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Risemberg EL, Smeekens JM, Cruz Cisneros MC, Hampton BK, Hock P, Linnertz CL, Miller DR, Orgel K, Shaw GD, de Villena FPM, Burks AW, Valdar W, Kulis MD, Ferris MT. A mutation in Themis contributes to anaphylaxis severity following oral peanut challenge in CC027 mice. J Allergy Clin Immunol 2024; 154:387-397. [PMID: 38670234 PMCID: PMC11323216 DOI: 10.1016/j.jaci.2024.03.027] [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: 09/07/2023] [Revised: 03/12/2024] [Accepted: 03/22/2024] [Indexed: 04/28/2024]
Abstract
BACKGROUND The development of peanut allergy is due to a combination of genetic and environmental factors, although specific genes have proven difficult to identify. Previously, we reported that peanut-sensitized Collaborative Cross strain CC027/GeniUnc (CC027) mice develop anaphylaxis upon oral challenge to peanut, in contrast to C3H/HeJ (C3H) mice. OBJECTIVE This study aimed to determine the genetic basis of orally induced anaphylaxis to peanut in CC027 mice. METHODS A genetic mapping population between CC027 and C3H mice was designed to identify the genetic factors that drive oral anaphylaxis. A total of 356 CC027xC3H backcrossed mice were generated, sensitized to peanut, then challenged to peanut by oral gavage. Anaphylaxis and peanut-specific IgE were quantified for all mice. T-cell phenotyping was conducted on CC027 mice and 5 additional Collaborative Cross strains. RESULTS Anaphylaxis to peanut was absent in 77% of backcrossed mice, with 19% showing moderate anaphylaxis and 4% having severe anaphylaxis. There were 8 genetic loci associated with variation in response to peanut challenge-6 associated with anaphylaxis (temperature decrease) and 2 associated with peanut-specific IgE levels. There were 2 major loci that impacted multiple aspects of the severity of acute anaphylaxis, at which the CC027 allele was associated with worse outcome. At one of these loci, CC027 has a private genetic variant in the Themis gene. Consistent with described functions of Themis, we found that CC027 mice have more immature T cells with fewer CD8+, CD4+, and CD4+CD25+CD127- regulatory T cells. CONCLUSIONS Our results demonstrate a key role for Themis in the orally reactive CC027 mouse model of peanut allergy.
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Affiliation(s)
- Ellen L Risemberg
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Johanna M Smeekens
- Division of Allergy and Immunology, Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Marta C Cruz Cisneros
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Brea K Hampton
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Pablo Hock
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Colton L Linnertz
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Darla R Miller
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Kelly Orgel
- Division of Allergy and Immunology, Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Ginger D Shaw
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Fernando Pardo Manuel de Villena
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - A Wesley Burks
- Division of Allergy and Immunology, Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - William Valdar
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC.
| | - Michael D Kulis
- Division of Allergy and Immunology, Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC.
| | - Martin T Ferris
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC.
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Pahlevan Kakhki M, Giordano A, Starvaggi Cucuzza C, Venkata S Badam T, Samudyata S, Lemée MV, Stridh P, Gkogka A, Shchetynsky K, Harroud A, Gyllenberg A, Liu Y, Boddul S, James T, Sorosina M, Filippi M, Esposito F, Wermeling F, Gustafsson M, Casaccia P, Hillert J, Olsson T, Kockum I, Sellgren CM, Golzio C, Kular L, Jagodic M. A genetic-epigenetic interplay at 1q21.1 locus underlies CHD1L-mediated vulnerability to primary progressive multiple sclerosis. Nat Commun 2024; 15:6419. [PMID: 39079955 PMCID: PMC11289459 DOI: 10.1038/s41467-024-50794-z] [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: 04/28/2023] [Accepted: 07/21/2024] [Indexed: 08/02/2024] Open
Abstract
Multiple Sclerosis (MS) is a heterogeneous inflammatory and neurodegenerative disease with an unpredictable course towards progressive disability. Treating progressive MS is challenging due to limited insights into the underlying mechanisms. We examined the molecular changes associated with primary progressive MS (PPMS) using a cross-tissue (blood and post-mortem brain) and multilayered data (genetic, epigenetic, transcriptomic) from independent cohorts. In PPMS, we found hypermethylation of the 1q21.1 locus, controlled by PPMS-specific genetic variations and influencing the expression of proximal genes (CHD1L, PRKAB2) in the brain. Evidence from reporter assay and CRISPR/dCas9 experiments supports a causal link between methylation and expression and correlation network analysis further implicates these genes in PPMS brain processes. Knock-down of CHD1L in human iPSC-derived neurons and knock-out of chd1l in zebrafish led to developmental and functional deficits of neurons. Thus, several lines of evidence suggest a distinct genetic-epigenetic-transcriptional interplay in the 1q21.1 locus potentially contributing to PPMS pathogenesis.
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Affiliation(s)
- Majid Pahlevan Kakhki
- Department of Clinical Neuroscience, Karolinska Institutet, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Antonino Giordano
- Department of Clinical Neuroscience, Karolinska Institutet, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
- Neurology and Neurorehabilitation Units, IRCCS San Raffaele Hospital, Milan, Italy
- Laboratory of Human Genetics of Neurological Disorders, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Università Vita-Salute San Raffaele, Milan, Italy
| | - Chiara Starvaggi Cucuzza
- Department of Clinical Neuroscience, Karolinska Institutet, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
- Center for Neurology, Academic Specialist Center, Stockholm, Sweden
| | - Tejaswi Venkata S Badam
- Department of Clinical Neuroscience, Karolinska Institutet, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
- Department of Bioinformatics, Institute for Physics chemistry and Biology (IFM), Linköping university, Linköping, Sweden
| | - Samudyata Samudyata
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Marianne Victoria Lemée
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Pernilla Stridh
- Department of Clinical Neuroscience, Karolinska Institutet, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Asimenia Gkogka
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Klementy Shchetynsky
- Department of Clinical Neuroscience, Karolinska Institutet, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Adil Harroud
- The Neuro (Montreal Neurological Institute-Hospital), Montréal, QC, Canada
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada
- Department of Human Genetics, McGill University, Montréal, QC, Canada
| | - Alexandra Gyllenberg
- Department of Clinical Neuroscience, Karolinska Institutet, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Yun Liu
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, Shanghai, China
| | - Sanjaykumar Boddul
- Department of Medicine, Solna, Karolinska Institutet, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Tojo James
- Department of Clinical Neuroscience, Karolinska Institutet, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Melissa Sorosina
- Laboratory of Human Genetics of Neurological Disorders, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Massimo Filippi
- Neurology and Neurorehabilitation Units, IRCCS San Raffaele Hospital, Milan, Italy
- Università Vita-Salute San Raffaele, Milan, Italy
- Neurophysiology Unit, IRCCS San Raffaele Hospital, Milan, Italy
- Neuroimaging Research Unit, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Federica Esposito
- Neurology and Neurorehabilitation Units, IRCCS San Raffaele Hospital, Milan, Italy
- Laboratory of Human Genetics of Neurological Disorders, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Fredrik Wermeling
- Department of Medicine, Solna, Karolinska Institutet, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Mika Gustafsson
- Department of Bioinformatics, Institute for Physics chemistry and Biology (IFM), Linköping university, Linköping, Sweden
| | - Patrizia Casaccia
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Jan Hillert
- Department of Clinical Neuroscience, Karolinska Institutet, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Tomas Olsson
- Department of Clinical Neuroscience, Karolinska Institutet, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Ingrid Kockum
- Department of Clinical Neuroscience, Karolinska Institutet, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Carl M Sellgren
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
- Center for Psychiatry Research, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
- Stockholm Health Care Services, Stockholm County Council, Stockholm, Sweden
| | - Christelle Golzio
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Lara Kular
- Department of Clinical Neuroscience, Karolinska Institutet, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden.
| | - Maja Jagodic
- Department of Clinical Neuroscience, Karolinska Institutet, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden.
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Foley GR, Marthick JR, Lucas SE, Raspin K, Banks A, Stanford JL, Ostrander EA, FitzGerald LM, Dickinson JL. Germline Sequencing of DNA Damage Repair Genes in Two Hereditary Prostate Cancer Cohorts Reveals New Disease Risk-Associated Gene Variants. Cancers (Basel) 2024; 16:2482. [PMID: 39001544 PMCID: PMC11240467 DOI: 10.3390/cancers16132482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 06/27/2024] [Accepted: 07/02/2024] [Indexed: 07/16/2024] Open
Abstract
Rare, inherited variants in DNA damage repair (DDR) genes have a recognised role in prostate cancer (PrCa) susceptibility. In addition, these genes are therapeutically targetable. While rare variants are informing clinical management in other common cancers, defining the rare disease-associated variants in PrCa has been challenging. Here, whole-genome and -exome sequencing data from two independent, high-risk Australian and North American familial PrCa datasets were interrogated for novel DDR risk variants. Rare DDR gene variants (predicted to be damaging and present in two or more family members) were identified and subsequently genotyped in 1963 individuals (700 familial and 459 sporadic PrCa cases, 482 unaffected relatives, and 322 screened controls), and association analyses accounting for relatedness (MQLS) undertaken. In the combined datasets, rare ERCC3 (rs145201970, p = 2.57 × 10-4) and BRIP1 (rs4988345, p = 0.025) variants were significantly associated with PrCa risk. A PARP2 (rs200603922, p = 0.028) variant in the Australian dataset and a MUTYH (rs36053993, p = 0.031) variant in the North American dataset were also associated with risk. Evaluation of clinicopathological characteristics provided no evidence for a younger age or higher-grade disease at diagnosis in variant carriers, which should be taken into consideration when determining genetic screening eligibility criteria for targeted, gene-based treatments in the future. This study adds valuable knowledge to our understanding of PrCa-associated DDR genes, which will underpin effective clinical screening and treatment strategies.
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Affiliation(s)
- Georgea R Foley
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS 7000, Australia
| | - James R Marthick
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS 7000, Australia
| | - Sionne E Lucas
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS 7000, Australia
| | - Kelsie Raspin
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS 7000, Australia
| | - Annette Banks
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS 7000, Australia
| | - Janet L Stanford
- Fred Hutchinson Cancer Center, 1100 Fairview Ave. N., M4-B874, Seattle, WA 98109, USA
| | - Elaine A Ostrander
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Liesel M FitzGerald
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS 7000, Australia
| | - Joanne L Dickinson
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS 7000, Australia
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D’Aiuto V, Mormile I, Granata F, Napolitano F, Lamagna L, Della Casa F, de Paulis A, Rossi FW. Worldwide Heterogeneity of Food Allergy: Focus on Peach Allergy in Southern Italy. J Clin Med 2024; 13:3259. [PMID: 38892968 PMCID: PMC11173152 DOI: 10.3390/jcm13113259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/25/2024] [Accepted: 05/30/2024] [Indexed: 06/21/2024] Open
Abstract
Food allergy (FA) has shown an increasing prevalence in the last decades, becoming a major public health problem. However, data on the prevalence of FA across the world are heterogeneous because they are influenced by several factors. Among IgE-mediated FA, an important role is played by FA related to plant-derived food which can result from the sensitization to a single protein (specific FA) or to homologous proteins present in different foods (cross-reactive FA) including non-specific lipid transfer proteins (nsLTPs), profilins, and pathogenesis-related class 10 (PR-10). In addition, the clinical presentation of FA is widely heterogeneous ranging from mild symptoms to severe reactions up to anaphylaxis, most frequently associated with nsLTP-related FA (LTP syndrome). Considering the potential life-threatening nature of nsLTP-related FA, the patient's geographical setting should always be taken into account; thereby, it is highly recommended to build a personalized approach for managing FA across the world in the precision medicine era. For this reason, in this review, we aim to provide an overview of the prevalence of nsLTP-mediated allergies in the Mediterranean area and to point out the potential reasons for the different geographical significance of LTP-driven allergies with a particular focus on the allergenic properties of food allergens and their cross reactivity.
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Affiliation(s)
- Valentina D’Aiuto
- Department of Translational Medical Sciences, University of Naples Federico II, 80131 Naples, Italy; (V.D.); (I.M.); (F.N.); (F.D.C.); (A.d.P.); (F.W.R.)
| | - Ilaria Mormile
- Department of Translational Medical Sciences, University of Naples Federico II, 80131 Naples, Italy; (V.D.); (I.M.); (F.N.); (F.D.C.); (A.d.P.); (F.W.R.)
| | - Francescopaolo Granata
- Department of Translational Medical Sciences, University of Naples Federico II, 80131 Naples, Italy; (V.D.); (I.M.); (F.N.); (F.D.C.); (A.d.P.); (F.W.R.)
| | - Filomena Napolitano
- Department of Translational Medical Sciences, University of Naples Federico II, 80131 Naples, Italy; (V.D.); (I.M.); (F.N.); (F.D.C.); (A.d.P.); (F.W.R.)
| | - Laura Lamagna
- Department of Clinical Medicine and Surgery, University of Naples Federico II, 80131 Naples, Italy;
| | - Francesca Della Casa
- Department of Translational Medical Sciences, University of Naples Federico II, 80131 Naples, Italy; (V.D.); (I.M.); (F.N.); (F.D.C.); (A.d.P.); (F.W.R.)
| | - Amato de Paulis
- Department of Translational Medical Sciences, University of Naples Federico II, 80131 Naples, Italy; (V.D.); (I.M.); (F.N.); (F.D.C.); (A.d.P.); (F.W.R.)
