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Long A, Bunning B, Sampath V, DeKruyff RH, Nadeau KC. Epigenetics and the Environment in Airway Disease: Asthma and Allergic Rhinitis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1253:153-181. [PMID: 32445095 DOI: 10.1007/978-981-15-3449-2_6] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Asthma and rhinitis are complex, heterogeneous diseases characterized by chronic inflammation of the upper and lower airways. While genome-wide association studies (GWAS) have identified a number of susceptible loci and candidate genes associated with the pathogenesis of asthma and allergic rhinitis (AR), the risk-associated alleles account for only a very small percent of the genetic risk. In allergic airway and other complex diseases, it is thought that epigenetic modifications, including DNA methylation, histone modifications, and non-coding microRNAs, caused by complex interactions between the underlying genome and the environment may account for some of this "missing heritability" and may explain the high degree of plasticity in immune responses. In this chapter, we will focus on the current knowledge of classical epigenetic modifications, DNA methylation and histone modifications, and their potential role in asthma and AR. In particular, we will review epigenetic variations associated with maternal airway disease, demographics, environment, and non-specific associations. The role of specific genetic haplotypes in environmentally induced epigenetic changes are also discussed. A major limitation of many of the current studies of asthma epigenetics is that they evaluate epigenetic modifications in both allergic and non-allergic asthma, making it difficult to distinguish those epigenetic modifications that mediate allergic asthma from those that mediate non-allergic asthma. Additionally, most DNA methylation studies in asthma use peripheral or cord blood due to poor accessibility of airway cells or tissue. Unlike DNA sequences, epigenetic alterations are quite cell- and tissue-specific, and epigenetic changes found in airway tissue or cells may be discordant from that of circulating blood. These two confounding factors should be considered when reviewing epigenetic studies in allergic airway disease.
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Affiliation(s)
- Andrew Long
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research at Stanford University, Stanford, CA, 94305, USA.,Department of Pharmacy, Lucile Packard Children's Hospital, Stanford, CA, 94304, USA
| | - Bryan Bunning
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research at Stanford University, Stanford, CA, 94305, USA
| | - Vanitha Sampath
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research at Stanford University, Stanford, CA, 94305, USA
| | - Rosemarie H DeKruyff
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research at Stanford University, Stanford, CA, 94305, USA
| | - Kari C Nadeau
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research at Stanford University, Stanford, CA, 94305, USA.
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Toki S, Goleniewska K, Zhang J, Zhou W, Newcomb DC, Zhou B, Kita H, Boyd KL, Peebles RS. TSLP and IL-33 reciprocally promote each other's lung protein expression and ILC2 receptor expression to enhance innate type-2 airway inflammation. Allergy 2020; 75:1606-1617. [PMID: 31975538 PMCID: PMC7354889 DOI: 10.1111/all.14196] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 11/16/2019] [Accepted: 11/28/2019] [Indexed: 01/10/2023]
Abstract
Background The epithelial cell‐derived danger signal mediators thymic stromal lymphopoietin (TSLP) and IL‐33 are consistently associated with adaptive Th2 immune responses in asthma. In addition, TSLP and IL‐33 synergistically promoted group 2 innate lymphoid cell (ILC2) activation to induce innate allergic inflammation. However, the mechanism of this synergistic ILC2 activation is unknown. Methods BALB/c WT and TSLP receptor‐deficient (TSLPR−/−) mice were challenged intranasally with Alternaria extract (Alt‐Ext) or PBS for 4 consecutive days to evaluate innate airway allergic inflammation. WT mice pre‐administered with rTSLP or vehicle, TSLPR−/− mice, and IL‐33 receptor‐deficient (ST2−/−) mice were challenged intranasally with Alt‐Ext or vehicle once or twice to evaluate IL‐33 release and TSLP expression in the lung. TSLPR and ST2 expression on lung ILC2 were measured by flow cytometry after treatment of rTSLP, rIL‐33, rTSLP + rIL‐33, or vehicle. Results Thymic stromal lymphopoietin receptor deficient mice had significantly decreased the number of lung ILC2 expressing IL‐5 and IL‐13 following Alt‐Ext‐challenge compared to WT mice. Further, eosinophilia, protein level of lung IL‐4, IL‐5, and IL‐13, and airway mucus score were also significantly decreased in TSLPR−/− mice compared to WT mice. Endogenous and exogenous TSLP increased Alt‐Ext‐induced IL‐33 release into BALF, and ST2 deficiency decreased Alt‐Ext‐induced TSLP expression in the lung. Further, rTSLP and rIL‐33 treatment reciprocally increased each other's receptor expression on lung ILC2 in vivo and in vitro. Conclusion Thymic stromal lymphopoietin and IL‐33 signaling reciprocally enhanced each other's protein release and expression in the lung following Alt‐Ext‐challenge and each other's receptor expression on lung ILC2 to enhance ILC2 activation.
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Affiliation(s)
- Shinji Toki
- Division of Allergy, Pulmonary, and Critical Care Medicine Vanderbilt University School of Medicine Nashville TN USA
| | - Kasia Goleniewska
- Division of Allergy, Pulmonary, and Critical Care Medicine Vanderbilt University School of Medicine Nashville TN USA
| | - Jian Zhang
- Division of Allergy, Pulmonary, and Critical Care Medicine Vanderbilt University School of Medicine Nashville TN USA
| | - Weisong Zhou
- Division of Allergy, Pulmonary, and Critical Care Medicine Vanderbilt University School of Medicine Nashville TN USA
| | - Dawn C. Newcomb
- Division of Allergy, Pulmonary, and Critical Care Medicine Vanderbilt University School of Medicine Nashville TN USA
- Department of Pathology, Microbiology, and Immunology Vanderbilt University School of Medicine Nashville TN USA
| | - Baohua Zhou
- Wells Center for Pediatric Research Department of Pediatrics Indiana University School of Medicine Indianapolis IN USA
| | - Hirohito Kita
- Division of Allergic Diseases Department of Internal Medicine Mayo Clinic Rochester MN USA
| | - Kelli L. Boyd
- Department of Pathology, Microbiology, and Immunology Vanderbilt University School of Medicine Nashville TN USA
| | - Ray S. Peebles
- Division of Allergy, Pulmonary, and Critical Care Medicine Vanderbilt University School of Medicine Nashville TN USA
- Department of Pathology, Microbiology, and Immunology Vanderbilt University School of Medicine Nashville TN USA
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103
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Chen J, Chen Q, Wu C, Jin Y. Genetic variants of the C11orf30-LRRC32 region are associated with childhood asthma in the Chinese population. Allergol Immunopathol (Madr) 2020; 48:390-394. [PMID: 31812328 DOI: 10.1016/j.aller.2019.09.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 09/11/2019] [Accepted: 09/16/2019] [Indexed: 12/12/2022]
Abstract
INTRODUCTION AND OBJECTIVES To investigate whether genetic polymorphisms of C11orf30-LRRC32 region are associated with the development of childhood asthma in the Chinese population. METHODS A total of 732 asthma children and 824 age-matched healthy controls were included in the study. Blood samples were collected from the subjects for total IgE analysis, DNA extraction and RNA extraction. Three previously reported asthma-related SNPs were genotyped, including rs7936070 (G/T), rs7927894 (A/G), and rs6592657 (A/G). Blood samples from 50 patients and 50 controls were randomly selected to detect the mRNA expression levels of C11orf30 and LRRC32 in serum. RESULTS There were significantly different genotype frequencies between the two groups in terms of rs7936070 and rs7927894. Compared with controls, patients were found to have remarkably higher risk allele frequencies of rs7936070 and rs7927894. Genotype GG of rs7936070 was indicative of remarkably elevated total IgE level as compared with genotype TT and genotype GT. Similarly, genotype AA of rs7927894 was also associated with significantly elevated total IgE level. The serum expression of C11orf30 was significantly lower in the patients than in the controls. The C11orf30 expression was significantly correlated with the total IgE level (r = -0.463, p = 0.01). CONCLUSIONS Variants of C11orf30 were associated with the risk of childhood asthma in the Chinese population. Besides, abnormally decreased expression of C11orf30 was detected in the serum of patients, which was correlated with the total IgE level. The C11orf30 might play a role in asthma via biological pathways involving the regulation of total serum IgE level.
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Affiliation(s)
- J Chen
- Department of Paediatrics, Jiangsu Taizhou People's Hospital, Hailing South Road No. 399, Taizhou, China
| | - Q Chen
- Department of Paediatrics, Jiangsu Taizhou People's Hospital, Hailing South Road No. 399, Taizhou, China
| | - C Wu
- Department of Paediatrics, Jiangsu Taizhou People's Hospital, Hailing South Road No. 399, Taizhou, China
| | - Y Jin
- Department of Paediatrics, Jiangsu Taizhou People's Hospital, Hailing South Road No. 399, Taizhou, China.
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104
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Developmental Origins of Health and Disease: Impact of environmental dust exposure in modulating microbiome and its association with non-communicable diseases. J Dev Orig Health Dis 2020; 11:545-556. [PMID: 32536356 DOI: 10.1017/s2040174420000549] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Non-communicable diseases (NCDs) including obesity, diabetes, and allergy are chronic, multi-factorial conditions that are affected by both genetic and environmental factors. Over the last decade, the microbiome has emerged as a possible contributor to the pathogenesis of NCDs. Microbiome profiles were altered in patients with NCDs, and shift in microbial communities was associated with improvement in these health conditions. Since the genetic component of these diseases cannot be altered, the ability to manipulate the microbiome holds great promise for design of novel therapies in the prevention and treatment of NCDs. Together, the Developmental Origins of Health and Disease concept and the microbial hypothesis propose that early life exposure to environmental stimuli will alter the development and composition of the human microbiome, resulting in health consequences. Recent studies indicated that the environment we are exposed to in early life is instrumental in shaping robust immune development, possibly through modulation of the human microbiome (skin, airway, and gut). Despite much research into human microbiome, the origin of their constituent microbiota remains unclear. Dust (also known as particulate matter) is a key determinant of poor air quality in the modern urban environment. It is ubiquitous and serves as a major source and reservoir of microbial communities that modulates the human microbiome, contributing to health and disease. There are evidence that reported significant associations between environmental dust and NCDs. In this review, we will focus on the impact of dust exposure in shaping the human microbiome and its possible contribution to the development of NCDs.
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105
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Mustapa Kamal Basha MA, Majid HA, Razali N, Yahya A. Risk of eczema, wheezing and respiratory tract infections in the first year of life: A systematic review of vitamin D concentrations during pregnancy and at birth. PLoS One 2020; 15:e0233890. [PMID: 32542014 PMCID: PMC7295196 DOI: 10.1371/journal.pone.0233890] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 05/14/2020] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Allergic conditions and respiratory tract infections (RTIs) are common causes of morbidity and mortality in childhood. The relationship between vitamin D status in pregnancy (mothers), early life (infants) and health outcomes such as allergies and RTIs in infancy is unclear. To date, studies have shown conflicting results. OBJECTIVE This systematic review aims to gather and appraise existing evidence on the associations between serum vitamin D concentrations during pregnancy and at birth and the development of eczema, wheezing, and RTIs in infants. DATA SOURCES PubMed, MEDLINE, ProQuest, Scopus, CINAHL, Cochrane Library and Academic Search Premier databases were searched systematically using specified search terms and keywords. STUDY SELECTION Articles on the associations between serum vitamin D concentrations during pregnancy and at birth and eczema, wheezing, and RTIs among infants (1-year-old and younger) published up to 31 March 2019 were identified, screened and retrieved. RESULTS From the initial 2678 articles screened, ten met the inclusion criteria and were included in the final analysis. There were mixed and conflicting results with regards to the relationship between maternal and cord blood vitamin D concentrations and the three health outcomes-eczema, wheezing and RTIs-in infants. CONCLUSION Current findings revealed no robust and consistent associations between vitamin D status in early life and the risk of developing eczema, wheezing and RTIs in infants. PROSPERO registration no. CRD42018093039.
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Affiliation(s)
- Muzaitul Akma Mustapa Kamal Basha
- Department of Social Preventive Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
- Department of Special Care Nursing, Kulliyyah of Nursing, International Islamic University Malaysia (IIUM), Kuantan Campus, Pahang, Malaysia
| | - Hazreen Abdul Majid
- Department of Social Preventive Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
- Department of Nutrition, Harvard Chan School of Public Health, Boston, Massachusetts, United States of America
- Department of Nutrition, Faculty of Public Health, University of Airlangga, Surabaya, Indonesia
| | - Nuguelis Razali
- Department of Obstetrics & Gynaecology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Abqariyah Yahya
- Department of Social Preventive Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
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106
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He M, Mirzakhani H, Chen L, Wu R, Litonjua AA, Bacharier L, Weiss ST, Nelson DM. Vitamin D Sufficiency Has a Limited Effect on Placental Structure and Pathology: Placental Phenotypes in the VDAART Trial. Endocrinology 2020; 161:5818078. [PMID: 32270179 PMCID: PMC7528633 DOI: 10.1210/endocr/bqaa057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 04/06/2020] [Indexed: 11/19/2022]
Abstract
Vitamin D insufficiency during pregnancy is widespread. The effects of active vitamin D on the human placenta in vivo are unknown. We test the hypotheses that 25(OH)D sufficiency (arbitrarily defined as 25(OH)D ≥32 ng/mL) modulates placental structure and function in vivo in a population of women whose offspring are at risk for childhood asthma, and that placental pathology is more common in offspring that evolve asthma at age 3. Pregnant volunteers in the St. Louis, MO, cohort of the Vitamin D Antenatal Asthma Reduction Trial (VDAART, NIH grant #HL091528) participated in a nested case-control study and consented for the study of placentas after delivery. Maternal concentrations of 25(OH)D were measured at trial entry and in the third trimester. The histopathology of the placentas from women with sufficient 25(OH)D, versus insufficient, showed no clinically significant differences, but morphometry revealed villi of women with sufficient third-trimester 25(OH)D had a higher villous surface density. Notably, analyses of transcripts, extracted from formalin-fixed paraffin-embedded specimens, revealed higher expression of INTS9, vWF, MACC1, and ARMS2, and diminished expression of the CNTN5 genes in the insufficient group. A larger proportion of placentas showed chronic chorioamnionitis in offspring with versus without asthma at age 3. These findings suggest that maternal 25(OH)D insufficiency has a limited effect on human placental villous histopathology and morphometry, but attenuates a small number of placental gene expression profiles in this selected population. The association of placental chronic chorioamnionitis and offspring asthma is worthy of further study.
