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Tomusiak A, Floro A, Tiwari R, Riley R, Matsui H, Andrews N, Kasler HG, Verdin E. Development of an epigenetic clock resistant to changes in immune cell composition. Commun Biol 2024; 7:934. [PMID: 39095531 PMCID: PMC11297166 DOI: 10.1038/s42003-024-06609-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 07/14/2024] [Indexed: 08/04/2024] Open
Abstract
Epigenetic clocks are age predictors that use machine-learning models trained on DNA CpG methylation values to predict chronological or biological age. Increases in predicted epigenetic age relative to chronological age (epigenetic age acceleration) are connected to aging-associated pathologies, and changes in epigenetic age are linked to canonical aging hallmarks. However, epigenetic clocks rely on training data from bulk tissues whose cellular composition changes with age. Here, we found that human naive CD8+ T cells, which decrease in frequency during aging, exhibit an epigenetic age 15-20 years younger than effector memory CD8+ T cells from the same individual. Importantly, homogenous naive T cells isolated from individuals of different ages show a progressive increase in epigenetic age, indicating that current epigenetic clocks measure two independent variables, aging and immune cell composition. To isolate the age-associated cell intrinsic changes, we created an epigenetic clock, the IntrinClock, that did not change among 10 immune cell types tested. IntrinClock shows a robust predicted epigenetic age increase in a model of replicative senescence in vitro and age reversal during OSKM-mediated reprogramming.
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Affiliation(s)
- Alan Tomusiak
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, 94945, CA, USA
- Department of Gerontology, University of Southern California, 3715 McClintock Ave, Los Angeles, 90089, CA, USA
| | - Ariel Floro
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, 94945, CA, USA
- Department of Gerontology, University of Southern California, 3715 McClintock Ave, Los Angeles, 90089, CA, USA
| | - Ritesh Tiwari
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, 94945, CA, USA
| | - Rebeccah Riley
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, 94945, CA, USA
| | - Hiroyuki Matsui
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, 94945, CA, USA
| | - Nicolas Andrews
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, 94945, CA, USA
| | - Herbert G Kasler
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, 94945, CA, USA
| | - Eric Verdin
- Buck Institute for Research on Aging, 8001 Redwood Blvd, Novato, 94945, CA, USA.
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Zhou P, Liu W, Ma J. Roles of Menin in T cell differentiation and function: Current knowledge and perspectives. Immunology 2024. [PMID: 39011567 DOI: 10.1111/imm.13837] [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: 04/17/2024] [Accepted: 06/28/2024] [Indexed: 07/17/2024] Open
Abstract
The commitment to specific T lymphocytes (T cell) lineages is governed by distinct transcription factors, whose expression is modulated through epigenetic mechanisms. Unravelling these epigenetic mechanisms that regulate T cell differentiation and function holds significant importance for understanding T cells. Menin, a multifunctional scaffolding protein, is implicated in various cellular processes, such as cell proliferation, cell cycle control, DNA repair and transcriptional regulation, primarily through epigenetic mechanisms. Existing research indicates Menin's impact on T cell differentiation and function, while a comprehensive and systematic review is currently lacking to consolidate these findings. In the current review, we have highlighted recent studies on the role of Menin in T cell differentiation and function, focusing mainly on its impact on the memory Th2 maintenance, Th17 differentiation and maintenance, CD4+ T cell senescence, and effector CD8+ T cell survival. Considering Menin's crucial function in maintaining effector T cell function, the potential of inhibiting Menin activity in mitigating inflammatory diseases associated with excessive T cell activation has also been emphasised.
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Affiliation(s)
- Pingping Zhou
- Department of Immunology, Eye Hospital, The First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, Heilongjiang, China
| | - Weiru Liu
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jian Ma
- Department of Immunology, Eye Hospital, The First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, Heilongjiang, China
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Yusipov I, Kalyakulina A, Trukhanov A, Franceschi C, Ivanchenko M. Map of epigenetic age acceleration: A worldwide analysis. Ageing Res Rev 2024; 100:102418. [PMID: 39002646 DOI: 10.1016/j.arr.2024.102418] [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: 04/17/2024] [Revised: 07/03/2024] [Accepted: 07/08/2024] [Indexed: 07/15/2024]
Abstract
We present a systematic analysis of epigenetic age acceleration based on by far the largest collection of publicly available DNA methylation data for healthy samples (93 datasets, 23 K samples), focusing on the geographic (25 countries) and ethnic (31 ethnicities) aspects around the world. We employed the most popular epigenetic tools for assessing age acceleration and examined their quality metrics and ability to extrapolate to epigenetic data from different tissue types and age ranges different from the training data of these models. In most cases, the models proved to be inconsistent with each other and showed different signs of age acceleration, with the PhenoAge model tending to systematically underestimate and different versions of the GrimAge model tending to systematically overestimate the age prediction of healthy subjects. Referring to data availability and consistency, most countries and populations are still not represented in GEO, moreover, different datasets use different criteria for determining healthy controls. Because of this, it is difficult to fully isolate the contribution of "geography/environment", "ethnicity" and "healthiness" to epigenetic age acceleration. Among the explored metrics, only the DunedinPACE, which measures aging rate, appears to adequately reflect the standard of living and socioeconomic indicators in countries, although it has a limited application to blood methylation data only. Invariably, by epigenetic age acceleration, males age faster than females in most of the studied countries and populations.
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Affiliation(s)
- Igor Yusipov
- Artificial Intelligence Research Center, Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University, Nizhny Novgorod 603022, Russia; Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod 603022, Russia.
| | - Alena Kalyakulina
- Artificial Intelligence Research Center, Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University, Nizhny Novgorod 603022, Russia; Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod 603022, Russia.
| | - Arseniy Trukhanov
- Mriya Life Institute, National Academy of Active Longevity, Moscow 124489, Russia.
| | - Claudio Franceschi
- Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod 603022, Russia.
| | - Mikhail Ivanchenko
- Artificial Intelligence Research Center, Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University, Nizhny Novgorod 603022, Russia; Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod 603022, Russia.
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Yang F, Zhang X, Xie Y, Yuan J, Gao J, Chen H, Li X. The pathogenesis of food allergy and protection offered by dietary compounds from the perspective of epigenetics. J Nutr Biochem 2024; 128:109593. [PMID: 38336123 DOI: 10.1016/j.jnutbio.2024.109593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 01/23/2024] [Accepted: 02/04/2024] [Indexed: 02/12/2024]
Abstract
Food allergy is a global food safety concern, with an increasing prevalence in recent decades. However, the immunological and cellular mechanisms involved in allergic reactions remain incompletely understood, which impedes the development of effective prevention and treatment strategies. Current evidence supports those epigenetic modifications regulate the activation of immune cells, and their dysregulation can contribute to the development of food allergies. Patients with food allergy show epigenetic alterations that lead to the onset, duration and recovery of allergic disease. Moreover, many preclinical studies have shown that certain dietary components exert nutriepigenetic effects in changing the course of food allergies. In this review, we provide an up-to-date overview of DNA methylation, noncoding RNA and histone modification, with a focus on their connections to food allergies. Following this, we discuss the epigenetic mechanisms that regulate the activation and differentiation of innate and adapted immune cell in the context of food allergies. Subsequently, this study specifically focuses on the multidimensional epigenetic effects of dietary components in modulating the immune response, which holds promise for preventing food allergies in the future.
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Affiliation(s)
- Fan Yang
- State Key Laboratory of Food Science and Resources, College of Food Science and Technology, Nanchang University, Nanchang 330047, China; Jiangxi Province Key Laboratory of Food Allergy, Nanchang University, Nanchang 330047, China
| | - Xing Zhang
- State Key Laboratory of Food Science and Resources, College of Food Science and Technology, Nanchang University, Nanchang 330047, China; Jiangxi Province Key Laboratory of Food Allergy, Nanchang University, Nanchang 330047, China
| | - Yanhai Xie
- Sino-German Joint Research Institute, College of Food Science and Technology, Nanchang University, Nanchang 330047, China; Jiangxi Province Key Laboratory of Food Allergy, Nanchang University, Nanchang 330047, China
| | - Juanli Yuan
- State Key Laboratory of Food Science and Resources, College of Food Science and Technology, Nanchang University, Nanchang 330047, China; School of Pharmacy, Jiangxi Medical College, Nanchang University, Nanchang 330047, China
| | - Jinyan Gao
- State Key Laboratory of Food Science and Resources, College of Food Science and Technology, Nanchang University, Nanchang 330047, China; Jiangxi Province Key Laboratory of Food Allergy, Nanchang University, Nanchang 330047, China
| | - Hongbing Chen
- Sino-German Joint Research Institute, College of Food Science and Technology, Nanchang University, Nanchang 330047, China; Jiangxi Province Key Laboratory of Food Allergy, Nanchang University, Nanchang 330047, China
| | - Xin Li
- State Key Laboratory of Food Science and Resources, College of Food Science and Technology, Nanchang University, Nanchang 330047, China; Jiangxi Province Key Laboratory of Food Allergy, Nanchang University, Nanchang 330047, China.
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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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Goldner Kabeli R, Zevin S, Abargel A, Zilberberg A, Efroni S. Self-supervised learning of T cell receptor sequences exposes core properties for T cell membership. SCIENCE ADVANCES 2024; 10:eadk4670. [PMID: 38669334 DOI: 10.1126/sciadv.adk4670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 03/26/2024] [Indexed: 04/28/2024]
Abstract
The T cell receptor (TCR) repertoire is an extraordinarily diverse collection of TCRs essential for maintaining the body's homeostasis and response to threats. In this study, we compiled an extensive dataset of more than 4200 bulk TCR repertoire samples, encompassing 221,176,713 sequences, alongside 6,159,652 single-cell TCR sequences from over 400 samples. From this dataset, we then selected a representative subset of 5 million bulk sequences and 4.2 million single-cell sequences to train two specialized Transformer-based language models for bulk (CVC) and single-cell (scCVC) TCR repertoires, respectively. We show that these models successfully capture TCR core qualities, such as sharing, gene composition, and single-cell properties. These qualities are emergent in the encoded TCR latent space and enable classification into TCR-based qualities such as public sequences. These models demonstrate the potential of Transformer-based language models in TCR downstream applications.
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Affiliation(s)
- Romi Goldner Kabeli
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Sarit Zevin
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Avital Abargel
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Alona Zilberberg
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Sol Efroni
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
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Mijač S, Banić I, Genc AM, Lipej M, Turkalj M. The Effects of Environmental Exposure on Epigenetic Modifications in Allergic Diseases. MEDICINA (KAUNAS, LITHUANIA) 2024; 60:110. [PMID: 38256371 PMCID: PMC10820670 DOI: 10.3390/medicina60010110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 12/27/2023] [Accepted: 01/05/2024] [Indexed: 01/24/2024]
Abstract
Allergic diseases are one of the most common chronic conditions and their prevalence is on the rise. Environmental exposure, primarily prenatal and early life influences, affect the risk for the development and specific phenotypes of allergic diseases via epigenetic mechanisms. Exposure to pollutants, microorganisms and parasites, tobacco smoke and certain aspects of diet are known to drive epigenetic changes that are essential for immune regulation (e.g., the shift toward T helper 2-Th2 cell polarization and decrease in regulatory T-cell (Treg) differentiation). DNA methylation and histone modifications can modify immune programming related to either pro-allergic interleukin 4 (IL-4), interleukin 13 (IL-13) or counter-regulatory interferon γ (IFN-γ) production. Differential expression of small non-coding RNAs has also been linked to the risk for allergic diseases and associated with air pollution. Certain exposures and associated epigenetic mechanisms play a role in the susceptibility to allergic conditions and specific clinical manifestations of the disease, while others are thought to have a protective role against the development of allergic diseases, such as maternal and early postnatal microbial diversity, maternal helminth infections and dietary supplementation with polyunsaturated fatty acids and vitamin D. Epigenetic mechanisms are also known to be involved in mediating the response to common treatment in allergic diseases, for example, changes in histone acetylation of proinflammatory genes and in the expression of certain microRNAs are associated with the response to inhaled corticosteroids in asthma. Gaining better insight into the epigenetic regulation of allergic diseases may ultimately lead to significant improvements in the management of these conditions, earlier and more precise diagnostics, optimization of current treatment regimes, and the implementation of novel therapeutic options and prevention strategies in the near future.
