington, Conn
| | | | - Ferdousey Aziz
- the Department of Pathology, Sidra Medicine, Doha, Qatar
| | - Fatima Al Ali
- Department of Human Immunology, Sidra Medicine, Doha, Qatar
| | | | - Manar Ata
- Department of Human Immunology, Sidra Medicine, Doha, Qatar
| | - Mohammed Yousuf Karim
- the Department of Pathology, Sidra Medicine, Doha, Qatar
- the College of Medicine, Qatar University, Doha, Qatar
| | - Nico Marr
- Department of Human Immunology, Sidra Medicine, Doha, Qatar
- the College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
- Institute of Translational Immunology, Brandenburg Medical School, Brandenburg an der Havel, Germany
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Prevention of food allergy in infancy: the role of maternal interventions and exposures during pregnancy and lactation. THE LANCET. CHILD & ADOLESCENT HEALTH 2023; 7:358-366. [PMID: 36871575 DOI: 10.1016/s2352-4642(22)00349-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/10/2022] [Accepted: 11/24/2022] [Indexed: 03/06/2023]
Abstract
There is increased focus on the role of maternal interventions in the prevention of food allergy in infancy. There is no role for maternal dietary modifications during pregnancy or lactation, such as allergen avoidance, as a means of infant allergy prevention. Although exclusive breastfeeding is the recommended infant nutrition source globally, the effect of breastfeeding on infant allergy prevention remains unclear. There is emerging evidence that irregular cow's milk exposure (ie, infrequent formula supplementation) might increase the risk of cow's milk allergy. Although further studies are required, there is also emerging evidence that maternal peanut ingestion during breastfeeding along with early peanut introduction in infancy might have a preventive role. The effect of maternal dietary supplementation with vitamin D, omega-3, and prebiotics or probiotics remains unclear.
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Margolis DJ, Duke JL, Mitra N, Berna RA, Hoffstad OJ, Wasserman JR, Dinou A, Damianos G, Kotsopoulou I, Tairis N, Ferriola DA, Mosbruger TL, Hayeck TJ, Yan AC, Monos DS. A combination of HLA-DP α and β chain polymorphisms paired with a SNP in the DPB1 3' UTR region, denoting expression levels, are associated with atopic dermatitis. Front Genet 2023; 14:1004138. [PMID: 36911412 PMCID: PMC9995861 DOI: 10.3389/fgene.2023.1004138] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 01/13/2023] [Indexed: 02/25/2023] Open
Abstract
Introduction: Components of the immune response have previously been associated with the pathophysiology of atopic dermatitis (AD), specifically the Human Leukocyte Antigen (HLA) Class II region via genome-wide association studies, however the exact elements have not been identified. Methods: This study examines the genetic variation of HLA Class II genes using next generation sequencing (NGS) and evaluates the resultant amino acids, with particular attention on binding site residues, for associations with AD. The Genetics of AD cohort was used to evaluate HLA Class II allelic variation on 464 subjects with AD and 384 controls. Results: Statistically significant associations with HLA-DP α and β alleles and specific amino acids were found, some conferring susceptibility to AD and others with a protective effect. Evaluation of polymorphic residues in DP binding pockets revealed the critical role of P1 and P6 (P1: α31M + (β84G or β84V) [protection]; α31Q + β84D [susceptibility] and P6: α11A + β11G [protection]) and were replicated with a national cohort of children consisting of 424 AD subjects. Independently, AD susceptibility-associated residues were associated with the G polymorphism of SNP rs9277534 in the 3' UTR of the HLA-DPB1 gene, denoting higher expression of these HLA-DP alleles, while protection-associated residues were associated with the A polymorphism, denoting lower expression. Discussion: These findings lay the foundation for evaluating non-self-antigens suspected to be associated with AD as they potentially interact with particular HLA Class II subcomponents, forming a complex involved in the pathophysiology of AD. It is possible that a combination of structural HLA-DP components and levels of expression of these components contribute to AD pathophysiology.
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Affiliation(s)
- David J. Margolis
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Jamie L. Duke
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Nandita Mitra
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Ronald A. Berna
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Ole J. Hoffstad
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Jenna R. Wasserman
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Amalia Dinou
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Georgios Damianos
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Ioanna Kotsopoulou
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Nikolaos Tairis
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Deborah A. Ferriola
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Timothy L. Mosbruger
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Tristan J. Hayeck
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Department of Pathology and Laboratory Medicine, Perelman Schools of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Albert C. Yan
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Section of Dermatology, Division of General Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Dimitri S. Monos
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Department of Pathology and Laboratory Medicine, Perelman Schools of Medicine, University of Pennsylvania, Philadelphia, PA, United States
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Xie Q, Xue W. IgE-Mediated food allergy: Current diagnostic modalities and novel biomarkers with robust potential. Crit Rev Food Sci Nutr 2022; 63:10148-10172. [PMID: 35587740 DOI: 10.1080/10408398.2022.2075312] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Food allergy (FA) is a serious public health issue afflicting millions of people globally, with an estimated prevalence ranging from 1-10%. Management of FA is challenging due to overly restrictive diets and the lack of diagnostic approaches with high accuracy and prediction. Although measurement of serum-specific antibodies combined with patient medical history and skin prick test is a useful diagnostic tool, it is still an imprecise predictor of clinical reactivity with a high false-positive rate. The double-blind placebo-controlled food challenge represents the gold standard for FA diagnosis; however, it requires large healthcare and involves the risk of acute onset of allergic reactions. Improvement in our understanding of the molecular mechanism underlying allergic disease pathology, development of omics-based methods, and advances in bioinformatics have boosted the generation of a number of robust diagnostic biomarkers of FA. In this review, we discuss how traditional diagnostic modalities guide appropriate diagnosis and management of FA in clinical practice, as well as uncover the potential of the latest biomarkers for the diagnosis, monitoring, and prediction of FA. We also raise perspectives for precise and targeted medical intervention to fill the gap in the diagnosis of FA.
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Affiliation(s)
- Qiang Xie
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, P.R. China
| | - Wentong Xue
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, P.R. China
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Cardwell FS, Elliott SJ, Chin R, Pierre YS, Ben-Shoshan M, Chan ES, Gerdts J, Harada L, Asai Y, La Vieille S, Clarke AE. Economic burden of food allergy in Canada: Estimating costs and identifying determinants. Ann Allergy Asthma Immunol 2022; 129:220-230.e6. [PMID: 35500863 DOI: 10.1016/j.anai.2022.04.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/20/2022] [Accepted: 04/21/2022] [Indexed: 01/17/2023]
Abstract
BACKGROUND Limited data exist on the economic burden of food allergy (FA). OBJECTIVE To assess FA-related direct (healthcare and out-of-pocket) and indirect (lost productivity) costs and their determinants in Canadian children and adults self-reporting FA. METHODS FA-individuals self-reporting a convincing history or physician diagnosis were recruited through FA registries, an anaphylaxis registry, and advocacy associations, and electronically surveyed regarding FA-related healthcare use, out-of-pocket expenditures, and time lost from paid and unpaid labor. Direct and indirect costs (2020 Canadian dollars [CAD]) were stratified on severe reaction vs mild, moderate or no reaction, and children vs adults; multivariate regressions assessed the association between costs and sociodemographic and disease characteristics. RESULTS Between May 2018 and July 2019, 2692 eligible individuals responded (2189 convincing history and 503 physician diagnosis only); 1020 experienced a severe reaction; 1752 were children. Per FA-individual, annual healthcare, out-of-pocket, and indirect costs were $1267, $2136, and $7950. Those with a severe reaction had higher healthcare and out-of-pocket costs than those with mild, moderate or no reaction. FA-children vs FA-adults had higher healthcare and out-of-pocket costs, and lower indirect costs. Multivariate results showed that lower age, a severe reaction ever, multiple FAs, and fair or poor general health were associated with higher healthcare and out-of-pocket costs. Higher age, lower household education and income, and fair or poor general health were associated with higher indirect costs. CONCLUSION The economic burden of FA in Canada is substantial, particularly for those with a severe reaction ever, multiple FAs, and fair or poor general health. It is crucial that those most adversely affected are allocated appropriate resources to support disease management.
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Affiliation(s)
- Francesca S Cardwell
- Department of Geography and Environmental Management, University of Waterloo, Waterloo, Ontario, Canada.
| | - Susan J Elliott
- Department of Geography and Environmental Management, University of Waterloo, Waterloo, Ontario, Canada
| | - Ricky Chin
- Division of Rheumatology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Yvan St Pierre
- Division of Clinical Epidemiology, Department of Medicine, McGill University Health Centre, Montréal, Quebec, Canada
| | - Moshe Ben-Shoshan
- Division of Allergy and Clinical Immunology, Department of Pediatrics, Montréal Children's Hospital, McGill University Health Centre, Montréal, Quebec, Canada
| | - Edmond S Chan
- Division of Allergy and Immunology, Department of Pediatrics, British Columbia Children's Hospital, The University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Laurie Harada
- At the time of research: Consultant, Food Allergy Canada, Toronto, Ontario, Canada
| | - Yuka Asai
- Division of Dermatology, Department of Medicine, Queen's University, Kingston, Ontario, Canada
| | - Sébastien La Vieille
- Food Directorate, Health Canada, Ottawa, Ontario, Canada; Food Science Department, Faculty of Agricultural and Nutrition Sciences, Laval University, Québec City, Quebec, Canada
| | - Ann E Clarke
- Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
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Isik Z, Leblebici A, Demir Karaman E, Karaca C, Ellidokuz H, Koc A, Ellidokuz EB, Basbinar Y. In silico identification of novel biomarkers for key players in transition from normal colon tissue to adenomatous polyps. PLoS One 2022; 17:e0267973. [PMID: 35486660 PMCID: PMC9053805 DOI: 10.1371/journal.pone.0267973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 04/19/2022] [Indexed: 11/18/2022] Open
Abstract
Adenomatous polyps of the colon are the most common neoplastic polyps. Although most of adenomatous polyps do not show malign transformation, majority of colorectal carcinomas originate from neoplastic polyps. Therefore, understanding of this transformation process would help in both preventive therapies and evaluation of malignancy risks. This study uncovers alterations in gene expressions as potential biomarkers that are revealed by integration of several network-based approaches. In silico analysis performed on a unified microarray cohort, which is covering 150 normal colon and adenomatous polyp samples. Significant gene modules were obtained by a weighted gene co-expression network analysis. Gene modules with similar profiles were mapped to a colon tissue specific functional interaction network. Several clustering algorithms run on the colon-specific network and the most significant sub-modules between the clusters were identified. The biomarkers were selected by filtering differentially expressed genes which also involve in significant biological processes and pathways. Biomarkers were also validated on two independent datasets based on their differential gene expressions. To the best of our knowledge, such a cascaded network analysis pipeline was implemented for the first time on a large collection of normal colon and polyp samples. We identified significant increases in TLR4 and MSX1 expressions as well as decrease in chemokine profiles with mostly pro-tumoral activities. These biomarkers might appear as both preventive targets and biomarkers for risk evaluation. As a result, this research proposes novel molecular markers that might be alternative to endoscopic approaches for diagnosis of adenomatous polyps.
