Juan C. Celedón

Genome-wide Association Analysis Identifies PDE4D as an Asthma-Susceptibility Gene

Asthma, a chronic airway disease with known heritability, affects more than 300 million people around the world. A genome-wide association (GWA) study of asthma with 359 cases from the Childhood Asthma Management Program (CAMP) and 846 genetically matched controls from the Illumina ICONdb public resource was performed. The strongest region of association seen was on chromosome 5q12 in PDE4D. The phosphodiesterase 4D, cAMP-specific (phosphodiesterase E3 dunce homolog, Drosophila) gene (PDE4D) is a regulator of airway smooth-muscle contractility, and PDE4 inhibitors have been developed as medications for asthma. Allelic p values for top SNPs in this region were 4.3 x 10(-07) for rs1588265 and 9.7 x 10(-07) for rs1544791. Replications were investigated in ten independent populations with different ethnicities, study designs, and definitions of asthma. In seven white and Hispanic replication populations, two PDE4D SNPs had significant results with p values less than 0.05, and five had results in the same direction as the original population but had p values greater than 0.05. Combined p values for 18,891 white and Hispanic individuals (4,342 cases) in our replication populations were 4.1 x 10(-04) for rs1588265 and 9.2 x 10(-04) for rs1544791. In three black replication populations, which had different linkage disequilibrium patterns than the other populations, original findings were not replicated. Further study of PDE4D variants might lead to improved understanding of the role of PDE4D in asthma pathophysiology and the efficacy of PDE4 inhibitor medications.

Exposure to cat allergen, maternal history of asthma, and wheezing in first 5 years of life

We looked for an association between early exposure to pets and asthma and wheezing in children whose mothers or fathers did or did not have a history of asthma. We followed up 448 children, who had at least one parent with a history of atopy, from birth to 5 years. Among children whose mothers had no history of asthma, exposure to a cat or a Fel d 1 concentration of at least 8 microg/g at the age of 2-3 months was associated with a reduced risk of wheezing between the ages of 1 and 5 years. However, among children whose mothers did have a history of asthma, such exposures were associated with an increased risk of wheezing at or after the age of 3 years. There was no association between wheezing and exposure to dog or dog allergen, and the fathers allergy status had no effect on the relation between childhood wheezing and cat exposure.

Allele-Specific Chromatin Remodeling in the ZPBP2/GSDMB/ORMDL3 Locus Associated with the Risk of Asthma and Autoimmune Disease

Common SNPs in the chromosome 17q12-q21 region alter the risk for asthma, type 1 diabetes, primary biliary cirrhosis, and Crohn disease. Previous reports by us and others have linked the disease-associated genetic variants with changes in expression of GSDMB and ORMDL3 transcripts in human lymphoblastoid cell lines (LCLs). The variants also alter regulation of other transcripts, and this domain-wide cis-regulatory effect suggests a mechanism involving long-range chromatin interactions. Here, we further dissect the disease-linked haplotype and identify putative causal DNA variants via a combination of genetic and functional analyses. First, high-throughput resequencing of the region and genotyping of potential candidate variants were performed. Next, additional mapping of allelic expression differences in Yoruba HapMap LCLs allowed us to fine-map the basis of the cis-regulatory differences to a handful of candidate functional variants. Functional assays identified allele-specific differences in nucleosome distribution, an allele-specific association with the insulator protein CTCF, as well as a weak promoter activity for rs12936231. Overall, this study shows a common disease allele linked to changes in CTCF binding and nucleosome occupancy leading to altered domain-wide cis-regulation. Finally, a strong association between asthma and cis-regulatory haplotypes was observed in three independent family-based cohorts (p = 1.78 x 10(-8)). This study demonstrates the requirement of multiple parallel allele-specific tools for the investigation of noncoding disease variants and functional fine-mapping of human disease-associated haplotypes.

Association of body mass index with the development of methacholine airway hyperresponsiveness in men: the Normative Aging Study

Background: The rising prevalence of asthma in developed nations may be associated with the rising prevalence of obesity in these same nations. The relationship between body mass index (BMI) and the development of an objective marker for asthma, methacholine airway hyperresponsiveness (AHR), was investigated in adult men. Methods: Sixty one men who had no AHR at initial methacholine challenge testing but who developed AHR about 4 years later and 244 matched controls participated in the study. The effects of initial BMI and change in BMI on development of AHR were examined in conditional logistic regression models. Results: Initial BMI was found to have a non-linear relationship with development of AHR. Compared with men with initial BMI in the middle quintile, men with BMI in the lowest quintile (BMI=19.8–24.3 kg/m2) and those with BMI in the highest quintile (BMI >29.4 kg/m2) were more likely to develop AHR: OR=7.0 (95% CI 1.8 to 27.7) and OR=10.0 (95% CI 2.6 to 37.9), respectively. These results remained significant after controlling for age, smoking, IgE level, and initial FEV1. In addition, there was a positive linear relationship between change in BMI over the period of observation and the subsequent development of AHR. Conclusions: In this cohort of adult men, both a low BMI and a high BMI were associated with the development of AHR. For men with a low initial BMI the increased risk for development of AHR appears to be partly mediated by a gain in weight. The effect of BMI on AHR may suggest mechanisms in the observed associations between obesity and asthma.

