Heterogeneity of chronic obstructive pulmonary disease: from phenotype to genotype

Incorporating External Information in Tissue Subtyping: A Topic Modeling Approach

Probabilistic topic models, have been widely deployed for various applications such as learning disease or tissue subtypes. Yet, learning the parameters of such models is usually an ill-posed problem and may result in losing valuable information about disease severity. A common approach is to add a discriminative loss term to the generative model's loss in order to learn a representation that is also predictive of disease severity. However, finding a balance between these two losses is not straightforward. We propose an alternative way in this paper. We develop a framework which allows for incorporating external covariates into the generative model's approximate posterior. These covariates can have more discriminative power for disease severity compared to the representation that we extract from the posterior distribution. For instance, they can be features extracted from a neural network which predicts disease severity from CT images. Effectively, we enforce the generative model's approximate posterior to reside in the subspace of these discriminative covariates. We illustrate our method's application on a large-scale lung CT study of Chronic Obstructive Pulmonary Disease (COPD), a highly heterogeneous disease. We aim at identifying tissue subtypes by using a variant of topic model as a generative model. We quantitatively evaluate the predictive performance of the inferred subtypes and demonstrate that our method outperforms or performs on par with some reasonable baselines. We also show that some of the discovered subtypes are correlated with genetic measurements, suggesting that the identified subtypes may characterize the disease's underlying etiology.

Evaluation Of HHIP Polymorphisms And Their Relationship With Chronic Obstructive Pulmonary Disease Phenotypes

Purpose

We aimed to correlate three polymorphisms of the Hedgehog Interacting Protein (HHIP) gene with the three main phenotypes of the chronic obstructive pulmonary disease (frequent exacerbator (FE), asthma/COPD overlap (ACO), and emphysema with hyperinflation).

Patients and methods

A cross-sectional study was carried out in the Department of Pulmonology at the Rio de Janeiro State University from February 2015 to July 2018. A total of 81 patients diagnosed with COPD according to the criteria of the Global Initiative for Chronic Obstructive Lung Disease (GOLD) were enrolled. The subjects were divided into three distinct groups according to their phenotypes (FE, ACO and emphysema-hyperinflation). Three polymorphisms of the HHIP gene that are often reported as allegedly involved in the pathogenesis of COPD were analysed: rs1828591, rs13118928, and rs6537296. Real-time PCR - TAQMAN SNP Genotyping Assay was performed. The statistical analysis was carried out with the SPSS program with a multivariate analysis with a 95% confidence interval.

Results

An increase in the frequency of the A allele of the rs13118928 HHIP gene polymorphism was observed in the group of subjects with COPD and emphysema-hyperinflation phenotype when compared with those in the FE phenotype (p=0.019) and subjects with ACO (p=0.04). However, the subjects with emphysema-hyperinflation phenotype presented more often the A allele (p=0.04). The genotypic analysis confirmed the difference between the emphysema-hyperinflation and ACO phenotypes, with a higher prevalence of the AA genotype in the emphysema-hyperinflation group (p=0.04). The ACO and FE phenotype subjects showed no difference in these polymorphisms. No difference was found in the frequency of the polymorphisms rs1828591 (p= 0.552) and rs6537296 (p=0.296) in the three phenotypes evaluated.

Conclusion

The presence of the A allele in the rs13118928 polymorphism of the HHIP gene may be related to the emphysema-hyperinflation phenotype.

Energy efficient physiologic coupling of gait and respiration is altered in chronic obstructive pulmonary disease

AIMS

Coupling between walking and breathing in humans is well established. In healthy systems, the ability to couple and uncouple leads to energy economization. It is unknown if physiologic efficiency is susceptible to alteration, particularly in individuals with airflow obstruction. The aim of this research was to determine if coupling was compromised in a disease characterized by abnormal airflow and dyspnoea, and if this was associated with reduced energy efficiency.

METHODS

As a model of airflow obstruction, 17 chronic obstructive pulmonary disease (COPD) patients and 23 control subjects were included and walked on a treadmill for 6 minutes at three speeds (preferred speed and ±20% preferred speed) while energy expenditure, breathing, and walking were recorded. Rating of perceived exertion was recorded at the end of each walking trial. The most commonly used frequency ratio (ie, strides:breath) and cross recurrence quantification analysis were used to quantify coupling. Linear regression models were used to determine associations.

RESULTS

Less complex frequency ratios, simpler ratios, (ie, 1:1 and 3:2) accompanied with stronger coupling were moderately associated with increased energy expenditure in COPD subjects. This was found for all three speeds.

