{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Georgina Espígol Frigolé"],"instrument_platform":["Affymetrix GeneTitan™ Instrument","Affymetrix GeneTitan™ System","-","Affymetrix WT PLUS Reagent Kit"],"study_type":["transcription profiling by array"],"organism":["Homo sapiens"],"species":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16277"],"description":["Eosinophilic granulomatosis with polyangiitis (EGPA) is a rare and heterogeneous disease of unknown etiology, classified among ANCA-associated vasculitis, with an insatisfactory response to treatment.   The aims of the current project are:  1) To investigate pathogenic pathways involved in EGPA that could be potentially druggable or provide clinically useful biomarkers by a cross-sectional study determining gene-expression profile of peripheral blood CD4+T lymphocytes in clinically stable patients with EGPA, patients with asthma and healthy controls. By using gene set expression analysis (GSEA) we will identify the main differentially expressed pathways. The most signficant differentially expressed transcripts will be validated as potential biomarkers by quantitative real time RT-PCR and by serum ELISA if encoding for a soluble product in an additional cohort.   2) To determine the heterogeneity of the EGPA by analyzing its transcriptome according to subgroups of patients defined by clinical variables and response to treatment. If we obtain significant differentially expressed genes for each category defined by clinical variables, these genes will be also validated in an additional cohort.    3) Moreover, an unsurpervised clustering analysis will be performed in order to identify non-predefined subtypes.   With this study, we aim to contribute to the characterization of the molecular basis of the heterogeneity of EGPA patients and to identify pathways potentially involved in disease pathogenesis."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Hybridization - Labeled ss-cDNA samples were hybridized onto the Affymetrix GeneChip™ Human Clariom™ S Array according to the manufacturer’s protocol. Hybridization was carried out in the Affymetrix GeneTitan™ Instrument for automated fluidics and washing steps.","Nucleic Acid Extraction - Once trizol was unfrozen, 200ul of Chloroform was added to the Eppendorf and mixed during 15-30seg. After 2 min at ambient temperature, the eppendorf was centrifuged during 15min at 12.000G and 4ºC. After centrifugation, the transparent phase is transferred to another eppendorf, and 500ul of isopropanol is then added and mixed. The mix is incubated during 10min at ambient temperature, and then centrifuged during 10 min at 12.000G and 4ºC. After centrifugation, supernatant is discarded and 1ml of OH75% is added. The new mix is centrifuged during 5 min at 7.500G. This last process is repeated 3 times. In the end, the remaining RNA is frozen for a later use.","Labeling - Total RNA was first assessed for quality and quantity. High-quality RNA samples were processed into single-stranded complementary DNA (ss-cDNA) using the Affymetrix WT PLUS Reagent Kit following the manufacturer’s instructions. The resulting labeled ss-cDNA was purified and quantified before hybridization.","Scaning - Arrays were scanned and processed using the Affymetrix GeneTitan™ System. Signal intensities were extracted and normalized following Affymetrix standard procedures for the Clariom S array.","Sample Collection - 50ml of blood in EDTA tube were collected per patient/healty control. No fasting was requiered. All patients had their disease stable at the moment of the blood extraction. 10ml were centrifuged and serum was subsequently frozen. The remaining 40ml were used to isolate PBMC by density gradient (Ficol). From the PBMC, CD4+ lymphocites were isolated using Dynabeads, and thereafter lysed with tryzol and frozen at -80ºC."],"figure_sub":["MIAME Score","Raw Data","Organization","Assays and Data","MAGE-TAB Files","Array Designs"],"pubmed_authors":["Georgina Espígol Frigolé"],"additional_accession":[]},"is_claimable":false,"name":"Gene expression profile of CD4+ T lymphocytes from patients with eosinophilic granulomatosis with polyangiitis (EGPA) or  Churg-Strauss syndrome","description":"Eosinophilic granulomatosis with polyangiitis (EGPA) is a rare and heterogeneous disease of unknown etiology, classified among ANCA-associated vasculitis, with an insatisfactory response to treatment.   The aims of the current project are:  1) To investigate pathogenic pathways involved in EGPA that could be potentially druggable or provide clinically useful biomarkers by a cross-sectional study determining gene-expression profile of peripheral blood CD4+T lymphocytes in clinically stable patients with EGPA, patients with asthma and healthy controls. By using gene set expression analysis (GSEA) we will identify the main differentially expressed pathways. The most signficant differentially expressed transcripts will be validated as potential biomarkers by quantitative real time RT-PCR and by serum ELISA if encoding for a soluble product in an additional cohort.   2) To determine the heterogeneity of the EGPA by analyzing its transcriptome according to subgroups of patients defined by clinical variables and response to treatment. If we obtain significant differentially expressed genes for each category defined by clinical variables, these genes will be also validated in an additional cohort.    3) Moreover, an unsurpervised clustering analysis will be performed in order to identify non-predefined subtypes.   With this study, we aim to contribute to the characterization of the molecular basis of the heterogeneity of EGPA patients and to identify pathways potentially involved in disease pathogenesis.","dates":{"release":"2025-12-15T00:00:00Z","modification":"2026-05-27T15:40:27.179Z","creation":"2025-11-24T22:49:16.529Z"},"accession":"E-MTAB-16277","cross_references":{"EFO":["EFO_0002768","EFO_0002944","EFO_0003814","EFO_0003813","EFO_0005518","EFO_0003815"]}}