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Affiliation(s)
- Zerrin Isik
- Faculty of Engineering, Department of Computer Engineering, Dokuz Eylul University, Izmir, Turkey
- * E-mail:
| | - Asım Leblebici
- Department of Translational Oncology, Institute of Health Sciences, Dokuz Eylul University, Izmir, Turkey
| | - Ezgi Demir Karaman
- Department of Computer Engineering, Institute of Natural and Applied Sciences, Dokuz Eylul University, Izmir, Turkey
| | - Caner Karaca
- Department of Translational Oncology, Institute of Health Sciences, Dokuz Eylul University, Izmir, Turkey
| | - Hulya Ellidokuz
- Department of Preventive Oncology, Institute of Oncology, Dokuz Eylul University, Izmir, Turkey
| | - Altug Koc
- Gentan Genetic Medical Genetics Diagnosis Center, Izmir, Turkey
| | - Ender Berat Ellidokuz
- Faculty of Medicine, Department of Gastroenterology, Dokuz Eylul University, Izmir, Turkey
| | - Yasemin Basbinar
- Department of Translational Oncology, Institute of Oncology, Dokuz Eylul University, Izmir, Turkey
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Abstract
INTRODUCTION As the prevalence of food allergies (FA) increases worldwide, our understanding of its pathophysiology and risk factors is markedly expanding. In the past decades, an increasing number of genes have been linked to FA. Identification of such genes may help in predicting the genetic risk for FA development, age of onset, clinical manifestation, causative allergen(s), and possibly the optimal treatment strategies. Furthermore, identification of these genetic factors can help to understand the complex interactions between genes and the environment in predisposition to FA. AREAS COVERED We outline the recent important progress in determining genetic variants and disease-associated genes in IgE-mediated FA. We focused on the monogenic inborn errors of immunity (IEI) where FA is one of the clinical manifestations, emphasizing the genes and gene variants which were linked to FA with some of the most robust evidence. EXPERT OPINION Genetics play a significant role, either directly or along with environmental factors, in the development of FA. Since FA is a multifactorial disease, it is expected that multiple genes and genetic loci contribute to the risk for its development. Identification of the involved genes should contribute to the area of FA regarding pathogenesis, prediction, recognition, prognosis, prevention, and possibly therapeutic interventions.
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Affiliation(s)
- Yesim Demirdag
- Division of Basic and Clinical Immunology, Department of Medicine University of California, Irvine, CA
| | - Sami Bahna
- Division of Basic and Clinical Immunology, Department of Medicine University of California, Irvine, CA
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Jiao L, Su CW, Cao T, Zheng S, Walker WA, Shi HN. Maternal Influences and Intervention Strategies on the Development of Food Allergy in Offspring. Front Immunol 2022; 13:817062. [PMID: 35281070 PMCID: PMC8904425 DOI: 10.3389/fimmu.2022.817062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 02/01/2022] [Indexed: 11/24/2022] Open
Abstract
Food allergies and other immune-mediated diseases have become serious health concerns amongst infants and children in developed and developing countries. The absence of available cures limits disease management to allergen avoidance and symptomatic treatments. Research has suggested that the presence of maternal food allergies may expose the offspring to genetic predisposition, making them more susceptible to allergen sensitization. The following review has focused on epidemiologic studies regarding maternal influences of proneness to develop food allergy in offspring. The search strategy was "food allergy OR maternal effects OR offspring OR prevention". A systematically search from PubMed/MEDLINE, Science Direct and Google Scholar was conducted. Specifically, it discussed the effects of maternal immunity, microbiota, breastfeeding, genotype and allergy exposure on the development of food allergy in offspring. In addition, several commonly utilized prenatal and postpartum strategies to reduce food allergy proneness were presented, including early diagnosis of high-risk infants and various dietary interventions.
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Affiliation(s)
- Lefei Jiao
- School of Marine Sciences, Ningbo University, Ningbo, China
- Mucosal Immunology and Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, United States
| | - Chien-Wen Su
- Mucosal Immunology and Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, United States
| | - Tinglan Cao
- Laboratory for Lipid Medicine and Technology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, United States
| | - Shasha Zheng
- Department of Nutrition, California Baptist University, Riverside, CA, United States
| | - W. Allan Walker
- Mucosal Immunology and Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, United States
| | - Hai Ning Shi
- Mucosal Immunology and Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, United States
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Fukunaga K, Chinuki Y, Hamada Y, Fukutomi Y, Sugiyama A, Kishikawa R, Fukunaga A, Oda Y, Ugajin T, Yokozeki H, Harada N, Suehiro M, Hide M, Nakagawa Y, Noguchi E, Nakamura M, Matsunaga K, Yagami A, Morita E, Mushiroda T. Genome-wide association study reveals an association between the HLA-DPB1 ∗02:01:02 allele and wheat-dependent exercise-induced anaphylaxis. Am J Hum Genet 2021; 108:1540-1548. [PMID: 34246321 PMCID: PMC8387458 DOI: 10.1016/j.ajhg.2021.06.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 06/15/2021] [Indexed: 12/27/2022] Open
Abstract
Wheat-dependent exercise-induced anaphylaxis (WDEIA) is a life-threatening food allergy triggered by wheat in combination with the second factor such as exercise. The identification of potential genetic risk factors for this allergy might help high-risk individuals before consuming wheat-containing food. We aimed to identify genetic variants associated with WDEIA. A genome-wide association study was conducted in a discovery set of 77 individuals with WDEIA and 924 control subjects via three genetic models. The associations were confirmed in a replication set of 91 affected individuals and 435 control individuals. Summary statistics from the combined set were analyzed by meta-analysis with a random-effect model. In the discovery set, a locus on chromosome 6, rs9277630, was associated with WDEIA in the dominant model (OR = 3.95 [95% CI, 2.31-6.73], p = 7.87 × 10-8). The HLA-DPB1∗02:01:02 allele displayed the most significant association with WDEIA (OR = 4.51 [95% CI, 2.66-7.63], p = 2.28 × 10-9), as determined via HLA imputation following targeted sequencing. The association of the allele with WDEIA was confirmed in replication samples (OR = 3.82 [95% CI, 2.33-6.26], p = 3.03 × 10-8). A meta-analysis performed in the combined set revealed that the HLA-DPB1∗02:01:02 allele was significantly associated with an increased risk of WDEIA (OR = 4.13 [95% CI, 2.89-5.93], p = 1.06 × 10-14). Individuals carrying the HLA-DPB1∗02:01:02 allele have a significantly increased risk of WDEIA. Further validation of these findings in independent multiethnic cohorts is needed.
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Affiliation(s)
- Koya Fukunaga
- Laboratory for Pharmacogenomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan
| | - Yuko Chinuki
- Department of Dermatology, Shimane University Faculty of Medicine, Shimane 693-0021, Japan
| | - Yuto Hamada
- Clinical Research Center for Allergy and Rheumatology, National Hospital Organization Sagamihara National Hospital, Kanagawa 252-0392, Japan
| | - Yuma Fukutomi
- Clinical Research Center for Allergy and Rheumatology, National Hospital Organization Sagamihara National Hospital, Kanagawa 252-0392, Japan
| | - Akiko Sugiyama
- Department of Allergology, National Hospital Organization Fukuoka National Hospital, Fukuoka 810-0062, Japan
| | - Reiko Kishikawa
- Department of Allergology, National Hospital Organization Fukuoka National Hospital, Fukuoka 810-0062, Japan
| | - Atsushi Fukunaga
- Division of Dermatology, Department of Internal Related, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan
| | - Yoshiko Oda
- Division of Dermatology, Department of Internal Related, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan
| | - Tsukasa Ugajin
- Department of Dermatology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Hiroo Yokozeki
- Department of Dermatology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Naoe Harada
- Department of Dermatology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8551, Japan
| | - Masataka Suehiro
- Department of Dermatology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8551, Japan
| | - Michihiro Hide
- Department of Dermatology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima 734-8551, Japan
| | - Yukinobu Nakagawa
- Department of Dermatology, Course of Integrated Medicine, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Emiko Noguchi
- Department of Medical Genetics, Faculty of Medicine, University of Tsukuba, Tsukuba 305-8575, Japan
| | - Masashi Nakamura
- Department of Integrative Medical Science for Allergic Disease, Fujita Health University School of Medicine, Nagoya 454-8509, Japan; General Research and Development Institute, Hoyu, Nagakute 454-8509, Japan
| | - Kayoko Matsunaga
- Department of Integrative Medical Science for Allergic Disease, Fujita Health University School of Medicine, Nagoya 454-8509, Japan
| | - Akiko Yagami
- Department of Allergology, Fujita Health University School of Medicine, Nagoya 454-8509, Japan; Fujita Health University General Allergy Center in Bantane Hospital, Nagoya 454-8509, Japan
| | - Eishin Morita
- Department of Dermatology, Shimane University Faculty of Medicine, Shimane 693-0021, Japan.
| | - Taisei Mushiroda
- Laboratory for Pharmacogenomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.
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Nielsen KR, Bojsen SR, Masmas TN, Fjordside AL, Baech J, Haunstrup TM, Steffensen R. Association between human leukocyte antigens (HLAs) and human neutrophil antigens (HNAs) and autoimmune neutropenia of infancy in Danish patients. Pediatr Allergy Immunol 2021; 32:756-761. [PMID: 33421202 PMCID: PMC8248029 DOI: 10.1111/pai.13450] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 12/09/2020] [Accepted: 12/16/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Autoimmune neutropenia of infancy (AIN) is a frequent cause of neutropenia in children. The disease is caused by antibodies against epitopes on the immunoglobulin G (IgG) Fc receptor type 3b (FcγIIIb). We investigated the possible association of human neutrophil antigens (HNA), human leukocyte antigen (HLA)-DR, and HLA-DQ alleles with AIN and the association of these genotypes with the presence of autoantibodies. METHODS Eighty AIN cases with a median age of 13.5 months were included. Controls were healthy unrelated Danish blood donors. Anti-HNA-1a autoantibodies were detected using a flow cytometric granulocyte immunofluorescence test (Flow-GIFT) with phenotyped donor cells for detection of antibody specificity. Molecular determination of HNA genotypes was determined using real-time polymerase chain reaction (q-PCR). High-resolution HLA-DRB1 and HLA-DQB1 were determined by next-generation sequencing. RESULTS Antibodies against HNA-1a were detected in 51% (n = 41) of AIN patients, and anti-HNA-1b was detected in 3% (n = 2) of cases. In 46% of cases, the antibodies were anti-FcγIIIb-reactive. FCGR3B*01+,*02-,*03- was more common (odds ratio, 6.70; P < .0001), and FCGR3B*01-,*02+,*03- was less common (odds ratio, 0.30; P < .0001) among AIN cases. HNA-1a antibodies were significantly more frequent among AIN cases with the FCGR3B*01+,*02-,*03- genotype (odds ratio, 3.86; P < .007). The HLA-DRB1*14 - HLA-DQB1*05:03 haplotype was significantly more common (odds ratio, 7.44; P < .0001) in AIN patients. CONCLUSION The HLA haplotype HLA-DRB1*14 - DQB1*05:03 is associated with Danish AIN cases. Among Danish AIN patients, anti-HNA-1a is the most common autoantibody, and the antibody is more common in cases with the FCGR3B*01+,*02-,*03- genotype.