- Center for Basic and Clinical Immunology Research (CISI), WAO Center of Excellence, University of Naples Federico II, 80131 Naples, Italy
| | - Francesca Wanda Rossi
- Department of Translational Medical Sciences, University of Naples Federico II, 80131 Naples, Italy; (V.D.); (I.M.); (F.N.); (F.D.C.); (A.d.P.); (F.W.R.)
- Center for Basic and Clinical Immunology Research (CISI), WAO Center of Excellence, University of Naples Federico II, 80131 Naples, Italy
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Castagnoli R, Taietti I, Leung ASY, Eigenmann P. Editorial comment on the special issue "Omics in food allergy". Pediatr Allergy Immunol 2024; 35:e14113. [PMID: 38519873 DOI: 10.1111/pai.14113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 03/07/2024] [Indexed: 03/25/2024]
Affiliation(s)
- Riccardo Castagnoli
- Pediatric Unit, Department of Clinical, Surgical, Diagnostic, and Pediatric Sciences, University of Pavia, Pavia, Italy
- Pediatric Clinic, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Ivan Taietti
- Pediatric Unit, Department of Clinical, Surgical, Diagnostic, and Pediatric Sciences, University of Pavia, Pavia, Italy
- Pediatric Clinic, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Agnes Sze-Yin Leung
- Department of Paediatrics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Philippe Eigenmann
- Pediatric Allergy Unit, Department of Pediatrics, Gynecology and Obstetrics, University Hospitals of Geneva, Geneva, Switzerland
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Carucci L, Coppola S, Carandente R, Canani RB. Targeting Food Allergy with Probiotics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1449:79-93. [PMID: 39060732 DOI: 10.1007/978-3-031-58572-2_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/28/2024]
Abstract
The globally dramatic increase in food allergy prevalence and severity is demanding effective preventive and therapeutic strategies. Food allergy derives from a defect of immune tolerance mechanisms. Immune tolerance is modulated by gut microbiome composition and function, and gut microbiome dysbiosis has been associated with the development of food allergy. Selected probiotic strains could regulate immune tolerance mechanisms. The mechanisms are multiple and are still not completely defined. Increasing evidence is providing useful information on the choice of optimal bacterial species/strains, dosage, and timing for intervention. The increased knowledge on the crucial role played by postbiotic gut microbiome-derived metabolites, such as butyrate, is also opening the way to a post- biotic approach in the stimulation of immune tolerance.
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Affiliation(s)
- Laura Carucci
- Department of Translational Medical Science at the University of Naples Federico II, Naples, Italy
| | - Serena Coppola
- Department of Translational Medical Science at the University of Naples Federico II, Naples, Italy
| | - Rosilenia Carandente
- Department of Translational Medical Science at the University of Naples Federico II, Naples, Italy
| | - Roberto Berni Canani
- Department of Translational Medical Science at the University of Naples Federico II, Naples, Italy.
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Chun Y, Lee JH, Bunyavanich S. Epigenomic and epigenetic investigations of food allergy. Pediatr Allergy Immunol 2024; 35:e14065. [PMID: 38284919 PMCID: PMC10825314 DOI: 10.1111/pai.14065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/05/2023] [Accepted: 12/07/2023] [Indexed: 01/30/2024]
Abstract
As a potential link between genetic predisposition, environmental exposures, and food allergy outcomes, epigenetics has been a molecular variable of interest in ongoing efforts to understand food allergy mechanisms and outcomes. Here we review population-based investigations of epigenetic loci associated with food allergy, focusing on established clinical food allergy. We first provide an overview of epigenetic mechanisms that have been studied in cohorts with food allergy, predominantly DNA methylation but also microRNA. We then discuss investigations that have implemented epigenome-wide approaches aimed at genome-wide profiling and discovery. Such epigenome-wide studies have collectively identified differentially methylated and differentially regulated loci associated with T cell development, antigen presentation, reaction severity, and causal mediation in food allergy. We then discuss candidate-gene investigations that have honed in on Th1, Th2, T regulatory, and innate genes of a priori interest in food allergy. These studies have highlighted methylation changes in specific candidate genes as associated with T regulatory cell activity as well as differential methylation of Type 1 and Type 2 cytokine genes associated with various food allergies. Intriguingly, epigenetic loci associated with food allergy have also been explored as potential biomarkers for the clinical management of food allergy. We conclude by highlighting several priority directions for advancing population-based epigenomic and epigenetic understandings of food allergy.
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Affiliation(s)
- Yoojin Chun
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jo Hsuan Lee
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Supinda Bunyavanich
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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Rao S, Chen X, Ou OY, Chair SY, Chien WT, Liu G, Waye MMY. A Positive Causal Effect of Shrimp Allergy on Major Depressive Disorder Mediated by Allergy- and Immune-Related Pathways in the East Asian Population. Nutrients 2023; 16:79. [PMID: 38201909 PMCID: PMC10780813 DOI: 10.3390/nu16010079] [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: 09/28/2023] [Revised: 12/11/2023] [Accepted: 12/14/2023] [Indexed: 01/12/2024] Open
Abstract
BACKGROUND Observational studies have implied a potential correlation between allergic diseases and major depressive disorder (MDD). However, the relationship is still inconclusive as it is likely to be interfered with by substantial confounding factors and potential reverse causality. The present study aimed to investigate causal correlation of the two diseases by a Mendelian randomization (MR) study and further elucidate the underlying molecular mechanisms. METHODS With the biggest summary datasets of a genome-wide association study (GWAS) in the East Asian population, we conducted a two-sample, bidirectional MR study to assess the causal correlation between shrimp allergy (SA) and MDD. Subsequently, we identified the pleiotropic genes' susceptibility to the two diseases at whole-genome and tissue-specific levels, respectively. Enriched GO sets and KEGG pathways were also discovered to elucidate the potential underlying mechanisms. RESULTS With the most suitable MR method, SA was identified as a causal risk factor for MDD based on three different groups of independent genetic instruments, respectively (p < 2.81 × 10-2). In contrast, we did not observe a significant causal effect of MDD on SA. The GWAS-pairwise program successfully identified seven pleiotropic genetic variants (PPA3 > 0.8), indicating that the two diseases indeed have a shared genetic basis. At a whole-genome level, the MAGMA program identified 44 pleiotropic genes, which were enriched in allergy-related pathways, such as antigen processing and presentation pathway (p = 1.46 × 10-2). In brain-specific tissue, the S-MultiXcan program found 17 pleiotropic genes that were significantly enriched in immune-related pathways and GO sets, including asthma-related pathway, T-cell activation-related, and major histocompatibility complex protein-related GO sets. Regarding whole-blood tissue, the program identified six pleiotropic genes that are significantly enriched in tolerance induction-related GO sets. CONCLUSIONS The present study for the first time indicated a significant causal effect of SA on the occurrence of MDD, but the reverse was not true. Enrichment analyses of pleiotropic genes at whole-genome and tissue-specific levels implied the involvement of allergy and immune-related pathways in the shared genetic mechanism of the two diseases. Elucidating the causal effect and the acting direction may be beneficial in reducing the incidence rate of MDD for the massive group of SA patients in the East Asian region.
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Affiliation(s)
- Shitao Rao
- Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, Institute of Precision Medicine, School of Medical Technology and Engineering, Fujian Medical University, Fuzhou 350122, China; (S.R.); (X.C.)
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Xiaotong Chen
- Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, Institute of Precision Medicine, School of Medical Technology and Engineering, Fujian Medical University, Fuzhou 350122, China; (S.R.); (X.C.)
| | - Olivia Yanlai Ou
- Department of Psychology, University of Toronto, Toronto, ON M5S 1A1, Canada;
| | - Sek Ying Chair
- Croucher Laboratory for Human Genomics, Asia-Pacific Genomic and Genetic Nursing Centre, The Nethersole School of Nursing, The Chinese University of Hong Kong, Hong Kong, China; (S.Y.C.); (W.T.C.)
| | - Wai Tong Chien
- Croucher Laboratory for Human Genomics, Asia-Pacific Genomic and Genetic Nursing Centre, The Nethersole School of Nursing, The Chinese University of Hong Kong, Hong Kong, China; (S.Y.C.); (W.T.C.)
| | - Guangming Liu
- College of Ocean Food and Biological Engineering, Xiamen Key Laboratory of Marine Functional Food, Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Jimei University, Xiamen 361021, China
| | - Mary Miu Yee Waye
- Croucher Laboratory for Human Genomics, Asia-Pacific Genomic and Genetic Nursing Centre, The Nethersole School of Nursing, The Chinese University of Hong Kong, Hong Kong, China; (S.Y.C.); (W.T.C.)
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Mrkić Kobal I, Plavec D, Vlašić Lončarić Ž, Jerković I, Turkalj M. Atopic March or Atopic Multimorbidity-Overview of Current Research. MEDICINA (KAUNAS, LITHUANIA) 2023; 60:21. [PMID: 38256282 PMCID: PMC10819021 DOI: 10.3390/medicina60010021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/11/2023] [Accepted: 12/18/2023] [Indexed: 01/24/2024]
Abstract
The atopic march encompasses a sequence of allergic conditions, including atopic dermatitis, food allergy, allergic rhinitis, and asthma, that frequently develop in a sequential pattern within the same individual. It was introduced as a conceptual framework aimed at elucidating the developmental trajectory of allergic conditions during childhood. Following the introduction of this concept, it was initially believed that the atopic march represented the sole and definitive trajectory of the development of allergic diseases. However, this perspective evolved with the emergence of new longitudinal studies, which revealed that the evolution of allergic diseases is far more intricate. It involves numerous immunological pathological mechanisms and may not align entirely with the traditional concept of the atopic march. The objective of our review is to portray the atopic march alongside other patterns in the development of childhood allergic diseases, with a specific emphasis on the potential for a personalized approach to the prevention, diagnosis, and treatment of atopic conditions.
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Affiliation(s)
- Iva Mrkić Kobal
- Clinic for Pediatric Medicine Helena, Ulica kneza Branimira 71, 10000 Zagreb, Croatia
- Faculty of Medicine, Josip Juraj Strossmayer University of Osijek, Josipa Huttlera 4, 31000 Osijek, Croatia
| | - Davor Plavec
- Faculty of Medicine, Josip Juraj Strossmayer University of Osijek, Josipa Huttlera 4, 31000 Osijek, Croatia
- Prima Nova, Zagrebačka cesta 132a, 10000 Zagreb, Croatia
| | - Željka Vlašić Lončarić
- Faculty of Medicine, Josip Juraj Strossmayer University of Osijek, Josipa Huttlera 4, 31000 Osijek, Croatia
- Children’s Hospital Srebrnjak, Srebrnjak 100, 10000 Zagreb, Croatia
| | - Ivana Jerković
- Faculty of Medicine, Josip Juraj Strossmayer University of Osijek, Josipa Huttlera 4, 31000 Osijek, Croatia
- Children’s Hospital Srebrnjak, Srebrnjak 100, 10000 Zagreb, Croatia
| | - Mirjana Turkalj
- Faculty of Medicine, Josip Juraj Strossmayer University of Osijek, Josipa Huttlera 4, 31000 Osijek, Croatia
- Children’s Hospital Srebrnjak, Srebrnjak 100, 10000 Zagreb, Croatia
- Faculty of Medicine, Catholic University of Croatia, Ilica 242, 10000 Zagreb, Croatia
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10
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Li S, Chu KH, Wai CYY. Genomics of Shrimp Allergens and Beyond. Genes (Basel) 2023; 14:2145. [PMID: 38136967 PMCID: PMC10742822 DOI: 10.3390/genes14122145] [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: 10/25/2023] [Revised: 11/21/2023] [Accepted: 11/23/2023] [Indexed: 12/24/2023] Open
Abstract
Allergy to shellfishes, including mollusks and crustaceans, is a growing health concern worldwide. Crustacean shellfish is one of the "Big Eight" allergens designated by the U.S. Food and Drug Administration and is the major cause of food-induced anaphylaxis. Shrimp is one of the most consumed crustaceans triggering immunoglobulin E (IgE)-mediated allergic reactions. Over the past decades, the allergen repertoire of shrimp has been unveiled based on conventional immunodetection methods. With the availability of genomic data for penaeid shrimp and other technological advancements like transcriptomic approaches, new shrimp allergens have been identified and directed new insights into their expression levels, cross-reactivity, and functional impact. In this review paper, we summarize the current knowledge on shrimp allergens, as well as allergens from other crustaceans and mollusks. Specific emphasis is put on the genomic information of the shrimp allergens, their protein characteristics, and cross-reactivity among shrimp and other organisms.