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Affiliation(s)
- Mai He
- Department of Pathology & Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri
- Correspondence: Mai He, MD, PhD, Department of Pathology & Immunology, 660 South Euclid, Campus Box 8118, Washington University School of Medicine in St. Louis, St. Louis, MO 63110.
| | - Hooman Mirzakhani
- Channing Division of Network Medicine, Department of Medicine, Harvard Medical School and Brigham and Women’s Hospital, Boston, Massachusetts
| | - Ling Chen
- Division of Biostatistics, Washington University School of Medicine in St. Louis, St. Louis, Missouri
| | - Robert Wu
- Penn State College of Medicine, Hershey, Pennsylvania
| | - Augusto A Litonjua
- Division of Pulmonary Medicine, Department of Pediatrics, University of Rochester, School of Medicine, Rochester, New York
| | - Leonard Bacharier
- Division of Allergy, Immunology and Pulmonary Medicine, Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, Missouri
| | - Scott T Weiss
- Channing Division of Network Medicine, Department of Medicine, Harvard Medical School and Brigham and Women’s Hospital, Boston, Massachusetts
| | - D Michael Nelson
- Department of Obstetrics & Gynecology, Washington University School of Medicine in St. Louis, St. Louis, Missouri
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107
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Johansson Å, Rask-Andersen M, Karlsson T, Ek WE. Genome-wide association analysis of 350 000 Caucasians from the UK Biobank identifies novel loci for asthma, hay fever and eczema. Hum Mol Genet 2020; 28:4022-4041. [PMID: 31361310 PMCID: PMC6969355 DOI: 10.1093/hmg/ddz175] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 05/29/2019] [Accepted: 06/03/2019] [Indexed: 12/19/2022] Open
Abstract
Even though heritability estimates suggest that the risk of asthma, hay fever and eczema is largely due to genetic factors, previous studies have not explained a large part of the genetics behind these diseases. In this genome-wide association study, we include 346 545 Caucasians from the UK Biobank to identify novel loci for asthma, hay fever and eczema and replicate novel loci in three independent cohorts. We further investigate if associated lead single nucleotide polymorphisms (SNPs) have a significantly larger effect for one disease compared to the other diseases, to highlight possible disease-specific effects. We identified 141 loci, of which 41 are novel, to be associated (P ≤ 3 × 10−8) with asthma, hay fever or eczema, analyzed separately or as disease phenotypes that includes the presence of different combinations of these diseases. The largest number of loci was associated with the combined phenotype (asthma/hay fever/eczema). However, as many as 20 loci had a significantly larger effect on hay fever/eczema only compared to their effects on asthma, while 26 loci exhibited larger effects on asthma compared with their effects on hay fever/eczema. At four of the novel loci, TNFRSF8, MYRF, TSPAN8, and BHMG1, the lead SNPs were in Linkage Disequilibrium (LD) (>0.8) with potentially casual missense variants. Our study shows that a large amount of the genetic contribution is shared between the diseases. Nonetheless, a number of SNPs have a significantly larger effect on one of the phenotypes, suggesting that part of the genetic contribution is more phenotype specific.
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Affiliation(s)
- Åsa Johansson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Mathias Rask-Andersen
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Torgny Karlsson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Weronica E Ek
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- To whom correspondence should be addressed at: Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, PO Box 815, 75108, Uppsala, Sweden. Tel: +46703519004; Fax: +46184714931;
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108
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van Sadelhoff JHJ, Wiertsema SP, Garssen J, Hogenkamp A. Free Amino Acids in Human Milk: A Potential Role for Glutamine and Glutamate in the Protection Against Neonatal Allergies and Infections. Front Immunol 2020; 11:1007. [PMID: 32547547 PMCID: PMC7270293 DOI: 10.3389/fimmu.2020.01007] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 04/28/2020] [Indexed: 12/12/2022] Open
Abstract
Breastfeeding is indicated to support neonatal immune development and to protect against neonatal infections and allergies. Human milk composition is widely studied in relation to these unique abilities, which has led to the identification of various immunomodulating components in human milk, including various bioactive proteins. In addition to proteins, human milk contains free amino acids (FAAs), which have not been well-studied. Of those, the FAAs glutamate and glutamine are by far the most abundant. Levels of these FAAs in human milk sharply increase during the first months of lactation, in contrast to most other FAAs. These unique dynamics are globally consistent, suggesting that their levels in human milk are tightly regulated throughout lactation and, consequently, that they might have specific roles in the developing neonate. Interestingly, free glutamine and glutamate are reported to exhibit immunomodulating capacities, indicating that these FAAs could contribute to neonatal immune development and to the unique protective effects of breastfeeding. This review describes the current understanding of the FAA composition in human milk. Moreover, it provides an overview of the effects of free glutamine and glutamate on immune parameters relevant for allergic sensitization and infections in early life. The data reviewed provide rationale to study the role of free glutamine and glutamate in human milk in the protection against neonatal allergies and infections.
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Affiliation(s)
- Joris H J van Sadelhoff
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | | | - Johan Garssen
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, Netherlands.,Danone Nutricia Research, Utrecht, Netherlands
| | - Astrid Hogenkamp
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, Netherlands
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109
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Fereidouni M, Ferns GA, Bahrami A. Current status and perspectives regarding the association between allergic disorders and cancer. IUBMB Life 2020; 72:1322-1339. [PMID: 32458542 DOI: 10.1002/iub.2285] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 03/05/2020] [Accepted: 03/19/2020] [Indexed: 12/18/2022]
Abstract
While activation of immune system may lead to a lower risk of some diseases, it has been shown that a history of atopic allergic disorders such as asthma, hay fever, eczema, and food allergies could be related to several types of cancer. However, the evidence is not entirely conclusive. Two proposals suggest a possible mechanism for the association between allergic disorders and cancers: immune surveillance and the antigenic stimulation. The association of allergy and cancer may vary by cancer site and the type of exposure. The aim of current review was to summarize the current knowledge of the association between allergic diseases and the risk of cancers with particular emphasis on case-controls and cohort studies to estimate the cancer risk associated with allergy.
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Affiliation(s)
- Mohammad Fereidouni
- Department of Immunology, Medical school Birjand University of Medical Sciences, Birjand, Iran.,Cellular and Molecular Research Center, Birjand University of Medical Sciences, Birjand, Iran
| | - Gordon A Ferns
- Division of Medical Education, Brighton & Sussex Medical School, Brighton, UK
| | - Afsane Bahrami
- Cellular and Molecular Research Center, Birjand University of Medical Sciences, Birjand, Iran
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110
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Resolving Clinical Phenotypes into Endotypes in Allergy: Molecular and Omics Approaches. Clin Rev Allergy Immunol 2020; 60:200-219. [PMID: 32378146 DOI: 10.1007/s12016-020-08787-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Allergic diseases are highly complex with respect to pathogenesis, inflammation, and response to treatment. Current efforts for allergic disease diagnosis have focused on clinical evidence as a binary outcome. Although outcome status based on clinical phenotypes (observable characteristics) is convenient and inexpensive to measure in large studies, it does not adequately provide insight into the complex molecular determinants of allergic disease. Individuals with similar clinical diagnoses do not necessarily have similar disease etiologies, natural histories, or responses to treatment. This heterogeneity contributes to the ineffective response to treatment leading to an annual estimated cost of $350 billion in the USA alone. There has been a recent focus to deconvolute the clinical heterogeneity of allergic diseases into specific endotypes using molecular and omics approaches. Endotypes are a means to classify patients based on the underlying pathophysiological mechanisms involving distinct functions or treatment response. The advent of high-throughput molecular omics, immunophenotyping, and bioinformatics methods including machine learning algorithms is facilitating the development of endotype-based diagnosis. As we move to the next decade, we should truly start treating clinical endotypes not clinical phenotype. This review highlights current efforts taking place to improve allergic disease endotyping via molecular omics profiling, immunophenotyping, and machine learning approaches in the context of precision diagnostics in allergic diseases. Graphical Abstract.
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111
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Guo H, An J, Yu Z. Identifying Shared Risk Genes for Asthma, Hay Fever, and Eczema by Multi-Trait and Multiomic Association Analyses. Front Genet 2020; 11:270. [PMID: 32373153 PMCID: PMC7176997 DOI: 10.3389/fgene.2020.00270] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 03/05/2020] [Indexed: 12/03/2022] Open
Abstract
Asthma, hay fever and eczema are three comorbid diseases with high prevalence and heritability. Their common genetic architectures have not been well-elucidated. In this study, we first conducted a linkage disequilibrium score regression analysis to confirm the strong genetic correlations between asthma, hay fever and eczema. We then integrated three distinct association analyses (metaCCA multi-trait association analysis, MAGMA genome-wide and MetaXcan transcriptome-wide gene-based tests) to identify shared risk genes based on the large-scale GWAS results in the GeneATLAS database. MetaCCA can detect pleiotropic genes associated with these three diseases jointly. MAGMA and MetaXcan were performed separately to identify candidate risk genes for each of the three diseases. We finally identified 150 shared risk genes, in which 60 genes are novel. Functional enrichment analysis revealed that the shared risk genes are enriched in inflammatory bowel disease, T cells differentiation and other related biological pathways. Our work may provide help on treatment of asthma, hay fever and eczema in clinical applications.
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Affiliation(s)
- Hongping Guo
- Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education and Hunan Key Laboratory for Computation and Simulation in Science and Engineering, Xiangtan University, Hunan, China.,School of Mathematics and Computer Science, Hanjiang Normal University, Hubei, China
| | - Jiyuan An
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
| | - Zuguo Yu
- Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education and Hunan Key Laboratory for Computation and Simulation in Science and Engineering, Xiangtan University, Hunan, China.,School of Electrical Engineering and Computer Science, Queensland University of Technology, Brisbane, QLD, Australia
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112
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Han Y, Jia Q, Jahani PS, Hurrell BP, Pan C, Huang P, Gukasyan J, Woodward NC, Eskin E, Gilliland FD, Akbari O, Hartiala JA, Allayee H. Genome-wide analysis highlights contribution of immune system pathways to the genetic architecture of asthma. Nat Commun 2020; 11:1776. [PMID: 32296059 PMCID: PMC7160128 DOI: 10.1038/s41467-020-15649-3] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 03/17/2020] [Indexed: 12/20/2022] Open
Abstract
Asthma is a chronic and genetically complex respiratory disease that affects over 300 million people worldwide. Here, we report a genome-wide analysis for asthma using data from the UK Biobank and the Trans-National Asthma Genetic Consortium. We identify 66 previously unknown asthma loci and demonstrate that the susceptibility alleles in these regions are, either individually or as a function of cumulative genetic burden, associated with risk to a greater extent in men than women. Bioinformatics analyses prioritize candidate causal genes at 52 loci, including CD52, and demonstrate that asthma-associated variants are enriched in regions of open chromatin in immune cells. Lastly, we show that a murine anti-CD52 antibody mimics the immune cell-depleting effects of a clinically used human anti-CD52 antibody and reduces allergen-induced airway hyperreactivity in mice. These results further elucidate the genetic architecture of asthma and provide important insight into the immunological and sex-specific relevance of asthma-associated risk variants. Asthma is a common disease of the airways for which numerous genetic loci have been identified. Here, Han et al. carry out a genome-wide analysis for asthma to identify additional loci, report sex-stratified and genetic risk score analyses, and functionally follow-up one locus using a murine model of airway hyperreactivity.
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Affiliation(s)
- Yi Han
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA.,Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Qiong Jia
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA.,Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Pedram Shafiei Jahani
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Benjamin P Hurrell
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Calvin Pan
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
| | - Pin Huang
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA.,Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Janet Gukasyan
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA.,Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Nicholas C Woodward
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA.,Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Eleazar Eskin
- Department of Computer Science and Inter-Departmental Program in Bioinformatics, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Frank D Gilliland
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Omid Akbari
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Jaana A Hartiala
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA.,Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Hooman Allayee
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA. .,Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA.
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113
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Miao K, Zhang L, Pan T, Wang Y. Update on the role of endoplasmic reticulum stress in asthma. Am J Transl Res 2020; 12:1168-1183. [PMID: 32355534 PMCID: PMC7191165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 03/23/2020] [Indexed: 06/11/2023]
Abstract
Asthma has long attracted extensive attention because of its recurring symptoms of reversible airflow obstruction, airway hyperresponsiveness (AHR) and airway inflammation. Although accumulating evidence has enabled gradual increases in understanding of the pathogenesis of asthma, many questions regarding the mechanisms underlying asthma onset and progression remain unanswered. Recent advances delineating the potential functions of endoplasmic reticulum (ER) stress in meeting the need for an airway hypersensitivity response have revealed critical roles of unfolded protein response (UPR) pathways in asthma. In this review, we highlight the roles of ER stress and UPR activation in the etiology, pathogenesis and treatment of asthma and discuss whether the related mechanisms could be targets for therapeutic strategies.
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Affiliation(s)
- Kang Miao
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Pulmonary Diseases of Health Ministry, Key Cite of National Clinical Research Center for Respiratory Disease, Wuhan Clinical Medical Research Center for Chronic Airway Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology 1095 Jiefang Ave, Wuhan 430030, China
| | - Lei Zhang
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Pulmonary Diseases of Health Ministry, Key Cite of National Clinical Research Center for Respiratory Disease, Wuhan Clinical Medical Research Center for Chronic Airway Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology 1095 Jiefang Ave, Wuhan 430030, China
| | - Ting Pan
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Pulmonary Diseases of Health Ministry, Key Cite of National Clinical Research Center for Respiratory Disease, Wuhan Clinical Medical Research Center for Chronic Airway Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology 1095 Jiefang Ave, Wuhan 430030, China
| | - Yi Wang
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Pulmonary Diseases of Health Ministry, Key Cite of National Clinical Research Center for Respiratory Disease, Wuhan Clinical Medical Research Center for Chronic Airway Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology 1095 Jiefang Ave, Wuhan 430030, China
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114
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Genetic profiling for disease stratification in chronic obstructive pulmonary disease and asthma. Curr Opin Pulm Med 2020; 25:317-322. [PMID: 30762612 DOI: 10.1097/mcp.0000000000000568] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
PURPOSE OF REVIEW In asthma and chronic obstructive pulmonary disease (COPD), the movement towards genetic profiling with a push towards 'personalized medicine' has been hindered by complex environment--gene interactions and lack of tools to identify clear causal genetic traits. In this review, we will discuss the need for genetic profiling in asthma and COPD, what methods are currently used in the clinics and the recent finding using new sequencing methods. RECENT FINDINGS Over the past 10-15 years, genome-wide association studies analysis of common variants has provide little in the way of new genetic profiling markers for asthma and COPD. Whole exome/genome sequencing has provided a new method to identify lowly abundant alleles, which might have a much higher impact. Although, low population numbers due to high costs has hindered early studies, recent studies have reached genome wide significance. SUMMARY The use of genetic profiling of COPD in the clinic is current limited to the identification of Alpha-1 antitrypsin deficiency, while being absent in asthma. Advances in sequencing technology provide new avenues to identify disease causes or therapy response altering variants that in the short-term will allow for the development of screening procedures for disease to identify patients at risk of developing asthma or COPD.