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Affiliation(s)
- Kaspar René Nielsen
- Department of Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark
| | - Signe Rolskov Bojsen
- Department of Clinical Genetics, Sygehus Lillebaelt Vejle Hospital, Vejle, Denmark
| | - Tania Nicole Masmas
- Pediatric Hematopoietic Stem Cell Transplantation and Immunodeficiency, The Child and Adolescent Clinic, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | | | - John Baech
- Department of Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark
| | - Thure Mors Haunstrup
- Department of Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark
| | - Rudi Steffensen
- Department of Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark
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12
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Mennini M, Arasi S, Fiocchi AG. Allergy prevention through breastfeeding. Curr Opin Allergy Clin Immunol 2021; 21:216-221. [PMID: 33394704 DOI: 10.1097/aci.0000000000000718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW To perform a nonsystematic review of the literature on the role of breastfeeding as primary prevention tool for allergic diseases. RECENT FINDINGS Human milk contains vast amounts of biologically active components that have a significant impact on the development of the gut microbiota. Exclusively breastfed infants show a different microbiota, with a predominance of Bifidobacterium species in their intestines.The mechanisms underlying the antiallergic effects of human milk are most probably complex, as human milk contains not only nutritional substances but also functional molecules including polysaccharides, cytokines, proteins, and other components which can produce an epigenetic modulation of the innate and adaptive immune responses of the infant in very early life. SUMMARY Currently, there is not sufficient strong evidence to guarantee its effectiveness in allergy prevention and therefore the main international scientific societies still do not count it among the recognized primary prevention strategies of allergy.
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Affiliation(s)
- Maurizio Mennini
- Multifactorial and Systemic Diseases Research Area, Predictive and Preventive Medicine Research Unit, Division of Allergy Bambino Gesù Children's Hospital IRCCS, Rome, Italy
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13
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Czolk R, Klueber J, Sørensen M, Wilmes P, Codreanu-Morel F, Skov PS, Hilger C, Bindslev-Jensen C, Ollert M, Kuehn A. IgE-Mediated Peanut Allergy: Current and Novel Predictive Biomarkers for Clinical Phenotypes Using Multi-Omics Approaches. Front Immunol 2021; 11:594350. [PMID: 33584660 PMCID: PMC7876438 DOI: 10.3389/fimmu.2020.594350] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 12/11/2020] [Indexed: 01/22/2023] Open
Abstract
Food allergy is a collective term for several immune-mediated responses to food. IgE-mediated food allergy is the best-known subtype. The patients present with a marked diversity of clinical profiles including symptomatic manifestations, threshold reactivity and reaction kinetics. In-vitro predictors of these clinical phenotypes are evasive and considered as knowledge gaps in food allergy diagnosis and risk management. Peanut allergy is a relevant disease model where pioneer discoveries were made in diagnosis, immunotherapy and prevention. This review provides an overview on the immune basis for phenotype variations in peanut-allergic individuals, in the light of future patient stratification along emerging omic-areas. Beyond specific IgE-signatures and basophil reactivity profiles with established correlation to clinical outcome, allergenomics, mass spectrometric resolution of peripheral allergen tracing, might be a fundamental approach to understand disease pathophysiology underlying biomarker discovery. Deep immune phenotyping is thought to reveal differential cell responses but also, gene expression and gene methylation profiles (eg, peanut severity genes) are promising areas for biomarker research. Finally, the study of microbiome-host interactions with a focus on the immune system modulation might hold the key to understand tissue-specific responses and symptoms. The immune mechanism underlying acute food-allergic events remains elusive until today. Deciphering this immunological response shall enable to identify novel biomarker for stratification of patients into reaction endotypes. The availability of powerful multi-omics technologies, together with integrated data analysis, network-based approaches and unbiased machine learning holds out the prospect of providing clinically useful biomarkers or biomarker signatures being predictive for reaction phenotypes.
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Affiliation(s)
- Rebecca Czolk
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Julia Klueber
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
- Department of Dermatology and Allergy Center, Odense Research Center for Anaphylaxis, University of Southern Denmark, Odense, Denmark
| | - Martin Sørensen
- Department of Pediatric and Adolescent Medicine, University Hospital of North Norway, Tromsø, Norway
- Pediatric Research Group, Department of Clinical Medicine, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Françoise Codreanu-Morel
- Department of Allergology and Immunology, Centre Hospitalier de Luxembourg-Kanner Klinik, Luxembourg, Luxembourg
| | - Per Stahl Skov
- Department of Dermatology and Allergy Center, Odense Research Center for Anaphylaxis, University of Southern Denmark, Odense, Denmark
- RefLab ApS, Copenhagen, Denmark
- Institute of Immunology, National University of Copenhagen, Copenhagen, Denmark
| | - Christiane Hilger
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Carsten Bindslev-Jensen
- Department of Dermatology and Allergy Center, Odense Research Center for Anaphylaxis, University of Southern Denmark, Odense, Denmark
| | - Markus Ollert
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
- Department of Dermatology and Allergy Center, Odense Research Center for Anaphylaxis, University of Southern Denmark, Odense, Denmark
| | - Annette Kuehn
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
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14
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Current insights into the genetics of food allergy. J Allergy Clin Immunol 2021; 147:15-28. [PMID: 33436162 DOI: 10.1016/j.jaci.2020.10.039] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 10/02/2020] [Accepted: 10/30/2020] [Indexed: 12/19/2022]
Abstract
Food allergy (FA), a growing public health burden in the United States, and familial aggregation studies support strong roles for both genes and environment in FA risk. Deepening our understanding of the molecular and cellular mechanisms driving FAs is paramount to improving its prevention, diagnosis, and clinical management. In this review, we document lessons learned from the genetics of FA that have aided our understanding of these mechanisms. Although current genetic association studies suffer from low power, heterogeneity in definition of FA, and difficulty in our ability to truly disentangle FA from food sensitization (FS) and general atopy genetics, they reveal a set of genetic loci, genes, and variants that continue to implicate the importance of barrier and immune function genes across the atopic march, and FA in particular. The largest reported effects on FA are from MALT1 (odds ratio, 10.99), FLG (average odds ratio, ∼2.9), and HLA (average odds ratio, ∼2.03). The biggest challenge in the field of FA genetics is to elucidate the specific mechanism of action on FA risk and pathogenesis for these loci, and integrative approaches including genetics/genomics with transcriptomics, proteomics, and metabolomics will be critical next steps to translating these genetic insights into practice.
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15
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Irizar H, Kanchan K, Mathias RA, Bunyavanich S. Advancing Food Allergy Through Omics Sciences. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. IN PRACTICE 2021; 9:119-129. [PMID: 32777389 PMCID: PMC7855623 DOI: 10.1016/j.jaip.2020.07.044] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 07/24/2020] [Indexed: 02/07/2023]
Abstract
Since the publication of the first draft of the human genome, there has been an explosion of new technologies with increasing power to interrogate the totality of biological molecules (eg, DNA, RNA, proteins, metabolites) and their modifications (eg, DNA methylation, histone modifications). These technologies, collectively called omics, have been widely applied in the last 2 decades to study biological systems to gain deeper insight into mechanisms driving the physiology and pathophysiology of human health and disease. Because of its complex, multifactorial nature, food allergy is especially well suited to be investigated using omics approaches. In this rostrum, we review how omic technologies have been applied to explore diverse aspects of food allergy, including adaptive and innate immune processes in food-allergic responses, the role of the microbiome in food allergy risk, metabolic changes in the gut and blood associated with food allergy, and the identification of biomarkers and potential therapeutic targets for the condition. We discuss the strengths and limitations of the studies performed thus far and the need to adopt systems biology approaches that integrate data from multiple omics to fully leverage the potential of these technologies to advance food allergy research and care.
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Affiliation(s)
- Haritz Irizar
- Division of Psychiatry, University College London, London, United Kingdom; Department of Genetics & Genomic Sciences and Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Kanika Kanchan
- Department of Medicine, Johns Hopkins University, Baltimore, Md
| | | | - Supinda Bunyavanich
- Department of Genetics & Genomic Sciences and Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY.
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16
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AllerScreener – A Server for Allergenicity and Cross-Reactivity Prediction. CYBERNETICS AND INFORMATION TECHNOLOGIES 2020. [DOI: 10.2478/cait-2020-0071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Abstract
Allergenicity of proteins is a subtle property encoded in their structures. The prediction of allergenicity of novel proteins saves time and resources for subsequent experimental work. In the host antigen-presenting cells, the allergens are processed as antigens by the means of Human Leukocyte Antigens (HLA) class II proteins. Sometimes, people allergic to a given protein show allergic reaction to a different protein, even when the two proteins have different routes of exposure. This phenomenon is termed cross-reactivity. Here, we describe a server for allergenicity and cross-reactivity prediction based on the abilities of allergenic proteins to generate binders to HLA class II proteins. The generated peptides are compared to HLA binders originating from known allergens. As a result, the server returns a list of common binders, origin proteins, and species. Different species generate common HLA binders and this determines their cross-reactivity. The server is named AllerScreener and is freely accessible at:
http://www.ddg-pharmfac.net/AllerScreener
.
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17
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Fleischer DM, Chan ES, Venter C, Spergel JM, Abrams EM, Stukus D, Groetch M, Shaker M, Greenhawt M. A Consensus Approach to the Primary Prevention of Food Allergy Through Nutrition: Guidance from the American Academy of Allergy, Asthma, and Immunology; American College of Allergy, Asthma, and Immunology; and the Canadian Society for Allergy and Clinical Immunology. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY-IN PRACTICE 2020; 9:22-43.e4. [PMID: 33250376 DOI: 10.1016/j.jaip.2020.11.002] [Citation(s) in RCA: 138] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 10/30/2020] [Accepted: 11/02/2020] [Indexed: 12/12/2022]
Abstract
Recently published data from high-impact randomized controlled trials indicate the strong potential of strategies to prevent the development of food allergy in high-risk individuals, but guidance in the United States at present is limited to a policy for only the prevention of peanut allergy, despite other data being available and several other countries advocating early egg and peanut introduction. Eczema is considered the highest risk factor for developing IgE-mediated food allergy, but children without risk factors still develop food allergy. To prevent peanut and/or egg allergy, both peanut and egg should be introduced around 6 months of life, but not before 4 months. Screening before introduction is not required, but may be preferred by some families. Other allergens should be introduced around this time as well. Upon introducing complementary foods, infants should be fed a diverse diet, because this may help foster prevention of food allergy. There is no protective benefit from the use of hydrolyzed formula in the first year of life against food allergy or food sensitization. Maternal exclusion of common allergens during pregnancy and/or lactation as a means to prevent food allergy is not recommended. Although exclusive breast-feeding is universally recommended for all mothers, there is no specific association between exclusive breast-feeding and the primary prevention of any specific food allergy.