CONCLUSION

The novel finding was that increased energy expenditure was associated with stronger and less complex coupling. Increased effort is needed when utilizing a frequency ratio of 1:1 or 3:2. The more stable the coupling, the more effort it takes to walk. In contrast to the complex energy efficient coupling of controls, those with airflow obstruction manifested simpler and stronger coupling associated with reduced energy efficiency.

Patients with Chronic Obstructive Pulmonary Disease Walk with Altered Step Time and Step Width Variability as Compared with Healthy Control Subjects

RATIONALE

Compared with control subjects, patients with chronic obstructive pulmonary disease (COPD) have an increased incidence of falls and demonstrate balance deficits and alterations in mediolateral trunk acceleration while walking. Measures of gait variability have been implicated as indicators of fall risk, fear of falling, and future falls.

OBJECTIVES

To investigate whether alterations in gait variability are found in patients with COPD as compared with healthy control subjects.

METHODS

Twenty patients with COPD (16 males; mean age, 63.6 ± 9.7 yr; FEV₁/FVC, 0.52 ± 0.12) and 20 control subjects (9 males; mean age, 62.5 ± 8.2 yr) walked for 3 minutes on a treadmill while their gait was recorded. The amount (SD and coefficient of variation) and structure of variability (sample entropy, a measure of regularity) were quantified for step length, time, and width at three walking speeds (self-selected and ±20% of self-selected speed). Generalized linear mixed models were used to compare dependent variables.

RESULTS

Patients with COPD demonstrated increased mean and SD step time across all speed conditions as compared with control subjects. They also walked with a narrower step width that increased with increasing speed, whereas the healthy control subjects walked with a wider step width that decreased as speed increased. Further, patients with COPD demonstrated less variability in step width, with decreased SD, compared with control subjects at all three speed conditions. No differences in regularity of gait patterns were found between groups.

CONCLUSIONS

Patients with COPD walk with increased duration of time between steps, and this timing is more variable than that of control subjects. They also walk with a narrower step width in which the variability of the step widths from step to step is decreased. Changes in these parameters have been related to increased risk of falling in aging research. This provides a mechanism that could explain the increased prevalence of falls in patients with COPD.

Gait analysis in patients with chronic obstructive pulmonary disease: a systematic review

BACKGROUND

Gait instability is a major fall-risk factor in patients with chronic obstructive pulmonary disease (COPD). Clinical gait analysis is a reliable tool to predict fall onsets. However, controversy still exists on gait impairments associated with COPD.

RESEARCH QUESTION

Thus, the aims of this review were to evaluate the current understanding of spatiotemporal, kinematic and kinetic gait features in patients with COPD.

METHODS

In line with PRISMA guidelines, a systematic literature search was performed throughout Web of Science, PubMed Medline, Scopus, PEDro and Scielo databases. We considered observational cross-sectional studies evaluating gait features in patients with COPD as their primary outcome. Risk of bias and applicability of these papers were assessed according to the QUADAS-2 tool.

RESULTS

Seven articles, cross-sectional studies published from 2011 to 2017, met the inclusion criteria. Sample size of patients with COPD ranged 14-196 (mean age range: 64-75 years). The main reported gait abnormalities were reduced step length and cadence, and altered variability of spatiotemporal parameters. Only subtle biomechanical changes were reported at the ankle level.

SIGNIFICANCE

A convincing mechanistic link between such gait impairments and falls in patients with COPD is still lacking. The paucity of studies, small sample sizes, gender and disease status pooling were the main risk of biases affecting the results uncertainty. Two research directions emerged: stricter cohorts characterization in terms of COPD phenotype and longitudinal studies. Quantitative assessment of gait would identify abnormalities and sensorimotor postural deficiencies that in turn may lead to better falling prevention strategies in COPD.

Risk Perceptions in Diabetic Patients Who Have Experienced Adverse Events: Implications for Patient Involvement in Regulatory Decisions

Background

Increasingly, patients are expected to influence decisions previously reserved for regulatory agencies, pharmaceutical companies, and healthcare professionals. Individual patients have previously represented their patient population when rare, serious adverse events (AEs) were weighed as part of a benefit-risk assessment. However, the degree of heterogeneity of the patient population is critical for how accurately they can be represented by individuals.

Objectives

This study aims to explore patients’ risk perception of rare, serious adverse effects of medicines with regard to blood glucose-lowering antidiabetics used by the individual patient.

