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Shook MS, Lu X, Chen X, Parameswaran S, Edsall L, Trimarchi MP, Ernst K, Granitto M, Forney C, Donmez OA, Diouf AA, VonHandorf A, Rothenberg ME, Weirauch MT, Kottyan LC. Systematic identification of genotype-dependent enhancer variants in eosinophilic esophagitis. Am J Hum Genet 2024; 111:280-294. [PMID: 38183988 PMCID: PMC10870143 DOI: 10.1016/j.ajhg.2023.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 12/01/2023] [Accepted: 12/05/2023] [Indexed: 01/08/2024] Open
Abstract
Eosinophilic esophagitis (EoE) is a rare atopic disorder associated with esophageal dysfunction, including difficulty swallowing, food impaction, and inflammation, that develops in a small subset of people with food allergies. Genome-wide association studies (GWASs) have identified 9 independent EoE risk loci reaching genome-wide significance (p < 5 × 10-8) and 27 additional loci of suggestive significance (5 × 10-8 < p < 1 × 10-5). In the current study, we perform linkage disequilibrium (LD) expansion of these loci to nominate a set of 531 variants that are potentially causal. To systematically interrogate the gene regulatory activity of these variants, we designed a massively parallel reporter assay (MPRA) containing the alleles of each variant within their genomic sequence context cloned into a GFP reporter library. Analysis of reporter gene expression in TE-7, HaCaT, and Jurkat cells revealed cell-type-specific gene regulation. We identify 32 allelic enhancer variants, representing 6 genome-wide significant EoE loci and 7 suggestive EoE loci, that regulate reporter gene expression in a genotype-dependent manner in at least one cellular context. By annotating these variants with expression quantitative trait loci (eQTL) and chromatin looping data in related tissues and cell types, we identify putative target genes affected by genetic variation in individuals with EoE. Transcription factor enrichment analyses reveal possible roles for cell-type-specific regulators, including GATA3. Our approach reduces the large set of EoE-associated variants to a set of 32 with allelic regulatory activity, providing functional insights into the effects of genetic variation in this disease.
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Affiliation(s)
- Molly S Shook
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Xiaoming Lu
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Xiaoting Chen
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Sreeja Parameswaran
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Lee Edsall
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Michael P Trimarchi
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Kevin Ernst
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Marissa Granitto
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Carmy Forney
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Omer A Donmez
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Arame A Diouf
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Andrew VonHandorf
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Marc E Rothenberg
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA; Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA; Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
| | - Leah C Kottyan
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA; Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
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Filimonova I, Innocenti G, Vogl T. Phage Immunoprecipitation Sequencing (PhIP-Seq) for Analyzing Antibody Epitope Repertoires Against Food Antigens. Methods Mol Biol 2024; 2717:101-122. [PMID: 37737980 DOI: 10.1007/978-1-0716-3453-0_7] [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] [Indexed: 09/23/2023]
Abstract
While thousands of food and environmental allergens have been reported, conventional methods for allergy testing typically rely on measuring immunoglobulin E (IgE) binding against panels of dozens to hundreds of antigens. Beyond IgE, also the specificity of other Ig (sub-)classes such as IgG4, has gained interest because of a potential protective role toward allergy.Phage immunoprecipitation sequencing (PhIP-Seq) allows to study hundreds of thousands of rationally selected peptide antigens and to resolve binding specificities of different Ig classes. This technology combines synthetic DNA libraries encoding antigens, with the display on the surface of T7 bacteriophages and next-generation sequencing (NGS) for quantitative readouts. Thereby binding of entire Ig repertoires can be measured to detect the exact epitopes of food allergens and to study potential cross-reactivity.In this chapter, we provide a summary of both the key experimental steps and various strategies for analyzing PhIP-Seq datasets, as well as comparing the advantages and disadvantages of this methodology for measuring antibody responses against food antigens.
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Affiliation(s)
- Ioanna Filimonova
- Medical University of Vienna, Center for Cancer Research, Vienna, Austria
| | - Gabriel Innocenti
- Medical University of Vienna, Center for Cancer Research, Vienna, Austria
| | - Thomas Vogl
- Medical University of Vienna, Center for Cancer Research, Vienna, Austria.