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Affiliation(s)
- David M Fleischer
- Section of Allergy & Immunology, Department of Pediatrics, Children's Hospital Colorado, University of Colorado School of Medicine, Aurora, Colo
| | - Edmond S Chan
- Division of Allergy & Immunology, Department of Pediatrics, University of British Columbia, BC Children's Hospital, Vancouver, BC, Canada
| | - Carina Venter
- Section of Allergy & Immunology, Department of Pediatrics, Children's Hospital Colorado, University of Colorado School of Medicine, Aurora, Colo
| | - Jonathan M Spergel
- Division of Allergy and Immunology, Children's Hospital of Philadelphia, Department of Pediatrics, Perelman School of Medicine at University of Pennsylvania, Philadelphia, Pa
| | - Elissa M Abrams
- Section of Allergy and Clinical Immunology, Department of Pediatrics, University of Manitoba, Winnipeg, MB, Canada
| | - David Stukus
- Division of Allergy and Immunology, Nationwide Children's Hospital and The Ohio State University College of Medicine, Columbus, Ohio
| | - Marion Groetch
- Division of Pediatric Allergy and Immunology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Marcus Shaker
- Section of Allergy and Clinical Immunology, Children's Hospital at Dartmouth-Hitchcock Medical Center, Lebanon, NH
| | - Matthew Greenhawt
- Section of Allergy & Immunology, Department of Pediatrics, Children's Hospital Colorado, University of Colorado School of Medicine, Aurora, Colo.
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18
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Laha A, Ghosh A, Moitra S, Biswas H, Saha NC, Bhattacharya S, Saha GK, Podder S. Association of HLA-DQ and IL13 gene variants with challenge-proven shrimp allergy in West Bengal, India. Immunogenetics 2020; 72:489-498. [PMID: 33175217 DOI: 10.1007/s00251-020-01185-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 11/02/2020] [Indexed: 10/23/2022]
Abstract
Little is known about genetic factors and mechanisms underlying shrimp allergy. Genome-wide association studies identified HLA class-II and IL13 genes as highly plausible candidates for shrimp allergy. The present study was designed to investigate potential associations of HLA-DQ rs9275596, IL13 rs20541, and IL13 rs1800925 polymorphisms with challenge-proven shrimp allergy using the data from 532 people of West Bengal, India; selected on basis of positive skin prick test, elevated specific IgE and medical history. Risk genotypes, i.e., HLA-DQ rs9275596 CC, IL13 rs20541 AA, and IL13 rs1800925 TT, were found to be significantly associated with challenge positive shrimp allergy (P = 0.04, 0.01, and 0.03, respectively). Distribution of genotypes for HLA-DQ and IL13 polymorphisms in allergic and control subjects showed significant difference between younger (20-40 years) and older (> 40 years) age group (P = 0.006). Risk genotypes significantly associated with elevated shrimp-specific IgE. IL13 TA haplotype significantly associated with shrimp allergy and elevated specific IgE (P = 0.02). Synergistic effect of IL13 TA haplotype-HLA-DQ rs9275596 CC genotype interaction significantly elevated specific IgE (P = 0.03). The present study suggests that HLA-DQ and IL13 polymorphisms pose major risk for shrimp allergic patients in West Bengal, India and thus could be helpful for early target-specific therapeutic intervention in near future.
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Affiliation(s)
- Arghya Laha
- Allergology and Applied Entomology Research Laboratory, Department of Zoology, University of Burdwan, Bardhaman, 713104, West Bengal, India
| | - Amlan Ghosh
- Department of Life Sciences, Presidency University, Kolkata, 700073, West Bengal, India
| | - Saibal Moitra
- Allergy and Asthma Research Centre, Kolkata- 700029, West Bengal, India
| | - Himani Biswas
- Post Graduate Department of Zoology, Krishnagar Government College, Krishnagar, 741101, West Bengal, India
| | - Nimai Chandra Saha
- Vice-Chancellor, University of Burdwan, Bardhaman, 713104, West Bengal, India
| | - Srijit Bhattacharya
- Post Graduate Department of Physics, Barasat Government College, Kolkata, 700124, West Bengal, India
| | - Goutam Kumar Saha
- Department of Zoology, University of Calcutta, Kolkata, 700019, West Bengal, India
| | - Sanjoy Podder
- Allergology and Applied Entomology Research Laboratory, Department of Zoology, University of Burdwan, Bardhaman, 713104, West Bengal, India.
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19
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Kostara M, Chondrou V, Sgourou A, Douros K, Tsabouri S. HLA Polymorphisms and Food Allergy Predisposition. J Pediatr Genet 2020; 9:77-86. [PMID: 32341809 DOI: 10.1055/s-0040-1708521] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 12/31/2019] [Indexed: 12/16/2022]
Abstract
Food allergy (FA) is a growing health problem that affects ∼8% of the children worldwide. Although the prevalence of FA is increasing, the underlying genetic mechanisms responsible for the onset of this immune disorder are not yet clarified. Genetic factors seem to play a leading role in the development of FA, though interaction with environmental factors cannot be excluded. The broader network of genetic loci mediating the risk of this complex disorder remains to be identified. The human leucocyte antigen (HLA) has been associated with various immune disorders, including FA. This review aims to unravel the potential associations between HLA gene functions and the manifestation and outcome of FA disorders. Exploring new aspects of FA development with the perspective to improve our understanding of the multifaceted etiology and the complex biological mechanisms involved in FA is essential.
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Affiliation(s)
- Maria Kostara
- Department of Paediatrics, Ioannina University Hospital, Ioannina, Greece
| | - Vasiliki Chondrou
- Laboratory of Biology, School of Science and Technology, Hellenic Open University, Patras, Greece
| | - Argyro Sgourou
- Laboratory of Biology, School of Science and Technology, Hellenic Open University, Patras, Greece
| | - Konstantinos Douros
- Allergology and Pulmonology Unit, 3rd Pediatric Department, Attikon Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Sophia Tsabouri
- Department of Paediatrics, Child Health Department, School of Medicine, University of Ioannina, Ioannina, Greece
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20
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Mikhail IJ. Implementation of Early Peanut Introduction Guidelines. Immunol Allergy Clin North Am 2019; 39:459-467. [DOI: 10.1016/j.iac.2019.07.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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21
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Agnihotri NT, Lei DK, Gupta RS. Managing Younger Siblings of Food Allergic Children. Immunol Allergy Clin North Am 2019; 39:469-480. [PMID: 31563182 DOI: 10.1016/j.iac.2019.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Current guidelines state that there is insufficient evidence to recommend testing siblings of food allergic children before introduction of potential allergic foods, but the topic continues to remain controversial. Although the proportion of siblings who are sensitized to a food without clinical reactivity is high in comparison to those with a true food allergy, there is still a known increased risk amongst siblings of children with food allergies that has led to much apprehension about management. The appropriateness of testing and further steps for management of sensitization in the absence of history of clinical reactivity should be discussed with parents.
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Affiliation(s)
- Neha T Agnihotri
- Department of Medicine, Division of Allergy and Immunology, Northwestern University, 211 E. Ontario, 10th Floor, Suite 1000, Chicago, IL 60611, USA
| | - Dawn K Lei
- Department of Medicine, Division of Allergy and Immunology, Northwestern University, 211 E. Ontario, 10th Floor, Suite 1000, Chicago, IL 60611, USA
| | - Ruchi S Gupta
- Institute for Public Health and Medicine, Northwestern University Feinberg School of Medicine, 750 North Lake Shore Drive, Suite #680, Chicago, IL 60611, USA.
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22
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Suaini NHA, Wang Y, Soriano VX, Martino DJ, Allen KJ, Ellis JA, Koplin JJ. Genetic determinants of paediatric food allergy: A systematic review. Allergy 2019; 74:1631-1648. [PMID: 30835860 DOI: 10.1111/all.13767] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 01/31/2019] [Accepted: 02/14/2019] [Indexed: 12/27/2022]
Abstract
BACKGROUND The genetic determinants of food allergy have not been systematically reviewed. We therefore systematically reviewed the literature on the genetic basis of food allergy, identifying areas for further investigation. METHODS We searched three electronic databases (MEDLINE, EMBASE and PubMed) on 9 January 2018. Two authors screened retrieved articles for review according to inclusion criteria and extracted relevant information on study characteristics and measures of association. Eligible studies included those that reported an unaffected nonatopic control group, had genetic information and were carried out in children. RESULTS Of the 2088 studies retrieved, 32 met our inclusion criteria. Five were genome-wide association studies, and the remaining were candidate gene studies. Twenty-two of the studies were carried out in a predominantly Caucasian population with the remaining 10 from Asian-specific populations or unspecified ethnicity. We found FLG, HLA, IL10, IL13, as well as some evidence for other variants (SPINK5, SERPINB and C11orf30) that are associated with food allergy. CONCLUSIONS Little genetic research has been carried out in food allergy, with FLG, HLA and IL13 being the most reproducible genes for an association with food allergy. Despite promising results, existing genetic studies on food allergy are inundated with issues such as inadequate sample size and absence of multiple testing correction. Few included replication analyses or population stratification measures. Studies addressing these limitations along with functional studies are therefore needed to unravel the mechanisms of action of the identified genes.
