Lung Tissue Multi-Layer Network Analysis Uncovers the Molecular Heterogeneity of COPD

BACKGROUND

Chronic Obstructive Pulmonary Disease (COPD) is a heterogeneous condition. We hypothesized that the unbiased integration of different COPD lung omics using a novel multi-layer approach may unravel mechanisms associated with clinical characteristics.

METHODS

We profiled mRNA, miRNA and methylome in lung tissue samples from 135 former smokers with COPD. For each omic (layer) we built a patient network based on molecular similarity. The three networks were used to build a multi-layer network, and optimization of multiplex-modularity was employed to identify patient communities across the three distinct layers. Uncovered communities were related to clinical features.

RESULTS

We identified five patient communities in the multi-layer network which were molecularly distinct and related to clinical characteristics, such as FEV1 and blood eosinophils. Two communities (C#3 and C#4) had both similarly low FEV1 values and emphysema, but were molecularly different: C#3, but not C#4, presented B and T cell signatures and a downregulation of secretory (SCGB1A1/SCGB3A1) and ciliated cells. A machine learning model was set up to discriminate C#3 and C#4 in our cohort, and to validate them in an independent cohort. Finally, using spatial transcriptomics we characterized the small airway differences between C#3 and C#4, identifying an upregulation of T/B cell homing chemokines, and bacterial response genes in C#3.

CONCLUSIONS

A novel multi-layer network analysis is able to identify clinically relevant COPD patient communities. Patients with similarly low FEV1 and emphysema can have molecularly distinct small airways and immune response patterns, indicating that different endotypes can lead to similar clinical presentation.

Susceptible Young Adults and Development of COPD Later in Life

RATIONALE

Chronic obstructive pulmonary disease (COPD) has its origin in early life, and the Global Initiative for Chronic Obstructive Lung Disease (GOLD) proposes a pre-disease state "pre-COPD".

OBJECTIVE

We tested the hypothesis that susceptible young adults identified with chronic bronchitis and subtle lung function impairment will develop COPD later in life.

METHODS

We followed random non-obstructive individuals aged 20-50years from two population-based cohorts from different smoking eras, the Copenhagen General Population Study from 2003(N=5497) and Copenhagen City Heart Study from 1976-78(N=2609), for 10 and 25years for development of COPD(forced expiratory volume in one second[FEV1]/forced vital capacity[FVC]<0.70) and COPD GOLD 2-4 (additionally FEV1<80% predicted).

MEASUREMENTS AND MAIN RESULTS

After 10 years follow-up, 28% developed COPD and 13% COPD GOLD 2-4 in individuals susceptible to COPD compared to 8% and 1% in those without any susceptibility to COPD. Correspondingly, after 25years, 22% versus 13% developed COPD and 20% versus 8% developed COPD GOLD 2-4. More than half of incident COPD cases developed from a susceptible state. Compared to those without susceptibility to COPD, multivariable adjusted odds ratios in those susceptible to COPD were 3.42(95% confidence interval:2.78-4.21) for COPD and 10.1(6.77-15.2) for COPD GOLD 2-4 after 10years, and 1.54(1.23-1.93) and 2.12(1.64-2.73) after 25years. The ability of a COPD risk score consisting of the susceptibility state to COPD with smoking and asthma as risk factors to predict COPD later in life was high.

CONCLUSIONS

Our study suggests the existence of a pre-disease state of COPD, which can be used for early identification of susceptible individuals at risk for COPD later in life.

Smoking-associated increase in mucins 1 and 4 in human airways

Rationale

Smoking-related chronic obstructive pulmonary disease (COPD) is associated with dysregulated production of mucus. Mucins (MUC) are important both for mucus secretion and epithelial defense. We have examined the distribution of MUC1 and MUC4 in the airway epithelial cells of never-smokers and smokers with and without COPD.

Methods

Mucosal biopsies and bronchial wash samples were obtained by bronchoscopy from age- and sex-matched COPD-patients (n = 38; GOLD I-II/A-B), healthy never-smokers (n = 40) and current smokers with normal lung function (n = 40) from the Karolinska COSMIC cohort (NCT02627872). Cell-specific expressions of MUC1, MUC4 and regulating factors, i.e., epithelial growth factor receptor (EGFR) 1 and 2, were analyzed by immunohistochemistry. Soluble MUC1 was measured by quantitative immunodetection on slot blot.

Results

The levels of cell-bound MUC1 expression in basal cells and in soluble MUC1 in bronchial wash were increased in smokers, regardless of airway obstruction. Patients with chronic bronchitis had higher MUC1 expression. The expression of MUC4 in cells with goblet cell phenotype was increased in smokers. The expression of EGFR2, but not that of EGFR1, was higher in never-smokers than in smokers.

Conclusions

Smoking history and the presence of chronic bronchitis, regardless of airway obstruction, affect both cellular and soluble MUC1 in human airways. Therefore, MUC1 may be a novel marker for smoking- associated airway disease.

Clinical Aspects of Upper and Lower Respiratory Tract Infections

Respiratory tract infections are among the most common illnesses leading to medical consultation, and are associated with significant mortality. Community-acquired pneumonia is a common illness and, while Streptococcus pneumoniae continues to be the most frequent causative agent, atypical pathogens such as Mycoplasma pneumoniae, Chlamydia pneumoniae and Legionella species are now identified as additional common aetiological agents. Since clinical and roentgenographic features poorly predict the aetiological agent in most cases of community-acquired pneumonia, empirical therapy is generally recommended. Nosocomial pneumonia is the second most common hospital-acquired infection and is associated with significant mortality. Aerobic Gram-negative bacilli and Staphylococcus aureus are the predominant causative pathogens. New techniques to improve the diagnosis of nosocomial pneumonia have been introduced, but their role has not been entirely clarified. Therapy directed toward the most likely pathogens (aerobic Gram-negative species and S. aureus) on an empirical basis is recommended until more specific information is obtained. Acute exacerbations of chronic bronchitis should be treated with antimicrobial therapy directed toward S. pneumoniae, Haemophilus influenzae or Moraxella catarrhalis. Because of the emergence of β-lactamase-producing strains of H. influenzae and M. catarrhalis, the choice of an antimicrobial agent has to be carefully considered. Group A β-haemolytic streptococci are the most common cause of bacterial pharyngitis and penicillin remains the drug of choice. Patients suffering from otitis media and sinusitis are infected with the same organisms as those patients with acute exacerbations of chronic bronchitis and antibacterial choices are therefore similar.