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Affiliation(s)
- Sandra Mijač
- Department of Medical Research, Srebrnjak Children’s Hospital, Srebrnjak 100, HR-10000 Zagreb, Croatia; (S.M.); (A.-M.G.)
| | - Ivana Banić
- Department of Medical Research, Srebrnjak Children’s Hospital, Srebrnjak 100, HR-10000 Zagreb, Croatia; (S.M.); (A.-M.G.)
- Department of Innovative Diagnostics, Srebrnjak Children’s Hospital, Srebrnjak 100, HR-10000 Zagreb, Croatia
| | - Ana-Marija Genc
- Department of Medical Research, Srebrnjak Children’s Hospital, Srebrnjak 100, HR-10000 Zagreb, Croatia; (S.M.); (A.-M.G.)
| | - Marcel Lipej
- IT Department, Srebrnjak Children’s Hospital, Srebrnjak 100, HR-10000 Zagreb, Croatia;
| | - Mirjana Turkalj
- Department of Pediatric Allergy and Pulmonology, Srebrnjak Children’s Hospital, Srebrnjak 100, HR-10000 Zagreb, Croatia;
- Faculty of Medicine, J.J. Strossmayer University of Osijek, J. Huttlera 4, HR-31000 Osijek, Croatia
- Faculty of Medicine, Catholic University of Croatia, Ilica 242, HR-10000 Zagreb, Croatia
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8
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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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Kolsun KP, Lee S, MacIsaac JL, Subbarao P, Moraes TJ, Mandhane PJ, Turvey SE, Kobor MS, Jones MJ, Simons E. DNA methylation is not associated with sensitization to or dietary introduction of highly allergenic foods in a subset of the CHILD cohort at age 1 year. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. GLOBAL 2023; 2:100130. [PMID: 37781669 PMCID: PMC10509901 DOI: 10.1016/j.jacig.2023.100130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 04/24/2023] [Accepted: 04/30/2023] [Indexed: 10/03/2023]
Abstract
Background In the first year of life, DNA methylation (DNAm) patterns are established and are particularly susceptible to exposure-induced changes. Some of these changes may leave lasting effects by persistently altering gene expression or cell type composition or function, contributing to disease. Objectives In this discovery study, we investigated DNAm associations with sensitization to peanut, egg, or cow's milk and hypothesized that genes demonstrating DNAm differences in immune cells may play a role in the development of food sensitization. Methods Infant sensitization (a skin prick test wheal size that is at least 2 mm greater than the negative control) was measured to peanut, egg, and cow's milk at age 1 year, and ages of food introduction were reported prospectively. PBMC DNAm was measured in blood samples at 1 year in 144 infants, oversampled for atopy or wheeze. Statistical analysis of Illumina 450k array DNAm data was conducted in R with adjustment for clinical and genetic covariables and a minimum effect size of 1%, false discovery rate of 5%, and medium-confidence false discovery rate threshold of 20%. Results There were no DNAm differences between infants with and without peanut, egg, or cow's milk sensitization. Borderline significant sites with high effect sizes were enriched for methylation quantitative trait loci, hinting at genetic factors influencing DNAm at these sites. DNAm patterns did not differ by peanut or egg introduction before or after 12 months. Conclusion This small pilot study did not show differences in methylation by food sensitization or introduction, but it did demonstrate DNAm patterns linked to genetic variants.
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Affiliation(s)
- Kurt P. Kolsun
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg
| | - Samantha Lee
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg
| | - Julia L. MacIsaac
- Department of Medical Genetics, University of British Columbia, Vancouver
| | - Padmaja Subbarao
- Division of Respiratory Medicine, Department of Pediatrics, Hospital for Sick Children and University of Toronto
| | - Theo J. Moraes
- Division of Respiratory Medicine, Department of Pediatrics, Hospital for Sick Children and University of Toronto
| | - Piushkumar J. Mandhane
- Division of Pediatric Respirology, Pulmonary, and Asthma, Department of Pediatrics, University of Alberta, Edmonton
| | - Stuart E. Turvey
- Division of Allergy and Immunology, Department of Pediatrics, British Columbia Children’s Hospital, Vancouver
| | - Michael S. Kobor
- Department of Medical Genetics, University of British Columbia, Vancouver
| | - Meaghan J. Jones
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg
- Children’s Hospital Research Institute of Manitoba, Winnipeg
| | - Elinor Simons
- Children’s Hospital Research Institute of Manitoba, Winnipeg
- Section of Allergy and Immunology, Department of Pediatrics and Child Health, University of Manitoba, Winnipeg
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Giri AK, Prasad G, Parekatt V, Rajashekar D, Tandon N, Bharadwaj D. Epigenome-wide methylation study identified two novel CpGs associated with T2DM risk and a network of co-methylated CpGs capable of patient's classifications. Hum Mol Genet 2023; 32:2576-2586. [PMID: 37184252 DOI: 10.1093/hmg/ddad084] [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: 09/02/2022] [Revised: 04/24/2023] [Accepted: 05/11/2023] [Indexed: 05/16/2023] Open
Abstract
Prevention of Type 2 diabetes mellitus (T2DM) pandemic needs markers that can precisely predict the disease risk in an individual. Alterations in DNA methylations due to exposure towards environmental risk factors are widely sought markers for T2DM risk prediction. To identify such individual DNA methylation signatures and their effect on disease risk, we performed an epigenome-wide association study (EWAS) in 844 Indian individuals of Indo-European origin. We identified and validated methylation alterations at two novel CpG sites in MIR1287 (cg01178710) and EDN2-SCMH1 (cg04673737) genes associated with T2DM risk at the epigenome-wide-significance-level (P < 1.2 × 10-7). Further, we also replicated the association of two known CpG sites in TXNIP, and CPT1A in the Indian population. With 535 EWAS significant CpGs (P < 1.2 × 10-7) identified in the discovery phase samples, we created a co-methylation network using weighted correlation network analysis and identified four modules among the CpGs. We observed that methylation of one of the module associates with T2DM risk factors (e.g. BMI, insulin and C-peptide) and can be used as markers to segregate T2DM patients with good glycemic control (e.g. low HbA1c) and dyslipidemia (low HDL and high TG) from the other patients. Additionally, an intronic SNP (rs6503650) in the JUP gene, a member of the same module, associated with methylation at all the 14 hub CpG sites of that module as methQTL. Our network-assisted EWAS is the first to systematically explore DNA methylation variations conferring risks to T2DM in Indians and use the identified risk CpG sites for patient segregation with different clinical outcomes. These findings can be useful for better stratification of patients to improve the clinical management and treatment effects.
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Affiliation(s)
- Anil K Giri
- Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Gauri Prasad
- Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Vaisak Parekatt
- Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Donaka Rajashekar
- Genomics and Molecular Medicine Unit, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Nikhil Tandon
- Department of Endocrinology and Metabolism, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Dwaipayan Bharadwaj
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Systems Genomics Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
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11
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Zheng Y, Jun J, Brennan K, Gevaert O. EpiMix is an integrative tool for epigenomic subtyping using DNA methylation. CELL REPORTS METHODS 2023; 3:100515. [PMID: 37533639 PMCID: PMC10391348 DOI: 10.1016/j.crmeth.2023.100515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 04/12/2023] [Accepted: 06/01/2023] [Indexed: 08/04/2023]
Abstract
DNA methylation (DNAme) is a major epigenetic factor influencing gene expression with alterations leading to cancer and immunological and cardiovascular diseases. Recent technological advances have enabled genome-wide profiling of DNAme in large human cohorts. There is a need for analytical methods that can more sensitively detect differential methylation profiles present in subsets of individuals from these heterogeneous, population-level datasets. We developed an end-to-end analytical framework named "EpiMix" for population-level analysis of DNAme and gene expression. Compared with existing methods, EpiMix showed higher sensitivity in detecting abnormal DNAme that was present in only small patient subsets. We extended the model-based analyses of EpiMix to cis-regulatory elements within protein-coding genes, distal enhancers, and genes encoding microRNAs and long non-coding RNAs (lncRNAs). Using cell-type-specific data from two separate studies, we discover epigenetic mechanisms underlying childhood food allergy and survival-associated, methylation-driven ncRNAs in non-small cell lung cancer.
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Affiliation(s)
- Yuanning Zheng
- Stanford Center for Biomedical Informatics Research (BMIR), Department of Medicine & Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - John Jun
- Stanford Center for Biomedical Informatics Research (BMIR), Department of Medicine & Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Kevin Brennan
- Stanford Center for Biomedical Informatics Research (BMIR), Department of Medicine & Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Olivier Gevaert
- Stanford Center for Biomedical Informatics Research (BMIR), Department of Medicine & Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
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12
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Tarrant I, Finlay BB. Human milk oligosaccharides: potential therapeutic aids for allergic diseases. Trends Immunol 2023:S1471-4906(23)00111-4. [PMID: 37438187 DOI: 10.1016/j.it.2023.06.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 06/08/2023] [Accepted: 06/09/2023] [Indexed: 07/14/2023]
Abstract
Childhood allergy, including asthma, eczema, and food allergies, is a major global health burden, with prevalence increasing dramatically and novel interventions needed. Emerging research suggests that human milk oligosaccharides (HMOs), complex glycans found in breastmilk, have allergy-protective properties, indicating exciting therapeutic potential. This review evaluates current literature on the role of HMOs in allergy, assesses underlying immunological mechanisms, and discusses future research needed to translate findings into clinical implications. HMOs may mediate allergy risk through multiple structure-specific mechanisms, including microbiome modification, intestinal barrier maturation, immunomodulation, and gene regulation. Findings emphasize the importance of breastfeeding encouragement and HMO-supplemented formula milk for high allergy-risk infants. Although further investigation is necessary to determine the most efficacious structures against varying allergy phenotypes and their long-term efficacy, HMOs may represent a promising complementary tool for childhood allergy prevention.
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Affiliation(s)
- Isabel Tarrant
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - B Brett Finlay
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada; Department of Biochemistry, University of British Columbia, Vancouver, BC, Canada.
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13
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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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14
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Imran S, Neeland MR, Martino DJ, Peng S, Koplin J, Dharmage SC, Tang MLK, Sawyer S, Dang T, McWilliam V, Peters RL, Prescott S, Perrett KP, Novakovic B, Saffery R. Epigenomic variability is associated with age-specific naïve CD4 T cell response to activation in infants and adolescents. Immunol Cell Biol 2023; 101:397-411. [PMID: 36760028 PMCID: PMC10952707 DOI: 10.1111/imcb.12628] [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: 04/20/2022] [Revised: 02/07/2023] [Accepted: 02/08/2023] [Indexed: 02/11/2023]
Abstract
Childhood is a critical period of immune development. During this time, naïve CD4 (nCD4) T cells undergo programmed cell differentiation, mediated by epigenetic changes, in response to external stimuli leading to a baseline homeostatic state that may determine lifelong disease risk. However, the ontogeny of epigenetic signatures associated with CD4 T cell activation during key developmental periods are yet to be described. We investigated genome-wide DNA methylation (DNAm) changes associated with nCD4 T activation following 72 h culture in media+anti-CD3/CD28 beads in healthy infants (aged 12 months, n = 18) and adolescents (aged 10-15 years, n = 15). We integrated these data with transcriptomic and cytokine profiling from the same samples. nCD4 T cells from both age groups show similar extensive epigenetic reprogramming following activation, with the majority of genes involved in the T cell receptor signaling pathway associated with differential methylation. Additionally, we identified differentially methylated probes showing age-specific responses, that is, responses in only infants or adolescents, including within a cluster of T cell receptor (TCR) genes. These encoded several TCR alpha joining (TRAJ), and TCR alpha variable (TRAV) genes. Cytokine data analysis following stimulation revealed enhanced release of IFN-γ, IL-2 and IL-10, in nCD4 T cells from adolescents compared with infants. Overlapping differential methylation and cytokine responses identified four probes potentially underpinning these age-specific responses. We show that DNAm in nCD4T cells in response to activation is dynamic in infancy and adolescence, with additional evidence for age-specific effects potentially driving variation in cytokine responses between these ages.