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Udoye CC, Ehlers M, Manz RA. The B Cell Response and Formation of Allergenic and Anti-Allergenic Antibodies in Food Allergy. BIOLOGY 2023; 12:1501. [PMID: 38132327 PMCID: PMC10740584 DOI: 10.3390/biology12121501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 11/30/2023] [Accepted: 12/05/2023] [Indexed: 12/23/2023]
Abstract
Food allergies are a growing public health concern worldwide, especially in children and young adults. Allergen-specific IgE plays a central role in the pathogenesis of food allergies, but their titers poorly correlate with allergy development. Host immune systems yield allergen-specific immunoglobulin (Ig)A, IgE and IgG subclasses with low or high affinities and differential Fc N-glycosylation patterns that can affect the allergic reaction to food in multiple ways. High-affinity IgE is required to induce strong mast cell activation eventually leading to allergic anaphylaxis, while low-affinity IgE can even inhibit the development of clinically relevant allergic symptoms. IgA and IgG antibodies can inhibit IgE-mediated mast cell activation through various mechanisms, thereby protecting IgE-positive individuals from allergy development. The production of IgE and IgG with differential allergenic potential seems to be affected by the signaling strength of individual B cell receptors, and by cytokines from T cells. This review provides an overview of the diversity of the B cell response and the diverse roles of antibodies in food allergy.
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Affiliation(s)
- Christopher C. Udoye
- Institute for Systemic Inflammation Research, University of Lübeck, 23562 Lübeck, Germany
| | - Marc Ehlers
- Laboratories of Immunology and Antibody Glycan Analysis, Institute for Nutritional Medicine, University of Lübeck and University Medical Center Schleswig-Holstein, 23538 Lübeck, Germany
| | - Rudolf A. Manz
- Institute for Systemic Inflammation Research, University of Lübeck, 23562 Lübeck, Germany
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Allergenic food protein consumption is associated with systemic IgG antibody responses in non-allergic individuals. Immunity 2022; 55:2454-2469.e6. [PMID: 36473469 DOI: 10.1016/j.immuni.2022.11.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 06/01/2022] [Accepted: 11/09/2022] [Indexed: 12/12/2022]
Abstract
Although food-directed immunoglobulin E (IgE) has been studied in the context of allergies, the prevalence and magnitude of IgG responses against dietary antigens are incompletely characterized in the general population. Here, we measured IgG binding against food and environmental antigens obtained from allergen databases and the immune epitope database (IEDB), represented in a phage displayed library of 58,233 peptides. By profiling blood samples of a large cohort representing the average adult Israeli population (n = 1,003), we showed that many food antigens elicited systemic IgG in up to 50% of individuals. Dietary intake of specific food protein correlated with antibody binding, suggesting that diet can shape the IgG epitope repertoire. Our work documents abundant systemic IgG responses against food antigens and provides a reference map of the exact immunogenic epitopes on a population scale, laying the foundation to unravel the role of food- and environmental antigen-directed antibody binding in disease contexts.
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Zhu H, Tang K, Chen G, Liu Z. Biomarkers in oral immunotherapy. J Zhejiang Univ Sci B 2022; 23:705-731. [PMID: 36111569 PMCID: PMC9483607 DOI: 10.1631/jzus.b2200047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Food allergy (FA) is a global health problem that affects a large population, and thus effective treatment is highly desirable. Oral immunotherapy (OIT) has been showing reasonable efficacy and favorable safety in most FA subjects. Dependable biomarkers are needed for treatment assessment and outcome prediction during OIT. Several immunological indicators have been used as biomarkers in OIT, such as skin prick tests, basophil and mast cell reactivity, T cell and B cell responses, allergen-specific antibody levels, and cytokines. Other novel indicators also could be potential biomarkers. In this review, we discuss and assess the application of various immunological indicators as biomarkers for OIT.
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Affiliation(s)
- Haitao Zhu
- Department of Pediatrics (No. 3 Ward), Northwest Women's and Children's Hospital, Xi'an 710061, China
| | - Kaifa Tang
- Department of Urology, the Affiliated Hospital of Guizhou Medical University, Guiyang 550004, China
| | - Guoqiang Chen
- Department of Pediatrics (No. 3 Ward), Northwest Women's and Children's Hospital, Xi'an 710061, China
| | - Zhongwei Liu
- Department of Cardiology, Shaanxi Provincial People's Hospital, Xi'an 710068, China.
