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Clinical

COPD-Specific Gene Expression Signatures of Alveolar Macrophages as well as Peripheral Blood Monocytes Overlap and Correlate with Lung Function-GSE16972

Purpose

Among inflammatory cell types, alveolar macrophages appear to have a key role in initiating and/or sustaining disease progression. These cells are derived from peripheral monocytes. Identification of disease and cell type specific gene expression profiles can be revealing and also practically useful in order to diagnose and characterize disease progression and the effect of drug treatment.

Hypothesis

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Experimental Design

Brochoalveolar lavage fluid samples were collected from of COPD and healthy control patients. Alveolar macrophages were isolated using Percoll gradient centrifugation, isolated using CD14+ magnetic beads, and total RNA was extracted using Qiagen RNeasy Kit. The monocyte samples represent a pool of RNA from 5 patients. Total RNA was labeled with biotin and individual samples were hybridized to Affymetrix HG U133A GeneChips.Affymetrix data files were analyzed using GeneSpring 7.3 software. Using a non-parametric statistical test, we compared the gene expression patterns of the COPD and the healthy control patients and identified a set a genes that showed differential expression between the two groups.

Experimental Variables

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Controls

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Methods

We used Affymetrix microarrays to obtain gene expression data of alveolar macrophages and circulating monocytes of COPD and healthy control patients. The microarray results were confirmed by quantitative real-time polymerase chain reaction in multiple patient collections.Measurements and Main Results: We have identified gene sets specifically associated with COPD in alveolar macrophages and also in monocytes. Immune function, responses to stimuli, and cell death related genes appear to be impacted in both cell types. Remarkably, there is an overlapping gene set between the two cell types.

Additional Information

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Microarray
Affymetrix HG-U133A
12 Samples Loaded: 12
Human (Homo sapiens)
Monocytes , Macrophages
Chronic Obstructive Pulmonary Disease
Sample Set Spreadsheet
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Samples Preview
Sample ID !Sample_title cell type disease status Conditions pooled rna
GSM424840 COPD1 alveolar macrophage COPD patient COPD-Macrophages
GSM424842 control1 alveolar macrophage control patient Healthy-Macrophages
GSM424844 control2 alveolar macrophage control patient Healthy-Macrophages
GSM424845 control3 alveolar macrophage control patient Healthy-Macrophages
GSM424850 COPD4 alveolar macrophage COPD patient COPD-Macrophages
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File
sampleset4000091_sampleannotations.csv
Sample Set Spreadsheet
Raw Signal
Raw Signal
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Sample ID !Sample Title Cell type Disease status Conditions Pooled rna
GSM424840
COPD1
alveolar macrophage
COPD patient
COPD-Macrophages
 
GSM424842
control1
alveolar macrophage
control patient
Healthy-Macrophages
 
GSM424844
control2
alveolar macrophage
control patient
Healthy-Macrophages
 
GSM424845
control3
alveolar macrophage
control patient
Healthy-Macrophages
 
GSM424850
COPD4
alveolar macrophage
COPD patient
COPD-Macrophages
 
GSM424852
control5
alveolar macrophage
control patient
Healthy-Macrophages
 
GSM424853
COPD5
alveolar macrophage
COPD patient
COPD-Macrophages
 
GSM424857
COPD7
alveolar macrophage
COPD patient
COPD-Macrophages
 
GSM424858
control8
alveolar macrophage
control patient
Healthy-Macrophages
 
GSM424860
COPD8
alveolar macrophage
COPD patient
COPD-Macrophages
 
GSM425395
control monocyte
peripheral blood monocyte
control patient
Healthy-Monocytes
from 5 patients
GSM425396
COPD monocyte
peripheral blood monocyte
COPD patient
COPD-Monocytes
from 5 patients

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