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Series GSE100500 Query DataSets for GSE100500
Status Public on Dec 01, 2017
Title Transcriptional Survey of Alveolar Macrophages in a Murine Model of Chronic Granulomatous Inflammation Reveals Common Themes with Human Sarcoidosis
Organism Mus musculus
Experiment type Expression profiling by array
Summary Rationale: A well-validated animal model of sarcoidosis can help advance our understanding of the pathobiology of this complex disease. We have developed a multiwall carbon nanotube (MWCNT) based murine model that shows marked histological and inflammatory signal similarities to human sarcoidosis. In this study, we compared the alveolar immune cell transcriptional signatures of our murine model with human sarcoidosis to comprehensively assess overlapping molecular programs.
Methods: Total RNA was extracted from alveolar macrophages of 6 MWCNT mice and 6 control mice and hybridized to Illumina Mouse WG-6 v2 microarrays. Transcriptional profiling of alveolar immune cells in 15 sarcoidosis patients and 12 healthy humans was previously performed using Affymetrix Human GeneChip U133A 2.0 microarrays. Rigorous statistical methods were used to identify differentially expressed genes. To better elucidate gene expression pathways, integrated network and gene set enrichment analysis (GSEA) were applied. To confirm differential expression of select network genes, we performed qPCR studies using the ABI Prism 7300 Detection.
Results: We identified over 1000 genes that were differentially expressed between the control and the MWCNT mice. Gene Ontology functional analysis showed over-representation of processes primarily involved in immunity and inflammation in MCWNT mice. Applying a more comprehensive pathway analysis using GSEA to both mouse and human samples revealed upregulation of 92 gene sets in MWCNT mice and 142 gene sets in sarcoidosis patients. Commonly activated pathways in both MWCNT mice and sarcoidosis included adaptive immunity, T-cell signaling, IL-12/IL-17 signaling and oxidative phosphorylation. Differences in selective gene set enrichment between MWCNT mice and sarcoidosis patients were also observed, among them IL-27 signaling, NK-mediated cytotoxicity and proteasome pathways. We applied network analysis to differentially expressed genes common between the MWCNT model and human sarcoidosis to identify key drivers of disease and putative therapeutic targets.
Conclusions: Our MWCNT murine model has an alveolar macrophage signature that varies significantly from control mice. Application of an unbiased transcriptomic approach revealed substantial functional similarities between a murine MWCNT model and human sarcoidosis particularly with respect to activation of immune-specific pathways.
 
Overall design C57Bl/6 mice underwent oropharyngeal instillation of 35% surfactant/saline (control, n = 6) or 35% surfactant/saline solution containing 100 μg of MWCNT (n = 6). At day 60 after instillation, mice underwent BAL and alveolar macrophages were isolated with >90% purity. Total RNA from each sample was isolated and hybridized to Illumina Mouse WG-6 v2 BeadChip (total number of samples = 12).
 
Contributor(s) Gharib SA
Citation(s) 29212802
Submission date Jun 26, 2017
Last update date Jul 25, 2021
Contact name Sina A Gharib
E-mail(s) sagharib@u.washington.edu
Phone 206-221-0630
Organization name University of Washington
Department Medicine
Street address 850 Republican
City Seattle
State/province WA
ZIP/Postal code 98109
Country USA
 
Platforms (1)
GPL6887 Illumina MouseWG-6 v2.0 expression beadchip
Samples (12)
GSM2685225 Alveolar macrophages from control mice_AM_Control_1
GSM2685226 Alveolar macrophages from control mice_AM_Control_2
GSM2685227 Alveolar macrophages from control mice_AM_Control_3
Relations
BioProject PRJNA391959

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
GSE100500_RAW.tar 15.8 Mb (http)(custom) TAR
GSE100500_non_normalized.txt.gz 2.3 Mb (ftp)(http) TXT
Raw data are available on Series record
Processed data included within Sample table

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