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Kostara M, Chondrou V, Fotopoulos V, Sgourou A, Tsabouri S. Epigenetic/genetic variations in CG-rich elements of immune-related genes contribute to food allergy development during childhood. Pediatr Allergy Immunol 2022; 33:e13812. [PMID: 35754135 DOI: 10.1111/pai.13812] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 05/03/2022] [Accepted: 05/24/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND Genetic areas of FOXP3 TSDR, human leukocyte antigen-G (HLA-G) upstream of CpG island 96, CpG41 and CpG73 islands of the HLA-DRB1 and HLA-DQB1 genes respectively, previously documented to display immune-modulatory properties, were subjected to epigenetic/genetic analysis to assess their influence in IgE-mediated food allergy (FA) development in children. METHODS Sixty-four orally challenged and IgE-tested food allergic subjects together with 44 controls were recruited. Targeted pyrosequencing analysis to detect DNA methylation status and genetic variations was utilized and experimental results obtained were analyzed by a statistical software platform and correlated to clinical data. Also, transcription factor (TF) binding sites in study areas were unmasked by the JASPAR prediction database. RESULTS Parents' smoking was significantly correlated with aberrant methylation patterns, regardless of food allergic or control status. HLA-G promoter region showed a trend for hypomethylation in food allergic subjects, with one of the CG sites displaying significantly decreased methylation values. Rs1233333, residing within the HLA-G promoter region preserved a protective role toward DNA methylation. Variable methylation patterns were recorded for CpG41 of the HLA-DRB1 gene and hypermethylation of the region was significantly correlated with the presence of single nucleotide polymorphisms (SNPs). TFs' recognition sites, located in studied genetic areas and exerting pivotal regulatory biological roles, are potentially affected by divergent DNA methylation status. CONCLUSIONS We propose that HLA-G expression is triggered by food-derived allergens, providing a TregFoxP3-/HLA-G+ subpopulation generation to promote direct immune tolerance. Furthermore, clear evidence is provided for the underlying co-operation of genetic polymorphisms with epigenetic events, mainly at the CpG41 island of the HLA-DRB1 gene, which needs an extended investigation and elucidation.
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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
| | - Vassilis Fotopoulos
- Digital Systems Laboratory, 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
| | - Sophia Tsabouri
- Department of Paediatrics, Faculty of Medicine, School of Health Sciences, University of Ioannina, Ioannina, Greece
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da Silva Antunes R, Sutherland A, Frazier A, Schulten V, Pomés A, Glesner J, Calatroni A, Altman MC, Wood RA, O'Connor GT, Pongracic JA, Khurana Hershey GK, Kercsmar CM, Gruchalla RS, Gill M, Liu AH, Zoratti E, Kattan M, Busse PJ, Bacharier LB, Teach SJ, Wheatley LM, Togias A, Busse WW, Jackson DJ, Sette A. Heterogeneity of magnitude, allergen immunodominance, and cytokine polarization of cockroach allergen-specific T cell responses in allergic sensitized children. Clin Transl Allergy 2021; 11:e12073. [PMID: 34691392 PMCID: PMC8514843 DOI: 10.1002/clt2.12073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 09/13/2021] [Accepted: 10/03/2021] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Characterization of allergic responses to cockroach (CR), a common aeroallergen associated with asthma, has focused mainly on IgE reactivity, but little is known about T cell responses, particularly in children. We conducted a functional evaluation of CR allergen-specific T cell reactivity in a cohort of CR allergic children with asthma. METHODS Peripheral blood mononuclear cells (PBMCs) were obtained from 71 children, with mild-to-moderate asthma who were enrolled in a CR immunotherapy (IT) clinical trial, prior to treatment initiation. PBMC were stimulated with peptide pools derived from 11 CR allergens, and CD4+ T cell responses assessed by intracellular cytokine staining. RESULTS Highly heterogeneous responses in T cell reactivity were observed among participants, both in terms of the magnitude of cytokine response and allergen immunodominance. Reactivity against Bla g 9 and Bla g 5 was most frequent. The phenotype of the T cell response was dominated by IL-4 production and a Th2 polarized profile in 54.9% of participants, but IFNγ production and Th1 polarization was observed in 25.3% of the participants. The numbers of regulatory CD4+ T cells were also highly variable and the magnitude of effector responses and Th2 polarization were positively correlated with serum IgE levels specific to a clinical CR extract. CONCLUSIONS Our results demonstrate that in children with mild-to-moderate asthma, CR-specific T cell responses display a wide range of magnitude, allergen dominance, and polarization. These results will enable examination of whether any of the variables measured are affected by IT and/or are predictive of clinical outcomes.