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Affiliation(s)
- Noor H. A. Suaini
- Department of Paediatrics University of Melbourne Parkville Victoria Australia
- Centre for Food and Allergy Research Murdoch Children’s Research Institute Parkville Victoria Australia
| | - Yichao Wang
- Department of Paediatrics University of Melbourne Parkville Victoria Australia
- Centre for Food and Allergy Research Murdoch Children’s Research Institute Parkville Victoria Australia
| | - Victoria X. Soriano
- Department of Paediatrics University of Melbourne Parkville Victoria Australia
- Centre for Food and Allergy Research Murdoch Children’s Research Institute Parkville Victoria Australia
| | - David J. Martino
- Department of Paediatrics University of Melbourne Parkville Victoria Australia
- Centre for Food and Allergy Research Murdoch Children’s Research Institute Parkville Victoria Australia
- Telethon Kids Institute University of Western Australia Perth Western Australia Australia
| | - Katrina J. Allen
- Department of Paediatrics University of Melbourne Parkville Victoria Australia
- Centre for Food and Allergy Research Murdoch Children’s Research Institute Parkville Victoria Australia
- Department of Allergy and Clinical Immunology Royal Children's Hospital Parkville Victoria Australia
- Institute of Inflammation and Repair University of Manchester Manchester UK
| | - Justine A. Ellis
- Department of Paediatrics University of Melbourne Parkville Victoria Australia
- Genes, Environment & Complex Disease Murdoch Children’s Research Institute Parkville Victoria Australia
- Centre for Social and Early Emotional Development, Faculty of Health Deakin University Burwood Victoria Australia
| | - Jennifer J. Koplin
- Centre for Food and Allergy Research Murdoch Children’s Research Institute Parkville Victoria Australia
- School of Population and Global Health University of Melbourne Parkville Victoria Australia
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23
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Dhondalay GK, Rael E, Acharya S, Zhang W, Sampath V, Galli SJ, Tibshirani R, Boyd SD, Maecker H, Nadeau KC, Andorf S. Food allergy and omics. J Allergy Clin Immunol 2019; 141:20-29. [PMID: 29307411 DOI: 10.1016/j.jaci.2017.11.007] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Revised: 11/09/2017] [Accepted: 11/14/2017] [Indexed: 01/06/2023]
Abstract
Food allergy (FA) prevalence has been increasing over the last few decades and is now a global health concern. Current diagnostic methods for FA result in a high number of false-positive results, and the standard of care is either allergen avoidance or use of epinephrine on accidental exposure, although currently with no other approved treatments. The increasing prevalence of FA, lack of robust biomarkers, and inadequate treatments warrants further research into the mechanism underlying food allergies. Recent technological advances have made it possible to move beyond traditional biological techniques to more sophisticated high-throughput approaches. These technologies have created the burgeoning field of omics sciences, which permit a more systematic investigation of biological problems. Omics sciences, such as genomics, epigenomics, transcriptomics, proteomics, metabolomics, microbiomics, and exposomics, have enabled the construction of regulatory networks and biological pathway models. Parallel advances in bioinformatics and computational techniques have enabled the integration, analysis, and interpretation of these exponentially growing data sets and opens the possibility of personalized or precision medicine for FA.
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Affiliation(s)
- Gopal Krishna Dhondalay
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, Calif
| | - Efren Rael
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, Calif
| | - Swati Acharya
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, Calif
| | - Wenming Zhang
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, Calif
| | - Vanitha Sampath
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, Calif
| | - Stephen J Galli
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; Department of Pathology, Stanford University School of Medicine, Stanford, Calif; Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, Calif
| | - Robert Tibshirani
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; Department of Biomedical Data Sciences, Stanford University School of Medicine, Stanford, Calif
| | - Scott D Boyd
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; Department of Pathology, Stanford University School of Medicine, Stanford, Calif; Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, Calif
| | - Holden Maecker
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, Calif; Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, Calif
| | - Kari Christine Nadeau
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, Calif.
| | - Sandra Andorf
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, Calif
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Should Younger Siblings of Peanut Allergic Children Be Screened for Peanut Allergy? THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY-IN PRACTICE 2018; 6:414-418. [DOI: 10.1016/j.jaip.2018.01.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 01/03/2018] [Accepted: 01/10/2018] [Indexed: 01/05/2023]
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25
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Liu X, Hong X, Tsai HJ, Mestan KK, Shi M, Kefi A, Hao K, Chen Q, Wang G, Caruso D, Geng H, Gao Y, He J, Kumar R, Wang H, Yu Y, Bartell T, Tan XD, Schleimer RP, Weeks DE, Pongracic JA, Wang X. Genome-wide association study of maternal genetic effects and parent-of-origin effects on food allergy. Medicine (Baltimore) 2018; 97:e0043. [PMID: 29489655 PMCID: PMC5851764 DOI: 10.1097/md.0000000000010043] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Previous genetic studies of food allergy (FA) have mainly focused on inherited genotypic effects. The role of parental genotypic effects remains largely unexplored. Leveraging existing genome-wide association study (GWAS) data generated from the Chicago Food Allergy Study, we examined maternal genotypic and parent-of-origin (PO) effects using multinomial likelihood ratio tests in 588 complete and incomplete Caucasian FA trios. We identified 1 single nucleotide polymorphism with significant (P < 5×10) maternal effect on any FA (rs4235235), which is located in a noncoding RNA (LOC101927947) with unknown function. We also identified 3 suggestive (P < 5×10) loci with maternal genetic effects: 1 for any FA (rs976078, in a gene desert region on 13q31.1) and 2 for egg allergy (rs1343795 and rs4572450, in the ZNF652 gene, where genetic variants have been associated with atopic dermatitis). Three suggestive loci with PO effect were observed: 1 for peanut allergy (rs4896888 in the ADGB gene) and 2 for any FA in boys only (rs1036504 and rs2917750 in the IQCE gene). Findings from this family-based GWAS of FA provided some preliminary evidence on maternal genotypic or PO effects on FA. Additional family-based studies are needed to confirm our findings and gain new insight into maternal and paternal genetic contribution to FA.
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Affiliation(s)
- Xin Liu
- Key Laboratory of Genomic and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- Mary Ann and J. Milburn Smith Child Health Research Program, Stanley Manne Children's Research Institute, Ann and Robert H. Lurie Children's Hospital of Chicago
- Department of Pediatrics
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiumei Hong
- Department of Population, Family and Reproductive Health, Center on the Early Life Origins of Disease, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD
| | - Hui-Ju Tsai
- Department of Pediatrics
- Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan
- Department of Public Health, China Medical University, Taichung, Taiwan
| | - Karen K. Mestan
- Division of Neonatology, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL
| | - Min Shi
- Biostatistics Branch, NIEHS, NIH, DHHS, Research Triangle Park, NC
| | - Amira Kefi
- Mary Ann and J. Milburn Smith Child Health Research Program, Stanley Manne Children's Research Institute, Ann and Robert H. Lurie Children's Hospital of Chicago
- Department of Bioinformatics, the University of Illinois at Chicago, Chicago, IL
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Qi Chen
- Mary Ann and J. Milburn Smith Child Health Research Program, Stanley Manne Children's Research Institute, Ann and Robert H. Lurie Children's Hospital of Chicago
| | - Guoying Wang
- Department of Population, Family and Reproductive Health, Center on the Early Life Origins of Disease, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD
| | - Deanna Caruso
- Department of Population, Family and Reproductive Health, Center on the Early Life Origins of Disease, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD
| | - Hua Geng
- Department of Pediatrics
- Center for Intestinal and Liver Inflammation Research, Stanley Manne Children's Research Institute
| | - Yufeng Gao
- Key Laboratory of Genomic and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jianlin He
- Key Laboratory of Genomic and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Rajesh Kumar
- Division of Allergy and Immunology, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL
| | - Hongjian Wang
- Mary Ann and J. Milburn Smith Child Health Research Program, Stanley Manne Children's Research Institute, Ann and Robert H. Lurie Children's Hospital of Chicago
- Department of Cardiovascular Internal Medicine, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing
| | - Yunxian Yu
- Mary Ann and J. Milburn Smith Child Health Research Program, Stanley Manne Children's Research Institute, Ann and Robert H. Lurie Children's Hospital of Chicago
- Department of Epidemiology and Health Statistics, School of Public Health, Zhejiang University, Hangzhou, Zhejiang, China
| | - Tami Bartell
- Mary Ann and J. Milburn Smith Child Health Research Program, Stanley Manne Children's Research Institute, Ann and Robert H. Lurie Children's Hospital of Chicago
| | - Xiao-Di Tan
- Department of Pediatrics
- Center for Intestinal and Liver Inflammation Research, Stanley Manne Children's Research Institute
| | - Robert P. Schleimer
- Division of Allergy-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Daniel E. Weeks
- Departments of Human Genetics and Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA
| | - Jacqueline A. Pongracic
- Division of Allergy and Immunology, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL
| | - Xiaobin Wang
- Department of Population, Family and Reproductive Health, Center on the Early Life Origins of Disease, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD
- Division of General Pediatrics and Adolescent Medicine, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD
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26
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Khor SS, Morino R, Nakazono K, Kamitsuji S, Akita M, Kawajiri M, Yamasaki T, Kami A, Hoshi Y, Tada A, Ishikawa K, Hine M, Kobayashi M, Kurume N, Kamatani N, Tokunaga K, Johnson TA. Genome-wide association study of self-reported food reactions in Japanese identifies shrimp and peach specific loci in the HLA-DR/DQ gene region. Sci Rep 2018; 8:1069. [PMID: 29348432 PMCID: PMC5773682 DOI: 10.1038/s41598-017-18241-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 12/07/2017] [Indexed: 12/20/2022] Open
Abstract
Food allergy is an increasingly important health problem in the world. Several genome-wide association studies (GWAS) focused on European ancestry samples have identified food allergy-specific loci in the HLA class II region. We conducted GWAS of self-reported reactivity with common foods using the data from 11011 Japanese women and identified shrimp and peach allergy-specific loci in the HLA-DR/DQ gene region tagged by rs74995702 (P = 6.30 × 10−17, OR = 1.91) and rs28359884 (P = 2.3 × 10−12, OR = 1.80), respectively. After HLA imputation using a Japanese population-specific reference, the most strongly associated haplotype was HLA-DRB1*04:05-HLA-DQB1*04:01 for shrimp allergy (P = 3.92 × 10−19, OR = 1.99) and HLA-DRB1*09:01-HLA-DQB1*03:03 for peach allergy (P = 1.15 × 10−7, OR = 1.68). Additionally, both allergies’ associated variants were eQTLs for several HLA genes, with HLA-DQA2 the single eQTL gene shared between the two traits. Our study suggests that allergy to certain foods may be related to genetic differences that tag both HLA alleles having particular epitope binding specificities as well as variants modulating expression of particular HLA genes. Investigating this further could increase our understanding of food allergy aetiology and potentially lead to better therapeutic strategies for allergen immunotherapies.
