Opportunities and challenges in the genetics of COPD 2010: an International COPD Genetics Conference report

Does Chronic Obstructive Pulmonary Disease Originate from Different Cell Types?

The onset of chronic obstructive pulmonary disease (COPD) is heterogeneous, and current approaches to define distinct disease phenotypes are lacking. In addition to clinical methodologies, subtyping COPD has also been challenged by the reliance on human lung samples from late-stage diseases. Different COPD phenotypes may be initiated from the susceptibility of different cell types to cigarette smoke, environmental pollution, and infections at early stages that ultimately converge at later stages in airway remodeling and destruction of the alveoli when the disease is diagnosed. This perspective provides discussion points on how studies to date define different cell types of the lung that can initiate COPD pathogenesis, focusing on the susceptibility of macrophages, T and B cells, mast cells, dendritic cells, endothelial cells, and airway epithelial cells. Additional cell types, including fibroblasts, smooth muscle cells, neuronal cells, and other rare cell types not covered here, may also play a role in orchestrating COPD. Here, we discuss current knowledge gaps, such as which cell types drive distinct disease phenotypes and/or stages of the disease and which cells are primarily affected by the genetic variants identified by whole genome-wide association studies. Applying new technologies that interrogate the functional role of a specific cell type or a combination of cell types as well as single-cell transcriptomics and proteomic approaches are creating new opportunities to understand and clarify the pathophysiology and thereby the clinical heterogeneity of COPD.

The causal association between genetically regulated 25OHD and chronic obstructive pulmonary disease: A meta-analysis and Mendelian randomization study

Backgrounds and objectives: Chronic obstructive pulmonary disease (COPD) is a multifactorial disease under genetic control. We present a meta-analysis to examine the associations of vitamin D binding protein (VDBP) gene rs7041 polymorphism with the risk of COPD and changes in circulating 25OHD concentrations.

Methods: A literature search, quality assessment, and data extraction were conducted independently by two investigators. Data are expressed as odds ratio (OR) or weighted mean difference (WMD) with a 95% confidence interval (CI). The inverse variance weighted method (IVW) in R (version 1.1.456) was applied to calculate the Mendelian randomization coefficient.

Results: A total of 13 articles with 3,667 participants were meta-analyzed. The rs7041-GT genotype was associated with a 49% reduced COPD risk (OR: 0.51, 95% CI: 0.30 to 0.88, p = 0.014) compared to the rs7041-TT genotype. Carriers of the rs7041-GT genotype had significantly higher concentrations of circulating 25OHD than those with the rs7041-TT genotype (WMD: 0.32 ng/ml, 95% CI: 0.09 to 0.55, p = 0.006). Under the assumptions of Mendelian randomization, and assuming a linear logistic relationship between circulating 25OHD and COPD, an inverse association was noted after using VDBP gene rs7041 polymorphism as an instrument (WMD: −2.07, 95% CI: −3.72 to −0.41, p = 0.015). There was a low probability of publication bias.

Conclusion: We observed significant associations of VDBP gene rs7041 polymorphism with the risk of COPD and changes in circulating 25OHD concentrations. Importantly, we found a causal relationship between genetically regulated 25OHD concentrations and COPD risk.

Cleaning the Flue in Wood-Burning Stoves Is a Key Factor in Reducing Household Air Pollution

In experimental settings, replacing old wood stoves with new wood stoves results in reduced personal exposure to household air pollution. We tested this assumption by measuring PM2.5 and levoglucosan concentrations inside homes and correlated them with wood stove age. Methods: Thirty homes in the Albuquerque, NM area were monitored over a seven-day period using in-home particulate monitors placed in a common living area during the winter months. Real-time aerosol monitoring was performed, and filter samples were analyzed gravimetrically to calculate PM2.5 concentrations and chemically to determine concentrations of levoglucosan. A linear regression model with backward stepwise elimination was performed to determine the factors that would predict household air pollution measures. Results: In this sample, 73.3% of the households used wood as their primary source of heating, and 60% burned daily or almost daily. The mean burn time over the test week was 50 ± 38 h, and only one household burned wood 24/day (168 h). The average PM2.5 concentration (standard deviation) for the 30 homes during the seven-day period was 34.6 µg/m3 (41.3 µg/m3), and median (min, max) values were 15.5 µg/m3 (7.3 µg/m3, 193 µg/m3). Average PM2.5 concentrations in 30 homes ranged from 0−15 μg/m3 to >100 μg/m3. Maximum PM2.5 concentrations ranged from 100−200 μg/m3 to >3000 μg/m3. The levoglucosan levels showed a linear correlation with the total PM2.5 collected by the filters (R2 = 0.92). However, neither mean nor peak PM2.5 nor levoglucosan levels were correlated with the age (10.85 ± 8.54 years) of the wood stove (R2 ≤ 0.07, p > 0.23). The final adjusted linear regression model showed that average PM2.5 was associated with reports of cleaning the flue with a beta estimate of 35.56 (3.47−67.65) and R2 = 0.16 (p = 0.04). Discussion: Cleaning the flue and not the wood stove age was associated with household air pollution indices. Education on wood stove maintenance and safe burning practices may be more important in reducing household air pollution than the purchase of new stoves.

Effects of Wood Smoke Constituents on Mucin Gene Expression in Mice and Human Airway Epithelial Cells and on Nasal Epithelia of Subjects with a Susceptibility Gene Variant in Tp53

BACKGROUND

Exposure to wood smoke (WS) increases the risk for chronic bronchitis more than exposure to cigarette smoke (CS), but the underlying mechanisms are unclear.