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Affiliation(s)
| | - Aaron Sutherland
- Division of Vaccine DiscoveryLa Jolla Institute for ImmunologyLa JollaCaliforniaUSA
| | - April Frazier
- Division of Vaccine DiscoveryLa Jolla Institute for ImmunologyLa JollaCaliforniaUSA
| | - Veronique Schulten
- Division of Vaccine DiscoveryLa Jolla Institute for ImmunologyLa JollaCaliforniaUSA
| | - Anna Pomés
- Basic ResearchIndoor Biotechnologies, Inc.CharlottesvilleVirginiaUSA
| | - Jill Glesner
- Basic ResearchIndoor Biotechnologies, Inc.CharlottesvilleVirginiaUSA
| | | | - Matthew C. Altman
- Benaroya Research Institute Systems Immunology DivisionDepartment of MedicineUniversity of WashingtonSeattleWashingtonUSA
| | - Robert A. Wood
- Division of Pediatric Allergy, Immunology and RheumatologyDepartment of PediatricsJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - George T. O'Connor
- Boston University School of MedicinePulmonary CenterBostonMassachusettsUSA
| | - Jacqueline A. Pongracic
- Advanced General Pediatrics and Primary CareAnn & Robert H. Lurie Children's Hospital of ChicagoChicagoIllinoisUSA
| | | | - Carolyn M. Kercsmar
- Division of Pulmonary MedicineCincinnati Children's HospitalCincinnatiOhioUSA
| | - Rebecca S. Gruchalla
- Divisions of Infectious Diseases and Pulmonary Vascular BiologyDepartment of PediatricsUniversity of Texas Southwestern Medical CenterDallasTexasUSA
| | - Michelle Gill
- Divisions of Infectious Diseases and Pulmonary Vascular BiologyDepartment of PediatricsUniversity of Texas Southwestern Medical CenterDallasTexasUSA
| | - Andrew H. Liu
- Department of PediatricsChildren's Hospital ColoradoUniversity of Colorado School of MedicineAuroraColoradoUSA
| | - Edward Zoratti
- Henry Ford Health System and Wayne State University School of MedicineDetroitMichiganUSA
| | - Meyer Kattan
- College of Physicians and SurgeonsColumbia UniversityNew YorkNew YorkUSA
| | - Paula J. Busse
- Division of Clinical Immunology and AllergyIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Leonard B. Bacharier
- Department of PediatricsMonroe Carell Jr Children's Hospital at Vanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Stephen J. Teach
- Center for Translational ResearchChildren's National HospitalWashingtonDCUSA
| | - Lisa M. Wheatley
- Division of Allergy, Immunology, and TransplantationNational Institute of Allergy and Infectious DiseasesNational Institutes of HealthRockvilleMarylandUSA
| | - Alkis Togias
- Division of Allergy, Immunology, and TransplantationNational Institute of Allergy and Infectious DiseasesNational Institutes of HealthRockvilleMarylandUSA
| | - William W. Busse
- Departments of Pediatrics and MedicineUniversity of Wisconsin School of Medicine and Public HealthMadisonWisconsinUSA
| | - Daniel J. Jackson
- Departments of Pediatrics and MedicineUniversity of Wisconsin School of Medicine and Public HealthMadisonWisconsinUSA
| | - Alessandro Sette
- Division of Vaccine DiscoveryLa Jolla Institute for ImmunologyLa JollaCaliforniaUSA
- Department of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
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