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Affiliation(s)
- Shanshan Li
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China; (S.L.); (K.H.C.)
| | - Ka Hou Chu
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China; (S.L.); (K.H.C.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 510000, China
| | - Christine Yee Yan Wai
- Department of Paediatrics, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Hong Kong, China
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11
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Risemberg EL, Smeekens JM, Cisneros MCC, Hampton BK, Hock P, Linnertz CL, Miller DR, Orgel K, Shaw GD, de Villena FPM, Burks AW, Valdar W, Kulis MD, Ferris MT. A mutation in Themis contributes to peanut-induced oral anaphylaxis in CC027 mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.13.557467. [PMID: 37745496 PMCID: PMC10515941 DOI: 10.1101/2023.09.13.557467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Background The development of peanut allergy is due to a combination of genetic and environmental factors, although specific genes have proven difficult to identify. Previously, we reported that peanut-sensitized CC027/GeniUnc (CC027) mice develop anaphylaxis upon oral challenge to peanut, unlike C3H/HeJ (C3H) mice. Objective To determine the genetic basis of orally-induced anaphylaxis to peanut in CC027 mice. Methods A genetic mapping population between CC027 and C3H mice was designed to identify the genetic factors that drive oral anaphylaxis. A total of 356 CC027xC3H backcrossed mice were generated, sensitized to peanut, then challenged to peanut by oral gavage. Anaphylaxis and peanut-specific IgE were quantified for all mice. T-cell phenotyping was conducted on CC027 and five additional CC strains. Results Anaphylaxis to peanut was absent in 77% of backcrossed mice, with 19% showing moderate anaphylaxis, and 4% having severe anaphylaxis. A total of eight genetic loci were associated with variation in response to peanut challenge, six associated with anaphylaxis (temperature decrease) and two associated with peanut-specific IgE levels. There were two major loci that impacted multiple aspects of the severity of acute anaphylaxis, at which the CC027 allele was associated with worse outcome. At one of these loci, CC027 has a private genetic variant in the Themis (thymocyte-expressed molecule involved in selection) gene. Consistent with Themis' described functions, we found that CC027 have more immature T cells with fewer CD8+, CD4+, and CD4+CD25+CD127- regulatory T cells. Conclusion Our results demonstrate a key role for Themis in the orally-reactive CC027 mouse model of peanut allergy.
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Affiliation(s)
- Ellen L. Risemberg
- Curriculum in Bioinformatics and Computational Biology, UNC Chapel Hill
- Department of Genetics, UNC Chapel Hill
| | - Johanna M. Smeekens
- Department of Pediatrics, Division of Allergy and Immunology, UNC Chapel Hill
| | - Marta C. Cruz Cisneros
- Department of Genetics, UNC Chapel Hill
- Curriculum in Genetics and Molecular Biology, UNC Chapel Hill
| | - Brea K. Hampton
- Department of Genetics, UNC Chapel Hill
- Curriculum in Genetics and Molecular Biology, UNC Chapel Hill
| | | | | | | | - Kelly Orgel
- Department of Pediatrics, Division of Allergy and Immunology, UNC Chapel Hill
| | - Ginger D. Shaw
- Department of Genetics, UNC Chapel Hill
- Lineberger Comprehensive Cancer Center, UNC Chapel Hill
| | | | - A. Wesley Burks
- Department of Pediatrics, Division of Allergy and Immunology, UNC Chapel Hill
| | - William Valdar
- Department of Genetics, UNC Chapel Hill
- Lineberger Comprehensive Cancer Center, UNC Chapel Hill
| | - Michael D. Kulis
- Department of Pediatrics, Division of Allergy and Immunology, UNC Chapel Hill
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12
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Kalomoiri M, Prakash CR, Lagström S, Hauschulz K, Ewing E, Shchetynsky K, Kular L, Needhamsen M, Jagodic M. Simultaneous detection of DNA variation and methylation at HLA class II locus and immune gene promoters using targeted SureSelect Methyl-Sequencing. Front Immunol 2023; 14:1251772. [PMID: 37691926 PMCID: PMC10484099 DOI: 10.3389/fimmu.2023.1251772] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 08/02/2023] [Indexed: 09/12/2023] Open
Abstract
The Human Leukocyte Antigen (HLA) locus associates with a variety of complex diseases, particularly autoimmune and inflammatory conditions. The HLA-DR15 haplotype, for example, confers the major risk for developing Multiple Sclerosis in Caucasians, pinpointing an important role in the etiology of this chronic inflammatory disease of the central nervous system. In addition to the protein-coding variants that shape the functional HLA-antigen-T cell interaction, recent studies suggest that the levels of HLA molecule expression, that are epigenetically controlled, also play a role in disease development. However, deciphering the exact molecular mechanisms of the HLA association has been hampered by the tremendous genetic complexity of the locus and a lack of robust approaches to investigate it. Here, we developed a method to specifically enrich the genomic DNA from the HLA class II locus (chr6:32,426,802-34,167,129) and proximal promoters of 2,157 immune-relevant genes, utilizing the Agilent RNA-based SureSelect Methyl-Seq Capture related method, followed by sequencing to detect genetic and epigenetic variation. We demonstrated successful simultaneous detection of the genetic variation and quantification of DNA methylation levels in HLA locus. Moreover, by the detection of differentially methylated positions in promoters of immune-related genes, we identified relevant pathways following stimulation of cells. Taken together, we present a method that can be utilized to study the interplay between genetic variance and epigenetic regulation in the HLA class II region, potentially, in a wide disease context.
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Affiliation(s)
- Maria Kalomoiri
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Chandana Rao Prakash
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Sonja Lagström
- Diagnostics and Genomics Group, Agilent Technologies Sweden AB, Sundbyberg, Sweden
| | - Kai Hauschulz
- Diagnostics and Genomics Group, Agilent Technologies Deutschland GmbH, Waldbronn, Germany
| | - Ewoud Ewing
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Klementy Shchetynsky
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Lara Kular
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Maria Needhamsen
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Maja Jagodic
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
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13
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Bogan SN, Strader ME, Hofmann GE. Associations between DNA methylation and gene regulation depend on chromatin accessibility during transgenerational plasticity. BMC Biol 2023; 21:149. [PMID: 37365578 DOI: 10.1186/s12915-023-01645-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 06/07/2023] [Indexed: 06/28/2023] Open
Abstract
BACKGROUND Epigenetic processes are proposed to be a mechanism regulating gene expression during phenotypic plasticity. However, environmentally induced changes in DNA methylation exhibit little-to-no association with differential gene expression in metazoans at a transcriptome-wide level. It remains unexplored whether associations between environmentally induced differential methylation and expression are contingent upon other epigenomic processes such as chromatin accessibility. We quantified methylation and gene expression in larvae of the purple sea urchin Strongylocentrotus purpuratus exposed to different ecologically relevant conditions during gametogenesis (maternal conditioning) and modeled changes in gene expression and splicing resulting from maternal conditioning as functions of differential methylation, incorporating covariates for genomic features and chromatin accessibility. We detected significant interactions between differential methylation, chromatin accessibility, and genic feature type associated with differential expression and splicing. RESULTS Differential gene body methylation had significantly stronger effects on expression among genes with poorly accessible transcriptional start sites while baseline transcript abundance influenced the direction of this effect. Transcriptional responses to maternal conditioning were 4-13 × more likely when accounting for interactions between methylation and chromatin accessibility, demonstrating that the relationship between differential methylation and gene regulation is partially explained by chromatin state. CONCLUSIONS DNA methylation likely possesses multiple associations with gene regulation during transgenerational plasticity in S. purpuratus and potentially other metazoans, but its effects are dependent on chromatin accessibility and underlying genic features.
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Affiliation(s)
- Samuel N Bogan
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, USA.
| | - Marie E Strader
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, USA
- Department of Biology, Texas A&M University, College Station, USA
| | - Gretchen E Hofmann
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, USA
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14
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Arzola-Martínez L, Ptaschinski C, Lukacs NW. Trained innate immunity, epigenetics, and food allergy. FRONTIERS IN ALLERGY 2023; 4:1105588. [PMID: 37304168 PMCID: PMC10251748 DOI: 10.3389/falgy.2023.1105588] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 05/10/2023] [Indexed: 06/13/2023] Open
Abstract
In recent years the increased incidence of food allergy in Western culture has been associated with environmental factors and an inappropriate immune phenotype. While the adaptive immune changes in food allergy development and progression have been well-characterized, an increase in innate cell frequency and activation status has also recently received greater attention. Early in prenatal and neonatal development of human immunity there is a reliance on epigenetic and metabolic changes that stem from environmental factors, which are critical in training the immune outcomes. In the present review, we discuss how trained immunity is regulated by epigenetic, microbial and metabolic factors, and how these factors and their impact on innate immunity have been linked to the development of food allergy. We further summarize current efforts to use probiotics as a potential therapeutic approach to reverse the epigenetic and metabolic signatures and prevent the development of severe anaphylactic food allergy, as well as the potential use of trained immunity as a diagnostic and management strategy. Finally, trained immunity is presented as one of the mechanisms of action of allergen-specific immunotherapy to promote tolerogenic responses in allergic individuals.
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Affiliation(s)
- Llilian Arzola-Martínez
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States
- Mary H. Weiser Food Allergy Center (MHWFAC), University of Michigan, Ann Arbor, MI, United States
| | - Catherine Ptaschinski
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States
- Mary H. Weiser Food Allergy Center (MHWFAC), University of Michigan, Ann Arbor, MI, United States
| | - Nicholas W. Lukacs
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States
- Mary H. Weiser Food Allergy Center (MHWFAC), University of Michigan, Ann Arbor, MI, United States
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15
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Gu S, Yang D, Liu C, Xue W. The role of probiotics in prevention and treatment of food allergy. FOOD SCIENCE AND HUMAN WELLNESS 2023. [DOI: 10.1016/j.fshw.2022.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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16
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Devonshire A, Gautam Y, Johansson E, Mersha TB. Multi-omics profiling approach in food allergy. World Allergy Organ J 2023; 16:100777. [PMID: 37214173 PMCID: PMC10199264 DOI: 10.1016/j.waojou.2023.100777] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 04/05/2023] [Accepted: 04/05/2023] [Indexed: 05/24/2023] Open
Abstract
The prevalence of food allergy (FA) among children is increasing, affecting nearly 8% of children, and FA is the most common cause of anaphylaxis and anaphylaxis-related emergency department visits in children. Importantly, FA is a complex, multi-system, multifactorial disease mediated by food-specific immunoglobulin E (IgE) and type 2 immune responses and involving environmental and genetic factors and gene-environment interactions. Early exposure to external and internal environmental factors largely influences the development of immune responses to allergens. Genetic factors and gene-environment interactions have established roles in the FA pathophysiology. To improve diagnosis and identification of FA therapeutic targets, high-throughput omics approaches have emerged and been applied over the past decades to screen for potential FA biomarkers, such as genes, transcripts, proteins, and metabolites. In this article, we provide an overview of the current status of FA omics studies, namely genomic, transcriptomic, epigenomic, proteomic, exposomic, and metabolomic. The current development of multi-omics integration of FA studies is also briefly discussed. As individual omics technologies only provide limited information on the multi-system biological processes of FA, integration of population-based multi-omics data and clinical data may lead to robust biomarker discovery that could translate into advances in disease management and clinical care and ultimately lead to precision medicine approaches.
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Affiliation(s)
- Ashley Devonshire
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Yadu Gautam
- Division of Asthma Research, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Elisabet Johansson
- Division of Asthma Research, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Tesfaye B. Mersha
- Division of Asthma Research, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
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17
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Anić P, Golubić Talić J, Božinović K, Dediol E, Mravak-Stipetić M, Grce M, Milutin Gašperov N. Methylation of Immune Gene Promoters in Oral and Oropharyngeal Cancer. Int J Mol Sci 2023; 24:ijms24097698. [PMID: 37175405 PMCID: PMC10178514 DOI: 10.3390/ijms24097698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/13/2023] [Accepted: 04/18/2023] [Indexed: 05/15/2023] Open
Abstract
The proportion of oral and oropharyngeal squamous cell carcinoma (OOSCC) that can be attributed to human papillomavirus (HPV) infection is growing nowadays. A potential factor indicating the occurrence of HPV-positive OSCC is a change in the degree of methylation of gene promoters that play a key role in the immune response. In this study, we investigated the difference in the methylation of EDARADD, GBP4, HAVCR2, HLA DPB1, IL12RB1, MARCO, and SIGLEC12 gene promoters in samples of healthy oral mucosa versus samples of oral and oropharyngeal cancer. The presence of HPV infection in samples was examined earlier. To determine the difference in methylation of those gene promotors, isolated and bisulfite-modified DNA was analysed by the methylation-specific PCR method. The investigated gene promoters were found to be more hypomethylated in the oral and oropharyngeal cancer samples in comparison to normal tissue. The proportion of unmethylated gene promoters was similar in HPV-positive and HPV-negative cancers, although the data should be confirmed on a larger set of samples. To conclude, in samples of healthy oral mucosa, the investigated gene promoters were found to be methylated in a high percentage (73.3% to 100%), while in oral and oropharyngeal cancer samples, they were methylated in a low percentage (11.1% to 37%), regardless of HPV infection.