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115
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Shao Y, Zhang Y, Liu M, Fernandez-Beros ME, Qian M, Reibman J. Gene-Environment Interaction between the IL1RN Variants and Childhood Environmental Tobacco Smoke Exposure in Asthma Risk. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17062036. [PMID: 32204425 PMCID: PMC7142766 DOI: 10.3390/ijerph17062036] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/16/2020] [Accepted: 03/17/2020] [Indexed: 12/14/2022]
Abstract
(1) Background: Variants of the interleukin-1 receptor antagonist (IL1RN) gene, encoding an anti-inflammatory cytokine, are associated with asthma. Asthma is a chronic inflammatory disease of the airway influenced by interactions between genetic variants and environmental factors. We discovered a gene-environment interaction (GEI) of IL1RN polymorphisms with childhood environmental tobacco smoke (ETS) exposure on asthma susceptibility in an urban adult population. (2) Methods: DNA samples from the NYU/Bellevue Asthma Registry were genotyped for tag SNPs in IL1RN in asthma cases and unrelated healthy controls. Logistic regressions were used to study the GEI between IL1RN variants and childhood ETS exposures on asthma and early onset asthma, respectively, adjusting for population admixture and other covariates. (3) Results: Whereas the rare genotypes of IL1RN SNPs (e.g., GG in SNP rs2234678) were associated with decreased risk for asthma among those without ETS exposure (odds ratio OR = 0.215, p = 0.021), they are associated with increased risk for early onset asthma among those with childhood ETS (OR = 4.467, p = 0.021). (4) Conclusions: We identified a GEI between polymorphisms of IL1RN and childhood ETS exposure in asthma. Analysis of GEI indicated that childhood ETS exposure disrupted the protective effect of some haplotypes/genotypes of IL1RN for asthma and turned them into high-risk polymorphisms for early onset asthma.
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Affiliation(s)
- Yongzhao Shao
- Division of Biostatistics, Department of Population Health, School of Medicine (SOM), New York University, New York, NY 10016, USA; (Y.Z.); (M.L.); (M.Q.)
- Department of Environmental Medicine, SOM, New York University, New York, NY 10016, USA
- Correspondence: (Y.S.); (J.R.)
| | - Yian Zhang
- Division of Biostatistics, Department of Population Health, School of Medicine (SOM), New York University, New York, NY 10016, USA; (Y.Z.); (M.L.); (M.Q.)
- Department of Environmental Medicine, SOM, New York University, New York, NY 10016, USA
| | - Mengling Liu
- Division of Biostatistics, Department of Population Health, School of Medicine (SOM), New York University, New York, NY 10016, USA; (Y.Z.); (M.L.); (M.Q.)
- Department of Environmental Medicine, SOM, New York University, New York, NY 10016, USA
| | - Maria-Elena Fernandez-Beros
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, SOM, New York University, New York, NY 10016, USA;
| | - Meng Qian
- Division of Biostatistics, Department of Population Health, School of Medicine (SOM), New York University, New York, NY 10016, USA; (Y.Z.); (M.L.); (M.Q.)
| | - Joan Reibman
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, SOM, New York University, New York, NY 10016, USA;
- Correspondence: (Y.S.); (J.R.)
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116
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Guillen-Guio B, Hernández-Beeftink T, Marcelino-Rodríguez I, Rodríguez-Pérez H, Lorenzo-Salazar JM, Espinilla-Peña M, Corrales A, Pino-Yanes M, Callero A, Perez-Rodriguez E, Villar J, González-Montelongo R, Flores C. Admixture mapping of asthma in southwestern Europeans with North African ancestry influences. Am J Physiol Lung Cell Mol Physiol 2020; 318:L965-L975. [PMID: 32186396 DOI: 10.1152/ajplung.00344.2019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The prevalence of asthma symptoms in Canary Islanders, a southwestern European population from Spain, is almost three times higher than the country average. Because the genetic risks identified so far explain <5% of asthma heritability, here we aimed to discover new asthma loci by completing the first admixture mapping study in Canary Islanders leveraging their distinctive genetic makeup, where significant northwest African influences coexist in the European genetic diversity landscape. A 2-stage study was conducted in 1,491 unrelated individuals self-declaring having a Canary Islands origin for the 4 grandparents. Local ancestry estimates were obtained for the shared positions with reference data from putative ancestral populations from Europe, North Africa, and sub-Saharan Africa. Case-control deviations in local ancestry were tested for each ancestry separately using logistic regressions adjusted for principal components, followed by fine-mapping analyses based on imputed genotypes and analyses of the likely deleterious exonic variants. The admixture mapping analysis of asthma detected that local North African ancestry in a locus spanning 365 kb of chromosome 16q23.3 was associated with asthma risk at study-wide significance [lowest P = 1.12 × 10-4; odds ratio (OR) = 2.05; 95% confidence interval (CI) = 1.41-3.00]. Fine-mapping studies identified a variant associated with asthma, and results were replicated in independent samples (rs3852738, OR = 1.34; 95% CI = 1.13-1.59, P = 7.58 × 10-4). Whole exome sequencing data from a subset of individuals revealed an enrichment of likely deleterious variants among asthma cases in 16q23.3, particularly in the phospholipase Cγ2 (PLCG2) gene (P = 3.67 × 10-4). By completing the first mapping study of asthma in admixed populations from Europe, our results revealed a new plausible asthma locus.
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Affiliation(s)
- Beatriz Guillen-Guio
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Tamara Hernández-Beeftink
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.,Research Unit, Hospital Universitario de Gran Canaria Doctor Negrín, Las Palmas de Gran Canaria, Spain
| | - Itahisa Marcelino-Rodríguez
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Héctor Rodríguez-Pérez
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Jose M Lorenzo-Salazar
- Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain
| | - Marta Espinilla-Peña
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Almudena Corrales
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Maria Pino-Yanes
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.,Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, La Laguna, Santa Cruz de Tenerife, Spain.,Instituto de Tecnologías Biomédicas, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Ariel Callero
- Allergy Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
| | - Eva Perez-Rodriguez
- Allergy Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
| | - Jesús Villar
- Research Unit, Hospital Universitario de Gran Canaria Doctor Negrín, Las Palmas de Gran Canaria, Spain.,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | | | - Carlos Flores
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.,Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain.,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.,Instituto de Tecnologías Biomédicas, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
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117
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Jones SJ, Stroshein S, Williams AM, Liu D, Spinelli JJ, Connors JM, Brooks-Wilson AR. Birth Order, Sibship Size, Childhood Environment and Immune-Related Disorders, and Risk of Lymphoma in Lymphoid Cancer Families. Cancer Epidemiol Biomarkers Prev 2020; 29:1168-1178. [PMID: 32169998 DOI: 10.1158/1055-9965.epi-19-1204] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 12/04/2019] [Accepted: 03/09/2020] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Familial aggregation of lymphoid cancers and immune-related disorders suggests a role for genetic susceptibility; however, few studies examine environmental factors. According to the hygiene hypothesis, adult-onset immune-related diseases may be a consequence of reduced childhood infectious exposures and aberrant immune development. In a cohort of 196 multiple-case lymphoid cancer families, we analyzed environmental factors related to the hygiene hypothesis. METHODS Family structure, childhood environment, and immune-related disorders were examined among 196 lymphoid cancer families, in relation to risk of lymphoid cancer. We report on 450 lymphoid cancer cases and 1,018 unaffected siblings using logistic regression models with generalized estimating equations to estimate ORs and 95% confidence intervals (CI) for association. RESULTS The risk of lymphoma tended to decrease with later birth order (OR = 0.83; 95% CI, 0.78-0.89) and larger sibship size (OR = 0.82; 95% CI, 0.79-0.85). High maternal education, above average family income during childhood, allergies (OR = 2.25; 95% CI, 1.44-3.51), and tonsillectomy (OR = 1.78; 95% CI, 1.14-2.78) were independent risk factors for lymphoma. Familial lymphoid cancer cases were more likely to report environment (OR = 1.90; 95% CI, 1.21-2.98) and drug (OR = 2.30; 95% CI, 1.41-3.73) allergies. CONCLUSIONS These associations underscore the complex etiology of familial lymphoma. To our knowledge, this is the largest multiple-case family-based study that supports the hygiene hypothesis contributing to lymphoid cancer risk. IMPACT Understanding the mechanism by which environmental and lifestyle factors affect lymphoid cancer risk may advance cancer prevention, even in the familial context.
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Affiliation(s)
- Samantha J Jones
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer, Vancouver, British Columbia, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sumara Stroshein
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Amy M Williams
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Dongmeng Liu
- Department of Statistics and Actuarial Science, Simon Fraser University, Burnaby, British Columbia, Canada
| | - John J Spinelli
- Population Oncology, British Columbia Cancer, Vancouver, British Columbia, Canada.,School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Joseph M Connors
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Angela R Brooks-Wilson
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer, Vancouver, British Columbia, Canada. .,Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, British Columbia, Canada
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118
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Tang HHF, Sly PD, Holt PG, Holt KE, Inouye M. Systems biology and big data in asthma and allergy: recent discoveries and emerging challenges. Eur Respir J 2020; 55:13993003.00844-2019. [PMID: 31619470 DOI: 10.1183/13993003.00844-2019] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 09/12/2019] [Indexed: 12/15/2022]
Abstract
Asthma is a common condition caused by immune and respiratory dysfunction, and it is often linked to allergy. A systems perspective may prove helpful in unravelling the complexity of asthma and allergy. Our aim is to give an overview of systems biology approaches used in allergy and asthma research. Specifically, we describe recent "omic"-level findings, and examine how these findings have been systematically integrated to generate further insight.Current research suggests that allergy is driven by genetic and epigenetic factors, in concert with environmental factors such as microbiome and diet, leading to early-life disturbance in immunological development and disruption of balance within key immuno-inflammatory pathways. Variation in inherited susceptibility and exposures causes heterogeneity in manifestations of asthma and other allergic diseases. Machine learning approaches are being used to explore this heterogeneity, and to probe the pathophysiological patterns or "endotypes" that correlate with subphenotypes of asthma and allergy. Mathematical models are being built based on genomic, transcriptomic and proteomic data to predict or discriminate disease phenotypes, and to describe the biomolecular networks behind asthma.The use of systems biology in allergy and asthma research is rapidly growing, and has so far yielded fruitful results. However, the scale and multidisciplinary nature of this research means that it is accompanied by new challenges. Ultimately, it is hoped that systems medicine, with its integration of omics data into clinical practice, can pave the way to more precise, personalised and effective management of asthma.
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Affiliation(s)
- Howard H F Tang
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Australia .,Cambridge Baker Systems Genomics Initiative, Dept of Public Health and Primary Care, University of Cambridge, Cambridge, UK.,School of BioSciences, The University of Melbourne, Parkville, Australia
| | - Peter D Sly
- Queensland Children's Medical Research Institute, The University of Queensland, Brisbane, Australia.,Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Patrick G Holt
- Queensland Children's Medical Research Institute, The University of Queensland, Brisbane, Australia.,Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Kathryn E Holt
- Dept of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Australia.,London School of Hygiene and Tropical Medicine, London, UK
| | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Australia.,Cambridge Baker Systems Genomics Initiative, Dept of Public Health and Primary Care, University of Cambridge, Cambridge, UK.,School of BioSciences, The University of Melbourne, Parkville, Australia.,The Alan Turing Institute, London, UK
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119
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Friedlander HM, Ford JA, Zaccardelli A, Terrio AV, Cho MH, Sparks JA. Obstructive lung diseases and risk of rheumatoid arthritis. Expert Rev Clin Immunol 2020; 16:37-50. [PMID: 31774329 DOI: 10.1080/1744666x.2019.1698293] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Introduction: Smoking is an established risk factor for both lung diseases and rheumatoid arthritis (RA). Chronic mucosal airway inflammation may result in immune tolerance loss, neoantigen formation, and production of RA-related autoantibodies that increase the subsequent risk of RA. In this review, we aimed to summarize the current evidence supporting the role of obstructive lung diseases and subsequent risk of RA.Areas covered: We identified scientific articles discussing the biologic mechanisms linking mucosal airway inflammation and RA risk. We also identified studies investigating asthma, chronic obstructive pulmonary disease, bronchiectasis, cystic fibrosis, chronic tuberculous and nontuberculous mycobacterial infections, and interstitial lung disease with subsequent risk for RA.Expert opinion: The current evidence supports the hypothesis that mucosal airway inflammation may increase the risk of developing RA. However, most studies investigating this relationship have been retrospective and may not have adequately addressed the role of smoking. Larger prospective studies may provide stronger evidence for obstructive lung disease and RA risk. Determining the role of obstructive lung disease in RA pathogenesis may provide opportunity for RA prevention and screening strategies, while identifying novel biologic mechanisms that could offer targets to improve treatment and outcomes.
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Affiliation(s)
- H Maura Friedlander
- Brigham and Women's Hospital, Division of Rheumatology, Immunology and Allergy, Boston, MA, USA
| | - Julia A Ford
- Brigham and Women's Hospital, Division of Rheumatology, Immunology and Allergy, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Alessandra Zaccardelli
- Brigham and Women's Hospital, Division of Rheumatology, Immunology and Allergy, Boston, MA, USA
| | - Alexsandra V Terrio
- Brigham and Women's Hospital, Division of Rheumatology, Immunology and Allergy, Boston, MA, USA
| | - Michael H Cho
- Harvard Medical School, Boston, MA, USA.,Brigham and Women's Hospital, Division of Pulmonary and Critical Care Medicine, Boston, MA, USA.,Brigham and Women's Hospital, Channing Division of Network Medicine, Boston, MA, USA
| | - Jeffrey A Sparks
- Brigham and Women's Hospital, Division of Rheumatology, Immunology and Allergy, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
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Sestito S, D'Auria E, Baldassarre ME, Salvatore S, Tallarico V, Stefanelli E, Tarsitano F, Concolino D, Pensabene L. The Role of Prebiotics and Probiotics in Prevention of Allergic Diseases in Infants. Front Pediatr 2020; 8:583946. [PMID: 33415087 PMCID: PMC7783417 DOI: 10.3389/fped.2020.583946] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 11/23/2020] [Indexed: 12/15/2022] Open
Abstract
Allergic diseases have been linked to genetic and/or environmental factors, such as antibiotic use, westernized high fat and low fiber diet, which lead to early intestinal dysbiosis, and account for the rise in allergy prevalence, especially in western countries. Allergic diseases have shown reduced microbial diversity, including fewer lactobacilli and bifidobacteria, within the neonatal microbiota, before the onset of atopic diseases. Raised interest in microbiota manipulating strategies to restore the microbial balance for atopic disease prevention, through prebiotics, probiotics, or synbiotics supplementation, has been reported. We reviewed and discussed the role of prebiotics and/or probiotics supplementation for allergy prevention in infants. We searched PubMed and the Cochrane Database using keywords relating to "allergy" OR "allergic disorders," "prevention" AND "prebiotics" OR "probiotics" OR "synbiotics." We limited our evaluation to papers of English language including children aged 0-2 years old. Different products or strains used, different period of intervention, duration of supplementation, has hampered the draw of definitive conclusions on the clinical impact of probiotics and/or prebiotics for prevention of allergic diseases in infants, except for atopic dermatitis in infants at high-risk. This preventive effect on eczema in high-risk infants is supported by clear evidence for probiotics but only moderate evidence for prebiotic supplementation. However, the optimal prebiotic or strain of probiotic, dose, duration, and timing of intervention remains uncertain. Particularly, a combined pre- and post-natal intervention appeared of stronger benefit, although the definition of the optimal intervention starting time during gestation, the timing, and duration in the post-natal period, as well as the best target population, are still an unmet need.
