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Series GSE93606 Query DataSets for GSE93606
Status Public on Jan 14, 2017
Title Host-Microbial interactions in Idiopathic Pulmonary Fibrosis
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Changes in the respiratory microbiome are associated with disease progression in Idiopathic pulmonary fibrosis (IPF). The role of the host response to the respiratory microbiome however remains unknown. The role of this study is to explore the host-microbial interaction in IPF. Network analysis of gene expression data identified two gene modules that strongly associate with a diagnosis of IPF, BAL bacterial burden (determined by 16S quantitative PCR) and specific microbial OTUs, as well as lavage and peripheral blood neutrophilia. Genes within these modules that are involved in the host defence response include NLRC4, PGLYRP1, MMP9, DEFA4. The modules also contain two genes encoding specific antimicrobial peptides (SLPI and CAMP). Many of these particular transcripts were associated with survival and showed longitudinal over expression in subjects experiencing disease progression, further strengthening their relationship with disease. Integrated analysis of the host transcriptome and microbial signatures demonstrates an apparent host response to the presence of an altered or more abundant microbiome. These responses remain elevated on longitudinal follow up, suggesting that the bacterial communities of the lower airways may be acting as persistent stimuli for repetitive alveolar injury in IPF.
Sixty patients diagnosed with IPF were prospectively enrolled, together with 20 matched controls. Subjects underwent bronchoalveolar lavage (BAL) and peripheral whole blood was collected into PAXgene tubes for all subjects at baseline. For IPF subjects additional samples were taken at 1, 3, and 6 months and (if alive) a year. Gene expression profiles were generated using Affymetrix Human Gene1.1ST Arrays.
Overall design Survival=Months from Recruitment to composite end point or censoring; Age=Age in years at recruitment; FVC= Percent predicted Forced Vital Capacity; DLCO=Percent predicted Diffusing capacity of the lungs for carbon monoxide; Composite_End_Point=Death or decline in FVC >10% over a six month period, 1=Event, 2=No event.
Contributor(s) Molyneaux PL, Cookson WO, Moffatt MF, Maher TM
Citation(s) 28085486
Submission date Jan 13, 2017
Last update date Jan 18, 2017
Contact name Philip Molyneaux
Organization name Imperial College London
Street address Dovehouse Street
City London
ZIP/Postal code SW3 6PT
Country United Kingdom
Platforms (1)
GPL11532 [HuGene-1_1-st] Affymetrix Human Gene 1.1 ST Array [transcript (gene) version]
Samples (174)
GSM2458563 Control_1, Timepoint 0
GSM2458564 Control_10, Timepoint 0
GSM2458565 Control_11, Timepoint 0
BioProject PRJNA361279

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Supplementary file Size Download File type/resource
GSE93606_RAW.tar 713.4 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table

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