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Affiliation(s)
- Petra Anić
- Research Department, Srebrnjak Children's Hospital, 10000 Zagreb, Croatia
| | | | - Ksenija Božinović
- Department of Molecular Biology, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Emil Dediol
- Department of Maxillofacial Surgery, Clinical Hospital Dubrava, 10000 Zagreb, Croatia
| | - Marinka Mravak-Stipetić
- Department of Oral Medicine, School of Dental Medicine, University of Zagreb, 10000 Zagreb, Croatia
| | - Magdalena Grce
- Department of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia
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18
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Sindher SB, Chin AR, Aghaeepour N, Prince L, Maecker H, Shaw GM, Stevenson DK, Nadeau KC, Snyder M, Khatri P, Boyd SD, Winn VD, Angst MS, Chinthrajah RS. Advances and potential of omics studies for understanding the development of food allergy. FRONTIERS IN ALLERGY 2023; 4:1149008. [PMID: 37034151 PMCID: PMC10080041 DOI: 10.3389/falgy.2023.1149008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/06/2023] [Indexed: 04/11/2023] Open
Abstract
The prevalence of food allergy continues to rise globally, carrying with it substantial safety, economic, and emotional burdens. Although preventative strategies do exist, the heterogeneity of allergy trajectories and clinical phenotypes has made it difficult to identify patients who would benefit from these strategies. Therefore, further studies investigating the molecular mechanisms that differentiate these trajectories are needed. Large-scale omics studies have identified key insights into the molecular mechanisms for many different diseases, however the application of these technologies to uncover the drivers of food allergy development is in its infancy. Here we review the use of omics approaches in food allergy and highlight key gaps in knowledge for applying these technologies for the characterization of food allergy development.
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Affiliation(s)
- Sayantani B Sindher
- Sean N. Parker Center for Allergy and Asthma Research at Stanford University, Palo Alto, CA, United States
| | - Andrew R Chin
- Sean N. Parker Center for Allergy and Asthma Research at Stanford University, Palo Alto, CA, United States
| | - Nima Aghaeepour
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Palo Alto, CA, United States
- Department of Pediatrics, Stanford University School of Medicine, Palo Alto, CA, United States
- Department of Biomedical Data Science, Stanford University School of Medicine, Palo Alto, CA, United States
| | - Lawrence Prince
- Department of Pediatrics, Stanford University School of Medicine, Palo Alto, CA, United States
| | - Holden Maecker
- Department of Medicine, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Palo Alto, CA, United States
| | - Gary M Shaw
- Department of Pediatrics, Stanford University School of Medicine, Palo Alto, CA, United States
| | - David K Stevenson
- Department of Pediatrics, Stanford University School of Medicine, Palo Alto, CA, United States
| | - Kari C Nadeau
- Sean N. Parker Center for Allergy and Asthma Research at Stanford University, Palo Alto, CA, United States
| | - Michael Snyder
- Department of Genetics, Stanford University, Palo Alto, CA, United States
| | - Purvesh Khatri
- Department of Medicine, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Palo Alto, CA, United States
| | - Scott D Boyd
- Sean N. Parker Center for Allergy and Asthma Research at Stanford University, Palo Alto, CA, United States
- Department of Pathology, Stanford University, Palo Alto, CA, United States
| | - Virginia D Winn
- Department of Obstetrics and Gynecology, Stanford University School of Medicine, Palo Alto, CA, United States
| | - Martin S Angst
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Palo Alto, CA, United States
| | - R Sharon Chinthrajah
- Sean N. Parker Center for Allergy and Asthma Research at Stanford University, Palo Alto, CA, United States
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19
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Wang J, Zhou Y, Zhang H, Hu L, Liu J, Wang L, Wang T, Zhang H, Cong L, Wang Q. Pathogenesis of allergic diseases and implications for therapeutic interventions. Signal Transduct Target Ther 2023; 8:138. [PMID: 36964157 PMCID: PMC10039055 DOI: 10.1038/s41392-023-01344-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 01/20/2023] [Accepted: 02/03/2023] [Indexed: 03/26/2023] Open
Abstract
Allergic diseases such as allergic rhinitis (AR), allergic asthma (AAS), atopic dermatitis (AD), food allergy (FA), and eczema are systemic diseases caused by an impaired immune system. Accompanied by high recurrence rates, the steadily rising incidence rates of these diseases are attracting increasing attention. The pathogenesis of allergic diseases is complex and involves many factors, including maternal-fetal environment, living environment, genetics, epigenetics, and the body's immune status. The pathogenesis of allergic diseases exhibits a marked heterogeneity, with phenotype and endotype defining visible features and associated molecular mechanisms, respectively. With the rapid development of immunology, molecular biology, and biotechnology, many new biological drugs have been designed for the treatment of allergic diseases, including anti-immunoglobulin E (IgE), anti-interleukin (IL)-5, and anti-thymic stromal lymphopoietin (TSLP)/IL-4, to control symptoms. For doctors and scientists, it is becoming more and more important to understand the influencing factors, pathogenesis, and treatment progress of allergic diseases. This review aimed to assess the epidemiology, pathogenesis, and therapeutic interventions of allergic diseases, including AR, AAS, AD, and FA. We hope to help doctors and scientists understand allergic diseases systematically.
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Affiliation(s)
- Ji Wang
- National Institute of TCM constitution and Preventive Medicine, School of Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 100029, P.R. China
| | - Yumei Zhou
- National Institute of TCM constitution and Preventive Medicine, School of Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 100029, P.R. China
| | - Honglei Zhang
- National Institute of TCM constitution and Preventive Medicine, School of Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 100029, P.R. China
| | - Linhan Hu
- National Institute of TCM constitution and Preventive Medicine, School of Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 100029, P.R. China
| | - Juntong Liu
- National Institute of TCM constitution and Preventive Medicine, School of Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 100029, P.R. China
| | - Lei Wang
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 1000210, China
| | - Tianyi Wang
- National Institute of TCM constitution and Preventive Medicine, School of Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 100029, P.R. China
| | - Haiyun Zhang
- National Institute of TCM constitution and Preventive Medicine, School of Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 100029, P.R. China
| | - Linpeng Cong
- National Institute of TCM constitution and Preventive Medicine, School of Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 100029, P.R. China
| | - Qi Wang
- National Institute of TCM constitution and Preventive Medicine, School of Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 100029, P.R. China.
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20
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Geng Q, Zhang Y, Song M, Zhou X, Tang Y, Wu Z, Chen H. Allergenicity of peanut allergens and its dependence on the structure. Compr Rev Food Sci Food Saf 2023; 22:1058-1081. [PMID: 36624611 DOI: 10.1111/1541-4337.13101] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 12/13/2022] [Accepted: 12/18/2022] [Indexed: 01/11/2023]
Abstract
Food allergies are a global food safety problem. Peanut allergies are common due, in part, to their popular utilization in the food industry. Peanut allergy is typically an immunoglobulin E-mediated reaction, and peanuts contain 17 allergens belonging to different families in peanut. In this review, we first introduce the mechanisms and management of peanut allergy, followed by the basic structures of associated allergens. Subsequently, we summarize methods of epitope localization for peanut allergens. These methods can be instrumental in speeding up the discovery of allergenicity-dependent structures. Many attempts have been made to decrease the allergenicity of peanuts. The structures of hypoallergens, which are manufactured during processing, were analyzed to strengthen the desensitization process and allergen immunotherapy. The identification of conformational epitopes is the bottleneck in both peanut and food allergies. Further, the identification and modification of such epitopes will lead to improved strategies for managing and preventing peanut allergy. Combining traditional wet chemistry research with structure simulation studies will help in the epitopes' localization.
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Affiliation(s)
- Qin Geng
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
- College of Food Science and Technology, Nanchang University, Nanchang, China
| | - Ying Zhang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
- College of Food Science and Technology, Nanchang University, Nanchang, China
| | - Min Song
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
- College of Food Science and Technology, Nanchang University, Nanchang, China
| | - Xiaoya Zhou
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
- College of Food Science and Technology, Nanchang University, Nanchang, China
| | - Yu Tang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
- College of Food Science and Technology, Nanchang University, Nanchang, China
| | - Zhihua Wu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
- Sino-German Joint Research Institute, Nanchang University, Nanchang, China
| | - Hongbing Chen
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
- Sino-German Joint Research Institute, Nanchang University, Nanchang, China
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21
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Safar R, Oussalah A, Mayorga L, Vieths S, Barber D, Torres MJ, Guéant JL. Epigenome alterations in food allergy: A systematic review of candidate gene and epigenome-wide association studies. Clin Exp Allergy 2023; 53:259-275. [PMID: 36756739 DOI: 10.1111/cea.14277] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 12/10/2022] [Accepted: 12/20/2022] [Indexed: 02/10/2023]
Abstract
OBJECTIVE The aim of this study was to systematically review the evidence across studies that assessed DNA methylome variations in association with food allergy (FA). DESIGN A systematic review of the literature and meta-analysis were carried out within several databases. However, the risk of bias in the included articles was not evaluated. DATA SOURCES PubMed, Cochrane Database of Systematic Reviews, and Web of Science were used to search up to July 2022. ELIGIBILITY CRITERIA We included targeted and epigenome-wide association studies (EWASs) that assessed DNA methylome alterations in association with FA in adult or paediatric populations. RESULTS Among 366 publications, only 16 were retained, which were mainly focused on FA in children. Seven candidate gene-targeted studies found associations in Th1/Th2 imbalance (IL4, IL5, IL10, INFG, IL2 and IL12B genes), regulatory T cell function (FOXP3 gene), Toll-like receptors pathway (TLR2, CD14 genes) and digestive barrier integrity (FLG gene). Nine EWAS assessed the association with peanut allergy (n = 3), cow's milk allergy (n = 2) or various food allergens (n = 4). They highlighted 11 differentially methylated loci in at least two studies (RPS6KA2, CAMTA1, CTBP2, RYR2, TRAPPC9, DOCK1, GALNTL4, HDAC4, UMODL1, ZAK and TNS3 genes). Among them, CAMTA1 and RPS6KA2, and CTBP2 are involved in regulatory T cell function and Th2 cell differentiation, respectively. Gene-functional analysis revealed two enriched gene clusters involved in immune responses and protein phosphorylation. ChIP-X Enrichment Analysis 3 showed eight significant transcription factors (RXRA, ZBTB7A, ESR1, TCF3, MYOD1, CTCF, GATA3 and CBX2). Ingenuity Pathway Analysis identified canonical pathways involved, among other, in B cell development, pathogen-induced cytokine storm signalling pathway and dendritic cell maturation. CONCLUSION This review highlights the involvement of epigenomic alterations of loci in Th1/Th2 and regulatory T cell differentiation in both candidate gene studies and EWAS. These alterations provide a better insight into the mechanistic aspects in FA pathogenesis and may guide the development of epigenome-based biomarkers for FA.