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Affiliation(s)
- Simona Sestito
- Pediatric Unit, Department of Medical and Surgical Sciences, University "Magna Graecia" of Catanzaro, Catanzaro, Italy
| | - Enza D'Auria
- Department of Pediatrics, Vittore Buzzi Children's Hospital-University of Milan, Milan, Italy
| | - Maria Elisabetta Baldassarre
- Neonatology and Neonatal Intensive Care Unit, Department of Biomedical Science and Human Oncology, "Aldo Moro" University of Bari, Bari, Italy
| | - Silvia Salvatore
- Department of Pediatrics, Ospedale "F. Del Ponte", University of Insubria, Varese, Italy
| | - Valeria Tallarico
- Pediatric Unit, Department of Medical and Surgical Sciences, University "Magna Graecia" of Catanzaro, Catanzaro, Italy
| | - Ettore Stefanelli
- Pediatric Unit, Department of Medical and Surgical Sciences, University "Magna Graecia" of Catanzaro, Catanzaro, Italy
| | - Flora Tarsitano
- Pediatric Unit, Department of Medical and Surgical Sciences, University "Magna Graecia" of Catanzaro, Catanzaro, Italy
| | - Daniela Concolino
- Pediatric Unit, Department of Medical and Surgical Sciences, University "Magna Graecia" of Catanzaro, Catanzaro, Italy.,Department of Health Sciences, School of Medicine and Surgery, University Magna Graecia of Catanzaro, Catanzaro, Italy
| | - Licia Pensabene
- Pediatric Unit, Department of Medical and Surgical Sciences, University "Magna Graecia" of Catanzaro, Catanzaro, Italy
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121
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Maazi H, Hartiala JA, Suzuki Y, Crow AL, Shafiei Jahani P, Lam J, Patel N, Rigas D, Han Y, Huang P, Eskin E, Lusis AJ, Gilliland FD, Akbari O, Allayee H. A GWAS approach identifies Dapp1 as a determinant of air pollution-induced airway hyperreactivity. PLoS Genet 2019; 15:e1008528. [PMID: 31869344 PMCID: PMC6944376 DOI: 10.1371/journal.pgen.1008528] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 01/06/2020] [Accepted: 11/15/2019] [Indexed: 02/07/2023] Open
Abstract
Asthma is a chronic inflammatory disease of the airways with contributions from genes, environmental exposures, and their interactions. While genome-wide association studies (GWAS) in humans have identified ~200 susceptibility loci, the genetic factors that modulate risk of asthma through gene-environment (GxE) interactions remain poorly understood. Using the Hybrid Mouse Diversity Panel (HMDP), we sought to identify the genetic determinants of airway hyperreactivity (AHR) in response to diesel exhaust particles (DEP), a model traffic-related air pollutant. As measured by invasive plethysmography, AHR under control and DEP-exposed conditions varied 3-4-fold in over 100 inbred strains from the HMDP. A GWAS with linear mixed models mapped two loci significantly associated with lung resistance under control exposure to chromosomes 2 (p = 3.0x10-6) and 19 (p = 5.6x10-7). The chromosome 19 locus harbors Il33 and is syntenic to asthma association signals observed at the IL33 locus in humans. A GxE GWAS for post-DEP exposure lung resistance identified a significantly associated locus on chromosome 3 (p = 2.5x10-6). Among the genes at this locus is Dapp1, an adaptor molecule expressed in immune-related and mucosal tissues, including the lung. Dapp1-deficient mice exhibited significantly lower AHR than control mice but only after DEP exposure, thus functionally validating Dapp1 as one of the genes underlying the GxE association at this locus. In summary, our results indicate that some of the genetic determinants for asthma-related phenotypes may be shared between mice and humans, as well as the existence of GxE interactions in mice that modulate lung function in response to air pollution exposures relevant to humans. The genetic factors that modulate risk of asthma through gene-environment (GxE) interactions are poorly understood, due in large part to the inherent difficulties in carrying out such studies in humans. To address these challenges, we used the Hybrid Mouse Diversity Panel to elucidate the genetic architecture of asthma-related phenotypes in mice and identify loci that are associated with airway hyperreactivity (AHR) under control exposure conditions and in response to diesel exhaust particles (DEP), as a model traffic-related air pollutant. In the absence of exposure, we identified two loci on chromosomes 2 and 19 for AHR. The locus on chromosome 19 harbors Il33 and is syntenic to association signals observed for asthma at the IL33 locus in humans. In response to DEP exposure, we mapped AHR to a region on chromosome 3 and used a genetically modified mouse model to functionally demonstrate that Dapp1 is one of the genes underlying the GxE association at this locus. Collectively, our results support the concept that some of the genetic determinants for asthma-related phenotypes may be shared between mice and humans as well as the existence of GxE interactions in mice that modulate lung function in response to air pollution exposures relevant to humans.
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Affiliation(s)
- Hadi Maazi
- Departments of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Jaana A. Hartiala
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Yuzo Suzuki
- Departments of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Amanda L. Crow
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Pedram Shafiei Jahani
- Departments of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Jonathan Lam
- Departments of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Nisheel Patel
- Departments of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Diamanda Rigas
- Departments of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Yi Han
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Pin Huang
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Eleazar Eskin
- Department of Computer Science and Inter-Departmental Program in Bioinformatics, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Aldons. J. Lusis
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
| | - Frank D. Gilliland
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Omid Akbari
- Departments of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- * E-mail: (OA); (HA)
| | - Hooman Allayee
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- * E-mail: (OA); (HA)
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Donovan BM, Bastarache L, Turi KN, Zutter MM, Hartert TV. The current state of omics technologies in the clinical management of asthma and allergic diseases. Ann Allergy Asthma Immunol 2019; 123:550-557. [PMID: 31494234 PMCID: PMC6931133 DOI: 10.1016/j.anai.2019.08.460] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 08/27/2019] [Accepted: 08/29/2019] [Indexed: 12/12/2022]
Abstract
OBJECTIVE To review the state of omics science specific to asthma and allergic diseases and discuss the current and potential applicability of omics in clinical disease prediction, treatment, and management. DATA SOURCES Studies and reviews focused on the use of omics technologies in asthma and allergic disease research and clinical management were identified using PubMed. STUDY SELECTIONS Publications were included based on relevance, with emphasis placed on the most recent findings. RESULTS Omics-based research is increasingly being used to differentiate asthma and allergic disease subtypes, identify biomarkers and pathological mediators, predict patient responsiveness to specific therapies, and monitor disease control. Although most studies have focused on genomics and transcriptomics approaches, increasing attention is being placed on omics technologies that assess the effect of environmental exposures on disease initiation and progression. Studies using omics data to identify biological targets and pathways involved in asthma and allergic disease pathogenesis have primarily focused on a specific omics subtype, providing only a partial view of the disease process. CONCLUSION Although omics technologies have advanced our understanding of the molecular mechanisms underlying asthma and allergic disease pathology, omics testing for these diseases are not standard of care at this point. Several important factors need to be addressed before these technologies can be used effectively in clinical practice. Use of clinical decision support systems and integration of these systems within electronic medical records will become increasingly important as omics technologies become more widely used in the clinical setting.
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Affiliation(s)
- Brittney M Donovan
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Lisa Bastarache
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Kedir N Turi
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Mary M Zutter
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Tina V Hartert
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee.
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Nibbering B, Ubags NDJ. Microbial interactions in the atopic march. Clin Exp Immunol 2019; 199:12-23. [PMID: 31777060 DOI: 10.1111/cei.13398] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/29/2019] [Indexed: 12/13/2022] Open
Abstract
The human body is populated by a large number of microorganisms and exist in symbiosis with these immensely diverse communities, which are suggested to influence health and disease. The microbiota plays an essential role in the maturation and function of the immune system. The prevalence of atopic diseases has increased drastically over the past decades, and the co-occurrence of multiple allergic diseases and allergic sensitization starting in early life has gained a great deal of attention. Immune responses in different organs affected by allergic diseases (e.g. skin, intestine and lung) may be linked to microbial changes in peripheral tissues. In the current review, we provide an overview of the current understanding of microbial interactions in allergic diseases and their potential role in the atopic march.
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Affiliation(s)
- B Nibbering
- Faculty of Biology and Medicine, University of Lausanne, Service de Pneumologie, CHUV, Lausanne, Switzerland
| | - N D J Ubags
- Faculty of Biology and Medicine, University of Lausanne, Service de Pneumologie, CHUV, Lausanne, Switzerland
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Hadebe S, Brombacher F. Environment and Host-Genetic Determinants in Early Development of Allergic Asthma: Contribution of Fungi. Front Immunol 2019; 10:2696. [PMID: 31824491 PMCID: PMC6879655 DOI: 10.3389/fimmu.2019.02696] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 11/01/2019] [Indexed: 12/16/2022] Open
Abstract
Asthma is a chronic debilitating airway disease affecting millions of people worldwide. Although largely thought to be a disease of the first world, it is now clear that it is on the rise in many middle- and lower-income countries. The disease is complex, and its etiology is poorly understood, which explains failure of most treatment strategies. We know that in children, asthma is closely linked to poor lung function in the first 3-years of life, when the lung is still undergoing post-natal alveolarization phase. Epidemiological studies also suggest that environmental factors around that age do play a critical part in the establishment of early wheezing which persists until adulthood. Some of the factors that contribute to early development of asthma in children in Western world are clear, however, in low- to middle-income countries this is likely to differ significantly. The contribution of fungal species in the development of allergic diseases is known in adults and in experimental models. However, it is unclear whether early exposure during perinatal or post-natal lung development influences a protective or promotes allergic asthma. Host immune cells and responses will play a crucial part in early development of allergic asthma. How immune cells and their receptors may recognize fungi and promote allergic asthma or protect by tolerance among other immune mechanisms is not fully understood in this early lung development stage. The aim of this review is to discuss what fungal species are present during early exposure as well as their contribution to the development of allergic responses. We also discuss how the host has evolved to promote tolerance to limit hyper-responsiveness to innocuous fungi, and how host evasion by fungi during early development consequentially results in allergic diseases.
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Affiliation(s)
- Sabelo Hadebe
- Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Frank Brombacher
- Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town, South Africa
- Division of Immunology, Faculty of Health Sciences, Institute of Infectious Diseases and Molecular Medicine (IDM), University of Cape Town, Cape Town, South Africa
- Faculty of Health Sciences, Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Institute of Infectious Diseases and Molecular Medicine (IDM), University of Cape Town, Cape Town, South Africa
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Rhinoconjunctivitis among Adolescents in Kuwait and Associated Risk Factors: A Cross-Sectional Study. BIOMED RESEARCH INTERNATIONAL 2019; 2019:3981064. [PMID: 31815136 PMCID: PMC6878814 DOI: 10.1155/2019/3981064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/13/2019] [Accepted: 10/21/2019] [Indexed: 01/01/2023]
Abstract
Rhinoconjunctivitis is a public health problem that causes major illness and disability worldwide. Epidemiological studies intended to determine the burden of rhinoconjunctivitis in Kuwait are limited. Hence, this study sought to estimate the prevalence of rhinoconjunctivitis among adolescents in Kuwait and explore its association with different risk factors. Schoolchildren aged 11–14 years (n = 3,864) were enrolled in a cross-sectional study. Parents completed questionnaires regarding their children's clinical history and symptoms of rhinoconjunctivitis and relevant exposures. Associations were assessed using Poisson regression with robust variance estimation, and adjusted prevalence ratios (aPRs) and 95% confidence intervals (CIs) were estimated. The 12-month (current) prevalence estimates of rhinitis, rhinoconjunctivitis, and severe rhinoconjunctivitis were 28.6% (1,040/3,643), 13.5% (497/3,689), and 1.2% (44/3,689), respectively. The prevalence of current rhinoconjunctivitis symptoms was higher in boys compared to girls (aPR = 1.19, 95% CI: 1.01–1.41). Parental history of rhinitis and asthma showed positive associations with rhinoconjunctivitis in offspring. Trend analyses showed that rhinoconjunctivitis prevalence decreased with increasing numbers of total siblings (aPR = 0.92, Ptrend < 0.001) and older siblings (aPR = 0.90, Ptrend < 0.001). Rhinoconjunctivitis is common among adolescents in Kuwait and its epidemiology is similar to that found in western countries.
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Mucha S, Baurecht H, Novak N, Rodríguez E, Bej S, Mayr G, Emmert H, Stölzl D, Gerdes S, Jung ES, Degenhardt F, Hübenthal M, Ellinghaus E, Kässens JC, Wienbrandt L, Lieb W, Müller-Nurasyid M, Hotze M, Dand N, Grosche S, Marenholz I, Arnold A, Homuth G, Schmidt CO, Wehkamp U, Nöthen MM, Hoffmann P, Paternoster L, Standl M, Bønnelykke K, Ahluwalia TS, Bisgaard H, Peters A, Gieger C, Waldenberger M, Schulz H, Strauch K, Werfel T, Lee YA, Wolfien M, Rosenstiel P, Wolkenhauer O, Schreiber S, Franke A, Weidinger S, Ellinghaus D. Protein-coding variants contribute to the risk of atopic dermatitis and skin-specific gene expression. J Allergy Clin Immunol 2019; 145:1208-1218. [PMID: 31707051 DOI: 10.1016/j.jaci.2019.10.030] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 09/09/2019] [Accepted: 10/07/2019] [Indexed: 12/27/2022]
Abstract
BACKGROUND Fifteen percent of atopic dermatitis (AD) liability-scale heritability could be attributed to 31 susceptibility loci identified by using genome-wide association studies, with only 3 of them (IL13, IL-6 receptor [IL6R], and filaggrin [FLG]) resolved to protein-coding variants. OBJECTIVE We examined whether a significant portion of unexplained AD heritability is further explained by low-frequency and rare variants in the gene-coding sequence. METHODS We evaluated common, low-frequency, and rare protein-coding variants using exome chip and replication genotype data of 15,574 patients and 377,839 control subjects combined with whole-transcriptome data on lesional, nonlesional, and healthy skin samples of 27 patients and 38 control subjects. RESULTS An additional 12.56% (SE, 0.74%) of AD heritability is explained by rare protein-coding variation. We identified docking protein 2 (DOK2) and CD200 receptor 1 (CD200R1) as novel genome-wide significant susceptibility genes. Rare coding variants associated with AD are further enriched in 5 genes (IL-4 receptor [IL4R], IL13, Janus kinase 1 [JAK1], JAK2, and tyrosine kinase 2 [TYK2]) of the IL13 pathway, all of which are targets for novel systemic AD therapeutics. Multiomics-based network and RNA sequencing analysis revealed DOK2 as a central hub interacting with, among others, CD200R1, IL6R, and signal transducer and activator of transcription 3 (STAT3). Multitissue gene expression profile analysis for 53 tissue types from the Genotype-Tissue Expression project showed that disease-associated protein-coding variants exert their greatest effect in skin tissues. CONCLUSION Our discoveries highlight a major role of rare coding variants in AD acting independently of common variants. Further extensive functional studies are required to detect all potential causal variants and to specify the contribution of the novel susceptibility genes DOK2 and CD200R1 to overall disease susceptibility.
