Inflammatory cells and remodeling in bronchial biopsies from COPD patients and controls
Data files
Oct 23, 2025 version files 147.55 KB
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README.md
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Stata_syntax_for_analyses_in_Tables.rtf
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syntax_for_analyses_DRYAD.do
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ToDRYAD_Oct25_2.dta
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ToDRYAD_Oct25_2.xls
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Abstract
The understanding of inflammation and remodeling in the bronchial wall of COPD patients with varying disease severity remains incomplete. 35 healthy controls and 47 volunteer COPD patients underwent bronchoscopy with bronchoalveolar lavage (BAL) and sampling by endobronchial biopsies in 2014-2015 as part of the MicroCOPD Study. Biopsies were embedded in glycol methyl acrylate (GMA) resin and examined by immunohistochemistry and staining for enumeration of CD3+, CD4+, CD8+, CD20+, CD68+, EG2+, and NE+ inflammatory cells, as well as endothelial cells (EN4) and smooth muscle actin (SMA). Mucus cells were stained by periodic acid-schiff (PAS) and toluidine blue to visualize the reticular basement membrane (RBM). The number of macrophages and eosinophils was higher, and vascularity increased in the submucosa in COPD patients compared with healthy controls. In healthy smokers, there were lower numbers of lymphocytes (CD3+, CD4+, CD8+, CD20+) than in never smokers. However, COPD patients with GOLD I/II had higher numbers of eosinophils and larger smooth muscle area compared with GOLD III/IV. COPD exacerbations the last year, blood eosinophils, and use of inhaled corticosteroids did not affect levels of inflammation or remodeling. Smoking alters inflammation in healthy controls, while specific patterns of macrophages, eosinophils, and vascularity distinguish COPD from non-COPD in bronchial biopsies.
Description of the data and file structure
Observational bronchoscopy study of COPD patients and Controls with bronchoalveolar lavage from the middle lobe and bronchial biopsies from the right lower lobe. Biopsies underwent GMA embedding and were subsequently stained for immunohistochemistry.
Files and variables
File: ToDRYAD_Oct25_2.dta
Description:
Stata (.dta) data file "ToDRYAD_Oct25_2.dta"
Stata (www.stata.com), which is a commercial software company, and use of its program require licensing.
File: ToDRYAD_Oct25_2.xls
Description: An export of the Stata file "ToDRYAD_Oct25_2.dta" (lack label values defined since excel does not have that), which can be opened by R or other readily available programs.
Variables within the "ToDRYAD_Oct25_2.dta" and "ToDRYAD_Oct25_2.xls" files:
- category - controls or COPD
- agecat - age in three categories; 1=less than 60 yrs, 2= 60-69.99 yrs; 3= 70 + yrs (at the time of data collection)
- smoking - smoking habits (at the time of data collection)
- packyears_cat - pack years smoked in three categories for ex or current smokers
- GOLD_2categories (GOLD stage for COPD based on FEV1 in % of predicted)
- fev1*fvc*ratio - FEV1/FVC (forced expiratory volume in 1 second / forced vital capacity)
- inhalsteroid - used of inhaled corticosteroids (at the time of data collection)
- exace - more than one serious COPD exacerbation the last 12 months (no/yes)
- CAT - CAT score (symptom score for COPD)
- CD3_man - number of stained CD3 cells/mm2 in the biopsy
- CD4_man - number of stained CD4 cells/mm2 in the biopsy
- CD8_man - number of stained CD8 cells/mm2 in the biopsy
- CD20_man - number of stained CD20 cells/mm2 in the biopsy
- CD68_man - number of stained CD68 cells/mm2 in the biopsy
- EG2_man - number of eosinophil cells/mm2 in the biopsy
- NOE1 - number of 10^6 positive pixels for neutrophils/mm2
- LamRet - thickness of basement membrane (lamina reticularis) in µm
- PAS - Mucus in the epithelium, 10^3 positive pixels/mm
- aSMA_p - area of smooth muscle cells in %
- EN4_fraction100- area of vascular cells in %
- bal_macrophages_perc - Percent macrophages in bronchalveolar lavage (BAL) [based on manual cell counts]
- bal_lymphocytes_perc - Percent lymphocytes in bronchalveolar lavage (BAL) [based on manual cell counts]
- bal_neutrophils_perc - Percent neutrophiles in bronchalveolar lavage (BAL) [based on manual cell counts]
- bal_eosinophils_perc - Percent eosinophiles in bronchalveolar lavage (BAL) [based on manual cell counts]
- blood_leukocytes - blood leukocytes Total count, 10^9/L
- blood_eosinophils - blood eosinophiles Total count, 10^9/L
Note: n/a denotes either missing values (for instance non-successful staining/biopsy for PAS) or non-relevant value (for instance GOLD stage in non-COPD subjects)
File: syntax_for_analyses_DRYAD.do
Description: the Stata syntax files for most all calculations presented in the Tables.
Note, in the original paper age and packers in exact value were analyzed, but for anonymization, age and packyears are here given in categories. This file can be opened using any text editor.
File: Stata_syntax_for_analyses_in_Tables.rtf
Description: rtf version of the Stata syntax file "syntax_for_analyses_DRYAD.do" for all calculations presented in the Tables, available to read for those not having access to a Stata license.
Code/software
Stata (www.stata.com), which is a commercial software company, and use of its program require licensing.
Access information
Other publicly accessible locations of the data:
- NA
Data was derived from the following sources:
- NA
Human subjects data
Participants permitted the publication of anonymized results from the study. All data is anonymized (the study ID number is not included, and one cannot back-track from the current data file to the original study participants. Only the metadata used for the publication in PLOS One is provided here, and only on a sub-sample of all study participants in the MicroCOPD study. Age has been binned into categories for an extra layer of anonymity.