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Affiliation(s)
- Ramia Safar
- INSERM, UMR_S1256, NGERE - Nutrition, Genetics, and Environmental Risk Exposure, Faculty of Medicine of Nancy, University of Lorraine, Vandoeuvre-lès-Nancy, France
| | - Abderrahim Oussalah
- INSERM, UMR_S1256, NGERE - Nutrition, Genetics, and Environmental Risk Exposure, Faculty of Medicine of Nancy, University of Lorraine, Vandoeuvre-lès-Nancy, France.,Department of Molecular Medicine, Division of Biochemistry, Molecular Biology, and Nutrition, University Hospital of Nancy, Vandoeuvre-lès-Nancy, France.,Reference Center for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, Vandoeuvre-lès-Nancy, France
| | - Lina Mayorga
- Allergy Unit, Hospital Regional Universitario de Malaga, Malaga, Spain.,Allergy Research Group, Instituto de Investigación Biomedica de Malaga-IBIMA and ARADyAL, Malaga, Spain.,Laboratory for Nanostructures for the Diagnosis and Treatment of Allergic Diseases, Andalusian Center for Nanomedicine and Biotechnology (BIONAND), Malaga, Spain
| | - Stefan Vieths
- Paul-Ehrlich-Institut, Federal Institute for Vaccines and Biomedicines, Langen, Germany
| | - Domingo Barber
- Departamento de Ciencias Médicas Básicas, Facultad de Medicina, IMMA, Universidad San Pablo CEU, CEU Universities, Madrid, Spain.,ARADyAL-RD16/0006/0015, Thematic Network and Cooperative Research Centers, ISCIII, Madrid, Spain
| | - Maria Jose Torres
- Allergy Unit, Hospital Regional Universitario de Malaga, Malaga, Spain.,Allergy Research Group, Instituto de Investigación Biomedica de Malaga-IBIMA and ARADyAL, Malaga, Spain.,Laboratory for Nanostructures for the Diagnosis and Treatment of Allergic Diseases, Andalusian Center for Nanomedicine and Biotechnology (BIONAND), Malaga, Spain
| | - Jean-Louis Guéant
- INSERM, UMR_S1256, NGERE - Nutrition, Genetics, and Environmental Risk Exposure, Faculty of Medicine of Nancy, University of Lorraine, Vandoeuvre-lès-Nancy, France.,Department of Molecular Medicine, Division of Biochemistry, Molecular Biology, and Nutrition, University Hospital of Nancy, Vandoeuvre-lès-Nancy, France.,Reference Center for Inborn Errors of Metabolism (ORPHA67872), University Hospital of Nancy, Vandoeuvre-lès-Nancy, France
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22
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Koplin JJ, McWilliam V, Soriano VX, Peters RL. Early peanut introduction: To test or not to test? Ann Allergy Asthma Immunol 2023; 130:565-570. [PMID: 36791959 DOI: 10.1016/j.anai.2023.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/30/2023] [Accepted: 02/06/2023] [Indexed: 02/15/2023]
Abstract
OBJECTIVE To review recent evidence and international guidelines on early peanut introduction for preventing peanut allergy and provide an update on the status of the debate around testing before early peanut introduction. DATA SOURCES Review of published literature documenting: infant feeding guidelines; impact of early peanut introduction on peanut allergy; risk factors for peanut allergy; and impact of early peanut introduction guidelines on infant feeding practices and allergy. STUDY SELECTION We used a narrative approach and present both pro and con arguments for testing before peanut introduction. Data from randomized controlled trials and post-hoc analyses of these trials and observational studies were included. RESULTS Allergy prevention guidelines around the world now consistently recommend introducing peanut into an infant's diet before 12 months of age for countries with high peanut allergy prevalence. In the US, guidelines recently shifted away from recommending allergy testing before introduction for those at risk of peanut allergy. There is evidence primarily from Australia that recommending early introduction without prior testing is safe and effective in increasing early peanut introduction for both high and low-risk infants, although the subsequent reduction in peanut allergy prevalence at the population level was less than expected. CONCLUSION Current evidence supports recommending early peanut introduction without routinely testing for peanut allergy. If testing is offered, this should be based on shared decision making between families and practitioners and only be undertaken where there is provision for rapid access to definitive diagnosis including oral food challenges.
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Affiliation(s)
- Jennifer J Koplin
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia; Child Health Research Centre, University of Queensland, Brisbane, Queensland, Australia.
| | - Vicki McWilliam
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia; Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Department of Allergy and Immunology, Royal Children's Hospital, Parkville, Victoria, Australia
| | | | - Rachel L Peters
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia; Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia.
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23
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Incorporating genetics in identifying peanut allergy risk and tailoring allergen immunotherapy: A perspective on the genetic findings from the LEAP trial. J Allergy Clin Immunol 2023; 151:841-847. [PMID: 36732171 DOI: 10.1016/j.jaci.2022.12.819] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 12/15/2022] [Accepted: 12/23/2022] [Indexed: 02/04/2023]
Abstract
Examining the genetics of peanut allergy (PA) in the context of clinical trial interventions and outcomes provides an opportunity to not only understand gene-environment interactions for PA risk but to also understand the benefit of allergen immunotherapy. A consistent theme in the genetics of food allergy is that in keeping with the dual allergen exposure hypothesis, barrier- and immune-related genes are most commonly implicated in food allergy and tolerance. With a focus on PA, we review how genetic risk factors across 3 genes (FLG, MALT1, and HLA-DQA1) have helped delineate distinct allergic characteristics and outcomes in the context of environmental interventions in the Learning Early about Peanut Allergy (LEAP) study and other clinical trials. We specifically consider and present a framework for genetic risk prediction for the development of PA and discuss how genetics, age, and oral consumption intertwine to predict PA outcome. Although there is some promise in this proposed framework, a better understanding of the mechanistic pathways by which PA develops and persists is needed to develop targeted therapeutics for established disease. Only by understanding the mechanisms by which PA develops, persists, and resolves can we identify adjuvants to oral immunotherapy to make older children and adults immunologically similar to their younger, more malleable counterparts and thus more likely to achieve long-term tolerance.
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24
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Akdis CA, Akdis M, Boyd SD, Sampath V, Galli SJ, Nadeau KC. Allergy: Mechanistic insights into new methods of prevention and therapy. Sci Transl Med 2023; 15:eadd2563. [PMID: 36652536 DOI: 10.1126/scitranslmed.add2563] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
In the past few decades, the prevalence of allergic diseases has increased worldwide. Here, we review the etiology and pathophysiology of allergic diseases, including the role of the epithelial barrier, the immune system, climate change, and pollutants. Our current understanding of the roles of early life and infancy; diverse diet; skin, respiratory, and gut barriers; and microbiome in building immune tolerance to common environmental allergens has led to changes in prevention guidelines. Recent developments on the mechanisms involved in allergic diseases have been translated to effective treatments, particularly in the past 5 years, with additional treatments now in advanced clinical trials.
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Affiliation(s)
- Cezmi A Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos CH-7265, Switzerland.,Christine Kühne-Center for Allergy Research and Education, Davos CH-7265, Switzerland
| | - Mübeccel Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos CH-7265, Switzerland
| | - Scott D Boyd
- Sean N. Parker Center for Allergy and Asthma Research at Stanford University, Stanford, CA 94305, USA.,Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Vanitha Sampath
- Sean N. Parker Center for Allergy and Asthma Research at Stanford University, Stanford, CA 94305, USA
| | - Stephen J Galli
- Sean N. Parker Center for Allergy and Asthma Research at Stanford University, Stanford, CA 94305, USA.,Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kari C Nadeau
- Sean N. Parker Center for Allergy and Asthma Research at Stanford University, Stanford, CA 94305, USA
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25
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Diversité des allergies alimentaires. REVUE FRANÇAISE D'ALLERGOLOGIE 2022. [DOI: 10.1016/s1877-0320(22)00484-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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26
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Islam N, Chu DK. What is causing the rise in food allergy? A narrative review of risk factors for the development of food allergy in infants and children. FRONTIERS IN ALLERGY 2022; 3:1037596. [PMID: 36506645 PMCID: PMC9731156 DOI: 10.3389/falgy.2022.1037596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 10/31/2022] [Indexed: 11/25/2022] Open
Affiliation(s)
- Nazmul Islam
- Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, Ontario, ON, Canada
| | - Derek K. Chu
- Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, Ontario, ON, Canada,Department of Medicine, McMaster University, Hamilton, Ontario, ON, Canada,Correspondence: Derek K. Chu
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27
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Ohara R, Sugahara T, Sugie Y, Onda H, Yoshino N, Nishi K, Ishida M, Kikuzaki H. Identification of components in coriander (Coriandrum sativum L.) inhibiting degranulation of RBL-2H3 cells. Fitoterapia 2022; 163:105298. [PMID: 36108951 DOI: 10.1016/j.fitote.2022.105298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/05/2022] [Accepted: 09/05/2022] [Indexed: 11/16/2022]
Abstract
We found that a water-soluble extract of coriander (Coriandrum sativum L.) (leaves, petioles and stems) inhibits antigen-induced degranulation of RBL-2H3 cells, a rat basophil leukemia cell line. The aim of this study was to elucidate the anti-degranulation active components in the extract. The methanol-eluate fraction obtained by fractionation of the water-soluble extract using MCI gel column chromatography had strong activity, and eight components were isolated and identified. Two of them were identified as new compounds, (3S)-3-methyl-6-hydroxyisocoumarin 8-O-β-D-glucopyranoside (compound 1) and (7S,8R)-7,8-dihydro-8-β-D-glucopyranosyloxy-4-methoxy-7-methyl-5H-fro[2,3-g][2]benzopyran-5-one (compound 2). As a result of evaluation of anti-degranulation activity of eight components, seven of them, such as tryptophan, phenylalanine, dihydroxycoumarin glucoside, quercetin glycoside, rutin, compound 1, and compound 2, had the activity. These results indicated that the water-soluble extract of coriander contains several anti-degranulation substances.
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Affiliation(s)
- Rika Ohara
- Department of Food and Nutritional Sciences, Graduate School of Humanities and Science, Nara Women's University, Kitauoya Nishimachi, Nara 630-8506, Japan
| | - Takuya Sugahara
- Department of Bioscience, Graduate School of Agriculture, Ehime University, Matsuyama, Ehime 790-8566, Japan
| | - Yuna Sugie
- Department of Food Science & Nutrition, Nara Women's University, Kitauoya Nishimachi, Nara 630-8506, Japan
| | - Hiroyuki Onda
- Central Research Institute, S&B Foods Inc., 38-8 Miyamoto-cho, Itabashi-ku, Tokyo 174-8651, Japan
| | - Nanami Yoshino
- Central Research Institute, S&B Foods Inc., 38-8 Miyamoto-cho, Itabashi-ku, Tokyo 174-8651, Japan
| | - Kosuke Nishi
- Department of Bioscience, Graduate School of Agriculture, Ehime University, Matsuyama, Ehime 790-8566, Japan
| | - Momoko Ishida
- Department of Bioscience, Graduate School of Agriculture, Ehime University, Matsuyama, Ehime 790-8566, Japan.
| | - Hiroe Kikuzaki
- Department of Food Science & Nutrition, Nara Women's University, Kitauoya Nishimachi, Nara 630-8506, Japan.
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28
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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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29
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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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30
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Application of (multi-)omics approaches for advancing food allergy: an updated review. Curr Opin Food Sci 2022. [DOI: 10.1016/j.cofs.2022.100854] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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31
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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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32
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Tovo P, Monti G, Daprà V, Montanari P, Calvi C, Alliaudi C, Sardo A, Galliano I, Bergallo M. Enhanced expression of endogenous retroviruses and of TRIM28 and SETDB1 in children with food allergy. Clin Transl Allergy 2022; 12:e12124. [PMID: 35344298 PMCID: PMC8967271 DOI: 10.1002/clt2.12124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 01/19/2022] [Accepted: 01/27/2022] [Indexed: 11/20/2022] Open
Abstract
Background Human endogenous retroviruses (HERVs) represent 8% of our genome. They originate from ancestral infections and although no longer contagious they can regulate transcription of adjacent cellular genes, produce viral RNAs sensed as non‐self by pattern recognition receptors, and encode viral proteins, such as Syncytin (SYN) 1 and 2, that exhibit potent immunomodulatory properties. Based on this, HERVs have been studied and proposed as relevant cofactors in several chronic inflammatory and immune‐mediated diseases. HERV transcription is regulated by host TRIM28 and SET domain bifurcated histone lysine methyltransferase 1 (SETDB1), which in turn exert crucial regulatory functions on the host immune system. No studies explored the expression of HERVs, TRIM28, and SETDB1 in allergic patients. Methods We assessed, through a polymerase chain reaction real time Taqman amplification assay, the transcription levels of pol genes of HERV‐H, HERV‐K, HERV‐W, and of env genes of SYN1 and SYN2, as well as of TRIM28 and SETDB1 in whole blood from 32 children with IgE‐mediated food allergy, 19 with food protein‐induced enterocolitis syndrome (FPIES), and in healthy control children. Results The expression levels of pol genes of HERV‐H, ‐K, and ‐W were significantly enhanced in patients with IgE‐mediated FA or FPIES as compared to control subjects, while the mRNA concentrations of SYN1 and SYN2 were comparable in each group of children. Both TRIM28 and SETDB1 mRNA levels were significantly higher in allergic patients. Conclusions Given the influence of HERVs and of TRIM28 and SETDB1 on innate and adaptive immune responses, their transcriptional activation in children with food allergies suggest that they might play important roles in the development of these diseases.