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Affiliation(s)
- Sören Mucha
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | - Hansjörg Baurecht
- Department of Dermatology, Venereology and Allergy, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany; Department for Epidemiology and Preventive Medicine, University of Regensburg, Regensburg, Germany
| | - Natalija Novak
- Department of Dermatology and Allergy, University Hospital Bonn, Bonn, Germany
| | - Elke Rodríguez
- Department of Dermatology, Venereology and Allergy, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Saptarshi Bej
- Department of Systems Biology and Bioinformatics, University of Rostock, Germany
| | - Gabriele Mayr
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | - Hila Emmert
- Department of Dermatology, Venereology and Allergy, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Dora Stölzl
- Department of Dermatology, Venereology and Allergy, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Sascha Gerdes
- Department of Dermatology, Venereology and Allergy, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Eun Suk Jung
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany; Department of Internal Medicine and Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Korea
| | - Frauke Degenhardt
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | - Matthias Hübenthal
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany; Department of Dermatology, Venereology and Allergy, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Eva Ellinghaus
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | - Jan Christian Kässens
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | - Lars Wienbrandt
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | - Wolfgang Lieb
- Institute of Epidemiology and Biobank PopGen, Christian Albrechts University of Kiel, Kiel, Germany
| | - Martina Müller-Nurasyid
- Institute of Genetic Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany; Chair of Genetic Epidemiology, IBE, Faculty of Medicine, Ludwig-Maximilians-University Munich, Germany; Department of Internal Medicine I (Cardiology), Hospital of the Ludwig-Maximilians-University Munich, Munich, Germany
| | - Melanie Hotze
- Department of Dermatology, Venereology and Allergy, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Nick Dand
- School of Basic & Medical Biosciences, Faculty of Life Sciences & Medicine, King's College London, London, United Kingdom
| | - Sarah Grosche
- Pediatric Allergology, Experimental and Clinical Research Center, Charité Universitätsmedizin Berlin, Berlin, Germany; Max-Delbrück-Centrum (MDC) for Molecular Medicine, Berlin, Germany
| | - Ingo Marenholz
- Pediatric Allergology, Experimental and Clinical Research Center, Charité Universitätsmedizin Berlin, Berlin, Germany; Max-Delbrück-Centrum (MDC) for Molecular Medicine, Berlin, Germany
| | - Andreas Arnold
- Clinic and Polyclinic of Dermatology, University Medicine Greifswald, Greifswald, Germany
| | - Georg Homuth
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine and Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany
| | - Carsten O Schmidt
- Institute for Community Medicine, Study of Health in Pomerania/KEF, University Medicine Greifswald, Greifswald, Germany
| | - Ulrike Wehkamp
- Department of Dermatology, Venereology and Allergy, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Lavinia Paternoster
- Medical Research Council (MRC) Integrative Epidemiology Unit, Bristol Medical School, and the School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Marie Standl
- Institute of Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | | | - Klaus Bønnelykke
- Copenhagen Prospective Studies on Asthma in Childhood (COPSAC), Herlev and Gentofte Hospital, Gentofte, Denmark
| | - Tarunveer S Ahluwalia
- Copenhagen Prospective Studies on Asthma in Childhood (COPSAC), Herlev and Gentofte Hospital, Gentofte, Denmark; Steno Diabetes Center Copenhagen, Gentofte, Denmark
| | - Hans Bisgaard
- Copenhagen Prospective Studies on Asthma in Childhood (COPSAC), Herlev and Gentofte Hospital, Gentofte, Denmark
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Christian Gieger
- Research Unit of Molecular Epidemiology and Institute of Epidemiology II, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology and Institute of Epidemiology II, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Holger Schulz
- Institute of Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany; Chair of Genetic Epidemiology, IBE, Faculty of Medicine, Ludwig-Maximilians-University Munich, Germany
| | - Thomas Werfel
- Steno Diabetes Center Copenhagen, Gentofte, Denmark; Department of Dermatology and Allergy, Division of Immunodermatology and Allergy Research, Hannover Medical School, Hannover, Germany
| | - Young-Ae Lee
- Department of Internal Medicine I (Cardiology), Hospital of the Ludwig-Maximilians-University Munich, Munich, Germany; School of Basic & Medical Biosciences, Faculty of Life Sciences & Medicine, King's College London, London, United Kingdom
| | - Markus Wolfien
- Department of Systems Biology and Bioinformatics, University of Rostock, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | - Olaf Wolkenhauer
- Department of Systems Biology and Bioinformatics, University of Rostock, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany; First Medical Department, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | - Stephan Weidinger
- Department of Dermatology, Venereology and Allergy, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany.
| | - David Ellinghaus
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany.
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Margolis DJ, Mitra N, Wubbenhorst B, D'Andrea K, Kraya AA, Hoffstad O, Shah S, Nathanson KL. Association of Filaggrin Loss-of-Function Variants With Race in Children With Atopic Dermatitis. JAMA Dermatol 2019; 155:1269-1276. [PMID: 31365035 DOI: 10.1001/jamadermatol.2019.1946] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Importance Atopic dermatitis (AD) is a common chronic illness that has been associated with variation in the filaggrin gene (FLG). Four variants are most often evaluated. Objectives To comprehensively describe and compare results from targeted sequencing of FLG loss-of-function (LoF) variants in children of African and European ancestry and the association of these variants with onset and persistence of AD. Design, Setting, and Participants This prospective US cohort study assessed the genetic subcohort of the Pediatric Eczema Elective Registry (PEER). Children with mild to moderate AD were included in the analysis. Massively parallel sequencing (MPS) was used to focus on FLG LoF variation in white and African American children. Patients were enrolled from June 2005 through July 2017. Data were analyzed from January 25 through May 10, 2019. Main Outcomes and Measures Associations of FLG LoF variation with white and African American ancestry and with the risk and persistence of AD. Results A total of 741 children were included in the analysis (394 [53.2%] female and 347 [46.8%] male; mean [SD] age at onset, 1.97 [2.72] years); of these, 394 (53.2%) were white, 326 (44.0%) were African American, and 21 (2.8%) were of other ancestries. Using MPS technology, 23 FLG LoF variants were found in children with AD. The prevalence of FLG LoF variants was 177 participants (23.9%) in the full cohort, 124 white participants (31.5%), and 50 African American participants (15.3%). The odds ratio for carrying any FLG LoF variant in a white child compared with an African American child with AD was 2.44 (95% CI, 1.76-3.39). Some FLG LoF variants are only found in children of a specific ancestry (eg, p.S3316* and p.R826* were not seen in white patients). Children with an FLG LoF were more likely to have persistent AD (odds ratio, 0.67; 95% CI, 0.56-0.80). Conclusions and Relevance The FLG LoF variants in a US cohort of children with mild to moderate AD differ significantly by race and their association with the persistence of AD. Conventional testing of the 4 frequently evaluated variants is inadequate. Any planned genetic diagnostic test for AD based on FLG LoF variants must be inclusive and not rely on the most frequently studied variants.
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Affiliation(s)
- David J Margolis
- Perelman School of Medicine, University of Pennsylvania, Philadelphia.,Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia.,Department of Dermatology, University of Pennsylvania, Philadelphia
| | - Nandita Mitra
- Perelman School of Medicine, University of Pennsylvania, Philadelphia.,Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia
| | - Bradley Wubbenhorst
- Perelman School of Medicine, University of Pennsylvania, Philadelphia.,Division of Translational Medicine and Human Genetics, Department of Medicine, University of Pennsylvania, Philadelphia
| | - Kurt D'Andrea
- Perelman School of Medicine, University of Pennsylvania, Philadelphia.,Division of Translational Medicine and Human Genetics, Department of Medicine, University of Pennsylvania, Philadelphia
| | - Adam A Kraya
- Perelman School of Medicine, University of Pennsylvania, Philadelphia.,Division of Translational Medicine and Human Genetics, Department of Medicine, University of Pennsylvania, Philadelphia
| | - Ole Hoffstad
- Perelman School of Medicine, University of Pennsylvania, Philadelphia.,Department of Dermatology, University of Pennsylvania, Philadelphia
| | - Saloni Shah
- Perelman School of Medicine, University of Pennsylvania, Philadelphia.,Department of Dermatology, University of Pennsylvania, Philadelphia
| | - Katherine L Nathanson
- Perelman School of Medicine, University of Pennsylvania, Philadelphia.,Division of Translational Medicine and Human Genetics, Department of Medicine, University of Pennsylvania, Philadelphia.,Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia
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128
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Ivanova O, Richards LB, Vijverberg SJ, Neerincx AH, Sinha A, Sterk PJ, Maitland‐van der Zee AH. What did we learn from multiple omics studies in asthma? Allergy 2019; 74:2129-2145. [PMID: 31004501 DOI: 10.1111/all.13833] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 03/25/2019] [Accepted: 04/12/2019] [Indexed: 12/13/2022]
Abstract
More than a decade has passed since the finalization of the Human Genome Project. Omics technologies made a huge leap from trendy and very expensive to routinely executed and relatively cheap assays. Simultaneously, we understood that omics is not a panacea for every problem in the area of human health and personalized medicine. Whilst in some areas of research omics showed immediate results, in other fields, including asthma, it only allowed us to identify the incredibly complicated molecular processes. Along with their possibilities, omics technologies also bring many issues connected to sample collection, analyses and interpretation. It is often impossible to separate the intrinsic imperfection of omics from asthma heterogeneity. Still, many insights and directions from applied omics were acquired-presumable phenotypic clusters of patients, plausible biomarkers and potential pathways involved. Omics technologies develop rapidly, bringing improvements also to asthma research. These improvements, together with our growing understanding of asthma subphenotypes and underlying cellular processes, will likely play a role in asthma management strategies.
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Affiliation(s)
- Olga Ivanova
- Department of Respiratory Medicine, Amsterdam University Medical Centres (AUMC) University of Amsterdam Amsterdam the Netherlands
| | - Levi B. Richards
- Department of Respiratory Medicine, Amsterdam University Medical Centres (AUMC) University of Amsterdam Amsterdam the Netherlands
| | - Susanne J. Vijverberg
- Department of Respiratory Medicine, Amsterdam University Medical Centres (AUMC) University of Amsterdam Amsterdam the Netherlands
| | - Anne H. Neerincx
- Department of Respiratory Medicine, Amsterdam University Medical Centres (AUMC) University of Amsterdam Amsterdam the Netherlands
| | - Anirban Sinha
- Department of Respiratory Medicine, Amsterdam University Medical Centres (AUMC) University of Amsterdam Amsterdam the Netherlands
| | - Peter J. Sterk
- Department of Respiratory Medicine, Amsterdam University Medical Centres (AUMC) University of Amsterdam Amsterdam the Netherlands
| | - Anke H. Maitland‐van der Zee
- Department of Respiratory Medicine, Amsterdam University Medical Centres (AUMC) University of Amsterdam Amsterdam the Netherlands
- Department of Paediatric Pulmonology Amsterdam UMC/ Emma Children's Hospital Amsterdam the Netherlands
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Clark H, Granell R, Curtin JA, Belgrave D, Simpson A, Murray C, Henderson AJ, Custovic A, Paternoster L. Differential associations of allergic disease genetic variants with developmental profiles of eczema, wheeze and rhinitis. Clin Exp Allergy 2019; 49:1475-1486. [PMID: 31441980 PMCID: PMC6899469 DOI: 10.1111/cea.13485] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/11/2019] [Accepted: 08/01/2019] [Indexed: 12/25/2022]
Abstract
BACKGROUND Allergic diseases (eczema, wheeze and rhinitis) in children often present as heterogeneous phenotypes. Understanding genetic associations of specific patterns of symptoms might facilitate understanding of the underlying biological mechanisms. OBJECTIVE To examine associations between allergic disease-related variants identified in a recent genome-wide association study and latent classes of allergic diseases (LCADs) in two population-based birth cohorts. METHODS Eight previously defined LCADs between birth and 11 years: "No disease," "Atopic march," "Persistent eczema and wheeze," "Persistent eczema with later-onset rhinitis," "Persistent wheeze with later-onset rhinitis," "Transient wheeze," "Eczema only" and "Rhinitis only" were used as the study outcome. Weighted multinomial logistic regression was used to estimate associations between 135 SNPs (and a polygenic risk score, PRS) and LCADs among 6345 individuals from The Avon Longitudinal Study of Parents and Children (ALSPAC). Heterogeneity across LCADs was assessed before and after Bonferroni correction. Results were replicated in Manchester Asthma and Allergy Study (MAAS) (n = 896) and pooled in a meta-analysis. RESULTS We found strong evidence for differential genetic associations across the LCADs; pooled PRS heterogeneity P-value = 3.3 × 10-14 , excluding "no disease" class. The associations between the PRS and LCADs in MAAS were remarkably similar to ALSPAC. Two SNPs (a protein-truncating variant in FLG and a SNP within an intron of GSDMB) had evidence for differential association (pooled P-values ≤ 0.006). The FLG locus was differentially associated across LCADs that included eczema, with stronger associations for LCADs with comorbid wheeze and rhinitis. The GSDMB locus in contrast was equally associated across LCADs that included wheeze. CONCLUSIONS AND CLINICAL RELEVANCE We have shown complex, but distinct patterns of genetic associations with LCADs, suggesting that heterogeneous mechanisms underlie individual disease trajectories. Establishing the combination of allergic diseases with which each genetic variant is associated may inform therapeutic development and/or predictive modelling.
