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Satitsuksanoa P, van de Veen W, Tan G, Lopez JF, Wirz O, Jansen K, Sokolowska M, Mirer D, Globinska A, Boonpiyathad T, Schneider SR, Barletta E, Spits H, Chang I, Babayev H, Tahralı İ, Deniz G, Yücel EÖ, Kıykım A, Boyd SD, Akdis CA, Nadeau K, Akdis M. Allergen-specific B cell responses in oral immunotherapy-induced desensitization, remission, and natural outgrowth in cow's milk allergy. Allergy 2024. [PMID: 38989779 DOI: 10.1111/all.16220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 06/04/2024] [Accepted: 06/10/2024] [Indexed: 07/12/2024]
Abstract
BACKGROUND Antigen-specific memory B cells play a key role in the induction of desensitization and remission to food allergens in oral immunotherapy and in the development of natural tolerance (NT). Here, we characterized milk allergen Bos d 9-specific B cells in oral allergen-specific immunotherapy (OIT) and in children spontaneously outgrowing cow's milk allergy (CMA) due to NT. METHODS Samples from children with CMA who received oral OIT (before, during, and after), children who naturally outgrew CMA (NT), and healthy individuals were received from Stanford biobank. Bos d 9-specific B cells were isolated by flow cytometry and RNA-sequencing was performed. Protein profile of Bos d 9-specific B cells was analyzed by proximity extension assay. RESULTS Increased frequencies of circulating milk allergen Bos d 9-specific B cells were observed after OIT and NT. Milk-desensitized subjects showed the partial acquisition of phenotypic features of remission, suggesting that desensitization is an earlier stage of remission. Within these most significantly expressed genes, IL10RA and TGFB3 were highly expressed in desensitized OIT patients. In both the remission and desensitized groups, B cell activation-, Breg cells-, BCR-signaling-, and differentiation-related genes were upregulated. In NT, pathways associated with innate immunity characteristics, development of marginal zone B cells, and a more established suppressor function of B cells prevail that may play a role in long-term tolerance. The analyses of immunoglobulin heavy chain genes in specific B cells demonstrated that IgG2 in desensitization, IgG1, IgA1, IgA2, IgG4, and IgD in remission, and IgD in NT were predominating. Secreted proteins from allergen-specific B cells revealed higher levels of regulatory cytokines, IL-10, and TGF-β after OIT and NT. CONCLUSION Allergen-specific B cells are essential elements in regulating food allergy towards remission in OIT-received and naturally resolved individuals.
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Affiliation(s)
| | - Willem van de Veen
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zürich, Davos, Switzerland
| | - Ge Tan
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zürich, Davos, Switzerland
- Functional Genomics Center Zürich, ETH Zürich, Zürich, Switzerland
| | - Juan-Felipe Lopez
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zürich, Davos, Switzerland
| | - Oliver Wirz
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zürich, Davos, Switzerland
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Kirstin Jansen
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zürich, Davos, Switzerland
| | - Milena Sokolowska
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zürich, Davos, Switzerland
- Christine Kühne-Center for Allergy Research and Education (CK-CARE), Davos, Switzerland
| | - David Mirer
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zürich, Davos, Switzerland
| | - Anna Globinska
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zürich, Davos, Switzerland
| | - Tadech Boonpiyathad
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zürich, Davos, Switzerland
| | - Stephan R Schneider
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zürich, Davos, Switzerland
| | - Elena Barletta
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zürich, Davos, Switzerland
- Swiss Institute of Bioinformatics, Laussane, Switzerland
| | - Hergen Spits
- Department of Experimental Immunology, Academic Medical Center of the University of Amsterdam, Amsterdam, the Netherlands
| | - Iris Chang
- Sean N. Parker Center for Allergy and Asthma Research, Stanford, California, USA
| | - Huseyn Babayev
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zürich, Davos, Switzerland
| | - İlhan Tahralı
- Department of Immunology, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Gunnur Deniz
- Department of Immunology, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Esra Özek Yücel
- Division of Pediatrics, Department of Pediatric Allergy and Immunology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
- Department of Pediatric Allergy and Immunology, Cerrahpasa Medical Faculty, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Ayca Kıykım
- Department of Pediatric Allergy and Immunology, Cerrahpasa Medical Faculty, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Scott D Boyd