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Affiliation(s)
- Pier‐Angelo Tovo
- Department of Pediatric Sciences and Public Health University of Turin Turin Italy
| | - Giovanna Monti
- Pediatric Allergy Unit Regina Margherita Children's Hospital Turin Italy
| | - Valentina Daprà
- Pediatric Laboratory Department of Pediatric Sciences and Public Health University of Turin Turin Italy
| | - Paola Montanari
- Department of Pediatric Sciences and Public Health University of Turin Turin Italy
- Pediatric Laboratory Department of Pediatric Sciences and Public Health University of Turin Turin Italy
| | - Cristina Calvi
- Department of Pediatric Sciences and Public Health University of Turin Turin Italy
- Pediatric Laboratory Department of Pediatric Sciences and Public Health University of Turin Turin Italy
| | - Carla Alliaudi
- Department of Pediatric Sciences and Public Health University of Turin Turin Italy
- Pediatric Laboratory Department of Pediatric Sciences and Public Health University of Turin Turin Italy
| | - Allegra Sardo
- Department of Pediatric Sciences and Public Health University of Turin Turin Italy
| | - Ilaria Galliano
- Department of Pediatric Sciences and Public Health University of Turin Turin Italy
- Pediatric Laboratory Department of Pediatric Sciences and Public Health University of Turin Turin Italy
| | - Massimiliano Bergallo
- Department of Pediatric Sciences and Public Health University of Turin Turin Italy
- Pediatric Laboratory Department of Pediatric Sciences and Public Health University of Turin Turin Italy
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33
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Krempski JW, Lama JK, Iijima K, Kobayashi T, Matsunaga M, Kita H. A Mouse Model of the “LEAP” Study Reveals a Role for CTLA-4 in Preventing Peanut Allergy Induced by Environmental Peanut Exposure. J Allergy Clin Immunol 2022; 150:425-439.e3. [PMID: 35288169 PMCID: PMC9378358 DOI: 10.1016/j.jaci.2022.02.024] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 01/10/2022] [Accepted: 02/03/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND A human study, Learning Early About Peanut Allergy (LEAP), showed that early introduction of peanut products decreases the prevalence of peanut allergy among children. However, the immunologic mechanisms mediating the protective effects of consuming peanut products are not well understood. OBJECTIVE The objective was to develop a mouse model that simulates the LEAP study and investigate the underlying mechanisms for the study observations. METHODS Adult naive BALB/c mice were fed a commercial peanut butter product (Skippy) or buffer control and concomitantly exposed to peanut flour through the airway or skin to mimic environmental exposure. The animals were analyzed for anaphylactic reaction and by molecular and immunologic approaches. RESULTS After exposure to peanut flour through the airway or skin, naive mice developed peanut allergy, as demonstrated by acute and systemic anaphylaxis in response to challenge with peanut extract. Ingestion of Skippy, however, nearly abolished the increase in peanut-specific IgE and IgG and protected animals from developing anaphylaxis. Skippy-fed mice showed reduced numbers of T follicular helper (Tfh) cells and germinal center B cells in their draining lymph nodes, and single-cell RNA sequencing revealed a CD4+ T-cell population expressing cytotoxic T lymphocyte-associated protein 4 (CTLA-4) in these animals. Critically, blocking CTLA-4 with antibody increased levels of peanut-specific antibodies and reversed the protective effects of Skippy. CONCLUSION Ingestion of a peanut product protects mice from peanut allergy induced by environmental exposure to peanuts, and the CTLA-4 pathway, which regulates Tfh cell responses, likely plays a pivotal role in this protection.
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34
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Kim C, Kim YJ, Choi W, Jang HM, Hwang MY, Jung S, Lim H, Hong SB, Yoon K, Kim BJ, Park HY, Han B. Phenome-wide association study of the major histocompatibility complex region in the Korean population identifies novel association signals. Hum Mol Genet 2022; 31:2655-2667. [PMID: 35043955 DOI: 10.1093/hmg/ddac016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 11/11/2021] [Accepted: 01/11/2022] [Indexed: 11/13/2022] Open
Abstract
Human leukocyte antigen (HLA) gene variants in the major histocompatibility complex (MHC) region are associated with numerous complex human diseases and quantitative traits. Previous phenome-wide association studies (PheWAS) for this region demonstrated that HLA association patterns to the phenome have both population-specific and population-shared components. We performed MHC PheWAS in the Korean population by analyzing associations between phenotypes and genetic variants in the MHC region using the Korea Biobank Array project data samples from the Korean Genome and Epidemiology Study (KoGES) cohorts. Using this single-population dataset, we curated and analyzed 82 phenotypes for 125 673 Korean individuals after imputing HLA using CookHLA, a recently developed imputation framework. More than one-third of these phenotypes showed significant associations, confirming 56 known associations and discovering 13 novel association signals that were not reported previously. In addition, we analyzed heritability explained by the variants in the MHC region and genetic correlations among phenotypes based on the MHC variants.
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Affiliation(s)
- Chanwoo Kim
- Department of Electrical and Computer Engineering, Seoul National University, Seoul 08826, Republic of Korea
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA 98195, USA
| | - Young Jin Kim
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju-si, Chungcheongbuk-do 28159,, Republic of Korea
| | - Wanson Choi
- Department of Biomedical Sciences, BK21 Plus Biomedical Science Project, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Hye-Mi Jang
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju-si, Chungcheongbuk-do 28159,, Republic of Korea
| | - Mi Yeong Hwang
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju-si, Chungcheongbuk-do 28159,, Republic of Korea
| | - Sunwoo Jung
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Hyunjoon Lim
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Sang Bin Hong
- Department of Neurology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Kyungheon Yoon
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju-si, Chungcheongbuk-do 28159,, Republic of Korea
| | - Bong-Jo Kim
- Division of Genome Science, Department of Precision Medicine, National Institute of Health, Cheongju-si, Chungcheongbuk-do 28159,, Republic of Korea
| | - Hyun-Young Park
- Department of Precision Medicine, National Institute of Health, Cheongju-si, Chungcheongbuk-do 28159, Republic of Korea
| | - Buhm Han
- Department of Biomedical Sciences, BK21 Plus Biomedical Science Project, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul 08826, Republic of Korea
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Kanchan K, Grinek S, Bahnson HT, Ruczinski I, Shankar G, Larson D, Du Toit G, Barnes KC, Sampson HA, Suarez-Farinas M, Lack G, Nepom GT, Cerosaletti K, Mathias RA. HLA alleles and sustained peanut consumption promote IgG4 responses in subjects protected from peanut allergy. J Clin Invest 2022; 132:e152070. [PMID: 34981778 PMCID: PMC8718139 DOI: 10.1172/jci152070] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 10/28/2021] [Indexed: 11/18/2022] Open
Abstract
We investigated the interplay between genetics and oral peanut protein exposure in the determination of the immunological response to peanut using the targeted intervention in the LEAP clinical trial. We identified an association between peanut-specific IgG4 and HLA-DQA1*01:02 that was only observed in the presence of sustained oral peanut protein exposure. The association between IgG4 and HLA-DQA1*01:02 was driven by IgG4 specific for the Ara h 2 component. Once peanut consumption ceased, the association between IgG4-specific Ara h 2 and HLA-DQA1*01:02 was attenuated. The association was validated by observing expanded IgG4-specific epitopes in people who carried HLA-DQA1*01:02. Notably, we confirmed the previously reported associations with HLA-DQA1*01:02 and peanut allergy risk in the absence of oral peanut protein exposure. Interaction between HLA and presence or absence of exposure to peanut in an allergen- and epitope-specific manner implicates a mechanism of antigen recognition that is fundamental to driving immune responses related to allergy risk or protection.
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Affiliation(s)
- Kanika Kanchan
- Division of Allergy and Clinical Immunology, Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Stepan Grinek
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Henry T. Bahnson
- Benaroya Research Institute at Virginia Mason, Seattle, Washington, USA
- The Immune Tolerance Network, Bethesda, Maryland, USA
| | - Ingo Ruczinski
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Gautam Shankar
- Division of Allergy and Clinical Immunology, Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - David Larson
- The Immune Tolerance Network, Bethesda, Maryland, USA
| | - George Du Toit
- The Department of Pediatric Allergy, Division of Asthma, Allergy and Lung Biology, King’s College London, and Guy’s and St. Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Kathleen C. Barnes
- The Department of Medicine, University of Colorado, Anschutz, Colorado, USA
| | | | - Mayte Suarez-Farinas
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Gideon Lack
- The Department of Pediatric Allergy, Division of Asthma, Allergy and Lung Biology, King’s College London, and Guy’s and St. Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Gerald T. Nepom
- Benaroya Research Institute at Virginia Mason, Seattle, Washington, USA
- The Immune Tolerance Network, Bethesda, Maryland, USA
| | - Karen Cerosaletti
- Benaroya Research Institute at Virginia Mason, Seattle, Washington, USA
| | - Rasika A. Mathias
- Division of Allergy and Clinical Immunology, Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
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Bermick J, Schaller M. Epigenetic regulation of pediatric and neonatal immune responses. Pediatr Res 2022; 91:297-327. [PMID: 34239066 DOI: 10.1038/s41390-021-01630-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/01/2021] [Accepted: 06/09/2021] [Indexed: 02/06/2023]
Abstract
Epigenetic regulation of transcription is a collective term that refers to mechanisms known to regulate gene transcription without changing the underlying DNA sequence. These mechanisms include DNA methylation and histone tail modifications which influence chromatin accessibility, and microRNAs that act through post-transcriptional gene silencing. Epigenetics is known to regulate a variety of biological processes, and the role of epigtenetics in immunity and immune-mediated diseases is becoming increasingly recognized. While DNA methylation is the most widely studied, each of these systems play an important role in the development and maintenance of appropriate immune responses. There is clear evidence that epigenetic mechanisms contribute to developmental stage-specific immune responses in a cell-specific manner. There is also mounting evidence that prenatal exposures alter epigenetic profiles and subsequent immune function in exposed offspring. Early life exposures that are associated with poor long-term health outcomes also appear to impact immune specific epigenetic patterning. Finally, each of these epigenetic mechanisms contribute to the pathogenesis of a wide variety of diseases that manifest during childhood. This review will discuss each of these areas in detail. IMPACT: Epigenetics, including DNA methylation, histone tail modifications, and microRNA expression, dictate immune cell phenotypes. Epigenetics influence immune development and subsequent immune health. Prenatal, perinatal, and postnatal exposures alter immune cell epigenetic profiles and subsequent immune function. Numerous pediatric-onset diseases have an epigenetic component. Several successful strategies for childhood diseases target epigenetic mechanisms.
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Affiliation(s)
- Jennifer Bermick
- Department of Pediatrics, Division of Neonatology, University of Iowa, Iowa City, IA, USA. .,Iowa Inflammation Program, University of Iowa, Iowa City, IA, USA.
| | - Matthew Schaller
- Department of Pulmonary, Critical Care & Sleep Medicine, University of Florida, Gainesville, FL, USA
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Wang F, Luo D, Chen J, Pan C, Wang Z, Fu H, Xu J, Yang M, Mo S, Zhuang L, Ye L, Wang W. Genome-Wide Association Analysis to Search for New Loci Associated with Lifelong Premature Ejaculation Risk in Chinese Male Han Population. World J Mens Health 2022; 40:330-339. [PMID: 35021295 PMCID: PMC8987137 DOI: 10.5534/wjmh.210084] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/23/2021] [Accepted: 07/31/2021] [Indexed: 11/15/2022] Open
Abstract
PURPOSE Genetic factors play an indispensable role in the pathogenesis of lifelong premature ejaculation (LPE). The susceptibility genes/SNPs that have been discovered are very limited and can only explain part of the genetic effects of LPE. Therefore, discovering more genetic polymorphisms associated with the occurrence and development of LPE will help reveal the pathogenesis of LPE. MATERIALS AND METHODS We conducted a genome-wide association study of LPE in 486 Chinese male Han people (cases and controls). We used Gene Titan multi-channel instrument and Axiom Analysis Suite 6.0 software for genotyping. Imputation was performed by IMPUTE2 software and the 1000 Genomes Project (Phase3) was used as reference for haplotype. Finally, logistic regression analysis was performed on all loci that passed the quality control. The odds ratio and 95% confidence interval were calculated to determine the association between each SNPs and Chinese male Han population LPE risk. RESULTS The results showed that a total of 33 genetic variants in 13 genes (LACTBL1, SSBP3, ACOT11, LINC02486, TMEM154, LINC01098, NONE, HCG27, HLA-C, TNFSF8, TNC, FAM53B, SULF2) have a suggestively significant genome-wide association with LPE risk (p<5×10-6). CONCLUSIONS This study is the first to conduct a GWAS on LPE in Chinese male Han population 33 genetic polymorphisms have a suggestive genome-wide association with LPE risk. This study have provided data supplement for the genetic loci of LPE risk, and laid a scientific foundation for the pathogenesis and the targeted therapy of LPE.
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Affiliation(s)
- Fei Wang
- Department of Urology, Hainan General Hospital, Affiliated Hainan Hospital of Hainan Medical University, Haikou, Hainan, China
| | - Defan Luo
- Department of Urology, Hainan General Hospital, Affiliated Hainan Hospital to University of South China, Hengyang, Hunan, China
| | - Jianxiang Chen
- Department of Urology, Affiliated Hospital of Xiangnan University, Chenzhou, Hunan, China
| | - Cuiqing Pan
- Department of Urology, Hainan General Hospital, Affiliated Hainan Hospital of Hainan Medical University, Haikou, Hainan, China
| | - Zhongyao Wang
- Department of Urology, Hainan General Hospital, Affiliated Hainan Hospital of Hainan Medical University, Haikou, Hainan, China
| | - Housheng Fu
- Department of Urology, Hainan General Hospital, Affiliated Hainan Hospital of Hainan Medical University, Haikou, Hainan, China
| | - Jianbing Xu
- Department of Urology, Hainan General Hospital, Affiliated Hainan Hospital of Hainan Medical University, Haikou, Hainan, China
| | - Meng Yang
- Department of Urology, Hainan General Hospital, Affiliated Hainan Hospital of Hainan Medical University, Haikou, Hainan, China
| | - Shaowei Mo
- Ministry of Science and education, Hainan Women and Children's Medical Center, Haikou, Hainan, China
| | - Liying Zhuang
- Library, Hainan Medical University, Haikou, Hainan, China
| | - Liefu Ye
- Department of Urology, Fujian Provincial Hospital, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, China, China.
| | - Weifu Wang
- Department of Urology, Hainan General Hospital, Affiliated Hainan Hospital of Hainan Medical University, Haikou, Hainan, China.