Methods

Semi-structured interviews were conducted with 18 patients with diabetes with self-perceived serious, but not necessarily rare, AEs (e.g. stroke or valve or bypass surgery). The interviews explored the patients’ history of disease, perceptions of the terms rare and serious, and overall levels of risk aversion. A thematic analysis of the interviews, including a consensus discussion, was carried out.

Results

Interestingly, respondents rarely made a clear distinction between medicines-induced AEs and complications related to disease progression. Concerns regarding AEs were apparently diverse but were systematically related to the personal experiences of the respondents. Respondents routinely ignored information about possible rare, serious AEs, unless it could be related to personal experience. In the absence of experience, concerns were focused on common and less serious AEs, thus disregarding rare and more serious events.

Conclusion

The study suggests that experience of AEs, related to either medicines or disease, constitutes an important factor of patient risk perception. We therefore propose that serious adverse experiences should be added to the traditional panel of socioeconomic factors that are accounted for when patients are invited to give input on regulatory decisions.

Sulfatase modifying factor 1 (SUMF1) is associated with Chronic Obstructive Pulmonary Disease

Background

It has been observed that mice lacking the sulfatase modifying factor (Sumf1) developed an emphysema-like phenotype. However, it is unknown if SUMF1 may play a role in Chronic Obstructive Pulmonary Disease (COPD) in humans. The aim was to investigate if the expression and genetic regulation of SUMF1 differs between smokers with and without COPD.

Methods

SUMF1 mRNA was investigated in sputum cells and whole blood from controls and COPD patients (all current or former smokers). Expression quantitative trait loci (eQTL) analysis was used to investigate if single nucleotide polymorphisms (SNPs) in SUMF1 were significantly associated with SUMF1 expression. The association of SUMF1 SNPs with COPD was examined in a population based cohort, Lifelines. SUMF1 mRNA from sputum cells, lung tissue, and lung fibroblasts, as well as lung function parameters, were investigated in relation to genotype.

Results

Certain splice variants of SUMF1 showed a relatively high expression in lung tissue compared to many other tissues. SUMF1 Splice variant 2 and 3 showed lower levels in sputum cells from COPD patients as compared to controls. Twelve SNPs were found significant by eQTL analysis and overlapped with the array used for genotyping of Lifelines. We found alterations in mRNA expression in sputum cells and lung fibroblasts associated with SNP rs11915920 (top hit in eQTL), which validated the results of the lung tissue eQTL analysis. Of the twelve SNPs, two SNPs, rs793391 and rs308739, were found to be associated with COPD in Lifelines. The SNP rs793391 was also confirmed to be associated with lung function changes.

Conclusions

We show that SUMF1 expression is affected in COPD patients compared to controls, and that SNPs in SUMF1 are associated with an increased risk of COPD. Certain COPD-associated SNPs have effects on either SUMF1 gene expression or on lung function. Collectively, this study shows that SUMF1 is associated with an increased risk of developing COPD.

Electronic supplementary material

The online version of this article (doi:10.1186/s12931-017-0562-5) contains supplementary material, which is available to authorized users.

From Systems Understanding to Personalized Medicine: Lessons and Recommendations Based on a Multidisciplinary and Translational Analysis of COPD

Systems medicine, using and adapting methods and approaches as developed within systems biology, promises to be essential in ongoing efforts of realizing and implementing personalized medicine in clinical practice and research. Here we review and critically assess these opportunities and challenges using our work on COPD as a case study. We find that there are significant unresolved biomedical challenges in how to unravel complex multifactorial components in disease initiation and progression producing different clinical phenotypes. Yet, while such a systems understanding of COPD is necessary, there are other auxiliary challenges that need to be addressed in concert with a systems analysis of COPD. These include information and communication technology (ICT)-related issues such as data harmonization, systematic handling of knowledge, computational modeling, and importantly their translation and support of clinical practice. For example, clinical decision-support systems need a seamless integration with new models and knowledge as systems analysis of COPD continues to develop. Our experience with clinical implementation of systems medicine targeting COPD highlights the need for a change of management including design of appropriate business models and adoption of ICT providing and supporting organizational interoperability among professional teams across healthcare tiers, working around the patient. In conclusion, in our hands the scope and efforts of systems medicine need to concurrently consider these aspects of clinical implementation, which inherently drives the selection of the most relevant and urgent issues and methods that need further development in a systems analysis of disease.

Gait mechanics in patients with chronic obstructive pulmonary disease

BACKGROUND

Chronic obstructive pulmonary disease (COPD) is characterized by the frequent association of disease outside the lung. The objective of this study was to determine the presence of biomechanical gait abnormalities in COPD patients compared to healthy controls while well rested and without rest.

