DOI: 10.5061/dryad.3n5tb2rvf
title: Inflammatory cells and remodeling in bronchial biopsies from COPD patients and controls

description: 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: # Inflammatory cells and remodeling in bronchial biopsies from COPD
 patients and controls #### 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](http://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](http://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.