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Affiliation(s)
- Samira Imran
- Murdoch Children's Research Institute, and Department of PaediatricsUniversity of Melbourne, Royal Children's HospitalFlemington RoadParkvilleVICAustralia
| | - Melanie R Neeland
- Murdoch Children's Research Institute, and Department of PaediatricsUniversity of Melbourne, Royal Children's HospitalFlemington RoadParkvilleVICAustralia
| | - David J. Martino
- Wal‐yan Respiratory Research Centre, Telethon Kids InstitutePerthAustralia
- University of Western AustraliaPerthWAAustralia
| | - Stephen Peng
- Murdoch Children's Research Institute, and Department of PaediatricsUniversity of Melbourne, Royal Children's HospitalFlemington RoadParkvilleVICAustralia
| | - Jennifer Koplin
- Murdoch Children's Research Institute, and Department of PaediatricsUniversity of Melbourne, Royal Children's HospitalFlemington RoadParkvilleVICAustralia
| | - Shyamali C Dharmage
- Murdoch Children's Research Institute, and Department of PaediatricsUniversity of Melbourne, Royal Children's HospitalFlemington RoadParkvilleVICAustralia
- Allergy and Lung Health UnitMelbourne School of Population and Global HealthUniversity of MelbourneMelbourneVICAustralia
| | - Mimi LK Tang
- Murdoch Children's Research Institute, and Department of PaediatricsUniversity of Melbourne, Royal Children's HospitalFlemington RoadParkvilleVICAustralia
- Department of Allergy and ImmunologyRoyal Children's HospitalMelbourneVICAustralia
| | - Susan Sawyer
- Murdoch Children's Research Institute, and Department of PaediatricsUniversity of Melbourne, Royal Children's HospitalFlemington RoadParkvilleVICAustralia
- Centre for Adolescent HealthRoyal Children's Hospital MelbourneMelbourneVICAustralia
| | - Thanh Dang
- Murdoch Children's Research Institute, and Department of PaediatricsUniversity of Melbourne, Royal Children's HospitalFlemington RoadParkvilleVICAustralia
| | - Vicki McWilliam
- Murdoch Children's Research Institute, and Department of PaediatricsUniversity of Melbourne, Royal Children's HospitalFlemington RoadParkvilleVICAustralia
- Department of Allergy and ImmunologyRoyal Children's HospitalMelbourneVICAustralia
| | - Rachel L Peters
- Murdoch Children's Research Institute, and Department of PaediatricsUniversity of Melbourne, Royal Children's HospitalFlemington RoadParkvilleVICAustralia
| | - Susan Prescott
- School of MedicineThe University of Western Australia35 Stirling HighwayCrawleyWAAustralia
- Telethon Kids Institute15 Hospital AvenueNedlandsWAAustralia
- Department of ImmunologyPerth Children's Hospital15 Hospital AvenueNedlandsWAAustralia
| | - Kirsten P Perrett
- Murdoch Children's Research Institute, and Department of PaediatricsUniversity of Melbourne, Royal Children's HospitalFlemington RoadParkvilleVICAustralia
- Department of Allergy and ImmunologyRoyal Children's HospitalMelbourneVICAustralia
| | - Boris Novakovic
- Murdoch Children's Research Institute, and Department of PaediatricsUniversity of Melbourne, Royal Children's HospitalFlemington RoadParkvilleVICAustralia
| | - Richard Saffery
- Murdoch Children's Research Institute, and Department of PaediatricsUniversity of Melbourne, Royal Children's HospitalFlemington RoadParkvilleVICAustralia
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15
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Liu S, Yang Y, Zeng L, Wang L, He C, Chen Z, Sun J, Lyu T, Wang M, Chen H, Zhang F. TOX promotes follicular helper T cell differentiation in patients with primary Sjögren's syndrome. Rheumatology (Oxford) 2023; 62:946-957. [PMID: 35713502 DOI: 10.1093/rheumatology/keac304] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/27/2022] [Accepted: 04/19/2022] [Indexed: 02/04/2023] Open
Abstract
OBJECTIVES Whether naive CD4+ T cells are dysregulated and associated with the overactivation of CD4+ T cells in primary SS (pSS) remains unclear. We aimed to explore the role and underlying mechanism of naive CD4+ T cells in pSS. METHODS We examined the activation, proliferation and differentiation of naive CD4+ T cells from pSS patients and healthy controls. Differentially expressed genes were identified using RNA sequencing, and were overexpressed or silenced to determine the gene regulating follicular helper T (Tfh) cells. Assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) with chromatin immunoprecipitation with high-throughput sequencing (ChIP-seq) was performed to explore the epigenetic mechanism. Naive CD4+ T cells were treated with pSS-related cytokines to explore the upstream signalling pathway. RESULTS pSS naive CD4+ T cells had higher potentials of activation, proliferation and differentiation towards Tfh cells. Thymocyte selection-associated high mobility group box protein (TOX) was upregulated in pSS naive CD4+ T cells and promoted T cell activation and Tfh cell polarization. TOX silencing in pSS naive CD4+ T cells downregulated B cell lymphoma 6 (BCL6) expression and altered levels of multiple Tfh-associated genes. ChIP-seq analysis implied that TOX bound to the BCL6 locus, where there were accessible regions found by ATAC-seq. IFN-α induced TOX overexpression, which was attenuated by Janus kinase (JAK) and signal transducer and activator of transcription 1 (STAT1) inhibitors. CONCLUSION Our data suggest that TOX in pSS naive CD4+ T cells is upregulated, which facilitates Tfh cell differentiation. Mechanistically, IFN-α induces TOX overexpression in naive CD4+ T cells through JAK-STAT1 signalling and TOX regulates BCL6 expression. Therefore, IFN-α-JAK-STAT1 signalling and TOX might be potential therapeutic targets in pSS.
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Affiliation(s)
- Suying Liu
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College.,Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education
| | - Yanlei Yang
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College.,Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education
| | - Liuting Zeng
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College.,Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education
| | - Li Wang
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College.,Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education
| | - Chengmei He
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College.,Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education
| | - Zhilei Chen
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College.,Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education
| | - Jinlei Sun
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College.,Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education
| | - Taibiao Lyu
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College.,Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education
| | - Mu Wang
- Department of Stomatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hua Chen
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College.,Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education
| | - Fengchun Zhang
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College.,Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education
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16
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Zheng Y, Jun J, Brennan K, Gevaert O. EpiMix: an integrative tool for epigenomic subtyping using DNA methylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.03.522660. [PMID: 36711917 PMCID: PMC9881910 DOI: 10.1101/2023.01.03.522660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
DNA methylation (DNAme) is a major epigenetic factor influencing gene expression with alterations leading to cancer, immunological, and cardiovascular diseases. Recent technological advances enable genome-wide quantification of DNAme in large human cohorts. So far, existing methods have not been evaluated to identify differential DNAme present in large and heterogeneous patient cohorts. We developed an end-to-end analytical framework named "EpiMix" for population-level analysis of DNAme and gene expression. Compared to existing methods, EpiMix showed higher sensitivity in detecting abnormal DNAme that was present in only small patient subsets. We extended the model-based analyses of EpiMix to cis-regulatory elements within protein-coding genes, distal enhancers, and genes encoding microRNAs and lncRNAs. Using cell-type specific data from two separate studies, we discovered novel epigenetic mechanisms underlying childhood food allergy and survival-associated, methylation-driven non-coding RNAs in non-small cell lung cancer.
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Affiliation(s)
- Yuanning Zheng
- Stanford Center for Biomedical Informatics Research (BMIR), Department of Medicine & Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - John Jun
- Stanford Center for Biomedical Informatics Research (BMIR), Department of Medicine & Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Kevin Brennan
- Stanford Center for Biomedical Informatics Research (BMIR), Department of Medicine & Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Olivier Gevaert
- Stanford Center for Biomedical Informatics Research (BMIR), Department of Medicine & Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
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17
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Differential CpG DNA methylation of peripheral B cells, CD4 + T cells, and salivary gland tissues in IgG4-related disease. Arthritis Res Ther 2023; 25:4. [PMID: 36609529 PMCID: PMC9824958 DOI: 10.1186/s13075-022-02978-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 12/12/2022] [Indexed: 01/09/2023] Open
Abstract
OBJECTIVES Immunoglobulin-G4-related disease (IgG4-RD) is a distinct systemic autoimmune-mediated disease manifesting as chronic inflammation and tissue fibrosis. Since the role of DNA methylation in the pathogenesis of IgG4-RD is still unclear, we conduct this study to investigate epigenetic modifications in IgG4-RD. METHODS A genome-wide DNA methylation study was conducted with B cells, CD4+ T cells, and salivary gland tissues from IgG4-RD patients and matched controls by using the Illumina HumanMethylation 850K BeadChip. We further performed pyrosequencing and immunohistochemistry assays to validate the methylation status of some targets of interest. RESULTS We identified differentially methylated CpG sites including 44 hypomethylated and 166 hypermethylated differentially methylated probes (DMPs) in B cells and 260 hypomethylated and 112 hypermethylated DMPs in CD4+ T cells from 10 IgG4-RD patients compared with 10 healthy controls. We also identified 36945 hypomethylated and 78380 hypermethylated DMPs in salivary gland tissues of 4 IgG4-RD patients compared with 4 controls. DPM2 (cg21181453), IQCK (cg10266221), and ABCC13 (cg05699681, cg04985582) were hypermethylated and MBP (cg18455083) was hypomethylated in B cells, CD4+ T cells, and salivary gland tissues of IgG4-RD patients. We also observed the hypomethylated HLA-DQB2 in CD4+ T cells from IgG4-RD patients. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of DMPs in salivary gland tissues of IgG4-RD patients revealed enrichment of pathways involved in the regulation of immune cell responses and fibrosis. CONCLUSION This is the first DNA methylation study in peripheral B cells, CD4+ T cells, and salivary gland tissues from IgG4-RD patients. Our findings highlighted the role of epigenetic modification of DNA methylation and identified several genes and pathways possibly involved in IgG4-RD pathogenesis.
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18
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Kazmi W, Berin MC. Oral tolerance and oral immunotherapy for food allergy: Evidence for common mechanisms? Cell Immunol 2023; 383:104650. [PMID: 36543052 DOI: 10.1016/j.cellimm.2022.104650] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/21/2022] [Accepted: 11/26/2022] [Indexed: 12/05/2022]
Abstract
Food allergies affect up to 10% of the US population, can be life-threatening, and have a significant negative impact on quality of life. Delayed dietary introduction of foods in childhood can hinder the induction of oral tolerance, an active regulatory response to foods that prevents the development of food allergy. Some children outgrow their food allergies naturally, while many others have persistent, lifelong food allergy for which there are few therapeutic options. Oral immunotherapy (OIT) is a therapeutic approach of giving increasing amounts of food to attempt to desensitize the allergic individual. In this review, we focus on the immune mechanisms common to oral tolerance and response to oral immunotherapy, with the objective of determining whether true tolerance can be achieved after food allergy has been established.
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Affiliation(s)
- Wajiha Kazmi
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - M Cecilia Berin
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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19
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Management of Adult Patients with Gastrointestinal Symptoms from Food Hypersensitivity-Narrative Review. J Clin Med 2022; 11:jcm11247326. [PMID: 36555942 PMCID: PMC9784954 DOI: 10.3390/jcm11247326] [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: 10/16/2022] [Revised: 11/29/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022] Open
Abstract
The incidence of food hypersensitivity has increased dramatically over the years not only among children but also in adults. Adult patients are usually less suspected of food hypersensitivity symptoms since food allergies are more typical for small children, with a tendency to outgrow the condition. The aim of this article is to increase awareness of hypersensitivity to food symptoms and their diagnosis and treatment possibilities among gastroenterologists and other health care professionals dealing with this type of patient. Symptoms of many gastrointestinal disorders, especially functional, may be driven by different types of mechanisms, and food intolerance or allergy should be considered as a potential cause. This article presents the current understanding of the epidemiology, diagnosis and treatment of immune- and non-immune-mediated food-induced diseases. Diagnosis of food hypersensitivity is based mainly on medical history, different types of sensitivity tests, e.g., hydrogen breath test, specific IgE (sIgE) serum concentration, tissue eosinophil count, skin tests and oral food challenges considered as a "gold standard" for food allergy. Elimination diet and pharmacologic treatment for allergy symptoms are first-line therapies. Eosinophilic gastrointestinal diseases are often caused by non-IgE-mediated food allergies, require endoscopic biopsy samples to confirm diagnosis and proper elimination diet often combined with steroids or proton pump inhibitor agents for treatment. Mast cell activation syndrome (MCAS) derives from pathologic reaction of mast cells with increased tryptase serum level as a marker. Symptoms may occur in the digestive, respiratory, skin, neurologic and cardiovascular system. Treatment is based on histamine type 1, type 2 (H1, H2) receptor antagonists and other mast cell stabilizing agents. Carbohydrate intolerances are the most common type of food hypersensitivity in adult patients, and an elimination diet is effective for reducing symptoms. Food additives hypersensitivity remains difficult to diagnose, but use of a diet low in chemical substances alleviates symptoms and helps to diagnose the triggering factors.
