Homo sapiens
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PROVIDER: PRJNA236769 | ENA |
REPOSITORIES: ENA
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Project description:Analysis of gene-expression profiles with microarrays can be very useful to dissect specific responses and to characterize with a global view, new elements for improving the diagnosis, treatment and understanding of allergic diseases. We have used this approach for studying the olive pollen response, taking advantage our previous results of T-cell epitope mapping on Ole e 1 molecule (the major allergen from olive pollen) in order to analyze the stimuli influence on the gene-expression of olive pollen allergic patients. Peripheral blood mononuclear cells (PBMCs) from 6 healthy controls and 6 allergic subjects were stimulated 24 hours with olive pollen stimuli: Ole e 1 molecule and two Ole e 1 peptides previously defined as P2+3 (aa10-31), mainly recognized by non-allergic subjects (possible immunoregulatory epitope) and P10+12+13 (aa90-130), immunodominant T-cell epitope. RNA extracted from basal and stimulated PBMCs was analyzed by HuGeU133 plus 2.0 GeneChip, Affymetrix (38.500genes). After assessment of data quality by standard quality checks and principal components analysis (PCA), differential gene-expression by experimental conditions was performed by multiple testing, using microarrays specific software. Differences in functional analysis were performed by KEGG, for pathways and Gene-Ontology for biological process. The results of gene-expression by PCA showed differential clusters that correlated with the experimental conditions from samples of allergic patients. Analysis of differential gene-expression by multiple testing, and functional analysis by KEGG and Gene-Ontology revealed differential genes and pathways among the 4 experimental conditions.
2014-12-30 | GSE54522 | GEO
Project description:Analysis of gene-expression profiles by microarrays can be very useful to characterize new potential candidate genes, key regulatory networks, and to define phenotypes or molecular signatures to improve the diagnosis or classification of the disease. We have used this approach in the study of one of the major causes of allergic diseases in Mediterranean countries, the olive pollen response, in order to find differential molecular markers among five clinical groups, Non-allergic, Asymptomatic, Allergic but not to olive pollen, Non-treated, olive pollen allergic patients and Olive pollen allergic patients (under specific-immunotherapy). The results of gene-expression by principal components analysis (PCA) clearly showed five clusters of samples that correlated with the five clinical groups. Analysis of differential gene-expression by multiple testing, and functional analysis by KEGG and Gene-Ontology revealed differential genes and pathways among the 5 clinical groups.
2013-02-28 | GSE37157 | GEO
Project description:Analysis of gene-expression profiles by microarrays can be very useful to characterize new potential candidate genes, key regulatory networks, and to define phenotypes or molecular signatures to improve the diagnosis or classification of the disease. We have used this approach in the study of one of the major causes of allergic diseases in Mediterranean countries, the olive pollen response, in order to find differential molecular markers among five clinical groups, Non-allergic, Asymptomatic, Allergic but not to olive pollen, Non-treated, olive pollen allergic patients and Olive pollen allergic patients (under specific-immunotherapy). The results of gene-expression by principal components analysis (PCA) clearly showed five clusters of samples that correlated with the five clinical groups. Analysis of differential gene-expression by multiple testing, and functional analysis by KEGG and Gene-Ontology revealed differential genes and pathways among the 5 clinical groups. The study population comprised 28 subjects, selected from a previous immunological study (Aguerri et al. Eur. J. Inflammation 2012, in press), from Andalusia, who were recruited in 2 olive pollen exposure situations: during (April-June) and outside the pollen season (October-December). We established 5 groups, and 6 subjects from each group were selected for gene-expression analysis: Group 1, non-allergic subjects; Group 2, asymptomatic subjects (diagnosed with olive pollen allergy by skin testing, with no seasonal respiratory symptoms [rhinitis and/or asthma], and who consulted for adverse reaction to drugs); Group 3, patients who were allergic, but not to olive pollen; Group 4, non-treated olive pollenM-bM-^@M-^Sallergic; and Group 5, olive pollenM-bM-^@M-^Sallergic patients (receiving olive pollenM-bM-^@M-^Sspecific immunotherapy).The subjects were unrelated and recruited at the Allergy Service of 4 hospitals in Andalusia (Granada, JaM-CM-)n, Sevilla, and MM-CM-!laga). Olive pollenM-bM-^@M-^Sallergic patients fulfilled the following criteria: seasonal rhinitis and/or asthma from April to June, a positive skin prick test result for O. europaea pollen extract (ALK AbellM-CM-3, Madrid, Spain), and no previous immunotherapy. Informed consent was obtained from each subject. Ethical approval for the study was obtained from the Ethical and Research Committee of the participating hospitals. PBMCs were isolated from heparin-containing peripheral blood samples taken during and outside pollen season, by gradient centrifugation on Lymphoprep (Comercial Rafer, Zaragoza, Spain) following the manufacturerM-bM-^@M-^Ys instructions.