OBJECTIVE

The effect of WS and CS on mucous cell hyperplasia in mice and in human primary airway epithelial cells (AECs) was compared with replicate the findings in human cohorts. Responsible WS constituents were identified to better delineate the pathway involved, and the role of a tumor protein p53 (Tp53) gene polymorphism was investigated.

METHODS

Mice and primary human AECs were exposed to WS or CS and the signaling receptor and pathway were identified using short hairpin structures, small molecule inhibitors, and Western analyses. Mass spectrometric analysis was used to identify active WS constituents. The role of a gene variant in Tp53 that modifies proline to arginine was examined using nasal brushings from study participants in the Lovelace Smokers Cohort, primary human AECs, and mice with a modified Tp53 gene.

RESULTS

WS at 25-fold lower concentration than CS increased mucin expression more efficiently in mice and in human AECs in a p53 pathway-dependent manner. Study participants who were homozygous for p53 arginine compared with the proline variant showed higher mucin 5AC (MUC5AC) mRNA levels in nasal brushings if they reported WS exposure. The WS constituent, oxalate, increased MUC5AC levels similar to the whole WS extract, especially in primary human AECs homozygous for p53 arginine, and in mice with a modified Tp53 gene. Further, the anion exchange protein, SLC26A9, when reduced, enhanced WS- and oxalate-induced mucin expression.

DISCUSSION

The potency of WS compared with CS in inducing mucin expression may explain the increased risk for chronic bronchitis in participants exposed to WS. Identification of the responsible compounds could help estimate the risk of pollutants in causing chronic bronchitis in susceptible individuals and provide strategies to improve management of lung diseases. https://doi.org/10.1289/EHP9446.

Associations of genetic risk and smoking with incident chronic obstructive pulmonary disease

BACKGROUND

Genetic and smoking contribute to chronic obstructive pulmonary disease (COPD), but whether a combined polygenic risk score (PRS) is associated with incident COPD and whether it has a synergistic effect on the smoking remains unclear. We aimed to investigate the association of PRS with COPD and explore whether smoking behaviors could modify such association.

METHODS

Multivariable Cox proportional models were used to estimate hazard ratios (HRs) and 95% confidence intervals (95% CIs) for the association of the PRS and smoking with COPD.

RESULTS

The study included 439 255 participants (mean age 56.5; 53.9% female), with a median follow-up of 9.0 years. The PRS_lasso containing 2.5 million variants showed better discrimination and a stronger association for incident COPD than the PRS₂₇₉ containing 279 genome-wide significance variants. Compared with the low genetic risk, the HRs of the medium and high genetic risk were 1.39 (95% CI, 1.31-1.48) and 2.40 (95% CI, 2.24-2.56), respectively. The HR of high genetic risk and current smoking was 11.62 (95% CI, 10.31-13.10) times of low genetic risk and never smoking. There were significant interactions between the PRS_lasso and smoking status for incident COPD (p for interaction<0.001). From low genetic risk to high genetic risk, the HRs of current smoking increased from 4.32 (95% CI, 3.69-5.06) to 6.89 (95% CI, 6.21-7.64), and the population-attributable risks of smoking increased from 42.7% to 61.1%.

CONCLUSION

PRS constructed from millions of variants below genome-wide significance showed significant associations with incident COPD. Participants with a high genetic risk may be more susceptible to developing COPD when exposed to smoking.

Influence of the CYP2J2 Gene Polymorphisms on Chronic Obstructive Pulmonary Disease Risk in the Chinese Han Population

INTRODUCTION

Cytochrome P450 (CYP) 2J2 is a major enzyme that controls epoxyeicosatrienoic acids biosynthesis, which may play a role in chronic obstructive pulmonary disease (COPD) development. In this study, we aimed to assess the influence of CYP2J2 polymorphisms with COPD susceptibility.

MATERIAL AND METHODS

A case-control study enrolled 313 COPD cases and 508 controls was to investigate the association between CYP2J2 polymorphisms and COPD risk. Agena MassARRAY platform was used to genotype CYP2J2 polymorphisms. Odds ratios (OR) and 95% confidence intervals (CI) were calculated to evaluate the association between CYP2J2 polymorphisms and COPD risk.

RESULTS

We observed rs11207535 (homozygote: OR=0.08, 95%CI=0.01-0.96, p=0.047; recessive: OR=0.08, 95%CI=0.01-0.94, p=0.044), rs10889159 (homozygote: OR=0.08, 95%CI=0.01-0.92, p=0.043; recessive: OR=0.08, 95%CI=0.01-0.90, p=0.040) and rs1155002 (heterozygote: OR=1.63, 95%CI=1.13-2.36, p=0.009; dominant: OR=1.64, 95%CI=1.15-2.35, p=0.006; additive: OR=1.45, 95%CI=1.09-1.92, p=0.011) were significantly associated with COPD risk. Allelic tests showed T allele of rs2280274 was related to a decreased risk of COPD and T allele of rs1155002 was associated with an increased COPD risk. Stratified analyses indicated the effects of CYP2J2 polymorphisms and COPD risk were dependent on gender and smoking status (p<0.05). Additionally, two haplotypes (A_rs11207535C_rs10889159T_rs1155002 and A_rs11207535C_rs10889159C_rs1155002) significantly decreased COPD risk.