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20
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Long Non-Coding RNAs Expressed in the Peanut Allergy for Understanding the Pathophysiology of Peanut Allergy Rat Model. Foods 2022; 11:foods11233760. [PMID: 36496569 PMCID: PMC9740276 DOI: 10.3390/foods11233760] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/11/2022] [Accepted: 11/18/2022] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Peanut allergy (PA) has become a clinical and public health problem, which is mainly regulated by genetics, immune responses, and environmental factors. Diagnosis and treatment for PA have always remained huge challenges due to its multiple triggers. Studies have shown that long non-coding RNAs (lncRNAs) play a critical role in the development of allergic diseases. METHOD AND RESULTS In the current study, we examined the plasma lncRNA expression profiles of peanut allergy Brown Norway rats and healthy controls and 496 differently expressed lncRNAs were identified, including 411 up-regulated genes and 85 down-regulated genes. We screened 8 lncRNAs based on the candidate principle and the candidates were verified in individual samples by quantitative real-time PCR. Then, the four lncRNA-based diagnostic model was established by least absolute shrinkage and selection operator (LASSO) and logistic regression, which was proved by area under the receiver operating characteristic curve (AUC). CONCLUSIONS In summary, we assessed the correlation between lncRNA expression levels and the diagnosis of peanut allergy, which may perform a vital role in guiding the management of peanut allergy.
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21
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Imran S, Neeland MR, Peng S, Vlahos A, Martino D, Dharmage SC, Tang MLK, Sawyer S, Dang TD, McWilliam V, Peters RL, Koplin JJ, Perrett KP, Novakovic B, Saffery R. Immuno-epigenomic analysis identifies attenuated interferon responses in naïve CD4 T cells of adolescents with peanut and multi-food allergy. Pediatr Allergy Immunol 2022; 33:e13890. [PMID: 36433861 DOI: 10.1111/pai.13890] [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: 01/26/2022] [Revised: 10/26/2022] [Accepted: 11/02/2022] [Indexed: 11/27/2022]
Abstract
BACKGROUND IgE-mediated food allergies have been linked to suboptimal naïve CD4 T (nCD4T) cell activation in infancy, underlined by epigenetic and transcriptomic variation. Similar attenuated nCD4T cell activation in adolescents with food allergy have also been reported, but these are yet to be linked to specific epigenetic or transcriptional changes. METHODS We generated genome-wide DNA methylation data in purified nCD4 T cells at quiescence and following activation in a cohort of adolescents (aged 10-15 years old) with peanut allergy (peanut only or peanut + ≥1 additional food allergy) (FA, n = 29), and age-matched non-food allergic controls (NA, n = 18). Additionally, we assessed transcriptome-wide gene expression and cytokine production in these cells following activation. RESULTS We found widespread changes in DNA methylation in both NA and FA nCD4T cells in response to activation, associated with the T cell receptor signaling pathway. Adolescents with FA exhibit unique DNA methylation signatures at quiescence and post-activation at key genes involved in Th1/Th2 differentiation (RUNX3, RXRA, NFKB1A, IL4R), including a differentially methylated region (DMR) at the TNFRSF6B promoter, linked to Th1 proliferation. Combined analysis of DNA methylation, transcriptomic data and cytokine output in the same samples identified an attenuated interferon response in nCD4T cells from FA individuals following activation, with decreased expression of several interferon genes, including IFN-γ and a DMR at a key downstream gene, BST2. CONCLUSION We find that attenuated nCD4T cell responses from adolescents with food allergy are associated with specific epigenetic variation, including disruption of interferon responses, indicating dysregulation of key immune pathways that may contribute to a persistent FA phenotype. However, we recognize the small sample size, and the consequent restraint on reporting adjusted p-value statistics as limitations of the study. Further study is required to validate these findings.
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Affiliation(s)
- Samira Imran
- Murdoch Children's Research Institute, and Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Melanie R Neeland
- Murdoch Children's Research Institute, and Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Stephen Peng
- Murdoch Children's Research Institute, and Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Amanda Vlahos
- Murdoch Children's Research Institute, and Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
| | - David Martino
- Murdoch Children's Research Institute, and Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia.,Telethon Kids Institute, University of Western, Perth, Nedlands, Australia
| | - Shyamali C Dharmage
- Murdoch Children's Research Institute, and Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia.,Allergy and Lung Health Unit, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Mimi L K Tang
- Murdoch Children's Research Institute, and Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia.,Department of Allergy and Immunology, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Susan Sawyer
- Murdoch Children's Research Institute, and Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia.,Centre for Adolescent Health, Royal Children's Hospital Melbourne, Melbourne, Victoria, Australia
| | - Thanh D Dang
- Murdoch Children's Research Institute, and Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Vicki McWilliam
- Murdoch Children's Research Institute, and Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia.,Department of Allergy and Immunology, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Rachel L Peters
- Murdoch Children's Research Institute, and Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Jennifer J Koplin
- Murdoch Children's Research Institute, and Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Kirsten P Perrett
- Murdoch Children's Research Institute, and Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia.,Department of Allergy and Immunology, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Boris Novakovic
- Murdoch Children's Research Institute, and Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Richard Saffery
- Murdoch Children's Research Institute, and Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Victoria, Australia
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22
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Ashley SE, Jones AC, Anderson D, Holt PG, Bosco A, Tang MLK. Remission of peanut allergy is associated with rewiring of allergen-driven T helper 2-related gene networks. Allergy 2022; 77:3015-3027. [PMID: 35615783 PMCID: PMC9790273 DOI: 10.1111/all.15324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 02/27/2022] [Accepted: 03/15/2022] [Indexed: 01/28/2023]
Abstract
BACKGROUND The immunological changes underpinning acquisition of remission (also called sustained unresponsiveness) following food immunotherapy remain poorly defined. Limited access to effective therapies and biosamples from treatment responders has prevented progress. Probiotic peanut oral immunotherapy is highly effective at inducing remission, providing an opportunity to investigate immune changes. METHODS Using a systems biology approach, we examined gene co-expression network patterns in peanut-specific CD4+ T cell responses before and after probiotic and peanut oral immunotherapy in subjects enrolled in the PPOIT-001 randomized trial: Responders who attained remission (n = 16), placebo-treated who remained allergic (n = 16). RESULTS Acquisition of remission was associated with rewiring of gene network patterns, which was characterized by integration of T helper 2 and interferon signalling modules, markedly reduced T helper 2 gene connectivity, and shutdown in co-expression activity between T helper 2 effectors and cell cycle regulators. CONCLUSION The immunological changes underlying remission following peanut oral immunotherapy are mediated by reprogramming of T helper 2-associated gene networks in the CD4+ T cell compartment. Findings provide insight into immune mechanisms driving the acquisition of remission following oral immunotherapy, paving the way for the development of improved approaches to induce remission/sustained unresponsiveness in patients with food allergy.
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Affiliation(s)
- Sarah E. Ashley
- Allergy ImmunologyMurdoch Children’s Research InstituteMelbourneVictoriaAustralia,Department of PaediatricsThe University of MelbourneMelbourneVictoriaAustralia,The Royal Children’s HospitalMelbourneVictoriaAustralia
| | - Anya C. Jones
- Telethon Kids InstitutePerthWestern AustraliaAustralia,The University of Western AustraliaPerthWestern AustraliaAustralia
| | - Denise Anderson
- Telethon Kids InstitutePerthWestern AustraliaAustralia,The University of Western AustraliaPerthWestern AustraliaAustralia
| | - Patrick G. Holt
- Telethon Kids InstitutePerthWestern AustraliaAustralia,The University of Western AustraliaPerthWestern AustraliaAustralia
| | - Anthony Bosco
- Telethon Kids InstitutePerthWestern AustraliaAustralia,The University of Western AustraliaPerthWestern AustraliaAustralia
| | - Mimi L. K. Tang
- Allergy ImmunologyMurdoch Children’s Research InstituteMelbourneVictoriaAustralia,Department of PaediatricsThe University of MelbourneMelbourneVictoriaAustralia,The Royal Children’s HospitalMelbourneVictoriaAustralia
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23
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Davis EC, Jackson CM, Ting T, Harizaj A, Järvinen KM. Predictors and biomarkers of food allergy and sensitization in early childhood. Ann Allergy Asthma Immunol 2022; 129:292-300. [PMID: 35490857 DOI: 10.1016/j.anai.2022.04.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/12/2022] [Accepted: 04/14/2022] [Indexed: 12/23/2022]
Abstract
OBJECTIVE To review existing literature on the early risk factors for and biomarkers of food allergy (FA) and food sensitization (FS) and highlight opportunities for future research that will further the understanding of FA pathogenesis in infancy and toddlerhood. DATA SOURCES PubMed search of English-language articles related to FA and atopic disease. STUDY SELECTIONS Human studies with outcomes related to FA, FS, and other atopic disease in childhood were selected and reviewed. Studies published after 2015 were prioritized. RESULTS The prevalence of FA has greatly increased in recent decades and is now a global public health concern. A complex network of early life risk factors has been associated with development of FA and FS in childhood. Food allergy has a genetic component, but recent evidence suggests that interactions between risk alleles and other environmental exposures are important for disease pathogenesis, potentially through epigenetic mechanisms. Lifestyle factors, such as delivery mode, antibiotic use, and pet exposure also influence FA risk, which may be through their effect on the early life gut microbiome. How these early life risk factors, along with route and timing of antigen exposure, collectively target the developing immune system remains an ongoing and important area of study. CONCLUSION The current body of evidence emphasizes the first 1000 days of life as a critical period for FA development. More observational studies and adequately powered clinical trials spanning early pregnancy through childhood are needed to identify novel biomarkers and risk factors that can predict susceptibility toward or protection against FA.
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Affiliation(s)
- Erin C Davis
- Division of Allergy and Immunology, Center for Food Allergy, Department of Pediatrics, University of Rochester School of Medicine and Dentistry, Golisano Children's Hospital, Rochester, New York
| | - Courtney M Jackson
- Division of Allergy and Immunology, Center for Food Allergy, Department of Pediatrics, University of Rochester School of Medicine and Dentistry, Golisano Children's Hospital, Rochester, New York
| | - Tiffany Ting
- Division of Allergy and Immunology, Center for Food Allergy, Department of Pediatrics, University of Rochester School of Medicine and Dentistry, Golisano Children's Hospital, Rochester, New York
| | - Albana Harizaj
- Division of Allergy and Immunology, Center for Food Allergy, Department of Pediatrics, University of Rochester School of Medicine and Dentistry, Golisano Children's Hospital, Rochester, New York; Division of Allergy, Immunology, and Rheumatology, Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, New York
| | - Kirsi M Järvinen
- Division of Allergy and Immunology, Center for Food Allergy, Department of Pediatrics, University of Rochester School of Medicine and Dentistry, Golisano Children's Hospital, Rochester, New York; Division of Allergy, Immunology, and Rheumatology, Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, New York; Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York.