2013-02-28 | E-GEOD-37157 | biostudies-arrayexpress
Project description:Gene expression (Npatients = 21, Ncontrols = 21) of CD4+ T-cells failed to seperate patients with seasonal allergic rhinitis (SAR) and healthy controls in an in vitro model system in which purified PBMCs from patients and healthy controls were challenged with allergen for 7 days. PBMCs from 21 patients (P) and 21 healthy controls (H) were challenged with grass pollen for 7 days. Diluent challenged control samples were obtained from all subjects. CD4+ cells were purified by MACS.
2013-08-28 | E-GEOD-50223 | biostudies-arrayexpress
Project description:Foxp3+ regulatory T cells (Treg) play a central role for tolerance against self and innocuous environmental antigens. However, the role of antigen-specificity for Treg-mediated tolerance is only incompletely understood. Here we show by direct ex vivo characterization of human CD4+ T cells, that the response against innocuous airborne antigens, such as plant pollen or fungal spores, is dominated by memory-like antigen-specific Treg. Surprisingly, breakdown of tolerance in atopic donors was not accompanied by a quantitatively or qualitatively altered Treg response, but instead correlated with a striking dichotomy of Treg versus Th2 target specificity. Allergenic proteins, are selectively targeted by Th2 cells, but not Treg. Thus human Treg specific for airborne antigens maintain tolerance at mucosal sites and the failure to generate specific Treg against a subgroup of antigens provides a window of opportunity for allergy development. PBMCs from sex and age matched birch pollen allergic patients and healthy controls, were stimulated (7h) with airborne fungal (A. fumigatus) or birch pollen antigen (birch) and sorted into antigen specific conventional and regulatory T cells according to their expression of CD154+ and CD137+ on CD4+ T cells, respectively. Number of samples per group in parentheses: Healthy controls stimulated with A. fumigatus (n=5), allergic patients stimulated with A. fumigatus (n=6), healthy controls stimulated with birch (n=6), allergic patients stimulated with birch (n=4).
2016-10-25 | E-GEOD-77018 | biostudies-arrayexpress
Project description:Allergen challenged CD4+ cells from allergic patients and healthy controls
| PRJNA217394 | ENA
Project description:The delineation of the olive pollen proteome and its allergogram can improve the clinical management of patients with this pollinosis. We here integrated the recently described wild olive genomic data in a comprehensive proteomic approach to get the annotated olive (Olea europaea) pollen proteome and complete its complex allergogram. Olive pollen proteins were identified by LC-MS/MS using predicted protein sequences from its genome. GO annotation, KEGG Pathway analysis and identification of allergen families were performed by bioinformatics. Recombinant DNA, protein expression and purification, and immunological analyses were used to characterize putative allergens. A total of 1,907 proteins were identified. 60% of the proteins were predicted to possess catalytic activity and be involved in metabolic processes. 203 proteins belonging to 47 allergen families were found, with 37 non-previously described in olive pollen. Of four potential allergens produced in Escherichia coli, a peptidyl-prolyl cis-trans isomerase -cyclophilin-, masked in the protein extract by the major allergen Ole e 1, was found as a new olive pollen allergen (Ole e 15). 63% of the Ole e 15-sensitized patients were children and showed strong IgE recognition of the allergen. Ole e 15 shared high sequence identity with other plant, animal and fungal cyclophilins and a high IgE cross-reactivity with pollen, plant food and animal extracts. Taken together, the combination of available genomic data with proteomics permitted the profiling of the olive pollen proteome, revealing the spectrum of allergen families and cyclophilin as a new relevant allergen implicated in cross-reactivity.