CONCLUSION

It suggested CYP2J2 polymorphisms were associated with COPD susceptibility in the Chinese Han population.

Genetic Advances in Chronic Obstructive Pulmonary Disease. Insights from COPDGene

Chronic obstructive pulmonary disease (COPD) is a common and progressive disease that is influenced by both genetic and environmental factors. For many years, knowledge of the genetic basis of COPD was limited to Mendelian syndromes, such as alpha-1 antitrypsin deficiency and cutis laxa, caused by rare genetic variants. Over the past decade, the proliferation of genome-wide association studies, the accessibility of whole-genome sequencing, and the development of novel methods for analyzing genetic variation data have led to a substantial increase in the understanding of genetic variants that play a role in COPD susceptibility and COPD-related phenotypes. COPDGene (Genetic Epidemiology of COPD), a multicenter, longitudinal study of over 10,000 current and former cigarette smokers, has been pivotal to these breakthroughs in understanding the genetic basis of COPD. To date, over 20 genetic loci have been convincingly associated with COPD affection status, with additional loci demonstrating association with COPD-related phenotypes such as emphysema, chronic bronchitis, and hypoxemia. In this review, we discuss the contributions of the COPDGene study to the discovery of these genetic associations as well as the ongoing genetic investigations of COPD subtypes, protein biomarkers, and post-genome-wide association study analysis.

Genetics of COPD

Although chronic obstructive pulmonary disease (COPD) risk is strongly influenced by cigarette smoking, genetic factors are also important determinants of COPD. In addition to Mendelian syndromes such as alpha-1 antitrypsin deficiency, many genomic regions that influence COPD susceptibility have been identified in genome-wide association studies. Similarly, multiple genomic regions associated with COPD-related phenotypes, such as quantitative emphysema measures, have been found. Identifying the functional variants and key genes within these association regions remains a major challenge. However, newly identified COPD susceptibility genes are already providing novel insights into COPD pathogenesis. Network-based approaches that leverage these genetic discoveries have the potential to assist in decoding the complex genetic architecture of COPD.

CYP2B6 genetic polymorphisms influence chronic obstructive pulmonary disease susceptibility in the Hainan population

Introduction

Chronic obstructive pulmonary disease (COPD) is a lung disease closely related to exposure to exogenous substances. CYP2B6 can activate many exogenous substances, which in turn affect lung cells. The aim of this study was to assess the association of single-nucleotide polymorphisms (SNPs) in CYP2B6 with COPD risk in a Chinese Han population.

Materials and methods

Genotypes of the five candidate SNPs in CYP2B6 were identified among 318 cases and 508 healthy controls with an Agena MassARRAY method. The association between CYP2B6 polymorphisms and COPD risk was evaluated using genetic models and haplotype analyses.

Results

In allele model, we observed that rs4803420 G and rs1038376 A were related to COPD risk. And rs4803420 G/T and G/T-T/T were related to a decreased COPD risk compared to GG genotype in the co-dominant and dominant models, respectively. When comparing with the AA genotype, rs1038376 A/T and A/T-T/T were associated with an increased COPD risk in the co-dominant and dominant models, respectively. Further gender stratification co-dominant and dominant models analysis showed that genotype G/T and G/T-T/T of rs4803420, and genotype A/T and A/T-T/T of rs1038376 were significantly associated with COPD risk compared to the wide type in males and females, while allele C of rs12979270 was only associated with COPD risk in females. Smoking status stratification analysis showed that rs12979270 C was significantly associated with an increased COPD risk under the allele model compared with allele A in the smoking subgroup. Haplotype analysis showed that haplotype GTA and TAA were related to COPD risk.

Conclusion

Our data is the first to demonstrate that CYP2B6 polymorphisms may exert effects on COPD susceptibility in the Chinese Han population.

Clinical Epidemiology of COPD: Insights From 10 Years of the COPDGene Study

The Genetic Epidemiology of COPD (COPDGene) study is a noninterventional, multicenter, longitudinal analysis of > 10,000 subjects, including smokers with a ≥ 10 pack-year history with and without COPD and healthy never smokers. The goal was to characterize disease-related phenotypes and explore associations with susceptibility genes. The subjects were extensively phenotyped with the use of comprehensive symptom and comorbidity questionnaires, spirometry, CT scans of the chest, and genetic and biomarker profiling. The objective of this review was to summarize the major advances in the clinical epidemiology of COPD from the first 10 years of the COPDGene study. We highlight the influence of age, sex, and race on the natural history of COPD, and the impact of comorbid conditions, chronic bronchitis, exacerbations, and asthma/COPD overlap.

TERT gene polymorphisms are associated with chronic obstructive pulmonary disease risk in the Chinese Li population

Background

Chronic obstructive pulmonary disease (COPD) is one of the leading causes of morbidity and mortality worldwide and is characterized by a partially reversible airflow limitation. Currently, many studies put forward that COPD is associated with both genetic and environmental factors. It has been reported that germline mutations in telomerase are risk factors for COPD susceptibility. In this study, we validated the association between TERT polymorphisms and COPD risk with a case–control study in the Chinese Li population.

Methods

A total of 279 COPD patients and 290 control individuals were recruited. We identified five single nucleotide polymorphisms (SNPs) in TERT that were associated with COPD. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated in logistic regression models after adjusting for age and gender to assess the association.

