Tumour necrosis factor gene complex polymorphisms in chronic obstructive pulmonary disease

Environment Changes Genetic Effects on Respiratory Conditions and Allergic Phenotypes

The prevalence of asthma and allergic diseases is disproportionately distributed among different populations, with an increasing trend observed in Western countries. Here we investigated how the environment affected genotype-phenotype association in a genetically homogeneous, but geographically separated population. We evaluated 18 single nucleotide polymorphisms (SNPs) corresponding to 8 genes (ADAM33, ALOX5, LT-α, LTC4S, NOS1, ORMDL3, TBXA2R and TNF-α), the lung function and five respiratory/allergic conditions (ever asthma, bronchitis, rhinitis, dermatitis and atopy) in two populations of Inuit residing either in the westernized environment of Denmark or in the rural area of Greenland. Our results showed that lung function was associated with genetic variants in ORMDL3, with polymorphisms having a significant interaction with place of residence. LT-α SNP rs909253 and rs1041981 were significantly associated with bronchitis risk. LT-α SNP rs2844484 was related to dermatitis susceptibility and was significantly influenced by the place of residence. The observed gene-phenotype relationships were exclusively present in one population and absent in the other population. We conclude that the genotype-phenotype associations relating to bronchitis and allergy susceptibility are dependent on the environment and that environmental factors/lifestyles modify genetic predisposition and change the genetic effects on diseases.

Paraoxonase-1 gene in patients with chronic obstructive pulmonary disease investigation Q192R and L55M polymorphisms

BACKGROUND

The effect of increased oxidative stress on the development of chronic obstructive pulmonary disease (COPD) is well known. One of the antioxidative systems against oxidative stress in human body is paraoxonase (PON) enzyme that protects low density lipoproteins (LDL) against oxidation. This study aimed to explore the polymorphisms on PON1, Q192R, L55M genes of patients with COPD.

METHODS

DNAs extraction was obtained from blood samples of 50 patients diagnosed with COPD and 50 patients as a control group who were presented to emergency clinic. Genotypes were obtained with polymerase chain reaction (PCR) and AIw I and Hsp92II restriction enzymes were used for Q192R and L55M polymorphisms, respectively. Analysis of data was done with the Chi-square test and Fisher's exact test.

RESULTS

A statistically significant difference in Q192R polymorphism was found between the COPD patients and the control group (P=0.05). There was no statistically significant difference in L55M polymorphisms between the patient and control groups (P>0.05). Q192R polymorphism was significantly correlated with the PON1 gene and cigarette smoking; however other risk factors did not show any significant correlation with this polymorphism. Though L55M polymorphism was significantly correlated with family history and tuberculosis, there was no significant correlation with other risk factors.

CONCLUSION

We believe that more studies are needed to study the correlation of L55M polymorphism with other factors.

Is TNF-α gene polymorphism related to pulmonary functions and prognosis as determined by FEV1, BMI, COPD exacerbation and hospitalization in patients with smoking-related COPD in a Turkish population?

INTRODUCTION

Some conflicting results have been published about the relationship between TNF-α-308 gene polymorphism and chronic obstructive pulmonary disease (COPD). The aim of this study was to determine whether TNF-α-308 gene polymorphism was associated with smoking-related COPD and whether it was associated with pulmonary function parameters (PFTs), body mass index (BMI), and prognosis.

METHODS

We studied the frequencies of TNF-α-308 gene polymorphism in 90 male subjects (60 subjects with COPD and 30 healthy smokers) in a Caucasian population.

RESULTS

There was no significant difference in the frequency of G/G and G/A gene polymorphisms in the COPD group compared with control subjects (p>0.05). We compared COPD patients as G/A gene polymorphism and G/G gene polymorphism; the PFTs and BMI before and after one year were not statistically significant (p>0.05). Also, the exacerbation and hospitalization data of COPD patients were not significant between these groups.

CONCLUSION

In conclusion, there was no difference between smoking-related COPD and the control group according to TNF α-308 gene polymorphism in a Caucasian population. In addition, it was shown that important determinants of prognosis of COPD such as FEV1, BMI, COPD exacerbation and hospitalization were not associated with TNF-α-308 gene polymorphism.

Genetic susceptibility

Why only 20% of smokers develop clinically relevant chronic obstructive pulmonary disease (COPD) was a puzzle for many years. Now, epidemiologic studies point clearly toward a large heritable component. The combination of genome-wide association studies and candidate gene analysis is helping to identify those genetic variants responsible for an individual's susceptibility to developing COPD. In this review, the current data implicating specific loci and genes in the pathogenesis of COPD are examined.

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.

Genetics of asthma susceptibility and severity

This article summarizes major findings in genome-wide studies of asthma susceptibility and severity. Two large meta-analyses identified four chromosomal regions which were consistently associated with development of asthma. Genes that are associated with asthma subphenotypes such as lung function, biomarker levels, and asthma therapeutic responses can provide insight into mechanisms of asthma severity and disease progression. Future genetic studies will incorporate sequencing in comprehensively phenotyped asthmatics to lead to the development of personalized therapy.

Genome-wide association and large-scale follow up identifies 16 new loci influencing lung function

Pulmonary function measures reflect respiratory health and are used in the diagnosis of chronic obstructive pulmonary disease. We tested genome-wide association with forced expiratory volume in 1 second and the ratio of forced expiratory volume in 1 second to forced vital capacity in 48,201 individuals of European ancestry with follow up of the top associations in up to an additional 46,411 individuals. We identified new regions showing association (combined P < 5 × 10(-8)) with pulmonary function in or near MFAP2, TGFB2, HDAC4, RARB, MECOM (also known as EVI1), SPATA9, ARMC2, NCR3, ZKSCAN3, CDC123, C10orf11, LRP1, CCDC38, MMP15, CFDP1 and KCNE2. Identification of these 16 new loci may provide insight into the molecular mechanisms regulating pulmonary function and into molecular targets for future therapy to alleviate reduced lung function.