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24
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Inhibition effect of PPAR-γ signaling on mast cell-mediated allergic inflammation through down-regulation of PAK1/ NF-κB activation. Int Immunopharmacol 2022; 108:108692. [DOI: 10.1016/j.intimp.2022.108692] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/17/2022] [Accepted: 03/07/2022] [Indexed: 12/14/2022]
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25
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Ponsonby AL, Collier F, O'Hely M, Tang MLK, Ranganathan S, Gray L, Morwitch E, Saffery R, Burgner D, Dwyer T, Sly PD, Harrison LC, Vuillermin P. Household size, T regulatory cell development, and early allergic disease: a birth cohort study. Pediatr Allergy Immunol 2022; 33:e13810. [PMID: 35754137 PMCID: PMC9545943 DOI: 10.1111/pai.13810] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 05/05/2022] [Accepted: 05/19/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND Children born to larger households have less allergic disease. T regulatory cell (Treg) development may be a relevant mechanism, but this has not been studied longitudinally. OBJECTIVE We aim to (i) describe how prenatal and postnatal environmental factors are associated with Treg development and (ii) investigate whether serial Treg measures predict allergic outcomes at 1 year of age. METHODS A birth cohort (n = 1074) with information on prenatal and postnatal early life factors. Both naïve Treg (nTreg) and activated Treg (aTreg) cell populations (as a proportion of CD4+ T cells) were available in 463 infants at birth (cord blood), 600 at 6 months, and 675 at 12 months. 191 infants had serial measures. Measures of allergic status at 12 months were polysensitization (sensitization to 2 or more allergens), clinically proven food allergy, atopic eczema, and atopic wheeze. RESULTS Infants born to larger households (3 or more residents) had higher longitudinal nTreg proportions over the first postnatal year with a mean difference (MD) of 0.67 (95% CI 0.30-1.04)%. Higher nTreg proportions at birth were associated with a reduced risk of infant allergic outcomes. Childcare attendance and breastfeeding were associated with higher longitudinal nTreg proportions (MD 0.48 (95% CI 0.08-0.80)%. CONCLUSION Multiple prenatal and postnatal microbial factors are associated with nTreg and aTreg development. Larger household size was associated with higher nTreg at birth which in turn was associated with reduced allergic sensitization and disease at 12 months of age.
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Affiliation(s)
- Anne-Louise Ponsonby
- The Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia.,Murdoch Children's Research Institute, Royal Children's Hospital, University of Melbourne, Parkville, Victoria, Australia
| | - Fiona Collier
- School of Medicine, Deakin University, Geelong, Victoria, Australia
| | - Martin O'Hely
- Murdoch Children's Research Institute, Royal Children's Hospital, University of Melbourne, Parkville, Victoria, Australia.,School of Medicine, Deakin University, Geelong, Victoria, Australia
| | - Mimi L K Tang
- Murdoch Children's Research Institute, Royal Children's Hospital, University of Melbourne, Parkville, Victoria, Australia
| | - Sarath Ranganathan
- Murdoch Children's Research Institute, Royal Children's Hospital, University of Melbourne, Parkville, Victoria, Australia
| | - Lawrence Gray
- School of Medicine, Deakin University, Geelong, Victoria, Australia.,Barwon Health, Geelong, Victoria, Australia
| | - Ellen Morwitch
- The Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia.,National Centre of Epidemiology and Population Health, Australian National University, Canberra, Australia
| | - Richard Saffery
- Murdoch Children's Research Institute, Royal Children's Hospital, University of Melbourne, Parkville, Victoria, Australia
| | - David Burgner
- Murdoch Children's Research Institute, Royal Children's Hospital, University of Melbourne, Parkville, Victoria, Australia
| | - Terence Dwyer
- Murdoch Children's Research Institute, Royal Children's Hospital, University of Melbourne, Parkville, Victoria, Australia.,The George Institute for Global Health, Oxford University, Oxford, UK
| | - Peter D Sly
- Murdoch Children's Research Institute, Royal Children's Hospital, University of Melbourne, Parkville, Victoria, Australia.,University of Queensland, South Brisbane, Queensland, Australia
| | | | - Peter Vuillermin
- Murdoch Children's Research Institute, Royal Children's Hospital, University of Melbourne, Parkville, Victoria, Australia.,School of Medicine, Deakin University, Geelong, Victoria, Australia.,Barwon Health, Geelong, Victoria, Australia
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26
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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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27
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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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28
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Eapen AA, Parameswaran S, Forney C, Edsall LE, Miller D, Donmez O, Dunn K, Lu X, Granitto M, Rowden H, Magier AZ, Pujato M, Chen X, Kaufman K, Bernstein DI, Devonshire AL, Rothenberg ME, Weirauch MT, Kottyan LC. Epigenetic and transcriptional dysregulation in CD4+ T cells in patients with atopic dermatitis. PLoS Genet 2022; 18:e1009973. [PMID: 35576187 PMCID: PMC9135339 DOI: 10.1371/journal.pgen.1009973] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 05/26/2022] [Accepted: 04/20/2022] [Indexed: 12/30/2022] Open
Abstract
Atopic dermatitis (AD) is one of the most common skin disorders among children. Disease etiology involves genetic and environmental factors, with 29 independent AD risk loci enriched for risk allele-dependent gene expression in the skin and CD4+ T cell compartments. We investigated the potential epigenetic mechanisms responsible for the genetic susceptibility of CD4+ T cells. To understand the differences in gene regulatory activity in peripheral blood T cells in AD, we measured chromatin accessibility (an assay based on transposase-accessible chromatin sequencing, ATAC-seq), nuclear factor kappa B subunit 1 (NFKB1) binding (chromatin immunoprecipitation with sequencing, ChIP-seq), and gene expression levels (RNA-seq) in stimulated CD4+ T cells from subjects with active moderate-to-severe AD, as well as in age-matched non-allergic controls. Open chromatin regions in stimulated CD4+ T cells were highly enriched for AD genetic risk variants, with almost half of the AD risk loci overlapping AD-dependent ATAC-seq peaks. AD-specific open chromatin regions were strongly enriched for NF-κB DNA-binding motifs. ChIP-seq identified hundreds of NFKB1-occupied genomic loci that were AD- or control-specific. As expected, the AD-specific ChIP-seq peaks were strongly enriched for NF-κB DNA-binding motifs. Surprisingly, control-specific NFKB1 ChIP-seq peaks were not enriched for NFKB1 motifs, but instead contained motifs for other classes of human transcription factors, suggesting a mechanism involving altered indirect NFKB1 binding. Using DNA sequencing data, we identified 63 instances of altered genotype-dependent chromatin accessibility at 36 AD risk variant loci (30% of AD risk loci) that might lead to genotype-dependent gene expression. Based on these findings, we propose that CD4+ T cells respond to stimulation in an AD-specific manner, resulting in disease- and genotype-dependent chromatin accessibility alterations involving NFKB1 binding.
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Affiliation(s)
- Amy A. Eapen
- Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Division of Allergy and Clinical Immunology, Henry Ford Health System, Detroit, Michigan, United States of America
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Sreeja Parameswaran
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Carmy Forney
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Lee E. Edsall
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Daniel Miller
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Omer Donmez
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Katelyn Dunn
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Xiaoming Lu
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Marissa Granitto
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Hope Rowden
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Adam Z. Magier
- Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Mario Pujato
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Xiaoting Chen
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Kenneth Kaufman
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- Cincinnati Veterans Administration, Cincinnati, Ohio, United States of America
| | - David I. Bernstein
- Division of Immunology, Allergy, and Rheumatology, University of Cincinnati, College of Medicine, Cincinnati, Ohio, United States of America
| | - Ashley L. Devonshire
- Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Marc E. Rothenberg
- Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Matthew T. Weirauch
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Leah C. Kottyan
- Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
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29
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A genome-wide association meta-analysis identifies new eosinophilic esophagitis loci. J Allergy Clin Immunol 2022; 149:988-998. [PMID: 34506852 PMCID: PMC9579995 DOI: 10.1016/j.jaci.2021.08.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 08/24/2021] [Accepted: 08/31/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND Eosinophilic esophagitis (EoE) is a chronic inflammatory disorder of the esophagus marked by eosinophilic infiltration. Cumulative evidence indicates that the risk of EoE involves the complex interplay of both genetic and environmental factors. Because only a few genetic loci have been identified in EoE, the genetic underpinning of EoE remains largely elusive. OBJECTIVE We sought to identify genetic loci associated with EoE. METHODS Four EoE cohorts were genotyped using the Illumina single nucleotide polymorphism array platform, totaling 1,930 cases and 13,634 controls of European ancestry. Genotype imputation was performed with the Michigan Imputation Server using the Trans-Omics for Precision Medicine reference panel including whole-genome sequencing data from more than 100,000 individuals. Meta-analysis was conducted to identify potential novel genetic loci associated with EoE. RESULTS Our study identified 11 new genome-wide significant loci, of which 6 are common variant loci, including 5q31.1 (rs2106984, P = 4.16 × 10-8; odds ratio [OR], 1.26, RAD50), 15q22.2 (rs2279293, P = 1.23 × 10-10; OR, 0.69, RORA), and 15q23 (rs56062135, P = 2.91 × 10-11; OR, 1.29, SMAD3), which have been previously associated with allergic conditions. Interestingly, a low-frequency synonymous mutation within the MATN2 gene was identified as the most significant single nucleotide polymorphism at the 8q22.1 locus. We also identified 5 sex-specific loci in the EoE cases, including an inflammatory bowel disease-associated locus at 9p24.1 (rs62541556, P = 4.4 × 10-8; OR, 1.11, JAK2). CONCLUSIONS Our findings demonstrate shared genetic underpinnings between EoE and other immune-mediated diseases and provide novel candidate genes for therapeutic target identification and prioritization.
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30
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Lee KH, Bosco A, O'Sullivan M, Song Y, Metcalfe J, Yu K, Mullins BJ, Loh R, Zhang G. Identifying gene network patterns and associated cellular immune responses in children with or without nut allergy. World Allergy Organ J 2022; 15:100631. [PMID: 35228856 PMCID: PMC8844301 DOI: 10.1016/j.waojou.2022.100631] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 11/23/2021] [Accepted: 01/18/2022] [Indexed: 11/17/2022] Open
Abstract
Background Although evidence suggests that the immune system plays a key role in the pathophysiology of nut allergy, the precise immunological mechanisms of nut allergy have not been systematically investigated. The aim of the present study was to identify gene network patterns and associated cellular immune responses in children with or without nut allergy. Methods Transcriptome profiling of whole blood cells was compared between children with and without nut allergy. Three genes were selected to be validated on a larger cohort of samples (n = 86) by reverse transcription-polymerase chain reactions (RT-qPCR). The composition of immune cells was inferred from the transcriptomic data using the CIBERSORTx algorithm. A co-expression network was constructed employing weighted gene co-expression network analysis (WGCNA) on the top 5000 most variable transcripts. The modules were interrogated with pathway analysis tools (InnateDB) and correlated with clinical phenotypes and cellular immune responses. Results Proportions of neutrophils were positively correlated and CD4+ T-cells and regulatory T-cells (Tregs) were negatively correlated with modules of nut allergy. We also identified 2 upregulated genes, namely Interferon Induced With Helicase C Domain 1 (IFIH1), DNA damage-regulated autophagy modulator 1 (DRAM1) and a downregulated gene Zinc Finger Protein 512B (ZNF512B) as hub genes for nut allergy. Further pathway analysis showed enrichment of type 1 interferon signalling in nut allergy. Conclusions Our findings suggest that upregulation of type 1 interferon signalling and neutrophil responses and downregulation of CD4+ T-cells and Tregs are features of the pathogenesis of nut allergy.
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Affiliation(s)
- Khui Hung Lee
- School of Public Health, Curtin University of Technology, Bentley, 6102, Western Australia, Australia
| | - Anthony Bosco
- Telethon Kids Institute, University of Western Australia, Crawley, 6000, Western Australia, Australia
| | - Michael O'Sullivan
- Department of Immunology, Perth Children's Hospital, Nedlands, 6009, Western Australia, Australia
| | - Yong Song
- The Menzies Institute for Medical Research, University of Tasmania, Hobart, 7000, Tasmania, Australia
| | - Jessica Metcalfe
- Department of Immunology, Perth Children's Hospital, Nedlands, 6009, Western Australia, Australia
| | - Kan Yu
- School of Science, Edith Cowan University, Joondalup, 6027, Western Australia, Australia
| | - Benjamin J. Mullins
- School of Public Health, Curtin University of Technology, Bentley, 6102, Western Australia, Australia
| | - Richard Loh
- Department of Immunology, Perth Children's Hospital, Nedlands, 6009, Western Australia, Australia
| | - Guicheng Zhang
- School of Public Health, Curtin University of Technology, Bentley, 6102, Western Australia, Australia
- Curtin Health Innovation Research Institute, Curtin University, Bentley, 6102, Western Australia, Australia
- Infection and Immunity, School of Biomedical Sciences, University of Western Australia, Crawley, 6000, Western Australia, Australia
- Corresponding author. School of Public Health, Curtin University of Technology, Kent St, Bentley, 6102, Western Australia, Australia.