Results

In the genetic model analysis, we found the “C/T‐T/T” genotype of rs10069690 in TERT was associated with an increased COPD risk in the dominant model (p = 0.046); the rs2853677 in TERT was significantly associated with increased COPD risk based on the codominant model (“A/G” genotype, p = 0.033), dominant model (A/G‐G/G genotype, p = 0.0091), and log‐additive model (p = 0.023). The rs2853676 in TERT could increase the risk of COPD in the dominant model (“C/T‐T/T” genotype, p = 0.026) and in the Log‐additive model (p = 0.022).

Conclusion

Our data shed new light on the association between TERT SNPs and COPD susceptibility in the Chinese Li population.

HIF1A gene rs10873142 polymorphism is associated with risk of chronic obstructive pulmonary disease in a Chinese Han population: a case-control study

Chronic obstructive pulmonary disease (COPD) is a type of obstructive lung disease characterized by long-term poor airflow. Recently, variants in the hypoxia inducible factor 1α (HIF1A) gene were found to be associated with COPD risk. The present study aimed to identify whether rs10873142 polymorphism (an intronic polymorphism) in HIF1A gene was related to COPD in a Chinese population. We genotyped HIF1A gene rs10873142 polymorphism in a case–control study with 235 COPD cases and 548 controls in a Chinese Han population. Odd ratios (ORs) and 95% confidence intervals (CIs) were estimated using the chi-squared (χ²) test, genetic model analysis, and stratification analysis. In the genetic model analysis, we found that the TT genotype (TT compared with CC: OR: 1.63; 95% CI: 1.02–2.60; P=0.042) and T allele (T compared with C: OR: 1.29; 95%CI, 1.02–1.60; P=0.032) showed significant correlation with the risk of COPD. However, in stratification analyses of age, BMI, and forced expiratory volume in 1 s (FEV1)/FEV, we failed to find any association between HIF1A gene rs10873142 polymorphism with COPD risk. The present study supports that HIF1A gene rs10873142 polymorphism may be associated with increased risk of COPD in a Chinese Han population. To the best of our knowledge, this is the first case–control study uncovering that the HIF1A gene rs10873142 polymorphism increases the risk of COPD in a Chinese Han population.

IREB2, CHRNA5, CHRNA3, FAM13A & hedgehog interacting protein genes polymorphisms & risk of chronic obstructive pulmonary disease in Tatar population from Russia

Background & objectives:

Chronic obstructive pulmonary disease (COPD) is a complex chronic inflammatory disease of the respiratory system affecting primarily distal respiratory pathways and lung parenchyma. This study was aimed at investigating the association of COPD with IREB2, CHRNA5, CHRNA3, FAM13A and hedgehog interacting protein (HHIP) genes in a Tatar population from Russia.

Methods:

Six single nucleotide polymorphisms (SNPs) (rs13180, rs16969968, rs1051730, rs6495309, rs7671167, rs13118928) were genotyped by the real-time polymerase chain reaction in this study (511 COPD patients and 508 controls). Logistic regression was used to detect the association of SNPs and haplotypes of linked loci in different models. Linear regression analyses were performed to estimate the relationship between SNPs and lung function parameters and pack-years.

Results:

The rs13180 (IREB2), rs16969968 (CHRNA5) and rs1051730 (CHRNA3) were significantly associated with COPD in additive model [P_adj=0.00001, odds ratio (OR)=0.64; P_adj=0.0001, OR=1.41 and P_adj=0.0001, OR=1.47]. The C-G haplotype by rs13180 and rs1051730 was a protective factor for COPD in our population (P_adj=0.0005, OR=0.61). These results were confirmed only in smokers. The rs16969968 and rs1051730 were associated with decrease of forced expiratory volume in 1 sec % predicted (P_adj=0.005 and P_adj=0.0019).

Interpretation & conclusions:

Our study showed the association of rs13180, rs16969968 and rs1051730 with COPD and lung function in Tatar population from Russia. Further studies need to be done in other ethnic populations.

Association between RTEL1 gene polymorphisms and COPD susceptibility in a Chinese Han population

Objective

We investigated the association between single-nucleotide polymorphisms in regulation of telomere elongation helicase 1 (RTEL1), which has been associated with telomere length in several brain cancers and age-related diseases, and the risk of chronic obstructive pulmonary disease (COPD) in a Chinese Han population.

Methods

In a case–control study that included 279 COPD cases and 290 healthy controls, five single-nucleotide polymorphisms in RTEL1 were selected and genotyped using the Sequenom MassARRAY platform. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated using unconditional logistic regression after adjusting for age and gender.

Results

In the genotype model analysis, we determined that rs4809324 polymorphism had a decreased effect on the risk of COPD (CC versus TT: OR =0.28; 95% CI =0.10–0.82; P=0.02). In the genetic model analysis, we found that the “C/C” genotype of rs4809324 was associated with a decreased risk of COPD based on the codominant model (OR =0.33; 95% CI =0.13–0.86; P=0.022) and recessive model (OR =0.32; 95% CI =0.12–0.80; P=0.009).

Conclusion

Our data shed new light on the association between genetic polymorphisms of RTEL1 and COPD susceptibility in the Chinese Han population.

