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Series GSE28042 Query DataSets for GSE28042
Status Public on Oct 15, 2013
Title Peripheral Blood Mononuclear Cell Gene Expression Profiles May Predict Poor Outcome in Idiopathic Pulmonary Fibrosis [Agilent]
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Background: In this study we aimed to identify peripheral blood mononuclear cell (PBMC) gene expression profiles predictive of poor outcomes in idiopathic pulmonary fibrosis (IPF)
Methods: Microarray analyses of PBMC were performed in 120 patients from discovery (n=45) and replication cohorts (n=75). Genes and pathways associated with transplant-free survival (TFS) were identified and confirmed by qRT-PCR.
Findings: 52 genes were predictive of TFS in a discovery cohort (FDR<5%, Cox score above 2.5 or below -2.5). Clustering the replication cohort samples using these genes distinguished two patient groups with significantly different TFS (hazard ratio 1.96, 95%CI 1.01-3.8, P=0.018). Decreased expression of “The co-stimulatory signaling during T cell activation” Biocarta pathway and in particular CD28, ICOS, LCK and ITK was associated with shorter TFS times in each cohort (FDR<5%). qRT-PCR expression of CD28, ICOS, LCK and ITK correlated with the microarray results in the discovery cohort (P<0.05) and their decreased expression was predictive of shorter TFS in the replication cohort (P<0.05). A genomic and clinical model demonstrated an area under the ROC curve of 78.5% at 2.4 months for death and lung transplant prediction.
Interpretation: Our results suggest that CD28, ICOS, LCK and ITK are outcome biomarkers in IPF.
 
Overall design PBMC from 75 patients with the diagnosis of IPF were obtained within 30 minutes from blood draw. Total RNA was extracted, labeled and hybridized to Agilent Whole Human Genome Oligo Microarray, 4 x 44K. Patients were followed from blood draw until death, transplant or last follow up. Hierarchical clustering and gene-set analysis with censored outcome data were used to study the association of gene expression and outcome in this cohort (replication cohort)
 
Contributor(s) Herazo Maya J
Citation(s) 24089408, 26589497
Submission date Mar 18, 2011
Last update date Mar 30, 2020
Contact name JOSE DAVID HERAZO MAYA
Organization name Yale University
Department Medicine
Lab Kaminski Lab
Street address 300 Cedar Street
City New Haven
State/province CT
ZIP/Postal code 06520
Country USA
 
Platforms (1)
GPL6480 Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Probe Name version)
Samples (94)
GSM693750 Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0002
GSM693751 Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0004
GSM693752 Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0007
This SubSeries is part of SuperSeries:
GSE28221 Peripheral Blood Mononuclear Cell Gene Expression Profiles May Predict Poor Outcome in Idiopathic Pulmonary Fibrosis
Relations
BioProject PRJNA141911

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE28042_RAW.tar 203.5 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table
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