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31
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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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32
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Wisgrill L, Werner P, Fortino V, Fyhrquist N. AIM in Allergy. Artif Intell Med 2022. [DOI: 10.1007/978-3-030-64573-1_90] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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33
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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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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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Ming Zhuo C, Liu C, Srivastava KD, Lin A, Lazarski C, Wang L, Maskey A, Song Y, Chen X, Yang N, Zambrano L, Bushko R, Nowak-Wegrzyn A, Cox A, Liu Z, Huang W, Dunkin D, Miao M, Li XM. Anti-IgE Effect of Small-Molecule-Compound Arctigenin on Food Allergy in association with a Distinct Transcriptome Profile. Clin Exp Allergy 2021; 52:250-264. [PMID: 34757674 DOI: 10.1111/cea.14048] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 10/28/2021] [Indexed: 11/30/2022]
Abstract
BACKGROUND Excessive production of IgE plays a major role in the pathology of food allergy. In an attempt to identify anti-IgE natural products, Arctium Lappa was one of the most effective herbs among approximately 300 screened medicinal herbs. However, little is known about its anti-IgE compounds. OBJECTIVE To identify compounds from Arctium Lappa for targeted therapy on IgE production and explore their underlying mechanisms. METHODS Liquid-liquid extraction and column chromatographic methods were used to purify the compounds. IgE inhibitory effects were determined on IgE producing human myeloma U266 cells, peanut-allergic murine model, and PBMCs from food-allergic patients. Genes involved in IgE inhibition in PBMCs were studied by RNA sequencing. RESULTS The main compounds isolated were identified as arctiin and arctigenin. Both compounds significantly inhibited IgE production in U266 cells, with arctigenin the most potent (IC50=5.09μg/mL). Arctigenin (at a dose of 13.3 mg/kg) markedly reduced peanut-specific IgE levels, blocked hypothermia and histamine release in a peanut-allergic mouse model. Arctigenin also significantly reduced IgE production and Th2 cytokines (IL5, IL13) by PBMCs. We found 479 differentially expressed genes in PBMCs with arctigenin treatment (p<0.001 and fold-change ≥1.5), involving 24 gene ontology terms (p<0.001, FDR <0.05); cell division was the most significant. Eleven genes including UBE2C and BCL6 were validated by qPCR. CONCLUSION Arctigenin markedly inhibited IgE production in U266 cells, peanut allergic murine model and PBMCs from allergic patients by down-regulating cell division, cell cycle-related genes and up-regulating anti-inflammatory factors.
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Affiliation(s)
- Cao Ming Zhuo
- Academy of Chinese Medicine Science, Henan University of Chinese Medicine, Zhengzhou, Henan, 450000, China
| | - Changda Liu
- Academy of Chinese Medicine Science, Henan University of Chinese Medicine, Zhengzhou, Henan, 450000, China.,Pediatric Department, Icahn School of Medicine at Mount Sinai, New York, New York, 10029, USA
| | - Kamal D Srivastava
- Department of Microbiology and Immunology, New York Medical College, New York, NY, 10595, USA.,General Nutraceutical Technology LLC, Elmsford, NY, 10523, USA
| | - Adora Lin
- Center for Cancer and Immunology Research, Children's National Research Institute, Washington, DC, 20010, USA
| | - Christopher Lazarski
- Center for Cancer and Immunology Research, Children's National Research Institute, Washington, DC, 20010, USA
| | - Lu Wang
- Center for Cancer and Immunology Research, Children's National Research Institute, Washington, DC, 20010, USA
| | - Anish Maskey
- Department of Microbiology and Immunology, New York Medical College, New York, NY, 10595, USA
| | - Ying Song
- Academy of Chinese Medicine Science, Henan University of Chinese Medicine, Zhengzhou, Henan, 450000, China.,Pediatric Department, Icahn School of Medicine at Mount Sinai, New York, New York, 10029, USA
| | - Xiaoke Chen
- Pediatric Department, Icahn School of Medicine at Mount Sinai, New York, New York, 10029, USA.,Department of Pulmonary and Critical Care Medicine, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518033, China
| | - Nan Yang
- Department of Microbiology and Immunology, New York Medical College, New York, NY, 10595, USA.,General Nutraceutical Technology LLC, Elmsford, NY, 10523, USA
| | - Linda Zambrano
- Pediatric Department, Icahn School of Medicine at Mount Sinai, New York, New York, 10029, USA
| | - Renna Bushko
- Pediatric Department, Icahn School of Medicine at Mount Sinai, New York, New York, 10029, USA
| | - Anna Nowak-Wegrzyn
- Allergy and Immunology, Department of Pediatrics, Hassenfeld Children's Hospital, New York University Grossman School of Medicine, New York, NY, 10029, USA.,Department of Pediatrics, Gastroenterology and Nutrition, Collegium Medicum, University of Warmia and Mazury, Olsztyn, Poland
| | - Amanda Cox
- Pediatric Department, Icahn School of Medicine at Mount Sinai, New York, New York, 10029, USA
| | - Zhigang Liu
- Department of Immunology, the First Affiliated Hospital of Shen Zhen University, Shenzhen, China, 518116
| | - Weihua Huang
- Department of Pathology, New York Medical College, New York, NY, 10595, USA
| | - David Dunkin
- Pediatric Department, Icahn School of Medicine at Mount Sinai, New York, New York, 10029, USA
| | - Mingsan Miao
- Academy of Chinese Medicine Science, Henan University of Chinese Medicine, Zhengzhou, Henan, 450000, China
| | - Xiu-Min Li
- Department of Microbiology and Immunology, New York Medical College, New York, NY, 10595, USA.,Department of Otolaryngology, New York Medical College, New York, NY, 10595, USA
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Lecamwasam A, Novakovic B, Meyer B, Ekinci EI, Dwyer KM, Saffery R. DNA methylation profiling identifies epigenetic differences between early versus late stages of diabetic chronic kidney disease. Nephrol Dial Transplant 2021; 36:2027-2038. [PMID: 33146725 DOI: 10.1093/ndt/gfaa226] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND We investigated a cross-sectional epigenome-wide association study of patients with early and late diabetes-associated chronic kidney disease (CKD) to identify possible epigenetic differences between the two groups as well as changes in methylation across all stages of diabetic CKD. We also evaluated the potential of using a panel of identified 5'-C-phosphate-G-3' (CpG) sites from this cohort to predict the progression of diabetic CKD. METHODS This cross-sectional study recruited 119 adults. DNA was extracted from blood using the Qiagen QIAampDNA Mini Spin Kit. Genome-wide methylation analysis was performed using Illumina Infinium MethylationEPIC BeadChips (HM850K). Intensity data files were processed and analysed using the minfi and MissMethyl packages for R. We examined the degree of methylation of CpG sites in early versus late diabetic CKD patients for CpG sites with an unadjusted P-value <0.01 and an absolute change in methylation of 5% (n = 239 CpG sites). RESULTS Hierarchical clustering of the 239 CpG sites largely separated the two groups. A heat map for all 239 CpG sites demonstrated distinct methylation patterns in the early versus late groups, with CpG sites showing evidence of progressive change. Based on our differentially methylated region (DMR) analysis of the 239 CpG sites, we highlighted two DMRs, namely the cysteine-rich secretory protein 2 (CRISP2) and piwi-like RNA-mediated gene silencing 1 (PIWIL1) genes. The best predictability for the two groups involved a receiver operating characteristics curve of eight CpG sites alone and achieved an area under the curve of 0.976. CONCLUSIONS We have identified distinct DNA methylation patterns between early and late diabetic CKD patients as well as demonstrated novel findings of potential progressive methylation changes across all stages (1-5) of diabetic CKD at specific CpG sites. We have also identified associated genes CRISP2 and PIWIL1, which may have the potential to act as stage-specific diabetes-associated CKD markers, and showed that the use of a panel of eight identified CpG sites alone helps to increase the predictability for the two groups.
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Affiliation(s)
| | - Boris Novakovic
- Epigenetics Research, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Braydon Meyer
- Epigenetics Research, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Elif I Ekinci
- Department of Endocrinology, Austin Health, Melbourne, Victoria, Australia.,Department of Medicine, University of Melbourne, Melbourne, Victoria, Australia
| | - Karen M Dwyer
- School of Medicine, Faculty of Health, Deakin University, Melbourne, Victoria, Australia
| | - Richard Saffery
- Epigenetics Research, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
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Holm SR, Jenkins BJ, Cronin JG, Jones N, Thornton CA. A role for metabolism in determining neonatal immune function. Pediatr Allergy Immunol 2021; 32:1616-1628. [PMID: 34170575 DOI: 10.1111/pai.13583] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 05/19/2021] [Accepted: 06/03/2021] [Indexed: 01/04/2023]
Abstract
Immune responses of neonates differ markedly to those of adults, with skewed cytokine phenotypes, reduced inflammatory properties and drastically diminished memory function. Recent research efforts have started to unravel the role of cellular metabolism in determining immune cell fate and function. For studies in humans, much of the work on metabolic mechanisms underpinning innate and adaptive immune responses by different haematopoietic cell types is in adults. Studies investigating the contribution of metabolic adaptation in the unique setting of early life are just emerging, and much more work is needed to elucidate the contribution of metabolism to neonatal immune responses. Here, we discuss our current understanding of neonatal immune responses, examine some of the latest developments in neonatal immunometabolism and consider the possible role of altered metabolism to the distinctive immune phenotype of the neonate. Understanding the role of metabolism in regulating immune function at this critical stage in life has direct benefit for the child by affording opportunities to maximize immediate and long-term health. Additionally, gaining insight into the diversity of human immune function and naturally evolved immunometabolic strategies that modulate immune function could be harnessed for a wide range of opportunities including new therapeutic approaches.
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Affiliation(s)
- Sean R Holm
- Institute of Life Science, Swansea University Medical School, Swansea University, Swansea, UK
| | - Ben J Jenkins
- Institute of Life Science, Swansea University Medical School, Swansea University, Swansea, UK
| | - James G Cronin
- Institute of Life Science, Swansea University Medical School, Swansea University, Swansea, UK
| | - Nicholas Jones
- Institute of Life Science, Swansea University Medical School, Swansea University, Swansea, UK
| | - Catherine A Thornton
- Institute of Life Science, Swansea University Medical School, Swansea University, Swansea, UK
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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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Devonshire AL, Fan H, Pujato M, Paranjpe A, Gursel D, Schipma M, Dunn JM, Andorf S, Pongracic JA, Kottyan LC, Kumar R. Whole blood transcriptomics identifies gene expression associated with peanut allergy in infants at high risk. Clin Exp Allergy 2021; 51:1396-1400. [PMID: 34473385 PMCID: PMC9290487 DOI: 10.1111/cea.14008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 08/08/2021] [Indexed: 12/16/2022]
Affiliation(s)
- Ashley L Devonshire
- Division of Allergy and Immunology, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA.,Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Hanli Fan
- Pathology Core Facility, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Mario Pujato
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Aditi Paranjpe
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Demirkan Gursel
- Pathology Core Facility, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Matthew Schipma
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Julia M Dunn
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Sandra Andorf
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.,Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Jacqueline A Pongracic
- Division of Allergy and Immunology, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA.,Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Leah C Kottyan
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.,Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Rajesh Kumar
- Division of Allergy and Immunology, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA.,Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
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Imran S, Neeland MR, Koplin J, Dharmage S, Tang MLK, Sawyer S, Dang T, McWilliam V, Peters R, Perrett KP, Novakovic B, Saffery R. Epigenetic programming underpins B-cell dysfunction in peanut and multi-food allergy. Clin Transl Immunology 2021; 10:e1324. [PMID: 34466226 PMCID: PMC8384135 DOI: 10.1002/cti2.1324] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 06/07/2021] [Accepted: 07/16/2021] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVE Rates of IgE-mediated food allergy (FA) have increased over the last few decades, and mounting evidence implicates disruption of epigenetic profiles in various immune cell types in FA development. Recent data implicate B-cell dysfunction in FA; however, few studies have examined epigenetic changes within these cells. METHODS We assessed epigenetic and transcriptomic profiles in purified B cells from adolescents with FA, comparing single-food-allergic (peanut only), multi-food-allergic (peanut and ≥1 other food) and non-allergic (control) individuals. Adolescents represent a phenotype of persistent and severe FA indicative of a common immune deviation. RESULTS We identified 144 differentially methylated probes (DMPs) and 116 differentially expressed genes (DEGs) that distinguish B cells of individuals with FA from controls, including differential methylation of the PM20D1 promoter previously associated with allergic disorders. Subgroup comparisons found 729 DMPs specific to either single-food- or multi-food-allergic individuals, suggesting epigenetic distinctions between allergy groups. This included two regions with increased methylation near three S100 genes in multi-food-allergic individuals. Ontology results of DEGs specific to multi-food-allergic individuals revealed enrichment of terms associated with myeloid cell activation. Motif enrichment analysis of promoters associated with DMPs and DEGs showed differential enrichment for motifs recognised by transcription factors regulating B- and T-cell development, B-cell lineage determination and TGF-β signalling pathway between the multi-food-allergic and single-food-allergic groups. CONCLUSION Our data highlight epigenetic changes in B cells associated with peanut allergy, distinguishing features of the epigenome between single-food- and multi-food-allergic individuals and revealing differential developmental pathways potentially underpinning these distinct phenotypes.