Genetic loci associated with chronic obstructive pulmonary disease overlap with loci for lung function and pulmonary fibrosis

Chronic obstructive pulmonary disease (COPD) is a leading cause of mortality worldwide. We performed a genetic association study in 15,256 cases and 47,936 controls, with replication of select top results (P < 5 × 10-6) in 9,498 cases and 9,748 controls. In the combined meta-analysis, we identified 22 loci associated at genome-wide significance, including 13 new associations with COPD. Nine of these 13 loci have been associated with lung function in general population samples, while 4 (EEFSEC, DSP, MTCL1, and SFTPD) are new. We noted two loci shared with pulmonary fibrosis (FAM13A and DSP) but that had opposite risk alleles for COPD. None of our loci overlapped with genome-wide associations for asthma, although one locus has been implicated in joint susceptibility to asthma and obesity. We also identified genetic correlation between COPD and asthma. Our findings highlight new loci associated with COPD, demonstrate the importance of specific loci associated with lung function to COPD, and identify potential regions of genetic overlap between COPD and other respiratory diseases.

A genome-wide association study identifies risk loci for spirometric measures among smokers of European and African ancestry

BACKGROUND

Pulmonary function decline is a major contributor to morbidity and mortality among smokers. Post bronchodilator FEV1 and FEV1/FVC ratio are considered the standard assessment of airflow obstruction. We performed a genome-wide association study (GWAS) in 9919 current and former smokers in the COPDGene study (6659 non-Hispanic Whites [NHW] and 3260 African Americans [AA]) to identify associations with spirometric measures (post-bronchodilator FEV1 and FEV1/FVC). We also conducted meta-analysis of FEV1 and FEV1/FVC GWAS in the COPDGene, ECLIPSE, and GenKOLS cohorts (total n = 13,532).

RESULTS

Among NHW in the COPDGene cohort, both measures of pulmonary function were significantly associated with SNPs at the 15q25 locus [containing CHRNA3/5, AGPHD1, IREB2, CHRNB4] (lowest p-value = 2.17 × 10(-11)), and FEV1/FVC was associated with a genomic region on chromosome 4 [upstream of HHIP] (lowest p-value = 5.94 × 10(-10)); both regions have been previously associated with COPD. For the meta-analysis, in addition to confirming associations to the regions near CHRNA3/5 and HHIP, genome-wide significant associations were identified for FEV1 on chromosome 1 [TGFB2] (p-value = 8.99 × 10(-9)), 9 [DBH] (p-value = 9.69 × 10(-9)) and 19 [CYP2A6/7] (p-value = 3.49 × 10(-8)) and for FEV1/FVC on chromosome 1 [TGFB2] (p-value = 8.99 × 10(-9)), 4 [FAM13A] (p-value = 3.88 × 10(-12)), 11 [MMP3/12] (p-value = 3.29 × 10(-10)) and 14 [RIN3] (p-value = 5.64 × 10(-9)).

CONCLUSIONS

In a large genome-wide association study of lung function in smokers, we found genome-wide significant associations at several previously described loci with lung function or COPD. We additionally identified a novel genome-wide significant locus with FEV1 on chromosome 9 [DBH] in a meta-analysis of three study populations.

Candidate genes for COPD: current evidence and research

COPD is a common complex disease characterized by progressive airflow limitation. Several genome-wide association studies (GWASs) have discovered genes that are associated with COPD. Recently, candidate genes for COPD identified by GWASs include CHRNA3/5 (cholinergic nicotine receptor alpha 3/5), IREB2 (iron regulatory binding protein 2), HHIP (hedgehog-interacting protein), FAM13A (family with sequence similarity 13, member A), and AGER (advanced glycosylation end product–specific receptor). Their association with COPD susceptibility has been replicated in multiple populations. Since these candidate genes have not been considered in COPD, their pathological roles are still largely unknown. Herein, we review some evidences that they can be effective drug targets or serve as biomarkers for diagnosis or subtyping. However, more study is required to understand the functional roles of these candidate genes. Future research is needed to characterize the effect of genetic variants, validate gene function in humans and model systems, and elucidate the genes’ transcriptional and posttranscriptional regulatory mechanisms.

Association of genetic polymorphisms with chronic obstructive pulmonary disease in the Hainan population: a case-control study

Purpose

Chronic obstructive pulmonary disease (COPD) is predicted to become the third most common cause of death and the fifth most common cause of disability in the world by 2020. Recently, variants in the hypoxia-inducible factor 1α (HIF1A), cholinergic receptor, neuronal nicotinic, alpha polypeptide-5, and iron-responsive element-binding protein 2 gene (IREB2) genes were found to be associated with COPD. This study aims to identify whether the variations in these genes are related to COPD in the Hainan population of the People’s Republic of China.

Patients and methods

We genotyped 12 single nucleotide polymorphisms in a case-control study with 200 COPD cases and 401 controls from Hainan, People’s Republic of China. Odds ratios and 95% confidence intervals were estimated using the chi-squared (χ²) test, genetic model analysis, haplotype analysis, and stratification analysis.

Results

In the genetic model analysis, we found that the genotype T/T of rs13180 of IREB2 decreased the COPD risk by 0.52-fold (P=0.025). But in the further stratification analysis, we failed to find the association between the selected single nucleotide polymorphisms with COPD risk in Han population. In addition, the haplotype analysis of HIF1A gene also was not found to be the possible haplotype associated with COPD risk.

Conclusion

Our results support that IREB2 rs13180 is associated with COPD in Hainan population. And this is the first time the HIF1A polymorphisms in COPD in a Chinese population has been reported, although we failed to find any significant result.