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Affiliation(s)
- Hannah Clark
- MRC Integrative Epidemiology Unit (IEU)Population Health SciencesBristol Medical SchoolUniversity of BristolBristolUK
| | - Raquel Granell
- MRC Integrative Epidemiology Unit (IEU)Population Health SciencesBristol Medical SchoolUniversity of BristolBristolUK
| | - John A. Curtin
- Division of Infection, Immunity and Respiratory MedicineSchool of Biological SciencesThe University of ManchesterManchester Academic Health Science Centre, and Manchester University NHS Foundation TrustManchesterUK
| | - Danielle Belgrave
- Section of PaediatricsDepartment of MedicineImperial College LondonLondonUK
| | - Angela Simpson
- Division of Infection, Immunity and Respiratory MedicineSchool of Biological SciencesThe University of ManchesterManchester Academic Health Science Centre, and Manchester University NHS Foundation TrustManchesterUK
| | - Clare Murray
- Division of Infection, Immunity and Respiratory MedicineSchool of Biological SciencesThe University of ManchesterManchester Academic Health Science Centre, and Manchester University NHS Foundation TrustManchesterUK
| | - A. John Henderson
- MRC Integrative Epidemiology Unit (IEU)Population Health SciencesBristol Medical SchoolUniversity of BristolBristolUK
| | - Adnan Custovic
- Section of PaediatricsDepartment of MedicineImperial College LondonLondonUK
| | - Lavinia Paternoster
- MRC Integrative Epidemiology Unit (IEU)Population Health SciencesBristol Medical SchoolUniversity of BristolBristolUK
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130
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Polos J, Fletcher J. Caesarean section and children's health: A quasi-experimental design. POPULATION STUDIES 2019; 73:353-368. [PMID: 31271341 PMCID: PMC7194009 DOI: 10.1080/00324728.2019.1624810] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 01/22/2019] [Indexed: 01/15/2023]
Abstract
The prevalence of inflammatory child health conditions-such as asthma, eczema, and food allergy-and their associated costs have increased rapidly over the last 30 years. While environmental factors likely underpin these increases, recent studies explain only a fraction of the trend and rely on associational methods. Caesarean (or C-) section rates increased dramatically in the period of interest, and this method of delivery is an understudied environmental factor linked to child health outcomes via the gut microbiome. We fuse 22 years of birth cohort data from the United States National Surveys of Children's Health with C-section rates from the National Vital Statistics System generated for subgroups based on state, sex, race, Hispanic origin, and birth year. Then, we model the effects of C-section on rates of asthma, eczema, and food allergy using a quasi-experimental fixed effects design. We find that C-section significantly predicts food allergy, with qualitatively significant implications.
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131
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Zhu Z, Camargo CA, Hasegawa K. Metabolomics in the prevention and management of asthma. Expert Rev Respir Med 2019; 13:1135-1138. [PMID: 31561725 DOI: 10.1080/17476348.2019.1674650] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Zhaozhong Zhu
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Carlos A Camargo
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Kohei Hasegawa
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
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132
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Seguel M, Beechler BR, Coon CC, Snyder PW, Spaan JM, Jolles AE, Ezenwa VO. Immune stability predicts tuberculosis infection risk in a wild mammal. Proc Biol Sci 2019; 286:20191401. [PMID: 31575363 DOI: 10.1098/rspb.2019.1401] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Immunity is one of the most variable phenotypic traits in animals; however, some individuals may show less fluctuation in immune traits, resulting in stable patterns of immune variation over time. It is currently unknown whether immune variation has consequences for infectious disease risk. In this study, we identified moderately stable immune traits in wild African buffalo and asked whether the stability of these traits affected bovine tuberculosis (TB) infection risk. We found that adaptive immune traits such as the level of interferon-γ (IFN-γ) released after white blood cell stimulation, the number of circulating lymphocytes and the level of antibodies against bovine adenovirus-3 were moderately repeatable (i.e. stable) over time, whereas parameters related to innate immunity either had low repeatability (circulating eosinophil numbers) or were not repeatable (e.g. neutrophil numbers, plasma bacteria killing capacity). Intriguingly, individuals with more repeatable IFN-γ and lymphocyte levels were at a significantly higher risk of acquiring TB infection. In stark contrast, average IFN-γ and lymphocyte levels were poor predictors of TB risk, indicating that immune variability rather than absolute response level better captured variation in disease susceptibility. This work highlights the important and under-appreciated role of immune variability as a predictor of infection risk.
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Affiliation(s)
- Mauricio Seguel
- Odum School of Ecology, University of Georgia, Athens, GA, USA
| | - Brianna R Beechler
- Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA
| | - Courtney C Coon
- Department of Veterinary Tropical Diseases, University of Pretoria, Onderstepoort, South Africa.,Felidae Conservation Fund, Mill Valley, CA, USA
| | - Paul W Snyder
- Odum School of Ecology, University of Georgia, Athens, GA, USA.,Department of Integrative Biology, Oregon State University, Corvallis, OR, USA
| | - Johannie M Spaan
- College of Osteopathic Medicine of the Pacific Northwest, Western University of Health Sciences, Lebanon, OR, USA
| | - Anna E Jolles
- Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA.,Department of Integrative Biology, Oregon State University, Corvallis, OR, USA
| | - Vanessa O Ezenwa
- Odum School of Ecology, University of Georgia, Athens, GA, USA.,Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
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133
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Bourdin A, Bjermer L, Brightling C, Brusselle GG, Chanez P, Chung KF, Custovic A, Diamant Z, Diver S, Djukanovic R, Hamerlijnck D, Horváth I, Johnston SL, Kanniess F, Papadopoulos N, Papi A, Russell RJ, Ryan D, Samitas K, Tonia T, Zervas E, Gaga M. ERS/EAACI statement on severe exacerbations in asthma in adults: facts, priorities and key research questions. Eur Respir J 2019; 54:13993003.00900-2019. [PMID: 31467120 DOI: 10.1183/13993003.00900-2019] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 07/17/2019] [Indexed: 01/05/2023]
Abstract
Despite the use of effective medications to control asthma, severe exacerbations in asthma are still a major health risk and require urgent action on the part of the patient and physician to prevent serious outcomes such as hospitalisation or death. Moreover, severe exacerbations are associated with substantial healthcare costs and psychological burden, including anxiety and fear for patients and their families. The European Academy of Allergy and Clinical Immunology (EAACI) and the European Respiratory Society (ERS) set up a task force to search for a clear definition of severe exacerbations, and to also define research questions and priorities. The statement includes comments from patients who were members of the task force.
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Affiliation(s)
- Arnaud Bourdin
- Université de Montpellier, CHU Montpellier, PhyMedExp, INSERM, CNRS, Montpellier, France
| | - Leif Bjermer
- Dept of Respiratory Medicine and Allergy, Lung and Allergy research Unit, Lund, Sweden
| | - Christopher Brightling
- Dept of Infection, Immunity and Inflammation, Institute for Lung Health, NIHR BRC Respiratory Medicine, University of Leicester, Leicester, UK
| | - Guy G Brusselle
- Dept of Respiratory Diseases, Ghent University Hospital, Ghent, Belgium
| | | | - Kian Fan Chung
- National Heart and Lung Institute, Imperial College, London, UK
| | - Adnan Custovic
- Dept of Paediatrics, Imperial College London, London, UK
| | - Zuzana Diamant
- Dept of Respiratory Medicine and Allergology, Skane University Hospital, Lund, Sweden.,Respiratory and Allergy Research, QPS Netherlands, The Netherlands
| | - Sarah Diver
- Dept of Respiratory Sciences, College of Life Sciences, Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, UK
| | - Ratko Djukanovic
- University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | | | - Ildikó Horváth
- National Koranyi Institute for Pulmonology, and Dept of Public Health, Semmelweis University, Budapest, Hungary
| | | | | | - Nikos Papadopoulos
- Division of Infection, Immunity and Respiratory Medicine, University of Manchester, Manchester, UK.,Allergy Dept, 2nd Pediatric Clinic, University of Athens, Athens, Greece
| | - Alberto Papi
- Respiratory Medicine, University of Ferrara, Ferrara, Italy
| | - Richard J Russell
- Institute for Lung Health, NIHR Leicester Biomedical Research Centre, Dept of Infection, Immunity and Inflammation, University of Leicester, Leicester, UK
| | - Dermot Ryan
- Allergy and Respiratory Research Group, Centre for Population Health Sciences, University of Edinburgh, Edinburgh, UK.,Woodbrook Medical Centre, Loughborough, UK
| | | | - Thomy Tonia
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | | | - Mina Gaga
- 7th Respiratory Medicine Dept, Athens Chest Hospital, Athens, Greece
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134
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Lou C, Mitra N, Wubbenhorst B, D'Andrea K, Hoffstad O, Kim BS, Yan A, Zaenglein AL, Fuxench ZC, Nathanson KL, Margolis DJ. Association between fine mapping thymic stromal lymphopoietin and atopic dermatitis onset and persistence. Ann Allergy Asthma Immunol 2019; 123:595-601.e1. [PMID: 31491540 DOI: 10.1016/j.anai.2019.08.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 08/20/2019] [Accepted: 08/24/2019] [Indexed: 12/18/2022]
Abstract
BACKGROUND Atopic dermatitis (AD) is a common chronic relapsing skin disease. Genetic variants have been associated with skin barrier function and immune regulation. Thymic stromal lymphopoietin (TSLP), an immune regulator, has been previously associated with AD. OBJECTIVE To fine map TSLP and evaluate associations with the onset and persistence of AD. METHODS TSLP variation was determined using targeted massively parallel sequencing in a longitudinal cohort of children with AD. Evaluations included linkage disequilibrium and the persistence of AD for as many as 10 years of follow-up. The association between the presence of AD and rs1898671 variation was evaluated in a second independent cohort. RESULTS The minor variant frequency for rs1898671 was 23.5% (95% CI, 21.4%-25.8%). This variant was not in linkage disequilibrium with other TSLP variants in the longitudinal cohort (n = 741). White children with AD were less likely to have rs1898671 variant (odds ratio [OR], 1.41; 95% CI, 1.20-1.66) than Genome Aggregation Database controls. Children with AD and the rs1898671 variant during follow-up were more likely to have remission than children who were wild type for rs1898671 (OR, 1.56; 95% CI, 1.26-1.91). In the second cohort (n = 585), the rs1898671 variant was less prevalent in those with AD than those without. The protective effect was greater in rs1898671 heterozygotes (OR, 1.91; 95% CI, 1.34-2.75) than homozygotes (OR, 1.28; 95% CI, 0.61-2.70). CONCLUSION TSLP and specifically rs1898671 are important in the pathogenesis of AD and could represent a potential clinical target for the development of therapies to treat individuals with AD.
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Affiliation(s)
- Carolyn Lou
- Department of Biostatistics, Epidemiology and Informatics, Perlman School of Medicine, Philadelphia, Pennsylvania
| | - Nandita Mitra
- Department of Biostatistics, Epidemiology and Informatics, Perlman School of Medicine, Philadelphia, Pennsylvania
| | - Bradley Wubbenhorst
- Department of Medicine, Division of Translational Medicine and Human Genetics, Perlman School of Medicine, Philadelphia, Pennsylvania
| | - Kurt D'Andrea
- Department of Medicine, Division of Translational Medicine and Human Genetics, Perlman School of Medicine, Philadelphia, Pennsylvania
| | - Ole Hoffstad
- Department of Biostatistics, Epidemiology and Informatics, Perlman School of Medicine, Philadelphia, Pennsylvania
| | - Brian S Kim
- Washington University School of Medicine, St Louis, Missouri
| | - Albert Yan
- Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Andrea L Zaenglein
- Departments of Dermatology and Pediatrics, Pennsylvania State University/Hershey Medical Center, Hershey, Pennsylvania
| | - Zelma Chiesa Fuxench
- Department of Dermatology, Perlman School of Medicine, Philadelphia, Pennsylvania
| | - Katherine L Nathanson
- Department of Medicine, Division of Translational Medicine and Human Genetics, Perlman School of Medicine, Philadelphia, Pennsylvania
| | - David J Margolis
- Department of Biostatistics, Epidemiology and Informatics, Perlman School of Medicine, Philadelphia, Pennsylvania; Department of Dermatology, Perlman School of Medicine, Philadelphia, Pennsylvania.
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135
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Hachim MY, Hachim IY, Elemam NM, Hamoudi RA. Toxicogenomic analysis of publicly available transcriptomic data can predict food, drugs, and chemical-induced asthma. PHARMACOGENOMICS & PERSONALIZED MEDICINE 2019; 12:181-199. [PMID: 31692590 PMCID: PMC6717055 DOI: 10.2147/pgpm.s217535] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 07/30/2019] [Indexed: 02/04/2023]
Abstract
Background : With the increasing incidence of asthma, more attention is focused on the diverse and complex nutritional and environmental triggers of asthma exacerbations. Currently, there are no established risk assessment tools to evaluate asthma triggering potentials of most of the nutritional and environmental triggers encountered by asthmatic patients. Purpose The objective of this study is to devise a reliable workflow, capable of estimating the toxicogenomic effect of such factors on key player genes in asthma pathogenesis. Methods Gene expression extracted from publicly available datasets of asthmatic bronchial epithelium were subjected to a comprehensive analysis of differential gene expression to identify significant genes involved in asthma development and progression. The identified genes were subjected to Gene Set Enrichment Analysis using a total of 31,826 gene sets related to chemical, toxins, and drugs to identify common agents that share similar asthma-related targets genes and signaling pathways. Results Our analysis identified 225 differentially expressed genes between severe asthmatic and healthy bronchial epithelium. Gene Set Enrichment Analysis of the identified genes showed that they are involved in response to toxic substances and organic cyclic compounds and are targeted by 41 specific diets, plants products, and plants related toxins (eg adenine, arachidonic acid, baicalein, caffeic acid, corilagin, curcumin, ellagic acid, luteolin, microcystin-RR, phytoestrogens, protoporphyrin IX, purpurogallin, rottlerin, and salazinic acid). Moreover, the identified chemicals share interesting inflammation-related pathways like NF-κB. Conclusion Our analysis was able to explain and predict the toxicity in terms of stimulating the differentially expressed genes between severe asthmatic and healthy epithelium. Such an approach can pave the way to generate a cost-effective and reliable source for asthma-specific toxigenic reports thus allowing the asthmatic patients, physicians, and medical researchers to be aware of the potential triggering factors with fatal consequences.