METHODS

Patients with COPD (N = 17) and aged-matched, healthy controls (N = 21) walked at their self-selected pace down a 10-meter walkway while biomechanical gait variables were collected. A one-minute rest was given between each of the five collected trials to prevent tiredness (REST condition). Patients with COPD then walked at a self-selected pace on a treadmill until the onset of self-reported breathlessness or leg tiredness. Subjects immediately underwent gait analysis with no rest between each of the five collected trials (NO REST condition). Statistical models with and without covariates age, gender, and smoking history were used.

RESULTS

After adjusting for covariates, COPD patients demonstrated more ankle power absorption in mid-stance (P = 0.006) than controls during both conditions. Both groups during NO REST demonstrated increased gait speed (P = 0.04), stride length (P = 0.03), and peak hip flexion (P = 0.04) with decreased plantarflexion moment (P = 0.04) and increased knee power absorption (P = 0.04) as compared to REST. A significant interaction revealed that peak ankle dorsiflexion moment was maintained from REST to NO REST for COPD but increased for controls (P < 0.01). Stratifying by disease severity did not alter these findings, except that step width decreased in NO REST as compared to REST (P = 0.01). Standardized effect sizes of significant effects varied from 0.5 to 0.98.

CONCLUSIONS

Patients with COPD appear to demonstrate biomechanical gait changes at the ankle as compared to healthy controls. This was seen not only in increased peak ankle power absorption during no rest but was also demonstrated by a lack of increase in peak ankle dorsiflexion moment from the REST to the NO REST condition as compared to the healthy controls. Furthermore, a wider step width has been associated with fall risk and this could account for the increased incidence of falls in patients with COPD.

Utility of animal and in vivo experimental infection of humans with rhinoviruses in the development of therapeutic agents for viral exacerbations of asthma and chronic obstructive pulmonary disease

There is an association with acute viral infection of the respiratory tract and exacerbations of asthma and chronic obstructive pulmonary disease (COPD). Although these exacerbations are associated with several types of viruses, human rhinoviruses (HRVs) are associated with the vast majority of disease exacerbations. Due to the lack of an animal species that is naturally permissive for HRVs to use as a facile model system, and the limitations associated with animal models of asthma and COPD, studies of controlled experimental infection of humans with HRVs have been used and conducted safely for decades. This review discusses how these experimental infection studies with HRVs have provided a means of understanding the pathophysiology underlying virus-induced exacerbations of asthma and COPD with the goal of developing agents for their prevention and treatment.

Tailoring of corticosteroids in COPD management

This literature review updates the reader on the new studies regarding steroid therapy over the last year in stable COPD and in exacerbations. In stable COPD, we critique the 2011 update and 2013 revision of the GOLD guidelines, discuss why combining inhaled corticosteroids (ICS) with long-acting beta-agonists (LABA) (ICS/LABA) is preferable over LABA alone and review the literature for intraclass differences, finding that the evidence does not clearly support superiority of any particular ICS/LABA. We also address other comparisons against ICS/LABA, including triple therapy. We briefly review which type of inhaler should be chosen. For exacerbations, we report the REDUCE trial findings favouring a 5-day course of systemic steroids, and other trials addressing which steroid and route to use, including in an intensive care setting. Lastly, the future lies in new anti-inflammatories and re-phenotyping the heterogeneous amalgamation of COPD. A Spanish guideline recommends distinguishing steroid-responsive eosinophilic exacerbators from other phenotypes.

The role of macrolides in asthma: current evidence and future directions

Macrolides, such as clarithromycin and azithromycin, possess antimicrobial, immunomodulatory, and potential antiviral properties. They represent a potential therapeutic option for asthma, a chronic inflammatory disorder characterised by airway hyper-responsiveness that leads to recurrent episodes of wheezing, breathlessness, chest tightness, and coughing. Results from clinical trials, however, have been contentious. The findings could be confounded by many factors, including the heterogeneity of asthma, treatment duration, dose, and differing outcome measures. Recent evidence suggests improved effectiveness of macrolides in patients with sub-optimally controlled severe neutrophilic asthma and in asthma exacerbations. We examine the evidence from clinical trials and discuss macrolide properties and their relevance to the pathophysiology of asthma. At present, the use of macrolides in chronic asthma or acute exacerbations is not justified. Further work, including proteomic, genomic, and microbiome studies, will advance our knowledge of asthma phenotypes, and help to identify a macrolide-responsive subgroup. Future clinical trials should target this subgroup and place emphasis on clinically relevant outcomes such as asthma exacerbations.