The independent and combined effects of lifetime smoke exposures and asthma as they relate to COPD

Chronic obstructive pulmonary disease (COPD) is part of a worldwide tobacco-related disease epidemic, and is associated with progressive airflow obstruction and varying degrees of emphysema and/or hyperinflation. Greater focus has been placed recently on the potential for early life factors to influence the development of COPD, based on the premise that delayed lung growth during childhood and adolescence might predispose to lung disease in later life. For most people, the adverse effects on lung function of adult and early childhood factors are additive, which provides no additional incentive for current smokers to quit. However, if there is a (synergistic) interaction between active smoking and asthma, smoking cessation is likely to have a greater lung function benefit for the smoker who is also asthmatic, especially if quitting occurs at an early age. This article critically evaluates the evidence for the independent associations of lifetime asthma, smoking and smoke exposures with airflow obstruction, plus their interaction when multiple factors are present.

Chronic Obstructive Pulmonary Disease Genetics: A Review of the Past and a Look Into the Future

Chronic obstructive pulmonary disease (COPD) affects over 10 million Americans.¹ This complex disorder demonstrates many different presentations in a wide variety of patients, and results from a combination of environmental exposures and genetic risk factors. Smoking alone does not result in COPD: not all smokers develop COPD and lung function decline among smokers is highly variable. There is growing evidence for genetic risk factors for COPD: early familial aggregation and linkage analysis studies strongly suggested genetic contributions to COPD, and recent genome-wide association studies have identified several genomic regions that are clearly related to COPD susceptibility. However, despite recent advances in COPD genetics, much of the heritability of COPD remains unexplained, and functional studies are only beginning to elucidate a role for the genetic associations that have been identified. Despite this, the future is bright for understanding the genetics of COPD. Improvements in COPD phenotyping, collaborations among COPD study cohorts, and novel integrative approaches to identifying genetic markers all promise to unravel much of this missing heritability and ultimately lead to improvements in our understanding of COPD susceptibility and treatment.

Clinical trial simulation to assist in COPD trial planning and design with a biomarker-based diagnostic: when to pull the trigger?

Chronic Obstructive Pulmonary Disease (COPD) is a heterogeneous disease with a wide range of clinical phenotypes that vary from predominantly airway disease (chronic bronchitis) to predominantly parenchymal disease (emphysema). Current advances for the treatment of COPD are increasingly focused on targeted treatments and development of novel biomarker-based diagnostics (Dx)'s to select the patients most likely to benefit. Clinical trial planning and design with biomarkers includes additional considerations beyond those for conventional trials in un-selected populations, e.g., the heterogeneity of COPD phenotypes in the population, the ability of a biomarker to predict clinically meaningful phenotypes that are differentially associated with the response to a targeted treatment, and the data needed to make Go/No Go decisions during clinical development. We developed the Clinical Trial Object Oriented Research Application (CTOORA), a computer-aided clinical trial simulator of COPD patient outcomes, to inform COPD trial planning with biomarkers. CTOORA provides serial projections of trial success for a range of hypothetical and plausible scenarios of interest. In the absence of data, CTOORA can identify characteristics of a biomarker-based Dx needed to provide a meaningful advantage when used in a clinical trial. We present a case study in which CTOORA is used to identify the scenarios for which a biomarker may be used successfully in clinical development. CTOORA is a tool for robust clinical trial planning with biomarkers, to guide early-to-late stage development that is positioned for success.

Relationship between the microsatellite D2S388-5 and D2S2232 polymorphisms and chronic obstructive pulmonary disease in the Chinese Kazakh population

BACKGROUND AND OBJECTIVE

Chronic obstructive pulmonary disease (COPD) is influenced by multiple genetic and environmental factors. The role of genetic susceptibility in the pathogenesis of COPD has recently gained more attention. The surface lung surfactant protein B plays an important role in COPD pathogenesis. Microsatellite DNA has been characterized in the surfactant protein B alleles D2S388-5 and D2S2232. The aim of this research was to investigate the distribution of the D2S388-5 and D2S2232 microsatellite polymorphisms in smokers of the Kazakh ethnic group in Xinjiang, China, with and without COPD to assess whether such polymorphisms are associated with COPD susceptibility.

METHODS

DNA was extracted from the blood of 197 smokers with COPD and 236 control smokers of Kazakh ethnicity. The smokers diagnosed with COPD were registered at the Department of Respiratory Medicine from four different hospitals. The control group was recruited at the medical examination centre from the same area. The polymorphisms of the D2S388-5 and D2S2232 microsatellite loci were measured by multiple short tandem repeat amplification using fluorescence-labelled polymerase chain reaction and capillary electrophoresis.

RESULTS

Nine alleles and 32 genotypes were identified in D2S388-5, while 9 alleles and 31 genotypes were identified in D2S2232. Both genotype distributions in control smokers were in accordance with Hardy-Weinberg equilibrium. The frequency of the 254 bp allele from the D2S388-5 locus was significantly higher in the COPD group versus the control (P < 0.001, odds ratio = 5.942).

CONCLUSIONS

D2S388-5 microsatellite polymorphism may be associated with susceptibility to COPD in Xinjiang Kazakhs.

Paired inspiratory-expiratory chest CT scans to assess for small airways disease in COPD

Background

Gas trapping quantified on chest CT scans has been proposed as a surrogate for small airway disease in COPD. We sought to determine if measurements using paired inspiratory and expiratory CT scans may be better able to separate gas trapping due to emphysema from gas trapping due to small airway disease.