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Affiliation(s)
- Mahmood Yaseen Hachim
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Ibrahim Yaseen Hachim
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Noha M Elemam
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Rifat A Hamoudi
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah 27272, United Arab Emirates.,Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates.,Division of Surgery and Interventional Science, University College London, London, UK
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136
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Replicated methylation changes associated with eczema herpeticum and allergic response. Clin Epigenetics 2019; 11:122. [PMID: 31443688 PMCID: PMC6706929 DOI: 10.1186/s13148-019-0714-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 07/22/2019] [Indexed: 01/06/2023] Open
Abstract
Background Although epigenetic mechanisms are important risk factors for allergic disease, few studies have evaluated DNA methylation differences associated with atopic dermatitis (AD), and none has focused on AD with eczema herpeticum (ADEH+). We will determine how methylation varies in AD individuals with/without EH and associated traits. We modeled differences in genome-wide DNA methylation in whole blood cells from 90 ADEH+, 83 ADEH−, and 84 non-atopic, healthy control subjects, replicating in 36 ADEH+, 53 ADEH−, and 55 non-atopic healthy control subjects. We adjusted for cell-type composition in our models and used genome-wide and candidate-gene approaches. Results We replicated one CpG which was significantly differentially methylated by severity, with suggestive replication at four others showing differential methylation by phenotype or severity. Not adjusting for eosinophil content, we identified 490 significantly differentially methylated CpGs (ADEH+ vs healthy controls, genome-wide). Many of these associated with severity measures, especially eosinophil count (431/490 sites). Conclusions We identified a CpG in IL4 associated with serum tIgE levels, supporting a role for Th2 immune mediating mechanisms in AD. Changes in eosinophil level, a measure of disease severity, are associated with methylation changes, providing a potential mechanism for phenotypic changes in immune response-related traits. Electronic supplementary material The online version of this article (10.1186/s13148-019-0714-1) contains supplementary material, which is available to authorized users.
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137
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Filaggrin sequencing and bioinformatics tools. Arch Dermatol Res 2019; 312:155-158. [PMID: 31372728 DOI: 10.1007/s00403-019-01956-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 07/13/2019] [Indexed: 12/30/2022]
Abstract
Atopic dermatitis (AD) is a common illness that most commonly originates in childhood, but can be seen in all ages. Filaggrin (FLG) loss of function variants have been associated with the onset and severity of atopic dermatitis and are the most common genetic association with AD. Previous studies have shown variability in the frequency of FLG variants. We have recently demonstrated that previous FLG genotyping methods were inadequate for proper genotyping. In this concise report, we show that genotyping using a popular older informatics program is problematic. In fact, publications that used the older program likely do not properly capture all FLG variants.
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138
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Cait A, Cardenas E, Dimitriu PA, Amenyogbe N, Dai D, Cait J, Sbihi H, Stiemsma L, Subbarao P, Mandhane PJ, Becker AB, Moraes TJ, Sears MR, Lefebvre DL, Azad MB, Kollmann T, Turvey SE, Mohn WW. Reduced genetic potential for butyrate fermentation in the gut microbiome of infants who develop allergic sensitization. J Allergy Clin Immunol 2019; 144:1638-1647.e3. [PMID: 31279007 DOI: 10.1016/j.jaci.2019.06.029] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 06/06/2019] [Accepted: 06/13/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND Allergic disease is the most frequent chronic health issue in children and has been linked to early-life gut microbiome dysbiosis. Many lines of evidence suggest that microbially derived short-chain fatty acids, and particularly butyrate, can promote immune tolerance. OBJECTIVE We sought to determine whether bacterial butyrate production in the gut during early infancy is protective against the development of atopic disease in children. METHODS We used shotgun metagenomic analysis to determine whether dysbiosis in butyrate fermentation could be identified in human infants, before their developing allergic disease. RESULTS We found that the microbiome of infants who went on to develop allergic sensitization later in childhood lacked genes encoding key enzymes for carbohydrate breakdown and butyrate production. CONCLUSIONS Our findings support the importance of microbial carbohydrate metabolism during early infancy in protecting against the development of allergies.
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Affiliation(s)
- Alissa Cait
- Department of Microbiology & Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Erick Cardenas
- Department of Microbiology & Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Pedro A Dimitriu
- Department of Microbiology & Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nelly Amenyogbe
- Department of Microbiology & Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Darlene Dai
- Department of Pediatrics, BC Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jessica Cait
- Biomedical Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hind Sbihi
- Department of Pediatrics, BC Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Leah Stiemsma
- Department of Microbiology & Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada; Department of Pediatrics, BC Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Padmaja Subbarao
- Department of Pediatrics & Physiology, University of Toronto, Toronto, Ontario, Canada; Hospital for Sick Children, Toronto, Ontario, Canada
| | - Piush J Mandhane
- Department of Pediatrics, University of Alberta, Edmonton, Alberta, Canada; School of Public Health, University of Alberta, Edmonton, Alberta, Canada
| | - Allen B Becker
- Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Theo J Moraes
- Department of Pediatrics & Physiology, University of Toronto, Toronto, Ontario, Canada; Hospital for Sick Children, Toronto, Ontario, Canada
| | - Malcolm R Sears
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Diana L Lefebvre
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Meghan B Azad
- Developmental Origins of Chronic Diseases in Children Network (DEVOTION), Department of Pediatrics and Child Health, Children's Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Tobias Kollmann
- Department of Pediatrics, BC Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Stuart E Turvey
- Department of Pediatrics, BC Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada.
| | - William W Mohn
- Department of Microbiology & Immunology, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada.
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139
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Krautenbacher N, Flach N, Böck A, Laubhahn K, Laimighofer M, Theis FJ, Ankerst DP, Fuchs C, Schaub B. A strategy for high-dimensional multivariable analysis classifies childhood asthma phenotypes from genetic, immunological, and environmental factors. Allergy 2019; 74:1364-1373. [PMID: 30737985 PMCID: PMC6767756 DOI: 10.1111/all.13745] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Revised: 12/22/2018] [Accepted: 01/06/2019] [Indexed: 12/14/2022]
Abstract
Background Associations between childhood asthma phenotypes and genetic, immunological, and environmental factors have been previously established. Yet, strategies to integrate high‐dimensional risk factors from multiple distinct data sets, and thereby increase the statistical power of analyses, have been hampered by a preponderance of missing data and lack of methods to accommodate them. Methods We assembled questionnaire, diagnostic, genotype, microarray, RT‐qPCR, flow cytometry, and cytokine data (referred to as data modalities) to use as input factors for a classifier that could distinguish healthy children, mild‐to‐moderate allergic asthmatics, and nonallergic asthmatics. Based on data from 260 German children aged 4‐14 from our university outpatient clinic, we built a novel multilevel prediction approach for asthma outcome which could deal with a present complex missing data structure. Results The optimal learning method was boosting based on all data sets, achieving an area underneath the receiver operating characteristic curve (AUC) for three classes of phenotypes of 0.81 (95%‐confidence interval (CI): 0.65‐0.94) using leave‐one‐out cross‐validation. Besides improving the AUC, our integrative multilevel learning approach led to tighter CIs than using smaller complete predictor data sets (AUC = 0.82 [0.66‐0.94] for boosting). The most important variables for classifying childhood asthma phenotypes comprised novel identified genes, namely PKN2 (protein kinase N2), PTK2 (protein tyrosine kinase 2), and ALPP (alkaline phosphatase, placental). Conclusion Our combination of several data modalities using a novel strategy improved classification of childhood asthma phenotypes but requires validation in external populations. The generic approach is applicable to other multilevel data‐based risk prediction settings, which typically suffer from incomplete data.
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Affiliation(s)
- Norbert Krautenbacher
- Institute of Computational Biology Helmholtz Zentrum München German Research Center for Environmental Health GmbH Neuherberg Germany
- Technische Universität München Center for Mathematics Chair of Mathematical Modeling of Biological Systems Garching Germany
| | - Nicolai Flach
- Institute of Computational Biology Helmholtz Zentrum München German Research Center for Environmental Health GmbH Neuherberg Germany
- Technische Universität München Center for Mathematics Chair of Mathematical Modeling of Biological Systems Garching Germany
| | - Andreas Böck
- Department of Pulmonary and Allergy Dr. von Hauner Children's Hospital LMU Munich Germany
| | - Kristina Laubhahn
- Department of Pulmonary and Allergy Dr. von Hauner Children's Hospital LMU Munich Germany
- Member of German Lung Centre (DZL) CPC Munich Germany
| | - Michael Laimighofer
- Institute of Computational Biology Helmholtz Zentrum München German Research Center for Environmental Health GmbH Neuherberg Germany
- Technische Universität München Center for Mathematics Chair of Mathematical Modeling of Biological Systems Garching Germany
| | - Fabian J. Theis
- Institute of Computational Biology Helmholtz Zentrum München German Research Center for Environmental Health GmbH Neuherberg Germany
- Technische Universität München Center for Mathematics Chair of Mathematical Modeling of Biological Systems Garching Germany
| | - Donna P. Ankerst
- Technische Universität München Center for Mathematics Chair of Mathematical Modeling of Biological Systems Garching Germany
- University of Texas Health Science Center at San Antonio San Antonio Texas
| | - Christiane Fuchs
- Institute of Computational Biology Helmholtz Zentrum München German Research Center for Environmental Health GmbH Neuherberg Germany
- Technische Universität München Center for Mathematics Chair of Mathematical Modeling of Biological Systems Garching Germany
- Faculty of Business Administration and Economics Bielefeld University Bielefeld Germany
| | - Bianca Schaub
- Department of Pulmonary and Allergy Dr. von Hauner Children's Hospital LMU Munich Germany
- Member of German Lung Centre (DZL) CPC Munich Germany
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Demirci M, Tokman H, Uysal H, Demiryas S, Karakullukcu A, Saribas S, Cokugras H, Kocazeybek B. Reduced Akkermansia muciniphila and Faecalibacterium prausnitzii levels in the gut microbiota of children with allergic asthma. Allergol Immunopathol (Madr) 2019; 47:365-371. [PMID: 30765132 DOI: 10.1016/j.aller.2018.12.009] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 11/11/2018] [Accepted: 12/04/2018] [Indexed: 02/07/2023]
Abstract
INTRODUCTION AND OBJECTIVES The amounts of Akkermansia muciniphila and Faecalibacterium prausnitzii in gut microbiota are reduced in patients with allergic diseases compared to healthy controls. We aimed to quantify levels of A. muciniphila and F. prausnitzii amounts using real-time quantitative PCR (qPCR) in the gut microbiota of children with allergic asthma and in healthy controls. MATERIALS AND METHODS In total, 92 children between the ages of three and eight who were diagnosed with asthma and 88 healthy children were included in the study and bacterial DNA was isolated from the stool samples using the stool DNA isolation Kit. qPCR assays were studied with the microbial DNA qPCR Kit for A. muciniphila and microbial DNA qPCR Kit for F. prausnitzii. RESULTS Both bacterial species showed a reduction in the patient group compared to healthy controls. A. muciniphila and F. prausnitzii were found to be 5.45±0.004, 6.74±0.01 and 5.71±0.002, 7.28±0.009 in the stool samples of the asthma and healthy control groups, respectively. CONCLUSIONS F. prausnitzii and A. muciniphila may have induced anti-inflammatory cytokine IL-10 and prevented the secretion of pro-inflammatory cytokines like IL-12. These findings suggest that A. muciniphila and F. prausnitzii may suppress inflammation through its secreted metabolites.
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141
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Willis-Owen SAG, Cookson WOC, Moffatt MF. The Genetics and Genomics of Asthma. Annu Rev Genomics Hum Genet 2019; 19:223-246. [PMID: 30169121 DOI: 10.1146/annurev-genom-083117-021651] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Asthma is a common, clinically heterogeneous disease with strong evidence of heritability. Progress in defining the genetic underpinnings of asthma, however, has been slow and hampered by issues of inconsistency. Recent advances in the tools available for analysis-assaying transcription, sequence variation, and epigenetic marks on a genome-wide scale-have substantially altered this landscape. Applications of such approaches are consistent with heterogeneity at the level of causation and specify patterns of commonality with a wide range of alternative disease traits. Looking beyond the individual as the unit of study, advances in technology have also fostered comprehensive analysis of the human microbiome and its varied roles in health and disease. In this article, we consider the implications of these technological advances for our current understanding of the genetics and genomics of asthma.
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Affiliation(s)
- Saffron A G Willis-Owen
- National Heart and Lung Institute, Imperial College London, London SW7 2AZ, United Kingdom; , ,
| | - William O C Cookson
- National Heart and Lung Institute, Imperial College London, London SW7 2AZ, United Kingdom; , ,
| | - Miriam F Moffatt
- National Heart and Lung Institute, Imperial College London, London SW7 2AZ, United Kingdom; , ,
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Abstract
PURPOSE OF REVIEW Recent studies demonstrate an important role of the secreted apolipoprotein A-I binding protein (AIBP) in regulation of cholesterol efflux and lipid rafts. The article discusses these findings in the context of angiogenesis and inflammation. RECENT FINDINGS Lipid rafts are cholesterol-rich and sphingomyelin-rich membrane domains in which many receptor complexes assemble upon activation. AIBP mediates selective cholesterol efflux, in part via binding to toll-like receptor-4 (TLR4) in activated macrophages and microglia, and thus reverses lipid raft increases in activated cells. Recent articles report AIBP regulation of vascular endothelial growth factor receptor-2, Notch1 and TLR4 function. In zebrafish and mouse animal models, AIBP deficiency results in accelerated angiogenesis, increased inflammation and exacerbated atherosclerosis. Spinal delivery of recombinant AIBP reduces neuraxial inflammation and reverses persistent pain state in a mouse model of chemotherapy-induced polyneuropathy. Inhalation of recombinant AIBP reduces lipopolysaccharide-induced acute lung injury in mice. These findings are discussed in the perspective of AIBP's proposed other function, as an NAD(P)H hydrate epimerase, evolving into a regulator of cholesterol trafficking and lipid rafts. SUMMARY Novel findings of AIBP regulatory circuitry affecting lipid rafts and related cellular processes may provide new therapeutic avenues for angiogenic and inflammatory diseases.