2019-06-17 | PXD012334 | Pride
Project description:The delineation of the olive pollen proteome and its allergogram can improve the clinical management of patients with this pollinosis. We here integrated the recently described wild olive genomic data in a comprehensive proteomic approach to get the annotated olive (Olea europaea) pollen proteome and complete its complex allergogram. Olive pollen proteins were identified by LC-MS/MS using predicted protein sequences from its genome. GO annotation, KEGG Pathway analysis and identification of allergen families were performed by bioinformatics. Recombinant DNA, protein expression and purification, and immunological analyses were used to characterize putative allergens. A total of 1,907 proteins were identified. 60% of the proteins were predicted to possess catalytic activity and be involved in metabolic processes. 203 proteins belonging to 47 allergen families were found, with 37 non-previously described in olive pollen. Of four potential allergens produced in Escherichia coli, a peptidyl-prolyl cis-trans isomerase -cyclophilin-, masked in the protein extract by the major allergen Ole e 1, was found as a new olive pollen allergen (Ole e 15). 63% of the Ole e 15-sensitized patients were children and showed strong IgE recognition of the allergen. Ole e 15 shared high sequence identity with other plant, animal and fungal cyclophilins and a high IgE cross-reactivity with pollen, plant food and animal extracts. Taken together, the combination of available genomic data with proteomics permitted the profiling of the olive pollen proteome, revealing the spectrum of allergen families and cyclophilin as a new relevant allergen implicated in cross-reactivity.
2019-06-17 | PXD012279 | Pride
Project description:The delineation of the olive pollen proteome and its allergogram can improve the clinical management of patients with this pollinosis. We here integrated the recently described wild olive genomic data in a comprehensive proteomic approach to get the annotated olive (Olea europaea) pollen proteome and complete its complex allergogram. Olive pollen proteins were identified by LC-MS/MS using predicted protein sequences from its genome. GO annotation, KEGG Pathway analysis and identification of allergen families were performed by bioinformatics. Recombinant DNA, protein expression and purification, and immunological analyses were used to characterize putative allergens. A total of 1,907 proteins were identified. 60% of the proteins were predicted to possess catalytic activity and be involved in metabolic processes. 203 proteins belonging to 47 allergen families were found, with 37 non-previously described in olive pollen. Of four potential allergens produced in Escherichia coli, a peptidyl-prolyl cis-trans isomerase -cyclophilin-, masked in the protein extract by the major allergen Ole e 1, was found as a new olive pollen allergen (Ole e 15). 63% of the Ole e 15-sensitized patients were children and showed strong IgE recognition of the allergen. Ole e 15 shared high sequence identity with other plant, animal and fungal cyclophilins and a high IgE cross-reactivity with pollen, plant food and animal extracts. Taken together, the combination of available genomic data with proteomics permitted the profiling of the olive pollen proteome, revealing the spectrum of allergen families and cyclophilin as a new relevant allergen implicated in cross-reactivity.
2019-06-17 | PXD012280 | Pride
Project description:Altered DNA methylation patterns in CD4+ T-cells indicate the importance of epigenetic mechanisms in inflammatory diseases. However, the identification of these alterations is complicated by the heterogeneity of most inflammatory diseases. Seasonal allergic rhinitis (SAR) is an optimal disease model for the study of DNA methylation because of its well-defined phenotype and etiology. We generated genome-wide DNA methylation (Npatients = 8, Ncontrols = 8) and gene expression (Npatients= 9, Ncontrols = 10) profiles of CD4+ T-cells from SAR patients and healthy controls using Illumina’s HumanMethylation450 and HT-12 microarrays, respectively. DNA methylation profiles clearly and robustly distinguished SAR patients from controls, during and outside the pollen season. Moreover, we found that this methylation signature correlated with symptom severity. In agreement with previously published studies, gene expression profiles of the same samples failed to separate patients and controls. Separation by methylation (Npatients = 12, Ncontrols = 12), but not by gene expression (Npatients = 21, Ncontrols = 21; GSE50223) was also observed in an in vitro model system in which purified PBMCs from patients and healthy controls were challenged with allergen. We observed changes in the proportions of memory T-cell populations between patients (Npatients = 35) and controls (Ncontrols= 9), which could explain the observed difference in DNA methylation. Our data highlight the potential of epigenomics in the stratification of immune disease and represents the first successful molecular classification of SAR using CD4+ T cells. Genomic DNA was isolated from CD4+ T-cells of patients with seasonal allergic rhinitis and healthy controls both during and outside the pollen season. Genomic DNA was bisulfite converted and hybridized to Illumina HumanMethylation450 BeadChip (Illumina, San Diego, CA) and scanned using the Illumina iScan.
2013-12-01 | E-GEOD-50222 | biostudies-arrayexpress