Methods

Smokers with and without COPD from the COPDGene Study underwent inspiratory and expiratory chest CT scans. Emphysema was quantified by the percent of lung with attenuation < −950HU on inspiratory CT. Four gas trapping measures were defined: (1) Exp₋₈₅₆, the percent of lung < −856HU on expiratory imaging; (2) E/I MLA, the ratio of expiratory to inspiratory mean lung attenuation; (3) RVC_856-950, the difference between expiratory and inspiratory lung volumes with attenuation between −856 and −950 HU; and (4) Residuals from the regression of Exp₋₈₅₆ on percent emphysema.

Results

In 8517 subjects with complete data, Exp₋₈₅₆ was highly correlated with emphysema. The measures based on paired inspiratory and expiratory CT scans were less strongly correlated with emphysema. Exp₋₈₅₆, E/I MLA and RVC_856-950 were predictive of spirometry, exercise capacity and quality of life in all subjects and in subjects without emphysema. In subjects with severe emphysema, E/I MLA and RVC_856-950 showed the highest correlations with clinical variables.

Conclusions

Quantitative measures based on paired inspiratory and expiratory chest CT scans can be used as markers of small airway disease in smokers with and without COPD, but this will require that future studies acquire both inspiratory and expiratory CT scans.

What can genetics tell us about the cause of fixed airflow obstruction?

Chronic obstructive pulmonary disease (COPD) is a major cause of chronic morbidity and mortality worldwide with smoking being the most important risk factor of the disease. However, lung function and COPD are known to also have a genetic component and a deeper knowledge of the genetic architecture of the disease could lead to further understanding of predisposition to COPD and also to development of new therapeutic interventions. Genetic linkage studies and candidate gene association studies have not provided evidence to convincingly identify the genes underlying lung function or COPD. However, recent large genome-wide association studies (GWAS) including tens of thousands of individuals have identified 26 variants at different loci in the human genome that show robust association with quantitative lung function measures in the general population. A growing number of these variants are being shown to be associated with COPD. Following the identification of these new lung function loci, the challenge now lies in refining the signals to identify the causative variants underlying the association signals and relating these signals to the molecular pathways that underlie lung function.

Emerging genetics of COPD

Since the discovery of alpha-1 antitrypsin in the early 1960s, several new genes have been suggested to play a role in chronic obstructive pulmonary disease (COPD) pathogenesis. Yet, in spite of those advances, much about the genetic basis of COPD still remains to be discovered. Unbiased approaches, such as genome-wide association (GWA) studies, are critical to identify genes and pathways and to verify suggested genetic variants. Indeed, most of our current understanding about COPD candidate genes originates from GWA studies. Experiments in form of cross-study replications and advanced meta-analyses have propelled the field towards unravelling details about COPD's pathogenesis. Here, we review the discovery of genetic variants in association with COPD phenotypes by discussing the available approaches and current findings. Limitations of current studies are considered and future directions provided.

Clinical applications of gene-based risk prediction for lung cancer and the central role of chronic obstructive pulmonary disease

Lung cancer is the leading cause of cancer death worldwide and nearly 90% of cases are attributable to smoking. Quitting smoking and early diagnosis of lung cancer, through computed tomographic screening, are the only ways to reduce mortality from lung cancer. Recent epidemiological studies show that risk prediction for lung cancer is optimized by using multivariate risk models that include age, smoking exposure, history of chronic obstructive pulmonary disease (COPD), family history of lung cancer, and body mass index. It has also been shown that COPD predates lung cancer in 65–70% of cases, conferring a four- to sixfold greater risk of lung cancer compared to smokers with normal lung function. Genome-wide association studies of smokers have identified a number of genetic variants associated with COPD or lung cancer. In a case–control study, where smokers with normal lungs were compared to smokers who had spirometry-defined COPD or histology confirmed lung cancer, several of these variants were shown to overlap, conferring the same susceptibility or protective effects on both COPD and lung cancer (independent of COPD status). In this perspective article, we show how combining clinical data with genetic variants can help identify heavy smokers at the greatest risk of lung cancer. Using this approach, we found that gene-based risk testing helped engage smokers in risk mitigating activities like quitting smoking and undertaking lung cancer screening. We suggest that such an approach could facilitate the targeted selection of smokers for cost-effective life-saving interventions.

Updates on the COPD gene list

A genetic contribution to develop chronic obstructive pulmonary disease (COPD) is well established. However, the specific genes responsible for enhanced risk or host differences in susceptibility to smoke exposure remain poorly understood. The goal of this review is to provide a comprehensive literature overview on the genetics of COPD, highlight the most promising findings during the last few years, and ultimately provide an updated COPD gene list. Candidate gene studies on COPD and related phenotypes indexed in PubMed before January 5, 2012 are tabulated. An exhaustive list of publications for any given gene was looked for. This well-documented COPD candidate-gene list is expected to serve many purposes for future replication studies and meta-analyses as well as for reanalyzing collected genomic data in the field. In addition, this review summarizes recent genetic loci identified by genome-wide association studies on COPD, lung function, and related complications. Assembling resources, integrative genomic approaches, and large sample sizes of well-phenotyped subjects is part of the path forward to elucidate the genetic basis of this debilitating disease.