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Affiliation(s)
- Longhou Fang
- Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, Houston Methodist DeBakey Heart and Vascular Center, Houston Methodist, 6550 Fannin St, TX77030
- Department of Cell and Developmental Biology, Weill Cornell Medical College, 407 E 61st St, New York, NY 10065
| | - Yury I. Miller
- Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093
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143
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Shen J, Zhao J, Ye QY, Gu XD. Interference of miR-943-3p with secreted frizzled-related proteins4 (SFRP4) in an asthma mouse model. Cell Tissue Res 2019; 378:67-80. [PMID: 31101982 DOI: 10.1007/s00441-019-03026-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 04/01/2019] [Indexed: 01/08/2023]
Abstract
The aim of this study is to investigate the potential roles of miR-943-3p and its target gene secreted frizzled-related proteins4 (SFRP4) in allergic asthma and elucidate its underlying mechanism, which may prompt a new clue about developing novel treatments of this disease. An allergic asthma mouse model was generated by challenging with ovalbumin (OVA); lung pathological features of mice were viewed using H&E staining; thickness of subepithelial fibrosis and smooth muscle was measured using Masson's trichrome staining. Inflammatory cells from bronchoalveolar lavage fluid (BALF) were counted based on Diff-Quik staining and morphometric analysis. Expressions of miR-943-3p, SFRP4 and Wnt signal pathway-associated proteins were detected using RT-PCR or immunoblotting, respectively. SFRP4 was downregulated in the bronchial biopsies of allergic asthma patients and represented a unique intersection between differentially expressed genes (DEGs) and genes in the Wnt signal pathway. Both miR-943-3p upregulation and SFRP4 downregulation were detected in allergic asthma patients and OVA-induced mice. Besides, OVA-induced mice possessed more inflammatory cells in BALF including macrophage (mac), eosinophil (eos), lymphocyte (lym) and neutrophil (neu), higher expression of collagen, β-catenin and c-Myc as well as thicker subepithelial fibrosis and smooth muscle in lung than control mice. In vivo delivery of miR-943-3p agomir worsened these symptoms, while both miR-943-3p antagomir and Ad-SFRP4 administration effectively alleviated this disease. Taken together, miR-943-3p accelerated the progression of airway inflammation and remodeling in allergic asthma via suppressing the activity of SFRP4 through Wnt signaling pathway in asthma patients and OVA-induced mice.
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Affiliation(s)
- Jian Shen
- Department of Pediatrics, Shuguang Hospital Affiliated to Shanghai Traditional Chinese Medical University, No. 528 Zhangheng Road, Pudong New Area, Shanghai, 201203, China.
| | - Jun Zhao
- Department of Pediatrics, Shuguang Hospital Affiliated to Shanghai Traditional Chinese Medical University, No. 528 Zhangheng Road, Pudong New Area, Shanghai, 201203, China
| | - Qing-Yan Ye
- Department of Pediatrics, Shuguang Hospital Affiliated to Shanghai Traditional Chinese Medical University, No. 528 Zhangheng Road, Pudong New Area, Shanghai, 201203, China
| | - Xi-Dong Gu
- Department of Clinical Laboratory, Shuguang Hospital Affiliated to Shanghai Traditional Chinese Medical University, Shanghai, 201203, China
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144
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Daya M, Barnes KC. African American ancestry contribution to asthma and atopic dermatitis. Ann Allergy Asthma Immunol 2019; 122:456-462. [PMID: 30772392 PMCID: PMC6500742 DOI: 10.1016/j.anai.2019.02.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 02/06/2019] [Accepted: 02/08/2019] [Indexed: 02/06/2023]
Abstract
OBJECTIVE Asthma and atopic dermatitis (AD) are complex diseases with striking disparities across racial and ethnic groups, which may be partly attributable to genetic factors. Here we summarize current knowledge from asthma and AD genome-wide association studies (GWAS) and pharmacogenetic studies in African ancestry populations. DATA SOURCES GWAS catalog; PUBMed. STUDY SELECTIONS GWAS catalog studies with trait annotations "asthma" and "atopic eczema" and African ancestry individuals in the discovery dataset; the recent CAAPA asthma GWAS; reports on pharmacogenetic studies in asthma and AD. RESULTS Although GWASs have revolutionized gene discovery for multiple complex traits, African Americans continue to be severely underrepresented in sufficiently powered genetics studies. Indeed, of the 16 asthma and 21 AD loci that reached genomewide significance in Europeans, very few have replicated in African ancestry populations. Challenges in comparing results from European vs African ancestry cohorts include modest sample size, differences in risk allele frequency, effect size, correlation between genetic variants, and environmental exposure in evolutionary history. African Americans also constitute a small percentage of dermatological and respiratory-focused clinical trials. Pharmacogenetic studies have similarly been focused largely on non-Hispanic whites, despite compelling evidence that genetic variation from different ancestral backgrounds may alter therapeutic efficacy of asthma and AD drugs. CONCLUSION Large-scale genetic studies of asthma and AD in African Americans are essential to reduce research and health disparities and empower scientific discoveries.
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Affiliation(s)
- Michelle Daya
- Department of Medicine, University of Colorado Denver, Aurora, Colorado
| | - Kathleen C Barnes
- Department of Medicine, University of Colorado Denver, Aurora, Colorado.
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145
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Li Y, Wu F, Tan Q, Guo M, Ma P, Wang X, Zhang S, Xu J, Luo P, Jin Y. The multifaceted roles of FOXM1 in pulmonary disease. Cell Commun Signal 2019; 17:35. [PMID: 30992007 PMCID: PMC6469073 DOI: 10.1186/s12964-019-0347-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 03/31/2019] [Indexed: 02/06/2023] Open
Abstract
Forkhead box M1 (FOXM1), a transcriptional regulator of G1/S and G2/M transition and M phase progression in the cell cycle, plays a principal role in many physiological and pathological processes. A growing number of studies have focused on the relationship between abnormal FOXM1 expression and pulmonary diseases, such as lung cancer, chronic obstructive pulmonary disease (COPD), asthma, acute lung injury (ALI), pulmonary fibrosis, and pulmonary arterial hypertension (PAH). These studies indicate that the FOXM1 regulatory network is a major predictor of poor outcomes, especially in lung cancer, and provide novel insight into various pulmonary diseases. For the first time, this review summarizes the mechanistic relationship between FOXM1 dysregulation and pulmonary diseases, the benefits of targeting abnormal FOXM1 expression, and the questions that remain to be addressed in the future.
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Affiliation(s)
- Yumei Li
- Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022, China
| | - Feng Wu
- Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022, China
| | - Qi Tan
- Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022, China
| | - Mengfei Guo
- Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022, China
| | - Pei Ma
- Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022, China
| | - Xuan Wang
- Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022, China
| | - Shuai Zhang
- Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022, China
| | - Juanjuan Xu
- Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022, China
| | - Ping Luo
- Center for Translational Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022, China
| | - Yang Jin
- Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022, China.
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146
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Kogan V, Millstein J, London SJ, Ober C, White SR, Naureckas ET, Gauderman WJ, Jackson DJ, Barraza-Villarreal A, Romieu I, Raby BA, Breton CV. Genetic-Epigenetic Interactions in Asthma Revealed by a Genome-Wide Gene-Centric Search. Hum Hered 2019; 83:130-152. [PMID: 30669148 PMCID: PMC7365350 DOI: 10.1159/000489765] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
OBJECTIVES There is evidence to suggest that asthma pathogenesis is affected by both genetic and epigenetic variation independently, and there is some evidence to suggest that genetic-epigenetic interactions affect risk of asthma. However, little research has been done to identify such interactions on a genome-wide scale. The aim of this studies was to identify genes with genetic-epigenetic interactions associated with asthma. METHODS Using asthma case-control data, we applied a novel nonparametric gene-centric approach to test for interactions between multiple SNPs and CpG sites simultaneously in the vicinities of 18,178 genes across the genome. RESULTS Twelve genes, PF4, ATF3, TPRA1, HOPX, SCARNA18, STC1, OR10K1, UPK1B, LOC101928523, LHX6, CHMP4B, and LANCL1, exhibited statistically significant SNP-CpG interactions (false discovery rate = 0.05). Of these, three have previously been implicated in asthma risk (PF4, ATF3, and TPRA1). Follow-up analysis revealed statistically significant pairwise SNP-CpG interactions for several of these genes, including SCARNA18, LHX6, and LOC101928523 (p = 1.33E-04, 8.21E-04, 1.11E-03, respectively). CONCLUSIONS Joint effects of genetic and epigenetic variation may play an important role in asthma pathogenesis. Statistical methods that simultaneously account for multiple variations across chromosomal regions may be needed to detect these types of effects on a genome-wide scale.
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Affiliation(s)
- Vladimir Kogan
- Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Joshua Millstein
- Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA,
| | - Stephanie J London
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, RTP, Research Triangle Park, North Carolina, USA
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
| | - Steven R White
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | | | - W James Gauderman
- Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Daniel J Jackson
- University of Wisconsin School of Medicine and Public Health, Madison, Illinois, USA
| | - Albino Barraza-Villarreal
- Department of Environmental Health, Population Health Center, National Institute of Public Health of Mexico, Cuernavaca, Mexico
| | - Isabelle Romieu
- International Agency for Research on Cancer, Section of Nutrition and Metabolism, Lyon, France
| | - Benjamin A Raby
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Carrie V Breton
- Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
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147
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Shakarami Z, Esmaeili Gouvrchin Ghaleh H, Mansouri Motlagh B, Sheikhian A, Jalali Kondori B. Evaluation of the protective and therapeutic effects of Pistacia atlantica gum aqueous extract on cellular and pathological aspects of experimental asthma in Balb/c mice. AVICENNA JOURNAL OF PHYTOMEDICINE 2019; 9:248-259. [PMID: 31143692 PMCID: PMC6526037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
OBJECTIVE The purpose of this study was to investigate the protective and therapeutic effects of aqueous extract of P. atlantica gum on an experimental asthma in BALB/c mice. MATERIALS AND METHODS Aqueous extract of dried and milled P. atlantica gum was assemble and evaluate by GC-MS. In order to investigate the effect of P. atlantica gum extract on cellular and pathological aspects of asthma, 60 BALB/c mice were divided into six groups as: negative control, asthmatic group, asthmatic group receiving dexamethasone (1mg/kg; intraperitoneal (IP)) and three asthmatic groups receiving different concentrations of the extract (100, 200 and 400 mg/kg, orally) from the beginning of the study and continued for 84 days. The examined parameters included cell population, IgE antibody production, levels of IL-4, IL-5, TGF-β, INF-γ, IL-10, and IL-17 cytokines, and lung tissue damage. RESULTS Regardless of the dose, aqueous extract of P. atlantica gum, caused significant decrease in the number of BALF eosinophilic cells and levels of anti-ovalbumin IgE, IL-4, IL-5 and IL-17 cytokine levels, as well as pathologic damage of the lung tissue. In addition, the amount of anti-inflammatory IL-10, TGF-β, and INF-γ Th1 cytokines significantly increased in the extract-treated groups compared to the asthmatic and dexamethasone-treated groups. Moreover, IFN-γ/IL-4 ratio significantly increased in a dose-dependent manner compared to the un-treated asthma group. CONCLUSION The aqueous extract of P. atlantica gum can be considered as a potent anti-inflammatory and immunomodulatory compound and may be used as a natural compound for treatment of immune system disorders.
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Affiliation(s)
- Zaynab Shakarami
- Department of Microbiology, Faculty of Veterinary Medicine, Urmia University, Urmia, Iran.,Razi Herbal Medicines Research Center, Lorestan University of Medical Sciences, Khorramabad, Iran.
| | | | | | - Ali Sheikhian
- Razi Herbal Medicines Research Center, Lorestan University of Medical Sciences, Khorramabad, Iran.,Corresponding Author: Tel: +989166616974, Fax: +986633120126 ,
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148
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Huang SSY, Al Ali F, Boughorbel S, Toufiq M, Chaussabel D, Garand M. A curated collection of transcriptome datasets to investigate the molecular mechanisms of immunoglobulin E-mediated atopic diseases. Database (Oxford) 2019; 2019:baz066. [PMID: 31290545 PMCID: PMC6616200 DOI: 10.1093/database/baz066] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 04/14/2019] [Accepted: 04/29/2019] [Indexed: 12/17/2022]
Abstract
Prevalence of allergies has reached ~20% of population in developed countries and sensitization rate to one or more allergens among school age children are approaching 50%. However, the combination of the complexity of atopic allergy susceptibility/development and environmental factors has made identification of gene biomarkers challenging. The amount of publicly accessible transcriptomic data presents an unprecedented opportunity for mechanistic discoveries and validation of complex disease signatures across studies. However, this necessitates structured methodologies and visual tools for the interpretation of results. Here, we present a curated collection of transcriptomic datasets relevant to immunoglobin E-mediated atopic diseases (ranging from allergies to primary immunodeficiencies). Thirty-three datasets from the Gene Expression Omnibus, encompassing 1860 transcriptome profiles, were made available on the Gene Expression Browser (GXB), an online and open-source web application that allows for the query, visualization and annotation of metadata. The thematic compositions, disease categories, sample number and platforms of the collection are described. Ranked gene lists and sample grouping are used to facilitate data visualization/interpretation and are available online via GXB (http://ige.gxbsidra.org/dm3/geneBrowser/list). Dataset validation using associated publications showed good concordance in GXB gene expression trend and fold-change.
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Affiliation(s)
| | - Fatima Al Ali
- Sidra Medicine, Al Gharrafa Street Ar-Rayyan, Doha, Qatar
| | | | | | | | - Mathieu Garand
- Sidra Medicine, Al Gharrafa Street Ar-Rayyan, Doha, Qatar
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149
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Milam EC, Jacob SE, Cohen DE. Contact Dermatitis in the Patient with Atopic Dermatitis. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY-IN PRACTICE 2019; 7:18-26. [DOI: 10.1016/j.jaip.2018.11.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 11/05/2018] [Accepted: 11/05/2018] [Indexed: 12/20/2022]
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150
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Hernandez-Pacheco N, Pino-Yanes M, Flores C. Genomic Predictors of Asthma Phenotypes and Treatment Response. Front Pediatr 2019; 7:6. [PMID: 30805318 PMCID: PMC6370703 DOI: 10.3389/fped.2019.00006] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 01/10/2019] [Indexed: 12/11/2022] Open
Abstract
Asthma is a complex respiratory disease considered as the most common chronic condition in children. A large genetic contribution to asthma susceptibility is predicted by the clustering of asthma and allergy symptoms among relatives and the large disease heritability estimated from twin studies, ranging from 55 to 90%. Genetic basis of asthma has been extensively investigated in the past 40 years using linkage analysis and candidate-gene association studies. However, the development of dense arrays for polymorphism genotyping has enabled the transition toward genome-wide association studies (GWAS), which have led the discovery of several unanticipated asthma genes in the last 11 years. Despite this, currently known risk variants identified using many thousand samples from distinct ethnicities only explain a small proportion of asthma heritability. This review examines the main findings of the last 2 years in genomic studies of asthma using GWAS and admixture mapping studies, as well as the direction of studies fostering integrative perspectives involving omics data. Additionally, we discuss the need for assessing the whole spectrum of genetic variation in association studies of asthma susceptibility, severity, and treatment response in order to further improve our knowledge of asthma genes and predictive biomarkers. Leveraging the individual's genetic information will allow a better understanding of asthma pathogenesis and will facilitate the transition toward a more precise diagnosis and treatment.
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Affiliation(s)
- Natalia Hernandez-Pacheco
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.,Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Maria Pino-Yanes
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.,Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Carlos Flores
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.,Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain
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