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Suarez-Pajes E, Díaz-García C, Rodríguez-Pérez H, Lorenzo-Salazar JM, Marcelino-Rodríguez I, Corrales A, Zheng X, Callero A, Perez-Rodriguez E, Garcia-Robaina JC, González-Montelongo R, Flores C, Guillen-Guio B. Targeted analysis of genomic regions enriched in African ancestry reveals novel classical HLA alleles associated with asthma in Southwestern Europeans. Sci Rep 2021; 11:23686. [PMID: 34880287 PMCID: PMC8654850 DOI: 10.1038/s41598-021-02893-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 11/24/2021] [Indexed: 12/30/2022] Open
Abstract
Despite asthma has a considerable genetic component, an important proportion of genetic risks remain unknown, especially for non-European populations. Canary Islanders have the largest African genetic ancestry observed among Southwestern Europeans and the highest asthma prevalence in Spain. Here we examined broad chromosomal regions previously associated with an excess of African genetic ancestry in Canary Islanders, with the aim of identifying novel risk variants associated with asthma susceptibility. In a two-stage cases-control study, we revealed a variant within HLA-DQB1 significantly associated with asthma risk (rs1049213, meta-analysis p = 1.30 × 10–7, OR [95% CI] = 1.74 [1.41–2.13]) previously associated with asthma and broad allergic phenotype. Subsequent fine-mapping analyses of classical HLA alleles revealed a novel allele significantly associated with asthma protection (HLA-DQA1*01:02, meta-analysis p = 3.98 × 10–4, OR [95% CI] = 0.64 [0.50–0.82]) that had been linked to infectious and autoimmune diseases, and peanut allergy. HLA haplotype analyses revealed a novel haplotype DQA1*01:02-DQB1*06:04 conferring asthma protection (meta-analysis p = 4.71 × 10–4, OR [95% CI] = 0.47 [0.29– 0.73]).
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Affiliation(s)
- Eva Suarez-Pajes
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Claudio Díaz-García
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Héctor Rodríguez-Pérez
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Jose M Lorenzo-Salazar
- Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Itahisa Marcelino-Rodríguez
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Almudena Corrales
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Xiuwen Zheng
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Ariel Callero
- Allergy Unit, Hospital Universitario N.S. de Candelaria, Santa Cruz de Tenerife, Spain
| | - Eva Perez-Rodriguez
- Allergy Unit, Hospital Universitario N.S. de Candelaria, Santa Cruz de Tenerife, Spain
| | - Jose C Garcia-Robaina
- Allergy Unit, Hospital Universitario N.S. de Candelaria, Santa Cruz de Tenerife, Spain
| | | | - Carlos Flores
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain. .,Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain. .,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.
| | - Beatriz Guillen-Guio
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain. .,Department of Health Sciences, University of Leicester, Leicester, UK.
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Cañas JA, Núñez R, Cruz-Amaya A, Gómez F, Torres MJ, Palomares F, Mayorga C. Epigenetics in Food Allergy and Immunomodulation. Nutrients 2021; 13:4345. [PMID: 34959895 PMCID: PMC8708211 DOI: 10.3390/nu13124345] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 11/27/2021] [Accepted: 11/29/2021] [Indexed: 12/30/2022] Open
Abstract
Food allergy (FA) is an increasing problem worldwide and, over recent years, its prevalence is rising in developed countries. Nowadays, the immunological and cellular processes that occur in the allergic reactions are not fully understood, which hampers the development of in vitro diagnostic tools and further treatment options. Moreover, allergic diseases could be reinforced by environmental exposure and genetic modifications. Gene expression can be controlled by different epigenetic mechanisms like DNA methylation, histone modifications, and microRNAs. In addition, several environmental factors such as dietary components (vitamin D, butyrate, folic acid) are able to regulate this epigenetic mechanism. All these factors produce modifications in immune genes that could alter the development and function of immune cells, and therefore the etiology of the disease. Furthermore, these epigenetic mechanisms have also an influence on immunomodulation, which could explain sustained responsiveness or unresponsiveness during immunotherapy due to epigenetic modifications in key genes that induce tolerance in several FA. Thus, in this review we focus on the different epigenetic mechanisms that occur in FA and on the influence of several dietary components in these gene modifications.
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Affiliation(s)
- José A. Cañas
- Allergy Research Group, Instituto de Investigación Biomédica de Málaga-IBIMA, 29009 Málaga, Spain; (J.A.C.); (R.N.); (A.C.-A.); (F.P.)
- Andalusian Centre for Nanomedicine and Biotechnology-BIONAND, 29590 Málaga, Spain;
| | - Rafael Núñez
- Allergy Research Group, Instituto de Investigación Biomédica de Málaga-IBIMA, 29009 Málaga, Spain; (J.A.C.); (R.N.); (A.C.-A.); (F.P.)
| | - Anyith Cruz-Amaya
- Allergy Research Group, Instituto de Investigación Biomédica de Málaga-IBIMA, 29009 Málaga, Spain; (J.A.C.); (R.N.); (A.C.-A.); (F.P.)
- Andalusian Centre for Nanomedicine and Biotechnology-BIONAND, 29590 Málaga, Spain;
| | - Francisca Gómez
- Allergy Clinical Unit, Hospital Regional Universitario de Málaga, 29009 Málaga, Spain;
| | - María J. Torres
- Andalusian Centre for Nanomedicine and Biotechnology-BIONAND, 29590 Málaga, Spain;
- Allergy Clinical Unit, Hospital Regional Universitario de Málaga, 29009 Málaga, Spain;
- Medicine Department, Universidad de Málaga-UMA, 29010 Málaga, Spain
| | - Francisca Palomares
- Allergy Research Group, Instituto de Investigación Biomédica de Málaga-IBIMA, 29009 Málaga, Spain; (J.A.C.); (R.N.); (A.C.-A.); (F.P.)
| | - Cristobalina Mayorga
- Allergy Research Group, Instituto de Investigación Biomédica de Málaga-IBIMA, 29009 Málaga, Spain; (J.A.C.); (R.N.); (A.C.-A.); (F.P.)
- Andalusian Centre for Nanomedicine and Biotechnology-BIONAND, 29590 Málaga, Spain;
- Allergy Clinical Unit, Hospital Regional Universitario de Málaga, 29009 Málaga, Spain;
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Allergic diseases in infancy: I - Epidemiology and current interpretation. World Allergy Organ J 2021; 14:100591. [PMID: 34820047 PMCID: PMC8593659 DOI: 10.1016/j.waojou.2021.100591] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 08/30/2021] [Accepted: 09/08/2021] [Indexed: 12/19/2022] Open
Abstract
Objective Among non-communicable diseases, the prevalence of allergic diseases has increased significantly in the new millennium. The increase of allergic diseases is linked to the changing environment of infants. Methods This narrative review summarizes the discussions and conclusions from the 8th Human Milk Workshop. Information from the fields of pediatrics, epidemiology, biology, microbiology, and immunology are summarized to establish a framework describing potential avenues for the prevention of allergic diseases in the future. Results Several environmental circumstances are linked to the development of allergic diseases. While cesarean section is increasing the risk of allergies, early childhood exposure to a farm environment has a protective effect. From their analysis, nutritive and non-nutritive factors influencing the allergy risk in later life have been identified. The effect of breastfeeding on food allergy development is non-univocal. Human milk components including immunoglobulins, cytokines, and prebiotics have been indicated as important for allergy prevention. Conclusion Many factors linked to the western lifestyle have been associated with the development of allergic diseases. This suggests several theories that may serve as a basis for new protective interventions. While it is indubitable that mother's milk protects from infectious diseases, its role in the prevention of allergic diseases is to be elucidated.
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Ali A, Hamzaid NH, Ismail NAS. The Interplay of Nutriepigenomics, Personalized Nutrition and Clinical Practice in Managing Food Allergy. Life (Basel) 2021; 11:1275. [PMID: 34833150 PMCID: PMC8623511 DOI: 10.3390/life11111275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/25/2021] [Accepted: 11/05/2021] [Indexed: 11/16/2022] Open
Abstract
Food allergy in children has been a common issue due to the challenges of prescribing personalized nutrition with a lack of nutriepigenomics data. This has indeed further influenced clinical practice for appropriate management. While allergen avoidance is still the main principle in food allergy management, we require more information to advance the science behind nutrition, genes, and the immune system. Many researchers have highlighted the importance of personalized nutrition but there is a lack of data on how the decision is made. Thus, this review highlights the relationship among these key players in identifying the solution to the clinical management of food allergy with current nutriepigenomics data. The discussion integrates various inputs, including clinical assessments, biomarkers, and epigenetic information pertaining to food allergy, to curate a holistic and personalized approach to food allergy management in particular.
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Affiliation(s)
- Adli Ali
- Department of Pediatrics, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia;
| | - Nur Hana Hamzaid
- Dietetic Program & Centre for Rehabilitation and Special Needs Studies (iCaRehab), Faculty of Health Sciences, Universiti Kebangsaan Malaysia, Kuala Lumpur 50300, Malaysia;
| | - Noor Akmal Shareela Ismail
- Department of Biochemistry, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia
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Childs CE, Munblit D, Ulfman L, Gómez-Gallego C, Lehtoranta L, Recker T, Salminen S, Tiemessen M, Collado MC. Potential Biomarkers, Risk Factors and their Associations with IgE-mediated Food Allergy in Early Life: A Narrative Review. Adv Nutr 2021; 13:S2161-8313(22)00081-3. [PMID: 34596662 PMCID: PMC8970818 DOI: 10.1093/advances/nmab122] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Food allergy affects the quality of life of millions of people worldwide and presents a significant psychological and financial burden for both national and international public health. In the past few decades, the prevalence of allergic disease has been on the rise worldwide. Identified risk factors for food allergy include family history, mode of delivery, variations in infant feeding practices, prior diagnosis of other atopic diseases such as eczema, and social economic status. Identifying reliable biomarkers which predict the risk of developing food allergy in early life would be valuable in both preventing morbidity and mortality and by making current interventions available at the earliest opportunity. There is also the potential to identify new therapeutic targets. This narrative review provides details on the genetic, epigenetic, dietary and microbiome influences upon the development of food allergy and synthesizes the currently available data indicating potential biomarkers. While there is a large body of research evidence available within each field of potential risk factors, there are very limited number of studies which span multiple methodological fields, for example including immunology, microbiome, genetic/epigenetic factors and dietary assessment. We recommend that further collaborative research with detailed cohort phenotyping is required to identify biomarkers, and whether these vary between at-risk populations and the wider population. The low incidence of oral food challenge confirmed food allergy in the general population, and the complexities of designing nutritional intervention studies will provide challenges for researchers to address in generating high quality, reliable and reproducible research findings. STATEMENT OF SIGNIFICANCE Food allergy affects the quality of life of millions of people worldwide and presents a significant psychological and financial burden for both national and international public health. Identifying reliable biomarkers which predict the risk of developing food allergy would be valuable in both preventing morbidity and mortality and by making current interventions available at the earliest opportunity. This review provides details on the genetic, epigenetic, dietary and microbiome influences upon the development of food allergy. This helps in identifying reliable biomarkers to predict the risk of developing food allergy, which could be valuable in both preventing morbidity and mortality and by making interventions available at the earliest opportunity.
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Affiliation(s)
- Caroline E Childs
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom,Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Daniel Munblit
- Imperial College London, London, United Kingdom,Department of Paediatrics and Paediatric Infectious Diseases, Institute of Child’s Health, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia,Inflammation, Repair and Development Section, National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London, United Kingdom
| | | | - Carlos Gómez-Gallego
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
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Clinical Manifestations of Pediatric Food Allergy: a Contemporary Review. Clin Rev Allergy Immunol 2021; 62:180-199. [PMID: 34519995 DOI: 10.1007/s12016-021-08895-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2021] [Indexed: 12/12/2022]
Abstract
Food allergies (FAs) are an emerging health care issue, and a "second wave of the allergy epidemic" was named. There are extensive data that documented the prevalence rate as high as approximately 10%. FAs are immunological adverse reactions, including IgE-mediated mechanisms, cell-mediated mechanisms, or mixed IgE- and cell-mediated mechanisms. A diagnosis of FA is made by specific symptoms encounter with food, detailed past history, sensitization tests, and oral food challenges (OFCs) if necessary. The component-resolved diagnostics (CRD) test can distinguish true or cross-reaction. "Minimal elimination" from the results of CRD and OFC could avoid unnecessary food restriction. Strict food limitation is harsh and stressful on patients and their families. Children with FAs experience a higher rate of post-traumatic stress symptoms (PTSS) and bullying than others. In the last 20 years, oral immunotherapy (OIT), sublingual immunotherapy (SLIT), and epicutaneous immunotherapy (EPIT) are treatment strategies. OIT and EPIT are the most two encouraging treatments for FA. This review aims to introduce FAs in diverse clinical disorders, new perspectives, and their practical implications in diagnosing and treating FA.