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Affiliation(s)
- Seik-Soon Khor
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Ryoko Morino
- EverGene Ltd., Shinjuku-ku, Tokyo, 163-1435, Japan
| | | | | | | | | | - Tatsuya Yamasaki
- Life Science Group, Healthcare Division, Department of Healthcare Business, MTI Ltd., Shinjuku-ku, Tokyo, 163-1435, Japan
| | - Azusa Kami
- EverGene Ltd., Shinjuku-ku, Tokyo, 163-1435, Japan
| | - Yuria Hoshi
- Life Science Group, Healthcare Division, Department of Healthcare Business, MTI Ltd., Shinjuku-ku, Tokyo, 163-1435, Japan
| | - Asami Tada
- EverGene Ltd., Shinjuku-ku, Tokyo, 163-1435, Japan
| | | | - Maaya Hine
- LunaLuna Division, Department of Healthcare Business, MTI Ltd., Shinjuku-ku, Tokyo, 163-1435, Japan
| | - Miki Kobayashi
- LunaLuna Division, Department of Healthcare Business, MTI Ltd., Shinjuku-ku, Tokyo, 163-1435, Japan
| | - Nami Kurume
- LunaLuna Division, Department of Healthcare Business, MTI Ltd., Shinjuku-ku, Tokyo, 163-1435, Japan
| | | | - Katsushi Tokunaga
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan
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27
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Marenholz I, Grosche S, Kalb B, Rüschendorf F, Blümchen K, Schlags R, Harandi N, Price M, Hansen G, Seidenberg J, Röblitz H, Yürek S, Tschirner S, Hong X, Wang X, Homuth G, Schmidt CO, Nöthen MM, Hübner N, Niggemann B, Beyer K, Lee YA. Genome-wide association study identifies the SERPINB gene cluster as a susceptibility locus for food allergy. Nat Commun 2017; 8:1056. [PMID: 29051540 PMCID: PMC5648765 DOI: 10.1038/s41467-017-01220-0] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 08/31/2017] [Indexed: 02/08/2023] Open
Abstract
Genetic factors and mechanisms underlying food allergy are largely unknown. Due to heterogeneity of symptoms a reliable diagnosis is often difficult to make. Here, we report a genome-wide association study on food allergy diagnosed by oral food challenge in 497 cases and 2387 controls. We identify five loci at genome-wide significance, the clade B serpin (SERPINB) gene cluster at 18q21.3, the cytokine gene cluster at 5q31.1, the filaggrin gene, the C11orf30/LRRC32 locus, and the human leukocyte antigen (HLA) region. Stratifying the results for the causative food demonstrates that association of the HLA locus is peanut allergy-specific whereas the other four loci increase the risk for any food allergy. Variants in the SERPINB gene cluster are associated with SERPINB10 expression in leukocytes. Moreover, SERPINB genes are highly expressed in the esophagus. All identified loci are involved in immunological regulation or epithelial barrier function, emphasizing the role of both mechanisms in food allergy.
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Affiliation(s)
- Ingo Marenholz
- Max-Delbrück-Center (MDC) for Molecular Medicine, 13125, Berlin, Germany.,Clinic for Pediatric Allergy, Experimental and Clinical Research Center, Charité University Medical Center, 13125, Berlin, Germany
| | - Sarah Grosche
- Max-Delbrück-Center (MDC) for Molecular Medicine, 13125, Berlin, Germany.,Clinic for Pediatric Allergy, Experimental and Clinical Research Center, Charité University Medical Center, 13125, Berlin, Germany
| | - Birgit Kalb
- Max-Delbrück-Center (MDC) for Molecular Medicine, 13125, Berlin, Germany.,Clinic for Pediatric Allergy, Experimental and Clinical Research Center, Charité University Medical Center, 13125, Berlin, Germany.,Department of Pediatric Pneumology and Immunology, Charité University Medical Center, 13353, Berlin, Germany
| | - Franz Rüschendorf
- Max-Delbrück-Center (MDC) for Molecular Medicine, 13125, Berlin, Germany
| | - Katharina Blümchen
- Department of Allergy, Pulmonology and Cystic Fibrosis, Children's Hospital, Goethe University, 60590, Frankfurt am Main, Germany
| | - Rupert Schlags
- Department of Pediatric Pneumology and Allergology, Wangen Hospital, 88239, Wangen, Germany
| | - Neda Harandi
- Department of Pediatric Pneumology and Allergology, Wangen Hospital, 88239, Wangen, Germany
| | - Mareike Price
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, 30625, Hannover, Germany
| | - Gesine Hansen
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, 30625, Hannover, Germany
| | - Jürgen Seidenberg
- Department of Pediatric Pneumology and Allergology, Neonatology and Intensive Care, Medical Campus of University Oldenburg, 26133, Oldenburg, Germany
| | - Holger Röblitz
- Department of Pediatrics and Adolescent Medicine, Sana Klinikum Lichtenberg, 10365, Berlin, Germany
| | - Songül Yürek
- Department of Pediatric Pneumology and Immunology, Charité University Medical Center, 13353, Berlin, Germany
| | - Sebastian Tschirner
- Department of Pediatric Pneumology and Immunology, Charité University Medical Center, 13353, Berlin, Germany
| | - Xiumei Hong
- Department of Population, Family and Reproductive Health, Center on the Early Life Origins of Disease, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Xiaobin Wang
- Department of Population, Family and Reproductive Health, Center on the Early Life Origins of Disease, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Georg Homuth
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine and Ernst-Moritz-Arndt-University Greifswald, 17487, Greifswald, Germany
| | - Carsten O Schmidt
- Institute for Community Medicine, Study of Health in Pomerania/KEF, University Medicine Greifswald, 17475, Greifswald, Germany
| | - Markus M Nöthen
- Institute of Human Genetics and Department of Genomics, Life & Brain Center, University of Bonn, 53127, Bonn, Germany
| | - Norbert Hübner
- Max-Delbrück-Center (MDC) for Molecular Medicine, 13125, Berlin, Germany
| | - Bodo Niggemann
- Department of Pediatric Pneumology and Immunology, Charité University Medical Center, 13353, Berlin, Germany
| | - Kirsten Beyer
- Department of Pediatric Pneumology and Immunology, Charité University Medical Center, 13353, Berlin, Germany
| | - Young-Ae Lee
- Max-Delbrück-Center (MDC) for Molecular Medicine, 13125, Berlin, Germany. .,Clinic for Pediatric Allergy, Experimental and Clinical Research Center, Charité University Medical Center, 13125, Berlin, Germany.
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28
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Genome-wide association study and meta-analysis in multiple populations identifies new loci for peanut allergy and establishes C11orf30/EMSY as a genetic risk factor for food allergy. J Allergy Clin Immunol 2017; 141:991-1001. [PMID: 29030101 DOI: 10.1016/j.jaci.2017.09.015] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Revised: 09/05/2017] [Accepted: 09/19/2017] [Indexed: 12/23/2022]
Abstract
BACKGROUND Peanut allergy (PA) is a complex disease with both environmental and genetic risk factors. Previously, PA loci were identified in filaggrin (FLG) and HLA in candidate gene studies, and loci in HLA were identified in a genome-wide association study and meta-analysis. OBJECTIVE We sought to investigate genetic susceptibility to PA. METHODS Eight hundred fifty cases and 926 hyper-control subjects and more than 7.8 million genotyped and imputed single nucleotide polymorphisms (SNPs) were analyzed in a genome-wide association study to identify susceptibility variants for PA in the Canadian population. A meta-analysis of 2 phenotypes (PA and food allergy) was conducted by using 7 studies from the Canadian, American (n = 2), Australian, German, and Dutch (n = 2) populations. RESULTS An SNP near integrin α6 (ITGA6) reached genome-wide significance with PA (P = 1.80 × 10-8), whereas SNPs associated with Src kinase-associated phosphoprotein 1 (SKAP1), matrix metallopeptidase 12 (MMP12)/MMP13, catenin α3 (CTNNA3), rho GTPase-activating protein 24 (ARHGAP24), angiopoietin 4 (ANGPT4), chromosome 11 open reading frame (C11orf30/EMSY), and exocyst complex component 4 (EXOC4) reached a threshold suggestive of association (P ≤ 1.49 × 10-6). In the meta-analysis of PA, loci in or near ITGA6, ANGPT4, MMP12/MMP13, C11orf30, and EXOC4 were significant (P ≤ 1.49 × 10-6). When a phenotype of any food allergy was used for meta-analysis, the C11orf30 locus reached genome-wide significance (P = 7.50 × 10-11), whereas SNPs associated with ITGA6, ANGPT4, MMP12/MMP13, and EXOC4 and additional C11orf30 SNPs were suggestive (P ≤ 1.49 × 10-6). Functional annotation indicated that SKAP1 regulates expression of CBX1, which colocalizes with the EMSY protein coded by C11orf30. CONCLUSION This study identifies multiple novel loci as risk factors for PA and food allergy and establishes C11orf30 as a risk locus for both PA and food allergy. Multiple genes (C11orf30/EMSY, SKAP1, and CTNNA3) identified by this study are involved in epigenetic regulation of gene expression.
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29
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Abstract
PURPOSE OF REVIEW Food allergy is common among children and adults worldwide. Recent studies have improved our understanding of the genetic mechanism of food allergy and further studies may result in clinical application through genetic testing. RECENT FINDINGS Genetic factors are important in the development of food allergy. An increasing number of genes have been associated with food allergy in recent years. These include mutations and genetic variants in the filaggrin gene, the association of human leukocyte antigen DR and DQ regions with food allergy, copy number variation impacting CTNNA3 and RBFOX1, DNA methylation that partially mediates single nucleotide polymorphism association at the HLA-DR and DQ loci, as well as other genes. Several studies have implicated differences in gut microbiota composition in food allergy. SUMMARY With the advance of high-throughput genotyping and sequencing techniques together with improved analytical methods, the contributions of genetic and environmental factors in development of food allergy are being clarified. Yet much remains to be explored and more studies with larger sample sizes, better phenotyping, and improved quality control genomics methods are needed. The ultimate goal is the development of a panel of reliable markers for genetic testing in food allergy to improve overall patient care.
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30
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Muraro A, Lemanske RF, Castells M, Torres MJ, Khan D, Simon HU, Bindslev-Jensen C, Burks W, Poulsen LK, Sampson HA, Worm M, Nadeau KC. Precision medicine in allergic disease-food allergy, drug allergy, and anaphylaxis-PRACTALL document of the European Academy of Allergy and Clinical Immunology and the American Academy of Allergy, Asthma and Immunology. Allergy 2017; 72:1006-1021. [PMID: 28122115 DOI: 10.1111/all.13132] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/22/2017] [Indexed: 12/30/2022]
Abstract
This consensus document summarizes the current knowledge on the potential for precision medicine in food allergy, drug allergy, and anaphylaxis under the auspices of the PRACTALL collaboration platform. PRACTALL is a joint effort of the European Academy of Allergy and Clinical Immunology and the American Academy of Allergy, Asthma and Immunology, which aims to synchronize the European and American approaches to allergy care. Precision medicine is an emerging approach for disease treatment based on disease endotypes, which are phenotypic subclasses associated with specific mechanisms underlying the disease. Although significant progress has been made in defining endotypes for asthma, definitions of endotypes for food and drug allergy or for anaphylaxis lag behind. Progress has been made in discovery of biomarkers to guide a precision medicine approach to treatment of food and drug allergy, but further validation and quantification of these biomarkers are needed to allow their translation into practice in the clinical management of allergic disease.
