COPD-Specific Gene Expression Signatures of Alveolar Macrophages as well as Peripheral Blood Monocytes Overlap and Correlate with Lung Function-GSE16972
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.
--
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.
--
--
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.
--
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 |
All fields are editable except the "Sample ID" column. To edit a cell, click within the cell. To edit a "date" cell, click on the calendar icon. To cancel an edit, press the ESC key.
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 |
Name | ||
---|---|---|
All Samples | View | |
Culture conditions | Default | View |
In order to make new Group Sets or change settings, please log in. |
Group Set | |
---|---|
All Samples | |
Culture conditions |