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Affiliation(s)
- Samira Imran
- Murdoch Children’s Research Institute, and Department of PaediatricsUniversity of MelbourneRoyal Children's HospitalParkvilleVICAustralia
| | - Melanie R Neeland
- Murdoch Children’s Research Institute, and Department of PaediatricsUniversity of MelbourneRoyal Children's HospitalParkvilleVICAustralia
| | - Jennifer Koplin
- Murdoch Children’s Research Institute, and Department of PaediatricsUniversity of MelbourneRoyal Children's HospitalParkvilleVICAustralia
| | - Shyamali Dharmage
- Murdoch Children’s Research Institute, and Department of PaediatricsUniversity of MelbourneRoyal Children's HospitalParkvilleVICAustralia
- Allergy and Lung Health UnitMelbourne School of Population and Global HealthUniversity of MelbourneCarltonVICAustralia
| | - Mimi LK Tang
- Murdoch Children’s Research Institute, and Department of PaediatricsUniversity of MelbourneRoyal Children's HospitalParkvilleVICAustralia
- Department of Allergy and ImmunologyRoyal Children's HospitalMelbourneVICAustralia
| | - Susan Sawyer
- Murdoch Children’s Research Institute, and Department of PaediatricsUniversity of MelbourneRoyal Children's HospitalParkvilleVICAustralia
- Centre for Adolescent HealthRoyal Children's HospitalMelbourneVICAustralia
| | - Thanh Dang
- Murdoch Children’s Research Institute, and Department of PaediatricsUniversity of MelbourneRoyal Children's HospitalParkvilleVICAustralia
| | - Vicki McWilliam
- Murdoch Children’s Research Institute, and Department of PaediatricsUniversity of MelbourneRoyal Children's HospitalParkvilleVICAustralia
- Department of Allergy and ImmunologyRoyal Children's HospitalMelbourneVICAustralia
| | - Rachel Peters
- Murdoch Children’s Research Institute, and Department of PaediatricsUniversity of MelbourneRoyal Children's HospitalParkvilleVICAustralia
| | - Kirsten P Perrett
- Murdoch Children’s Research Institute, and Department of PaediatricsUniversity of MelbourneRoyal Children's HospitalParkvilleVICAustralia
- Department of Allergy and ImmunologyRoyal Children's HospitalMelbourneVICAustralia
| | - Boris Novakovic
- Murdoch Children’s Research Institute, and Department of PaediatricsUniversity of MelbourneRoyal Children's HospitalParkvilleVICAustralia
| | - Richard Saffery
- Murdoch Children’s Research Institute, and Department of PaediatricsUniversity of MelbourneRoyal Children's HospitalParkvilleVICAustralia
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Comparisons of Vitreal Angiogenic, Inflammatory, Profibrotic Cytokines, and Chemokines Profile between Patients with Epiretinal Membrane and Macular Hole. J Ophthalmol 2021; 2021:9947250. [PMID: 34336263 PMCID: PMC8294982 DOI: 10.1155/2021/9947250] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 06/28/2021] [Indexed: 12/22/2022] Open
Abstract
Objectives Idiopathic epiretinal membrane (iERM) or idiopathic macular hole (iMH) is frequently used as a “healthy” control in comparison of vitreous cytokines with other vitreoretinal diseases. This study aimed to investigate if there is a difference in vitreal cytokines expression between patients with iERM and iMH. Methods In this prospective study, all subjects received standard pars plana vitrectomy surgery, and 0.5 ml of native vitreous sample was extracted during the vitrectomy. Luminex technology and enzyme-linked immunosorbent assay were used to profile the concentration of 52 classic angiogenic, inflammatory, and profibrotic cytokines and chemokines. Statistical analyses were performed by the Mann–Whitney U test, followed by multiple comparisons by the Bonferroni correction. Results Vitreal samples from 13 iERM and 24 iMH were studied. Of the 52 tested cytokines, 41 were similar in expression, and 5 were under the detection limit, while 6 cytokines (MMP-8, Eotaxin, MIP-1a, RANTES, TGF-β2, and IL-4) were differently expressed between two groups (p < 0.05). Nevertheless, these significances disappeared after the adjustment of Bonferroni correction. Conclusion The tested cytokines showed similar expression between iERM and iMH patients. This indicates that eyes with iERM or iMH can be together served as “healthy” controls.
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Mapping the landscape of chromatin dynamics during naïve CD4+ T-cell activation. Sci Rep 2021; 11:14101. [PMID: 34238961 PMCID: PMC8266878 DOI: 10.1038/s41598-021-93509-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 06/22/2021] [Indexed: 12/23/2022] Open
Abstract
T-cell activation induces context-specific gene expression programs that promote energy generation and biosynthesis, progression through the cell cycle and ultimately cell differentiation. The aim of this study was to apply the omni ATAC-seq method to characterize the landscape of chromatin changes induced by T-cell activation in mature naïve CD4+ T-cells. Using a well-established ex vivo protocol of canonical T-cell receptor signaling, we generated genome-wide chromatin maps of naïve T-cells from pediatric donors in quiescent or recently activated states. We identified thousands of individual chromatin accessibility peaks that are associated with T-cell activation, the majority of which were annotated intronic and intergenic enhancer regions. A core set of 3268 gene promoters underwent chromatin remodeling and concomitant changes in gene expression in response to activation, and were enriched in multiple pathways controlling cell cycle regulation, metabolism, inflammatory response genes and cell survival. Leukemia inhibitory factor (LIF) was among those factors that gained the highest accessibility and expression, in addition to IL2-STAT5 dependent chromatin remodeling in the T-cell activation response. Using publicly available data we found the chromatin response was far more dynamic at 24-h compared with 72-h post-activation. In total 546 associations were reproduced at both time-points with similar strength of evidence and directionality of effect. At the pathways level, the IL2-STAT5, KRAS signalling and UV response pathways were replicable at both time-points, although differentially modulated from 24 to 72 h post-activation.
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43
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Combined prenatal Lactobacillus reuteri and ω-3 supplementation synergistically modulates DNA methylation in neonatal T helper cells. Clin Epigenetics 2021; 13:135. [PMID: 34193262 PMCID: PMC8247185 DOI: 10.1186/s13148-021-01115-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 06/15/2021] [Indexed: 02/08/2023] Open
Abstract
Background Environmental exposures may alter DNA methylation patterns of T helper cells. As T helper cells are instrumental for allergy development, changes in methylation patterns may constitute a mechanism of action for allergy preventive interventions. While epigenetic effects of separate perinatal probiotic or ω-3 fatty acid supplementation have been studied previously, the combined treatment has not been assessed. We aimed to investigate epigenome-wide DNA methylation patterns from a sub-group of children in an on-going randomised double-blind placebo-controlled allergy prevention trial using pre- and postnatal combined Lactobacillus reuteri and ω-3 fatty acid treatment. To this end, > 866000 CpG sites (MethylationEPIC 850K array) in cord blood CD4+ T cells were examined in samples from all four study arms (double-treatment: n = 18, single treatments: probiotics n = 16, ω-3 n = 15, and double placebo: n = 14). Statistical and bioinformatic analyses identified treatment-associated differentially methylated CpGs and genes, which were used to identify putatively treatment-induced network modules. Pathway analyses inferred biological relevance, and comparisons were made to an independent allergy data set. Results Comparing the active treatments to the double placebo group, most differentially methylated CpGs and genes were hypermethylated, possibly suggesting induction of transcriptional inhibition. The double-treated group showed the largest number of differentially methylated CpGs, of which many were unique, suggesting synergy between interventions. Clusters within the double-treated network module consisted of immune-related pathways, including T cell receptor signalling, and antigen processing and presentation, with similar pathways revealed for the single-treatment modules. CpGs derived from differential methylation and network module analyses were enriched in an independent allergy data set, particularly in the double-treatment group, proposing treatment-induced DNA methylation changes as relevant for allergy development. Conclusion Prenatal L. reuteri and/or ω-3 fatty acid treatment results in hypermethylation and affects immune- and allergy-related pathways in neonatal T helper cells, with potentially synergistic effects between the interventions and relevance for allergic disease. Further studies need to address these findings on a transcriptional level, and whether the results associate to allergy development in the children. Understanding the role of DNA methylation in regulating effects of perinatal probiotic and ω-3 interventions may provide essential knowledge in the development of efficacious allergy preventive strategies. Trial registration ClinicalTrials.gov, ClinicalTrials.gov-ID: NCT01542970. Registered 27th of February 2012—Retrospectively registered, https://clinicaltrials.gov/ct2/show/NCT01542970. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01115-4.
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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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Neeland MR, Andorf S, Dang TD, McWilliam VL, Perrett KP, Koplin JJ, Saffery R. Altered immune cell profiles and impaired CD4 T-cell activation in single and multi-food allergic adolescents. Clin Exp Allergy 2021; 51:674-684. [PMID: 33626189 DOI: 10.1111/cea.13857] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/10/2021] [Accepted: 02/17/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND Approximately 5% of adolescents have a food allergy, with peanut and tree nut allergies the most common. Having two or more food allergies in adolescence also doubles the risk of any adverse food reaction, and is associated with increased dietary and social burden. Investigations of immune function in persistently food allergic children are rare. OBJECTIVE In the present study, we aimed to investigate the immune mechanisms that underlie food allergy in adolescence. METHODS We used high-dimensional flow cytometry, unsupervised computational analysis and functional studies to comprehensively phenotype a range of non-antigen-specific immune parameters in a group of well-characterized adolescents with clinically defined single peanut allergy, multi-food allergy and aged-matched non-food allergic controls. RESULTS We show that food allergic adolescents have higher circulating proportions of dendritic cells (p = .0084, FDR-adjusted p = .087, median in no FA: 0.63% live cells, in FA: 0.93%), and higher frequency of activated, memory-like Tregs relative to non-food allergic adolescents (p = .011, FDR-adjusted p = .087, median in no FA: 0.49% live cells, in FA: 0.65%). Cytokine profiling revealed that CD3/CD28 stimulated naïve CD4 T cells from food allergic adolescents produced less IL-6 (p = .0020, FDR-adjusted p = .018, median log2 fold change [stimulated/unstimulated] in no FA: 3.03, in FA: 1.92) and TNFα (p = .0044, FDR-adjusted p = .020, median in no FA: 9.16, in FA: 8.64) and may secrete less IFNγ (p = .035, FDR-adjusted p = .11, median in no FA: 6.29, in FA: 5.67) than naïve CD4 T cells from non-food allergic controls. No differences between clinical groups were observed for LPS-stimulated monocyte secretion of cytokines. CONCLUSIONS These results have important implications for understanding the evolution of the immune response in food allergy throughout childhood, revealing that dendritic cell and T-cell signatures previously identified in early life may persist through to adolescence.