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Xu S, Pan Z, Huang L, Chen Y, Xie H, Wang F, Zhou T, Yu L, Kong J, Xu S, Pan F. Association of FOXO3a gene polymorphisms and ankylosing spondylitis susceptibility in Eastern Chinese Han population. Gene 2021; 800:145832. [PMID: 34274476 DOI: 10.1016/j.gene.2021.145832] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/26/2021] [Accepted: 07/13/2021] [Indexed: 12/12/2022]
Abstract
OBJECTIVE To investigate the association of FOXO3a polymorphisms and ankylosing spondylitis (AS) susceptibility in Eastern Chinese Han population. METHODS FOXO3a polymorphisms rs12206094, rs12212067, rs2253310, rs3800232, and rs4946933 were genotyped in 650 AS patients and 646 controls by the improved Multiple Ligase Detection Reaction. RESULTS The distribution of genotype in rs12212067 polymorphism was significantly different between AS patients and controls (P = 0.020), especially in male population (P = 0.009). There was significant difference of the genotype frequency distribution at rs3800232 between patients and controls in male population. The results of binary regression analysis showed that the rs12212067 GG genotype and rs3800232 TT genotype were obviously correlated with elevated AS risk, and the associations were still significant after being adjusted by age and gender (all P < 0.05). Interestingly, rs12212067 and rs3800232 genotypes were associated with disease activity of patients. Additionally, haplotype block rs12212067G- rs3800232T (OR = 1.403, 95%CI = 1.011-1.949) was further shown to confer promoting effect on developing AS. CONCLUSION Among Eastern Chinese Han population, FOXO3a polymorphism rs12212067 and rs3800232 may contribute to increased risk of developing AS, but well-designed multicenter studies are needed to further confirm these preliminary findings in the future.
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Affiliation(s)
- Shanshan Xu
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, Anhui 230032, China; The Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, 81 Meishan Road, Hefei, Anhui 230032, China
| | - Zhipeng Pan
- Department of Medical Oncology, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, China
| | - Li Huang
- Anhui Medical College, 387 Wuhu Road, Hefei, Anhui 230032, China
| | - Yuting Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, Anhui 230032, China; The Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, 81 Meishan Road, Hefei, Anhui 230032, China
| | - Huimin Xie
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, Anhui 230032, China; The Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, 81 Meishan Road, Hefei, Anhui 230032, China
| | - Feier Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, Anhui 230032, China; The Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, 81 Meishan Road, Hefei, Anhui 230032, China
| | - Tingting Zhou
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, Anhui 230032, China; The Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, 81 Meishan Road, Hefei, Anhui 230032, China
| | - Lingxiang Yu
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, Anhui 230032, China; The Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, 81 Meishan Road, Hefei, Anhui 230032, China
| | - Jiangpiang Kong
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, Anhui 230032, China; The Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, 81 Meishan Road, Hefei, Anhui 230032, China
| | - Shengqian Xu
- Department of Rheumatism and Immunity, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, China
| | - Faming Pan
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, Anhui 230032, China; The Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, 81 Meishan Road, Hefei, Anhui 230032, China.
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Association of methylation level and transcript level in TRAF5 gene with ankylosing spondylitis: a case-control study. Genes Immun 2021; 22:101-107. [PMID: 34021268 DOI: 10.1038/s41435-021-00135-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/27/2021] [Accepted: 05/10/2021] [Indexed: 02/04/2023]
Abstract
To explore the association between methylation level and transcript level of TNF receptor-associated factor 5 (TRAF5) gene with ankylosing spondylitis (AS) in Chinese Han population. Methylation and mRNA expression level of the TRAF5 gene were tested in 98 patients and 98 healthy controls. Among the 21 CpG sites, methylation levels at eight sites were significantly different between AS patients and healthy controls. However, only three sites remained significantly different after the correction by the Benjamini-Hochberg method. Compared with controls, the CpG island of TRAF5 gene promoter was highly methylated in AS patients, and the relative mRNA expression level of TRAF5 was significantly reduced in AS patients. And the mRNA level was negatively correlated with the methylation level of TRAF5 gene in AS patients (rs = -0.453, P < 0.001). Subgroup analyses indicated that there was no significant difference in the level of methylation between groups of different status of HLA-B27 and medications in AS patients. Multiple linear regression showed that disease-modifying antirheumatic drugs could reduce methylation levels of AS patients after adjusting for the effects of other drugs. In conclusion, the hypermethylation of the TRAF5 might contribute to the pathogenesis of AS, but many open questions remain.
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Single nucleotide polymorphisms of TRAF2 and TRAF5 gene in ankylosing spondylitis: a case-control study. Clin Exp Med 2021; 21:645-653. [PMID: 33997937 DOI: 10.1007/s10238-021-00719-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 05/05/2021] [Indexed: 12/16/2022]
Abstract
Objective To investigate the role of eight locus polymorphisms of tumor necrosis factor receptor-associated factor 2 (TRAF2) and TRAF5 gene and their interaction in the susceptibility to ankylosing spondylitis (AS) in Chinese Han population. Methods Eight single nucleotide polymorphisms (SNPs) of TRAF2 (rs3750511, rs10781522, rs17250673, rs59471504) and TRAF5 (rs6540679, rs12569232, rs4951523, rs7514863) gene were genotyped in 673 AS patients and 687 controls. Results The SNPs of TRAF2 and TRAF5 do not indicate a correlation with the susceptibility of AS in Chinese Han population. Genotype frequencies of rs3750511 were statistically significant in females between patients and controls. The allele frequencies of rs10781522 and genotype frequencies of rs3750511 were statistically significant between groups of different diseases activity. One three-locus model, TRAF2 (rs10781522, rs17250673) and TRAF5 (rs12569232), had a maximum testing accuracy of 52.67% and a maximum cross-validation consistency (10/10) that was significant at the level of P = 0.0001, after determined empirically by permutation testing. As to environmental variables, only marginal association was found between sleep quality and AS susceptibility. Conclusion TRAF2 rs3750511 polymorphism may be associated with the susceptibility and severity of AS. Besides, the interaction of TRAF2 and TRAF5 genes may be associated with AS susceptibility, but many open questions remain.
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Krempski JW, Warren C, Han X, Zhang W, He Z, Lejeune S, Nadeau K. Food Allergies: An Example of Translational Research. Immunol Allergy Clin North Am 2021; 41:143-163. [PMID: 33863476 DOI: 10.1016/j.iac.2021.01.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Food allergies have been rising in prevalence since the 1990s, imposing substantial physical, psychosocial, and economic burdens on affected patients and their families. Until recently, the only therapy for food allergy was strict avoidance of the allergenic food. Recent advances in translational studies, however, have led to insights into allergic sensitization and tolerance. This article provides an overview of cutting-edge research into food allergy and immune tolerance mechanisms utilizing mouse models, human studies, and systems biology approaches. This research is being translated and implemented in the clinical setting to improve diagnosis and reduce food allergy's public health burden.
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Affiliation(s)
- James Walter Krempski
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University, Stanford, CA, USA.
| | - Christopher Warren
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University, Stanford, CA, USA
| | - Xiaorui Han
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University, Stanford, CA, USA
| | - Wenming Zhang
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University, Stanford, CA, USA
| | - Ziyuan He
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University, Stanford, CA, USA
| | - Stéphanie Lejeune
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University, Stanford, CA, USA
| | - Kari Nadeau
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University, Stanford, CA, USA
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Raspin K, FitzGerald LM, Marthick JR, Field MA, Malley RC, Banks A, Donovan S, Thomson RJ, Foley GR, Stanford JL, Dickinson JL. A rare variant in EZH2 is associated with prostate cancer risk. Int J Cancer 2021; 149:1089-1099. [PMID: 33821477 DOI: 10.1002/ijc.33584] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 02/26/2021] [Accepted: 03/09/2021] [Indexed: 11/11/2022]
Abstract
Prostate cancer (PrCa) is highly heritable, and although rare variants contribute significantly to PrCa risk, few have been identified to date. Herein, whole-genome sequencing was performed in a large PrCa family featuring multiple affected relatives spanning several generations. A rare, predicted splice site EZH2 variant, rs78589034 (G > A), was identified as segregating with disease in all but two individuals in the family, one of whom was affected with lymphoma and bowel cancer and a female relative. This variant was significantly associated with disease risk in combined familial and sporadic PrCa datasets (n = 1551; odds ratio [OR] = 3.55, P = 1.20 × 10-5 ). Transcriptome analysis was performed on prostate tumour needle biopsies available for two rare variant carriers and two wild-type cases. Although no allele-dependent differences were detected in EZH2 transcripts, a distinct differential gene expression signature was observed when comparing prostate tissue from the rare variant carriers with the wild-type samples. The gene expression signature comprised known downstream targets of EZH2 and included the top-ranked genes, DUSP1, FOS, JUNB and EGR1, which were subsequently validated by qPCR. These data provide evidence that rs78589034 is associated with increased PrCa risk in Tasmanian men and further, that this variant may be associated with perturbed EZH2 function in prostate tissue. Disrupted EZH2 function is a driver of tumourigenesis in several cancers, including prostate, and is of significant interest as a therapeutic target.
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Affiliation(s)
- Kelsie Raspin
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Liesel M FitzGerald
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - James R Marthick
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Matt A Field
- Australian Institute of Tropical Health and Medicine and Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Cairns, Queensland, Australia.,John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Roslyn C Malley
- Hobart Pathology, Hobart, Tasmania, Australia.,Tasmanian School of Medicine, University of Tasmania, Hobart, Tasmania, Australia
| | - Annette Banks
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | | | - Russell J Thomson
- Centre for Research in Mathematics and Data Science, Western Sydney University, Sydney, New South Wales, Australia
| | - Georgea R Foley
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Janet L Stanford
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Joanne L Dickinson
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
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Abstract
The risk factors for food allergy (FA) include both genetic variants and environmental factors. Advances using both candidate-gene association studies and genome-wide approaches have led to the identification of FA-associated genes involved in immune responses and skin barrier functions. Epigenetic changes have also been associated with the risk of FA. In this chapter, we outline current understanding of the genetics, epigenetics and the interplay with environmental risk factors associated with FA. Future studies of gene-environment interactions, gene-gene interactions, and multi-omics integration may help shed light on the mechanisms of FA, and lead to improved diagnostic and treatment strategies.
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Affiliation(s)
- Elisabet Johansson
- Division of Asthma Research, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, 3333 Burnet Avenue, Cincinnati, OH 45229-3026, USA
| | - Tesfaye B Mersha
- Division of Asthma Research, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, 3333 Burnet Avenue, Cincinnati, OH 45229-3026, USA.
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Zhou X, Han X, Lyu SC, Bunning B, Kost L, Chang I, Cao S, Sampath V, Nadeau KC. Targeted DNA methylation profiling reveals epigenetic signatures in peanut allergy. JCI Insight 2021; 6:143058. [PMID: 33571165 PMCID: PMC8026193 DOI: 10.1172/jci.insight.143058] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 02/10/2021] [Indexed: 12/14/2022] Open
Abstract
DNA methylation (DNAm) has been shown to play a role in mediating food allergy; however, the mechanism by which it does so is poorly understood. In this study, we used targeted next-generation bisulfite sequencing to evaluate DNAm levels in 125 targeted highly informative genomic regions containing 602 CpG sites on 70 immune-related genes to understand whether DNAm can differentiate peanut allergy (PA) versus nonallergy (NA). We found PA-associated DNAm signatures associated with 12 genes (7 potentially novel to food allergy, 3 associated with Th1/Th2, and 2 associated with innate immunity), as well as DNAm signature combinations with superior diagnostic potential compared with serum peanut–specific IgE for PA versus NA. Furthermore, we found that, following peanut protein stimulation, peripheral blood mononuclear cell (PBMCs) from PA participants showed increased production of cognate cytokines compared with NA participants. The varying responses between PA and NA participants may be associated with the interaction between the modification of DNAm and the interference of environment. Using Euclidean distance analysis, we found that the distances of methylation profile comprising 12 DNAm signatures between PA and NA pairs in monozygotic (MZ) twins were smaller than those in randomly paired genetically unrelated individuals, suggesting that PA-related DNAm signatures may be associated with genetic factors.
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