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Cezmi A Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zürich, Davos, Switzerland
- Christine Kühne-Center for Allergy Research and Education (CK-CARE), Davos, Switzerland
| | - Kari Nadeau
- Sean N. Parker Center for Allergy and Asthma Research, Stanford, California, USA
| | - Mübeccel Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zürich, Davos, Switzerland
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The association of TAP polymorphisms with non-small-cell lung cancer in the Han Chinese population. Hum Immunol 2021; 82:917-922. [PMID: 34373132 DOI: 10.1016/j.humimm.2021.07.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 11/24/2022]
Abstract
The host immune system plays a crucial role in multiple types of cancer, including non-small-cell lung cancer (NSCLC). Transporter associated with antigen processing (TAP) protein heterodimer complexes might promote intracellular antigen peptide binding with class I major histocompatibility complex (MHC-I) molecules, and in recent years, TAP1 and TAP2 have been reported to be associated with multiple cancer risks. In the current study, we investigated the association of single-nucleotide polymorphisms (SNPs) in TAP1 and TAP2 with NSCLC in a Han Chinese population. Six and seven TAP1 and TAP2 SNPs, respectively, were genotyped and analysed in healthy controls and NSCLC patients. Based on our data, none of the six SNPs in TAP1 is associated with NSCLC risk (P > 0.0038). However, rs2228396 alleles in TAP2 were significantly different between NSCLC patients and healthy controls, and the A allele might be associated with an increased risk of this cancer (P = 0.001, OR = 1.65, 95%CI: 1.23 ∼ 2.21). Moreover, the genotype frequencies of rs2228396 were significantly different between patients and healthy controls (P = 7 × 10-4). Additionally, TAP2 rs241441 alleles exhibited a trend of difference between NSCLC patients and healthy controls, with the C allele possibly being associated with increased risk of NSCLC (P = 0.013; OR = 1.30, 95%CI: 1.06 ∼ 1.60). Moreover, the genotypes of rs241441 in TAP2 showed a significant difference between NSCLC patients and healthy controls (P = 1 × 10-4). In haplotype analysis, the TAP2 SNP haplotype (CAC, TAP2*0102) was significantly associated with increased NSCLC risk in the Han Chinese population (P = 0.003; OR = 1.57, 95%CI: 1.17 ∼ 2.10). Our results indicate that TAP2 SNPs (rs2228396 and rs241441) have a potential role in NSCLC pathogenesis.
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Ma X, Wang P, Xu G, Yu F, Ma Y. Integrative genomics analysis of various omics data and networks identify risk genes and variants vulnerable to childhood-onset asthma. BMC Med Genomics 2020; 13:123. [PMID: 32867763 PMCID: PMC7457797 DOI: 10.1186/s12920-020-00768-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 08/17/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Childhood-onset asthma is highly affected by genetic components. In recent years, many genome-wide association studies (GWAS) have reported a large group of genetic variants and susceptible genes associated with asthma-related phenotypes including childhood-onset asthma. However, the regulatory mechanisms of these genetic variants for childhood-onset asthma susceptibility remain largely unknown. METHODS In the current investigation, we conducted a two-stage designed Sherlock-based integrative genomics analysis to explore the cis- and/or trans-regulatory effects of genome-wide SNPs on gene expression as well as childhood-onset asthma risk through incorporating a large-scale GWAS data (N = 314,633) and two independent expression quantitative trait loci (eQTL) datasets (N = 1890). Furthermore, we applied various bioinformatics analyses, including MAGMA gene-based analysis, pathway enrichment analysis, drug/disease-based enrichment analysis, computer-based permutation analysis, PPI network analysis, gene co-expression analysis and differential gene expression analysis, to prioritize susceptible genes associated with childhood-onset asthma. RESULTS Based on comprehensive genomics analyses, we found 31 genes with multiple eSNPs to be convincing candidates for childhood-onset asthma risk; such as, PSMB9 (cis-rs4148882 and cis-rs2071534) and TAP2 (cis-rs9267798, cis-rs4148882, cis-rs241456, and trans-10,447,456). These 31 genes were functionally interacted with each other in our PPI network analysis. Our pathway enrichment analysis showed that numerous KEGG pathways including antigen processing and presentation, type I diabetes mellitus, and asthma were significantly enriched to involve in childhood-onset asthma risk. The co-expression patterns among 31 genes were remarkably altered according to asthma status, and 25 of 31 genes (25/31 = 80.65%) showed significantly or suggestively differential expression between asthma group and control group. CONCLUSIONS We provide strong evidence to highlight 31 candidate genes for childhood-onset asthma risk, and offer a new insight into the genetic pathogenesis of childhood-onset asthma.