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Affiliation(s)
- Melanie R Neeland
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Vic, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Vic, Australia
| | - Sandra Andorf
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.,Divisions of Biomedical Informatics and Allergy & Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Thanh D Dang
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Vic, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Vic, Australia
| | - Vicki L McWilliam
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Vic, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Vic, Australia
| | - Kirsten P Perrett
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Vic, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Vic, Australia.,Department of Allergy and Immunology, Royal Children's Hospital, Melbourne, Vic, Australia
| | - Jennifer J Koplin
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Vic, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Vic, Australia
| | - Richard Saffery
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Vic, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Vic, Australia
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Acevedo N, Scala G, Merid SK, Frumento P, Bruhn S, Andersson A, Ogris C, Bottai M, Pershagen G, Koppelman GH, Melén E, Sonnhammer E, Alm J, Söderhäll C, Kere J, Greco D, Scheynius A. DNA Methylation Levels in Mononuclear Leukocytes from the Mother and Her Child Are Associated with IgE Sensitization to Allergens in Early Life. Int J Mol Sci 2021; 22:ijms22020801. [PMID: 33466918 PMCID: PMC7830007 DOI: 10.3390/ijms22020801] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/22/2020] [Accepted: 12/23/2020] [Indexed: 12/23/2022] Open
Abstract
DNA methylation changes may predispose becoming IgE-sensitized to allergens. We analyzed whether DNA methylation in peripheral blood mononuclear cells (PBMC) is associated with IgE sensitization at 5 years of age (5Y). DNA methylation was measured in 288 PBMC samples from 74 mother/child pairs from the birth cohort ALADDIN (Assessment of Lifestyle and Allergic Disease During INfancy) using the HumanMethylation450BeadChip (Illumina). PBMCs were obtained from the mothers during pregnancy and from their children in cord blood, at 2 years and 5Y. DNA methylation levels at each time point were compared between children with and without IgE sensitization to allergens at 5Y. For replication, CpG sites associated with IgE sensitization in ALADDIN were evaluated in whole blood DNA of 256 children, 4 years old, from the BAMSE (Swedish abbreviation for Children, Allergy, Milieu, Stockholm, Epidemiology) cohort. We found 34 differentially methylated regions (DMRs) associated with IgE sensitization to airborne allergens and 38 DMRs associated with sensitization to food allergens in children at 5Y (Sidak p ≤ 0.05). Genes associated with airborne sensitization were enriched in the pathway of endocytosis, while genes associated with food sensitization were enriched in focal adhesion, the bacterial invasion of epithelial cells, and leukocyte migration. Furthermore, 25 DMRs in maternal PBMCs were associated with IgE sensitization to airborne allergens in their children at 5Y, which were functionally annotated to the mTOR (mammalian Target of Rapamycin) signaling pathway. This study supports that DNA methylation is associated with IgE sensitization early in life and revealed new candidate genes for atopy. Moreover, our study provides evidence that maternal DNA methylation levels are associated with IgE sensitization in the child supporting early in utero effects on atopy predisposition.
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Affiliation(s)
- Nathalie Acevedo
- Department of Clinical Science and Education, Karolinska Institutet, and Sachs’ Children and Youth Hospital, Södersjukhuset, SE-118 83 Stockholm, Sweden; (N.A.); (S.K.M.); (E.M.); (J.A.)
- Institute for Immunological Research, University of Cartagena, 130014 Cartagena, Colombia
| | - Giovanni Scala
- Department of Biology, University of Naples Federico II, 80138 Napoli, Italy;
- Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland;
- Institute of Biosciences and Medical Technologies (BioMediTech), Tampere University, 33520 Tampere, Finland
| | - Simon Kebede Merid
- Department of Clinical Science and Education, Karolinska Institutet, and Sachs’ Children and Youth Hospital, Södersjukhuset, SE-118 83 Stockholm, Sweden; (N.A.); (S.K.M.); (E.M.); (J.A.)
| | - Paolo Frumento
- Department of Political Sciences, University of Pisa, 56126 Pisa, Italy;
| | - Sören Bruhn
- Department of Medicine Solna, Translational Immunology Unit, Karolinska Institutet, SE-171 77 Stockholm, Sweden; (S.B.); (A.A.)
| | - Anna Andersson
- Department of Medicine Solna, Translational Immunology Unit, Karolinska Institutet, SE-171 77 Stockholm, Sweden; (S.B.); (A.A.)
| | - Christoph Ogris
- Stockholm Bioinformatics Center, Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, SE-17121 Solna, Sweden; (C.O.); (E.S.)
- Institute of Computational Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Matteo Bottai
- Institute of Environmental Medicine, Karolinska Institutet, SE-171 77 Stockholm, Sweden; (M.B.); (G.P.)
| | - Göran Pershagen
- Institute of Environmental Medicine, Karolinska Institutet, SE-171 77 Stockholm, Sweden; (M.B.); (G.P.)
| | - Gerard H. Koppelman
- Section of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children’s Hospital, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands;
- Groningen Research Institute of Asthma and COPD (GRIAC), University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands
| | - Erik Melén
- Department of Clinical Science and Education, Karolinska Institutet, and Sachs’ Children and Youth Hospital, Södersjukhuset, SE-118 83 Stockholm, Sweden; (N.A.); (S.K.M.); (E.M.); (J.A.)
- Institute of Environmental Medicine, Karolinska Institutet, SE-171 77 Stockholm, Sweden; (M.B.); (G.P.)
| | - Erik Sonnhammer
- Stockholm Bioinformatics Center, Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, SE-17121 Solna, Sweden; (C.O.); (E.S.)
| | - Johan Alm
- Department of Clinical Science and Education, Karolinska Institutet, and Sachs’ Children and Youth Hospital, Södersjukhuset, SE-118 83 Stockholm, Sweden; (N.A.); (S.K.M.); (E.M.); (J.A.)
| | - Cilla Söderhäll
- Department of Biosciences and Nutrition, Karolinska Institutet, SE-171 77 Stockholm, Sweden; (C.S.); (J.K.)
- Department of Women’s and Children’s Health, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, SE-171 77 Stockholm, Sweden; (C.S.); (J.K.)
- Folkhälsan Research Institute, Stem Cells and Metabolism Research Program, University of Helsinki, 00014 Helsinki, Finland
| | - Dario Greco
- Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland;
- Institute of Biosciences and Medical Technologies (BioMediTech), Tampere University, 33520 Tampere, Finland
- Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland
| | - Annika Scheynius
- Department of Clinical Science and Education, Karolinska Institutet, and Sachs’ Children and Youth Hospital, Södersjukhuset, SE-118 83 Stockholm, Sweden; (N.A.); (S.K.M.); (E.M.); (J.A.)
- Science for Life Laboratory, Karolinska Institutet, SE-171 65 Solna, Sweden
- Correspondence:
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Wisgrill L, Werner P, Fortino V, Fyhrquist N. AIM in Allergy. Artif Intell Med 2021. [DOI: 10.1007/978-3-030-58080-3_90-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Irizar H, Kanchan K, Mathias RA, Bunyavanich S. Advancing Food Allergy Through Omics Sciences. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. IN PRACTICE 2021; 9:119-129. [PMID: 32777389 PMCID: PMC7855623 DOI: 10.1016/j.jaip.2020.07.044] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 07/24/2020] [Indexed: 02/07/2023]
Abstract
Since the publication of the first draft of the human genome, there has been an explosion of new technologies with increasing power to interrogate the totality of biological molecules (eg, DNA, RNA, proteins, metabolites) and their modifications (eg, DNA methylation, histone modifications). These technologies, collectively called omics, have been widely applied in the last 2 decades to study biological systems to gain deeper insight into mechanisms driving the physiology and pathophysiology of human health and disease. Because of its complex, multifactorial nature, food allergy is especially well suited to be investigated using omics approaches. In this rostrum, we review how omic technologies have been applied to explore diverse aspects of food allergy, including adaptive and innate immune processes in food-allergic responses, the role of the microbiome in food allergy risk, metabolic changes in the gut and blood associated with food allergy, and the identification of biomarkers and potential therapeutic targets for the condition. We discuss the strengths and limitations of the studies performed thus far and the need to adopt systems biology approaches that integrate data from multiple omics to fully leverage the potential of these technologies to advance food allergy research and care.
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Affiliation(s)
- Haritz Irizar
- Division of Psychiatry, University College London, London, United Kingdom; Department of Genetics & Genomic Sciences and Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Kanika Kanchan
- Department of Medicine, Johns Hopkins University, Baltimore, Md
| | | | - Supinda Bunyavanich
- Department of Genetics & Genomic Sciences and Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY.
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Liu JQ, Hu TY, Diao KY, Yu D, Song YN, Mo LH, Yang G, Liu ZQ, Liu ZG, Yang PC. Cold stress promotes IL-33 expression in intestinal epithelial cells to facilitate food allergy development. Cytokine 2020; 136:155295. [PMID: 32977238 DOI: 10.1016/j.cyto.2020.155295] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 08/23/2020] [Accepted: 09/08/2020] [Indexed: 12/11/2022]
Abstract
BACKGROUND The causative factors and pathogenesis of food allergy (FA) is not fully understood yet. Cold stress (CS) occurs frequently in human life that influences physiological activities in the body. In this study, we aimed to investigate the chronic CS (CS) effects on promoting the expression of IL-33 in intestinal epithelial cells. METHODS CS was carried out by placing mice at 4 °C for 1 h daily for 7 consecutive days. We developed a mouse model used to test the effects of CS on the FA development. RESULTS We found that, similar to conventional FA mouse model, CS induced the core body temperature to drop markedly in mice, increased intestinal epithelial barrier permeability and facilitated FA development. CS promoted interleukin (IL)-33 expression in intestinal epithelial cells through the adrenocorticotropic hormone (ACTH)/cortisol axis and via inducing the Il33 promoter methylation. CS facilitated the FA development in mice, that could be blocked by depletion of IL-33 expression in intestinal epithelial cells. CONCLUSIONS CS induces IL-33 expression in intestinal epithelial cells to promote Th2 polarization in the intestinal tissues and facilitates FA development.
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Affiliation(s)
- Jiang-Qi Liu
- Department of Allergy, Longgang ENT Hospital and Shenzhen ENT Institute, Shenzhen, China; Research Center of Allergy & Immunology, Shenzhen University School of Medicine, Shenzhen, China
| | - Tian-Yong Hu
- Department of Allergy, Longgang ENT Hospital and Shenzhen ENT Institute, Shenzhen, China; Research Center of Allergy & Immunology, Shenzhen University School of Medicine, Shenzhen, China
| | - Kai-Yuan Diao
- Department of Pediatric Otolaryngology, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Dian Yu
- Department of Allergy, Longgang ENT Hospital and Shenzhen ENT Institute, Shenzhen, China
| | - Yan-Nan Song
- Department of Allergy, Longgang ENT Hospital and Shenzhen ENT Institute, Shenzhen, China
| | - Li-Hua Mo
- Department of Allergy, Longgang ENT Hospital and Shenzhen ENT Institute, Shenzhen, China; Department of Pediatric Otolaryngology, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Gui Yang
- Department of Otolaryngology, Longgagn Central Hospital, Shenzhen, China
| | - Zhi-Qiang Liu
- Department of Allergy, Longgang ENT Hospital and Shenzhen ENT Institute, Shenzhen, China; Research Center of Allergy & Immunology, Shenzhen University School of Medicine, Shenzhen, China.
| | - Zhi-Gang Liu
- Department of Allergy, Longgang ENT Hospital and Shenzhen ENT Institute, Shenzhen, China.
| | - Ping-Chang Yang
- Department of Allergy, Longgang ENT Hospital and Shenzhen ENT Institute, Shenzhen, China; Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Shenzhen, China.
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50
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Patil SU, Bunyavanich S, Cecilia Berin M. Emerging Food Allergy Biomarkers. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. IN PRACTICE 2020; 8:2516-2524. [PMID: 32888527 PMCID: PMC7479640 DOI: 10.1016/j.jaip.2020.04.054] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/17/2020] [Accepted: 04/18/2020] [Indexed: 12/12/2022]
Abstract
The management of food allergy is complicated by the lack of highly predictive biomarkers for diagnosis and prediction of disease course. The measurement of food-specific IgE is a useful tool together with clinical history but is an imprecise predictor of clinical reactivity. The gold standard for diagnosis and clinical research is a double-blind placebo-controlled food challenge. Improvement in our understanding of immune mechanisms of disease, development of high-throughput technologies, and advances in bioinformatics have yielded a number of promising new biomarkers of food allergy. In this review, we will discuss advances in immunoglobulin measurements, the utility of the basophil activation test, T-cell profiling, and the use of -omic technologies (transcriptome, epigenome, microbiome, and metabolome) as biomarker tools in food allergy.
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Affiliation(s)
- Sarita U. Patil
- Food Allergy Center, Department of Pediatrics, Massachusetts General Hospital, Boston, MA 02114
- Center for Immunological and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114
| | - Supinda Bunyavanich
- Jaffe Food Allergy Institute, Department of Pediatrics; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - M. Cecilia Berin
- Jaffe Food Allergy Institute, Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
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