Using genetics to predict the natural history of asthma?

Clinical practice reminds us that there is considerable variability in the course of asthma over time. Treatment of patients with asthma would be considerably improved if one could accurately predict the likely course of disease over the life course. Recently, with the advent of the era of genome-wide association studies, there has been a monumental shift in our understanding of the genetic factors that underlie inherited susceptibility to asthma. Genes have been identified that modulate many aspects of the natural history of asthma, such as susceptibility to atopy, altered lung development, and susceptibility to more severe disease. Heritability studies have even suggested a role for genetic factors in remission of asthma. However, although the discovery of novel genetic factors underlying disease susceptibility has undoubtedly improved our understanding of disease pathogenesis, whether these advances have improved the ability to predict the natural history in individual patients is questionable, and the application of genetic testing to clinical practice remains some way off.

Recommendations for using standardised phenotypes in genetic association studies

Genetic association studies of complex traits often rely on standardised quantitative phenotypes, such as percentage of predicted forced expiratory volume and body mass index to measure an underlying trait of interest (eg lung function, obesity). These phenotypes are appealing because they provide an easy mechanism for comparing subjects, although such standardisations may not be the best way to control for confounders and other covariates. We recommend adjusting raw or standardised phenotypes within the study population via regression. We illustrate through simulation that optimal power in both population- and family-based association tests is attained by using the residuals from within-study adjustment as the complex trait phenotype. An application of family-based association analysis of forced expiratory volume in one second, and obesity in the Childhood Asthma Management Program data, illustrates that power is maintained or increased when adjusted phenotype residuals are used instead of typical standardised quantitative phenotypes.

Meta-analyses on suspected chronic obstructive pulmonary disease genes: a summary of 20 years' research

RATIONALE

Chronic obstructive pulmonary disease (COPD) is a complex disorder with high mortality worldwide. Studies on the role of candidate genes and their polymorphisms in COPD development have so far produced ambiguous results.

OBJECTIVES

The aim of this study was to reveal the role of COPD candidate genes using data collected in previous research.

METHODS

We performed meta-analyses on 20 polymorphisms in 12 genes, after searching the PubMed and Embase databases for publications on COPD. These genes involve three main pathways associated with COPD development: the inflammatory, protease-antiprotease balance, and antioxidant pathways.

MEASUREMENTS AND MAIN RESULTS

We obtained significant results for three TGFB1 polymorphisms, although these were based only on a few studies. The IL1RN VNTR polymorphism increases the risk for COPD (odds ratio [OR], 1.7; 95% confidence interval [CI], 1.09-2.65), whereas the TNFA -308 G/A polymorphism does so only in Asian populations (OR, 2.01; 95% CI, 1.21-3.31). The GSTP1 I105V polymorphism was protective for COPD in Asian populations only (OR, 0.69; 95% CI, 0.56-0.85).

CONCLUSIONS

These results demonstrate the importance of ethnicity in identifying specific COPD genes.

National Emphysema Treatment Trial state of the art: genetics of emphysema

Although a hereditary contribution to emphysema has been long suspected, severe alpha1-antitrypsin deficiency remains the only conclusively proven genetic risk factor for chronic obstructive pulmonary disease (COPD). Recently, genome-wide linkage analysis has led to the identification of two promising candidate genes for COPD: TGFB1 and SERPINE2. Like multiple other COPD candidate gene associations, even these positionally identified genes have not been universally replicated across all studies. Differences in phenotype definition may contribute to nonreplication in genetic studies of heterogeneous disorders such as COPD. The use of precisely measured phenotypes, including emphysema quantification on high-resolution chest computed tomography scans, has aided in the discovery of additional genes for clinically relevant COPD-related traits. The use of computed tomography scans to assess emphysema and airway disease as well as newer genetic technologies, including gene expression microarrays and genome-wide association studies, has great potential to detect novel genes affecting COPD susceptibility, severity, and response to treatment.

Interpatient variability in rates of asthma progression: can genetics provide an answer?

Asthma is a heterogeneous disorder with a variable natural history. In children 3 patterns of the natural history of asthma have been described: early onset but transient, persistent, and later onset, with only the former leading to persistent asthma later in childhood. In adults a range of different asthma phenotypes differing in their environmental, inflammatory, and prognostic characteristics have also been described. These extend beyond allergic (extrinsic) and nonallergic (intrinsic) asthma to include persistent airflow obstruction and accelerated decrease in lung function over time. Asthma progression can be defined as the change in an individual's phenotype along a continuum ranging from nonasthmatic to asthmatic and subsequent development of severe chronic disease. It is clear that for prevention of asthma progression in patients, there is a need for both better understanding of the pathophysiology of asthma and identification of predictors of progression. Interpatient genetic variability has been shown to affect multiple facets of asthma progression, including increased susceptibility to atopy and subsequent asthma, progression to severe disease, and modification of the response to treatment. Thus genetic testing might provide a means for predicting the likely progression of an individual along the continuum, allowing targeting of preventative treatment. However, the prospect of the use of genetic information in clinical practice raises important social and ethical issues that will need to be addressed before genetic testing can be used to inform the preventative treatment of patients to prevent the development of progression of asthma in individuals.