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Affiliation(s)
- Xiuqing Ma
- Department of Pulmonary & Critical Care Medicine, Chinese PLA General Hospital, Beijing, 100853 China
| | - Peilan Wang
- Outpatient Department, Chinese PLA General Hospital, Beijing, 100853 China
| | - Guobing Xu
- Department of Cardiovascular Medicine, Zhongxiang People’s Hospital, Zhongxiang, 431900 Hubei Province China
| | - Fang Yu
- Department of Pediatrics, Chinese PLA General Hospital, Beijing, 100853 China
| | - Yunlong Ma
- Institute of Biomedical Big Data, School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027 P. R. China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University School of Medicine, Hangzhou, China
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Wang WT, Zhang DJ, Liu ZG, Peng FG, Wang L, Fu B, Wu SH, Li ZQ, Guo ZH, Liu D. Identification of differentially expressed genes in adipose tissue of min pig and large white pig using RNA-seq. ACTA AGR SCAND A-AN 2019. [DOI: 10.1080/09064702.2019.1611912] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- W. T. Wang
- College of Wildlife Resource, Northeast Forestry University, Harbin, People’s Republic of China
- Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - D. J. Zhang
- Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Z. G. Liu
- Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - F. G. Peng
- Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - L. Wang
- Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - B. Fu
- Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - S. H. Wu
- Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Z. Q. Li
- Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Z. H. Guo
- Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - D. Liu
- College of Wildlife Resource, Northeast Forestry University, Harbin, People’s Republic of China
- Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin, People’s Republic of China
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Liu R, Chen X, Qi J. Associations of TAP1 genetic polymorphisms with atopic diseases: asthma, rhinitis and dermatitis. Oncotarget 2018; 9:1553-1562. [PMID: 29416713 PMCID: PMC5788581 DOI: 10.18632/oncotarget.23458] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 12/06/2017] [Indexed: 01/06/2023] Open
Abstract
Controversial findings have been reported regarding to the effect of the transporter associated with antigen processing 1 (TAP1) polymorphisms exerted on the atopic diseases susceptibility. To gain a better understanding of the effects of TAP1 polymorphisms on the risk of atopic diseases, a retrospective study was carried out to evaluate the association of the most common TAP1 polymorphisms, rs1057141 and rs1135216, with the risk of atopic diseases. From studies published in PubMed, Embase, and Web of Science up to July 2017, ten eligible studies were selected for meta-analysis. The pooled results from rs1135216 polymorphism showed increased risk of atopic diseases in homozygote and recessive comparison. From the subgroup analysis by ethnicity, it was found that rs1135216 polymorphism contributed to atopic diseases susceptibility among Africans in all the five genetic models. Subgroup analysis by atopic types indicated significant association of TAP1 polymorphism rs1135216 with asthma in the allele, dominant and recessive models and with allergic rhinitis in the recessive model. As to rs1057141, increased risk of atopic disease in the allelic, dominant and heterozygous model was found in African population. Overall, this meta-analysis study demonstrated that rs1135216 polymorphism may contribute to atopic diseases susceptibility in Asians and Africans as assessed in this study. However, well designed large-scale case-control studies are needed to confirm such preliminary findings.
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Affiliation(s)
- Rongzeng Liu
- Department of Immunology, Medical College, Henan University of Science and Technology, Luoyang, China
| | - Xiafei Chen
- Network Information Center, Henan University of Science and Technology, Luoyang, China
| | - Jingjiao Qi
- Department of Immunology, Medical College, Henan University of Science and Technology, Luoyang, China
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Association analysis of tapasin polymorphisms with aspirin-exacerbated respiratory disease in asthmatics. Pharmacogenet Genomics 2014; 23:341-8. [PMID: 23736108 DOI: 10.1097/fpc.0b013e328361d4bb] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Aspirin-exacerbated respiratory disease (AERD) is characterized by the development of airway obstruction in asthmatic individuals following the ingestion of aspirin or other nonsteroidal anti-inflammatory drugs. TAPBP (TAP-binding protein, tapasin) is upregulated by eicosanoids, which act as potent inflammatory molecules in aspirin-related reactions. Thus, functional alterations in the TAPBP gene may contribute toward AERD. OBJECTIVES We examined the relationship between the single nucleotide polymorphisms on the TAPBP gene and AERD. MATERIALS AND METHODS A group of asthmatic patients (n=1252) underwent the oral aspirin challenge. Oral aspirin challenge reactions were categorized into two groups as follows: 15% or greater decreases in forced expiratory volume in 1 s or naso-ocular and skin reactions (AERD), or 15% or less decreases in forced expiratory volume in 1 s without naso-ocular and skin reactions (aspirin-tolerant asthma). Five single nucleotide polymorphisms of the TAPBP gene were genotyped. RESULTS Logistic regression analysis showed that the minor allele frequencies of TAPBP rs2071888 C>G (Thr260Arg) on exon 4 (P>0.05), which was in absolute linkage disequilibrium with rs1059288 T>C on 3'UTR, were significantly higher in the AERD group than in the aspirin-tolerant asthma group, and the P values remained significant after multiple comparisons (Pcorr=0.006, odds ratio: 1.37, 95% confidence interval: 1.11-1.69, additive model; Pcorr=0.009, odds ratio: 1.52, 95% confidence interval: 1.14-2.03, dominant model). Alpha-helical wheel plotting showed that 260Arg had greater hydrophilic helical property than 260Thr. CONCLUSION TAPBP polymorphisms may play a role in the development of AERD.
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