Genetic predisposition to chronic obstructive pulmonary disease and/or lung cancer: important considerations when evaluating risk

Chronic obstructive pulmonary disease (COPD) is defined as a disease causing an airflow limitation that is not fully reversible. COPD is phenotypically complex and characterized by small-airway disease and/or emphysema that result from the interaction between host genetic susceptibility and environmental exposures. As in lung cancer, smoking exposure is the most important risk factor for the development of COPD, accounting for 80% to 90% of all cases. COPD affects an estimated 8% to 10% of the general adult population, 15% to 20% of the smoking population, and 50% to 80% of lung cancer patients (with substantial smoking histories). In prospective studies, COPD has been found to be an independent risk factor for lung cancer, conferring a three- to 10-fold increased risk of lung cancer when compared with smokers without COPD. These findings suggest that smokers have a host susceptibility to COPD alone, COPD and lung cancer (i.e., overlap), and lung cancer in the absence of COPD. This minireview focuses on important points that need to be addressed when studying genetic susceptibility factors for COPD and its complex relationship with susceptibility to lung cancer.

CHRNA3/5, IREB2, and ADCY2 are associated with severe chronic obstructive pulmonary disease in Poland

We examined the association between single-nucleotide polymorphisms (SNPs) previously associated with chronic obstructive pulmonary disease (COPD) and/or lung function with COPD and COPD-related phenotypes in a novel cohort of patients with severe to very severe COPD. We examined 315 cases of COPD and 330 Caucasian control smokers from Poland. We included three SNPs previously associated with COPD: rs7671167 (FAM13A), rs13180 (IREB2), and rs8034191 (CHRNA 3/5), and four SNPs associated with lung function in a genome-wide association study of general population samples: rs2070600 (AGER), rs11134242 (ADCY2), rs4316710 (THSD4), and rs17096090 (INTS12). We tested for associations with severe COPD and COPD-related phenotypes, including lung function, smoking behavior, and body mass index. Subjects with COPD were older (average age 62 versus 58 years, P < 0.01), with more pack-years of smoking (45 versus 33 pack-years, P < 0.01). CHRNA3/5 (odds ratio [OR], 1.89; 95% confidence interval [CI], 1.5-2.4; P = 7.4 × 10(-7)), IREB2 (OR, 0.69; 95% CI, 0.5-0.9; P = 3.4 × 10(-3)), and ADCY2 (OR, 1.35; 95% CI, 1.1-1.7; P = 0.01) demonstrated significant associations with COPD. FAM13A (OR, 0.8; 95% CI, 0.7-1.0; P = 0.11) approached statistical significance. FAM13A and ADCY2 also demonstrated a significant association with lung function. Thus, in severe to very severe COPD, we demonstrate a replication of association between two SNPs previously associated with COPD (CHRNA3/5 and IREB2), as well as an association with COPD of one locus initially associated with lung function (ADCY2).

The importance of epigenetics in the development of chronic obstructive pulmonary disease

It is generally accepted that genetic predisposition plays a role in COPD development in susceptible individuals. Therefore, many candidate genes that could be linked to the development of disease have been examined in COPD. However, inconsistent results in different study populations often limit this approach, suggesting that not only genetics, but also other factors, may be contributed to the susceptibility to COPD. Epigenetic mechanisms can affect the transcriptional activity of specific genes, at different points in time, and in different organs. Moreover, these mechanisms can have an effect on people's health. Recently, there is emerging evidence supporting a role of epigenetics for the regulation of inflammatory genes in diseases such as asthma and COPD. Moreover, recent studies suggest that the currently used treatments including corticosteroids may work through epigenetic mechanisms. Epigenetic regulation can be reprogrammed, potentially affecting the risk, aetiology and treatment of various disease states. The epigenetically influenced phenotype could be reversed with demethylating or deacetylating agents, consistent with epigenetic plasticity. The postnatal reversibility of these methylation or acetylation events may therefore provide good opportunities for intervention. The recognition of the role of genetic and epigenetic mechanisms in the development of COPD may identify novel targets that hatch new therapies for patients with COPD.

A genome-wide association study of COPD identifies a susceptibility locus on chromosome 19q13

The genetic risk factors for chronic obstructive pulmonary disease (COPD) are still largely unknown. To date, genome-wide association studies (GWASs) of limited size have identified several novel risk loci for COPD at CHRNA3/CHRNA5/IREB2, HHIP and FAM13A; additional loci may be identified through larger studies. We performed a GWAS using a total of 3499 cases and 1922 control subjects from four cohorts: the Evaluation of COPD Longitudinally to Identify Predictive Surrogate Endpoints (ECLIPSE); the Normative Aging Study (NAS) and National Emphysema Treatment Trial (NETT); Bergen, Norway (GenKOLS); and the COPDGene study. Genotyping was performed on Illumina platforms with additional markers imputed using 1000 Genomes data; results were summarized using fixed-effect meta-analysis. We identified a new genome-wide significant locus on chromosome 19q13 (rs7937, OR = 0.74, P = 2.9 × 10(-9)). Genotyping this single nucleotide polymorphism (SNP) and another nearby SNP in linkage disequilibrium (rs2604894) in 2859 subjects from the family-based International COPD Genetics Network study (ICGN) demonstrated supportive evidence for association for COPD (P = 0.28 and 0.11 for rs7937 and rs2604894), pre-bronchodilator FEV(1) (P = 0.08 and 0.04) and severe (GOLD 3&4) COPD (P = 0.09 and 0.017). This region includes RAB4B, EGLN2, MIA and CYP2A6, and has previously been identified in association with cigarette smoking behavior.