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Affiliation(s)
- A. Muraro
- Food Allergy Referral Centre Veneto Region; Department of Women and Child Health; Padua General University Hospital; Padua Italy
| | - R. F. Lemanske
- Department of Pediatrics; University of Wisconsin School of Medicine and Public Health; Madison WI USA
| | - M. Castells
- Drug Hypersensitivity and Desensitization Center; Brigham & Women's Hospital; Harvard Medical School; Boston MA USA
| | - M. J. Torres
- Allergy Unit; Regional University Hospital of Malaga-IBIMA; UMA; Malaga Spain
| | - D. Khan
- Division of Allergy & Immunology; Department of Internal Medicine; University of Texas Southwestern Medical Center; Dallas TX USA
| | - H.-U. Simon
- Institute of Pharmacology; University of Bern; Bern Switzerland
| | - C. Bindslev-Jensen
- Department of Dermatology and Allergy Centre; Odense Research Center for Anaphylaxis (ORCA); Odense University Hospital; Odense Denmark
| | - W. Burks
- Department of Pediatrics; University of North Carolina; Chapel Hill NC USA
| | - L. K. Poulsen
- Allergy Clinic; Copenhagen University Hospital at Gentofte Hospital; Copenhagen Denmark
| | - H. A. Sampson
- Icahn School of Medicine at Mount Sinai; New York NY USA
| | - M. Worm
- Klinik für Dermatologie; Charité - Universitätsmedizin Berlin; Berlin Germany
| | - K. C. Nadeau
- Department of Medicine; Stanford University School of Medicine; Stanford CA USA
- Sean N. Parker Center for Allergy and Asthma Research; Stanford University School of Medicine; Stanford CA USA
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31
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Benedé S, Garrido-Arandia M, Martín-Pedraza L, Bueno C, Díaz-Perales A, Villalba M. Multifactorial Modulation of Food-Induced Anaphylaxis. Front Immunol 2017; 8:552. [PMID: 28559894 PMCID: PMC5432630 DOI: 10.3389/fimmu.2017.00552] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 04/25/2017] [Indexed: 01/26/2023] Open
Abstract
Prevalence of food-induced anaphylaxis increases progressively and occurs in an unpredictable manner, seriously affecting the quality of life of patients. Intrinsic factors including age, physiological, and genetic features of the patient as well as extrinsic factors such as the intake of drugs and exposure to environmental agents modulate this disorder. It has been proven that diseases, such as mastocytosis, defects in HLA, or filaggrin genes, increase the risk of severe allergic episodes. Certain allergen families such as storage proteins, lipid transfer proteins, or parvalbumins have also been linked to anaphylaxis. Environmental factors such as inhaled allergens or sensitization through the skin can exacerbate or trigger acute anaphylaxis. Moreover, the effect of dietary habits such as the early introduction of certain foods in the diet, and the advantage of the breastfeeding remain as yet unresolved. Interaction of allergens with the intestinal cell barrier together with a set of effector cells represents the primary pathways of food-induced anaphylaxis. After an antigen cross-links the IgEs on the membrane of effector cells, a complex intracellular signaling cascade is initiated, which leads cells to release preformed mediators stored in their granules that are responsible for the acute symptoms of anaphylaxis. Afterward, they can also rapidly synthesize lipid compounds such as prostaglandins or leukotrienes. Cytokines or chemokines are also released, leading to the recruitment and activation of immune cells in the inflammatory microenvironment. Multiple factors that affect food-induced anaphylaxis are discussed in this review, paying special attention to dietary habits and environmental and genetic conditions.
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Affiliation(s)
- Sara Benedé
- Dpto. Bioquímica y Biología Molecular I, Universidad Complutense de Madrid, Madrid, Spain
| | - María Garrido-Arandia
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), Campus de Montegancedo, Pozuelo de Alarcón, Madrid, Spain
| | - Laura Martín-Pedraza
- Dpto. Bioquímica y Biología Molecular I, Universidad Complutense de Madrid, Madrid, Spain
| | - Cristina Bueno
- Dpto. Bioquímica y Biología Molecular I, Universidad Complutense de Madrid, Madrid, Spain
| | - Araceli Díaz-Perales
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), Campus de Montegancedo, Pozuelo de Alarcón, Madrid, Spain
| | - Mayte Villalba
- Dpto. Bioquímica y Biología Molecular I, Universidad Complutense de Madrid, Madrid, Spain
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32
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Martino DJ, Ashley S, Koplin J, Ellis J, Saffery R, Dharmage SC, Gurrin L, Matheson MC, Kalb B, Marenholz I, Beyer K, Lee Y, Hong X, Wang X, Vukcevic D, Motyer A, Leslie S, Allen KJ, Ferreira MAR. Genomewide association study of peanut allergy reproduces association with amino acid polymorphisms in
HLA
‐
DRB
1. Clin Exp Allergy 2017; 47:217-223. [DOI: 10.1111/cea.12863] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 11/06/2016] [Accepted: 11/07/2016] [Indexed: 02/02/2023]
Affiliation(s)
- D. J. Martino
- Department of Paediatrics Murdoch Childrens Research Institute The Royal Children's Hospital The University of Melbourne Melbourne Vic. Australia
| | - S. Ashley
- Department of Paediatrics Murdoch Childrens Research Institute The Royal Children's Hospital The University of Melbourne Melbourne Vic. Australia
- Hudson Institute of Medical Research Clayton Vic. Australia
| | - J. Koplin
- Department of Paediatrics Murdoch Childrens Research Institute The Royal Children's Hospital The University of Melbourne Melbourne Vic. Australia
- School of Population and Global Health The University of Melbourne Melbourne Vic. Australia
| | - J. Ellis
- Department of Paediatrics Murdoch Childrens Research Institute The Royal Children's Hospital The University of Melbourne Melbourne Vic. Australia
| | - R. Saffery
- Department of Paediatrics Murdoch Childrens Research Institute The Royal Children's Hospital The University of Melbourne Melbourne Vic. Australia
| | - S. C. Dharmage
- School of Population and Global Health The University of Melbourne Melbourne Vic. Australia
| | - L. Gurrin
- School of Population and Global Health The University of Melbourne Melbourne Vic. Australia
| | - M. C. Matheson
- School of Population and Global Health The University of Melbourne Melbourne Vic. Australia
| | - B. Kalb
- Pediatric Pneumology and Immunology Charité Universitätsmedizin Berlin Berlin Germany
- Clinic for Pediatric Allergy, Experimental and Clinical Research Center of MDC Charité Berlin Germany
- Max‐Delbrück‐Center for Molecular Medicine (MDC) Berlin Germany
| | - I. Marenholz
- Clinic for Pediatric Allergy, Experimental and Clinical Research Center of MDC Charité Berlin Germany
- Max‐Delbrück‐Center for Molecular Medicine (MDC) Berlin Germany
| | - K. Beyer
- Pediatric Pneumology and Immunology Charité Universitätsmedizin Berlin Berlin Germany
| | - Y.‐A. Lee
- Clinic for Pediatric Allergy, Experimental and Clinical Research Center of MDC Charité Berlin Germany
- Max‐Delbrück‐Center for Molecular Medicine (MDC) Berlin Germany
| | - X. Hong
- Department of Population, Family and Reproductive Health Center on the Early Life Origins of Disease Johns Hopkins University Bloomberg School of Public Health Baltimore MD USA
| | - X. Wang
- Department of Population, Family and Reproductive Health Center on the Early Life Origins of Disease Johns Hopkins University Bloomberg School of Public Health Baltimore MD USA
| | - D. Vukcevic
- Department of Paediatrics Murdoch Childrens Research Institute The Royal Children's Hospital The University of Melbourne Melbourne Vic. Australia
- Centre for Systems Genomics Schools of Mathematics and Statistics and Biosciences The University of Melbourne Melbourne Vic. Australia
| | - A. Motyer
- Department of Paediatrics Murdoch Childrens Research Institute The Royal Children's Hospital The University of Melbourne Melbourne Vic. Australia
- Centre for Systems Genomics Schools of Mathematics and Statistics and Biosciences The University of Melbourne Melbourne Vic. Australia
| | - S. Leslie
- Department of Paediatrics Murdoch Childrens Research Institute The Royal Children's Hospital The University of Melbourne Melbourne Vic. Australia
- Centre for Systems Genomics Schools of Mathematics and Statistics and Biosciences The University of Melbourne Melbourne Vic. Australia
| | - K. J. Allen
- Department of Paediatrics Murdoch Childrens Research Institute The Royal Children's Hospital The University of Melbourne Melbourne Vic. Australia
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Epidemiology of food allergy and food-induced anaphylaxis: is there really a Western world epidemic? Curr Opin Allergy Clin Immunol 2016; 15:409-16. [PMID: 26258921 DOI: 10.1097/aci.0000000000000196] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
PURPOSE OF REVIEW Food-induced anaphylaxis continues to be an important cause of hospital admissions, particularly in children. This review outlines recent advances in understanding the epidemiology of IgE-mediated food allergy and potential mechanisms for its rise in prevalence. RECENT FINDINGS The rise in food allergy prevalence in Western countries has happened more quickly than changes to the genome can occur; thus, environmental changes are likely to be important. Recent studies, however, suggest that genetic risk determines responses to environmental risk factors. Environmental peanut exposure has been associated with increased peanut allergy risk in individuals with filaggrin null mutations, consistently with sensitization occurring through a damaged skin barrier. Reduced microbial and vitamin D exposure is also leading candidates for risk factors for food allergy in the context of genetic susceptibility. In addition, HLA-DR and HLA-DQ gene region variants appear to play a role in peanut allergy, although no studies have yet assessed their susceptibility to environmental cues. Finally, findings from observational cohorts and the first large-scale intervention trials for food allergy prevention support early oral allergen exposure to reduce the prevalence of specific food allergies, which is informing changes in public health guidelines at the population level. Further research will be required to assess the impact of these guideline changes on the population prevalence of food allergy. SUMMARY New studies are providing important insights into the prevalence, causes, and mechanisms of food allergy. Recent findings are informing changes to population health guidelines in developed countries, which have the potential to halt or reverse the increase in food allergy prevalence. By contrast, food allergy in the developing world remains understudied.
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Dimitrov I, Doytchinova I. Associations between Milk and Egg Allergens and the HLA-DRB1/DQ Polymorphism: A Bioinformatics Approach. Int Arch Allergy Immunol 2016; 169:33-9. [DOI: 10.1159/000444172] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 01/20/2016] [Indexed: 11/19/2022] Open
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The evolving story of human leukocyte antigen and the immunogenetics of peanut allergy. Ann Allergy Asthma Immunol 2015; 115:471-6. [PMID: 26522257 DOI: 10.1016/j.anai.2015.10.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 08/28/2015] [Accepted: 10/06/2015] [Indexed: 01/08/2023]
Abstract
OBJECTIVE Peanut allergy (PA) clearly has a heritable component. Specific genetic contributions are unknown, but human leukocyte antigen (HLA) loci are obvious candidates. This review focuses on emerging studies of HLA associations with PA. DATA SOURCES PubMed was searched with no time limitations using key terms human leukocyte antigen, HLA, MHC, peanut, peanut hypersensitivity, and peanut allergy. STUDY SELECTIONS Qualifying studies were English-language reports of genetic analyses examining PA and HLA associations. RESULTS Seven relevant citations were identified, which were published from 1996 to 2015. Early studies using candidate gene approaches found associations between PA and HLA-DR and -DQ alleles (HLA-DRB1*08 and DQB1*06:03P) when comparing subjects with peanut allergy with nonallergic unrelated control groups. No significant associations were found between siblings with and without peanut allergy. However, a recent large genomewide association study of patients with peanut allergy and their family members found 2 PA-associated single-nucleotide polymorphisms (rs9275596 and rs7192) mapping to regions involving the HLA-DR and HLA-DQ genes. Associations with differential DNA methylation partly mediated the associations between PA and single-nucleotide polymorphisms. CONCLUSION Early studies using candidate gene approaches identified HLA associations with PA compared with the general population, suggesting a link with atopy but failing to identify a PA-specific association. These studies had various limitations that included small samples. The most compelling evidence for a PA-specific HLA association comes from a genomewide association study, which examined the entire genome in large, well-defined, related cohorts. More research is needed to validate and replicate these findings, to perform fine genetic mapping of specific HLA loci, and to demonstrate underlying mechanisms of HLA contributions to PA.
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Affiliation(s)
- M. C. Berin
- Pediatric Allergy and Immunology; Icahn School of Medicine at Mount Sinai; New York NY USA
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Margolis DJ, Mitra N, Kim B, Gupta J, Hoffstad OJ, Papadopoulos M, Wubbenhorst B, Nathanson KL, Duke JL, Monos DS, Kamoun M. Association of HLA-DRB1 genetic variants with the persistence of atopic dermatitis. Hum Immunol 2015; 76:571-7. [PMID: 26307177 PMCID: PMC4593755 DOI: 10.1016/j.humimm.2015.08.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 04/27/2015] [Accepted: 08/21/2015] [Indexed: 10/23/2022]
Abstract
Atopic dermatitis (AD) is a waxing and waning illness of childhood that is likely caused by interactions between an altered skin barrier and immune dysregulation. The goal of our study was to evaluate the association of DRB1 genetic variants and the persistence of AD using whole exome sequencing and high resolution typing. DRB1 was interrogated based on previous reports that utilized high throughput techniques. We evaluated an ongoing nation-wide long-term cohort of children with AD in which patients are asked every 6months about their medication use and their AD symptoms. In total, 87 African-American and 50 European-American children were evaluated. Genetic association analysis was performed using a software tool focusing on amino acid variable positions shared by HLA-DRB1 alleles covering the antigen presenting domain. Amino acid variations at position 9 (pocket 9), position 26, and position 78 (pocket 4) were marginally associated with the prevalence of AD. However, the odds ratio was 0.30 (0.14, 0.68; p=0.003) for residue 78, 0.27 (0.10, 0.69; p=0.006) for residue 26 and not significant for residue 9 with respect to the persistence of AD. In conclusion, amino acid variations at peptide-binding pockets of HLA-DRB1 were associated with the persistence of AD in African-American children.
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Affiliation(s)
- David J Margolis
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States; Department of Dermatology, University of Pennsylvania, Philadelphia, PA, United States; Department of Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, PA, United States.
| | - Nandita Mitra
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States; Department of Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, PA, United States
| | - Brian Kim
- Division of Dermatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States; Department of Anesthesiology, Washington University School of Medicine, St. Louis, MO, United States
| | - Jayanta Gupta
- Division of Biostatistics and Epidemiology, Department of Biomedical Sciences, Texas Tech University Health Sciences Center, El Paso, TX, United States
| | - Ole J Hoffstad
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States; Department of Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, PA, United States
| | - Maryte Papadopoulos
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States; Department of Dermatology, University of Pennsylvania, Philadelphia, PA, United States
| | - Bradley Wubbenhorst
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States; Division of Translational Medicine and Human Genetics, Department of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Katherine L Nathanson
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States; Division of Translational Medicine and Human Genetics, Department of Medicine, University of Pennsylvania, Philadelphia, PA, United States; Abramson Cancer Center, Hospital of the University of Pennsylvania, Philadelphia, PA, United States
| | - Jamie L Duke
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Dimitri S Monos
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States; Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, United States; Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Malek Kamoun
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States; Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, United States
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Hong X, Hao K, Ladd-Acosta C, Hansen KD, Tsai HJ, Liu X, Xu X, Thornton TA, Caruso D, Keet CA, Sun Y, Wang G, Luo W, Kumar R, Fuleihan R, Singh AM, Kim JS, Story RE, Gupta RS, Gao P, Chen Z, Walker SO, Bartell TR, Beaty TH, Fallin MD, Schleimer R, Holt PG, Nadeau KC, Wood RA, Pongracic JA, Weeks DE, Wang X. Genome-wide association study identifies peanut allergy-specific loci and evidence of epigenetic mediation in US children. Nat Commun 2015; 6:6304. [PMID: 25710614 PMCID: PMC4340086 DOI: 10.1038/ncomms7304] [Citation(s) in RCA: 157] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 01/16/2015] [Indexed: 12/17/2022] Open
Abstract
Food allergy (FA) affects 2–10% of U.S. children and is a growing clinical and public health problem. Here we conduct the first genome-wide association study of well-defined FA, including specific subtypes (peanut, milk, and egg) in 2,759 U.S. participants (1,315 children; 1,444 parents) from the Chicago Food Allergy Study; and identify peanut allergy (PA)-specific loci in the HLA-DR and -DQ gene region at 6p21.32, tagged by rs7192 (p=5.5×10−8) and rs9275596 (p=6.8×10−10), in 2,197 participants of European ancestry. We replicate these associations in an independent sample of European ancestry. These associations are further supported by meta-analyses across the discovery and replication samples. Both single-nucleotide polymorphisms (SNPs) are associated with differential DNA methylation levels at multiple CpG sites (p<5×10−8); and differential DNA methylation of the HLA-DQB1 and HLA-DRB1 genes partially mediate the identified SNP-PA associations. This study suggests that the HLA-DR and -DQ gene region likely poses significant genetic risk for PA.
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Affiliation(s)
- Xiumei Hong
- Department of Population, Family and Reproductive Health, Center on the Early Life Origins of Disease, Johns Hopkins University Bloomberg School of Public Health, 615 North Wolfe Street, E4132, Baltimore, Maryland 21205, USA
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Christine Ladd-Acosta
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
| | - Kasper D Hansen
- 1] Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health Baltimore, Baltimore, Maryland 21205, USA [2] McKusick-Nathans Insitute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Hui-Ju Tsai
- 1] Mary Ann and J. Milburn Smith Child Health Research Program, Department of Pediatrics, Northwestern University Feinberg School of Medicine and Stanley Manne Children's Research Institute, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois 60611, USA [2] Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan 35053, Taiwan [3] Department of Public Health, China Medical University, Taichung 40402, Taiwan
| | - Xin Liu
- 1] Mary Ann and J. Milburn Smith Child Health Research Program, Department of Pediatrics, Northwestern University Feinberg School of Medicine and Stanley Manne Children's Research Institute, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois 60611, USA [2] Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Xin Xu
- Guangdong Provincial Institute of Nephrology, Southern Medical University, Guangzhou 510515, China
| | - Timothy A Thornton
- Department of Biostatistics, University of Washington, Seattle, Washington 98195, USA
| | - Deanna Caruso
- Department of Population, Family and Reproductive Health, Center on the Early Life Origins of Disease, Johns Hopkins University Bloomberg School of Public Health, 615 North Wolfe Street, E4132, Baltimore, Maryland 21205, USA
| | - Corinne A Keet
- 1] Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland 21205, USA [2] Division of Pediatric Allergy and Immunology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Yifei Sun
- Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health Baltimore, Baltimore, Maryland 21205, USA
| | - Guoying Wang
- Department of Population, Family and Reproductive Health, Center on the Early Life Origins of Disease, Johns Hopkins University Bloomberg School of Public Health, 615 North Wolfe Street, E4132, Baltimore, Maryland 21205, USA
| | - Wei Luo
- 1] Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA [2] College of Computer Science and Technology, Huaqiao University, Xiamen 361021, China
| | - Rajesh Kumar
- Division of Allergy and Immunology, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois 60611, USA
| | - Ramsay Fuleihan
- Division of Allergy and Immunology, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois 60611, USA
| | - Anne Marie Singh
- Department of Pediatrics and Medicine, Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern Feinberg School of Medicine, Chicago, Illinois 61611, USA
| | - Jennifer S Kim
- 1] Division of Allergy and Immunology, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois 60611, USA [2] NorthShore University HealthSystem, Evanston, Illinois 60201, USA
| | - Rachel E Story
- 1] Division of Allergy and Immunology, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois 60611, USA [2] NorthShore University Health Systems, Pritzker School of Medicine, University of Chicago, Chicago, Illinois 60637, USA
| | - Ruchi S Gupta
- Mary Ann and J. Milburn Smith Child Health Research Program, Department of Pediatrics, Northwestern University Feinberg School of Medicine and Stanley Manne Children's Research Institute, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois 60611, USA
| | - Peisong Gao
- Division of Allergy and Clinical Immunology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21224, USA
| | - Zhu Chen
- Department of Population, Family and Reproductive Health, Center on the Early Life Origins of Disease, Johns Hopkins University Bloomberg School of Public Health, 615 North Wolfe Street, E4132, Baltimore, Maryland 21205, USA
| | - Sheila O Walker
- Department of Population, Family and Reproductive Health, Center on the Early Life Origins of Disease, Johns Hopkins University Bloomberg School of Public Health, 615 North Wolfe Street, E4132, Baltimore, Maryland 21205, USA
| | - Tami R Bartell
- Mary Ann and J. Milburn Smith Child Health Research Program, Department of Pediatrics, Northwestern University Feinberg School of Medicine and Stanley Manne Children's Research Institute, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois 60611, USA
| | - Terri H Beaty
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
| | - M Daniele Fallin
- Department of Mental Health, Wendy Klag Center for Autism and Developmental Disabilities, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, USA
| | - Robert Schleimer
- Division of Allergy-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Patrick G Holt
- Telethon Kids Institute, University of Western Australia; Perth and Queensland Children's Medical Research Institute, University of Queensland, Brisbane, Queensland 4029, Australia
| | - Kari Christine Nadeau
- Division of Allergy, Immunology and Rheumatology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Robert A Wood
- Division of Pediatric Allergy and Immunology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Jacqueline A Pongracic
- Division of Allergy and Immunology, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois 60611, USA
| | - Daniel E Weeks
- Departments of Human Genetics and Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
| | - Xiaobin Wang
- 1] Department of Population, Family and Reproductive Health, Center on the Early Life Origins of Disease, Johns Hopkins University Bloomberg School of Public Health, 615 North Wolfe Street, E4132, Baltimore, Maryland 21205, USA [2] Division of General Pediatrics and Adolescent Medicine, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
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