The SERPINE2 Gene Is Associated with Chronic Obstructive Pulmonary Disease

RATIONALEnChronic obstructive pulmonary disease (COPD) is a complex disease influenced by multiple genes and environmental factors. A region on chromosome 2q has been shown to be linked to COPD. A positional candidate gene from the chromosome 2q region SERPINE2 (Serpin peptidase inhibitor, clade E [nexin, plasminogen activator inhibitor type 1], member 2), was previously evaluated as a susceptibility gene for COPD in two association studies, but the results were contradictory.nnnOBJECTIVESnTo identify the relationship between SERPINE2 polymorphisms and COPD-related phenotypes using family-based and case-control association studies.nnnMETHODSnIn the present study, we genotyped 25 single nucleotide polymorphisms (SNPs) from SERPINE2 and analyzed qualitative and quantitative COPD phenotypes in 635 pedigrees with 1,910 individuals and an independent case-control population that included 973 COPD cases and 956 control subjects. The family data were analyzed using family-based association tests. The case-control data were analyzed using logistic regression and linear models.nnnMEASUREMENTS AND MAIN RESULTSnSix SNPs demonstrated significant associations with COPD phenotypes in the family-based association analysis (0.0016<or=p<or=0.042). Five of these SNPs demonstrated replicated associations in the case-control analysis (0.021<or=p<or=0.031). In addition, the results of haplotype analyses supported the results from single SNP analyses.nnnCONCLUSIONSnThese data provide further support for SERPINE2 as a COPD susceptibility gene.

The Association of a SNP Upstream of INSIG2 with Body Mass Index is Reproduced in Several but Not All Cohorts

A SNP upstream of the INSIG2 gene, rs7566605, was recently found to be associated with obesity as measured by body mass index (BMI) by Herbert and colleagues. The association between increased BMI and homozygosity for the minor allele was first observed in data from a genome-wide association scan of 86,604 SNPs in 923 related individuals from the Framingham Heart Study offspring cohort. The association was reproduced in four additional cohorts, but was not seen in a fifth cohort. To further assess the general reproducibility of this association, we genotyped rs7566605 in nine large cohorts from eight populations across multiple ethnicities (total n = 16,969). We tested this variant for association with BMI in each sample under a recessive model using family-based, population-based, and case-control designs. We observed a significant (p < 0.05) association in five cohorts but saw no association in three other cohorts. There was variability in the strength of association evidence across examination cycles in longitudinal data from unrelated individuals in the Framingham Heart Study Offspring cohort. A combined analysis revealed significant independent validation of this association in both unrelated (p = 0.046) and family-based (p = 0.004) samples. The estimated risk conferred by this allele is small, and could easily be masked by small sample size, population stratification, or other confounders. These validation studies suggest that the original association is less likely to be spurious, but the failure to observe an association in every data set suggests that the effect of SNP rs7566605 on BMI may be heterogeneous across population samples.

Decreased response to inhaled steroids in overweight and obese asthmatic children

BACKGROUNDnThe mechanisms and consequences of the observed association between obesity and childhood asthma are unclear.nnnOBJECTIVESnWe sought to determine the effect of obesity on treatment responses to inhaled corticosteroids in asthmatic children.nnnMETHODSnWe performed a post hoc analysis to evaluate the interaction between body mass index (BMI) and treatment with inhaled budesonide on lung function in the Childhood Asthma Management Program trial. Participants were then stratified into overweight/obese and nonoverweight groups, and their response to inhaled budesonide was analyzed longitudinally over the 4 years of the trial.nnnRESULTSnThere was a significant interaction between BMI and budesonide for prebronchodilator FEV(1)/forced vital capacity (FVC) ratio (P = .0007) and bronchodilator response (BDR; P = .049) and a nonsignificant trend for an interaction between BMI and budesonide on prebronchodilator FEV(1) (P = .15). Nonoverweight children showed significant improvement with inhaled budesonide in lung function (FEV(1), FEV(1)/FVC ratio, and BDR) during the early (years 1-2) and late (years 3-4) stages of the trial. Overweight/obese children had improved FEV(1) and BDR during the early but not the late stage of the trial and showed no improvement in FEV(1)/FVC ratio. When comparing time points at which both groups showed a significant response, the degree of improvement among nonoverweight children was significantly greater than in overweight/obese children at most visits. Nonoverweight children had a 44% reduction in the risk of emergency department visits or hospitalizations throughout the trial (P = .001); there was no reduction in risk among overweight/obese children (P = .97).nnnCONCLUSIONSnCompared with children of normal weight, overweight/obese children in the Childhood Asthma Management Program showed a decreased response to inhaled budesonide on measures of lung function and emergency department visits/hospitalizations for asthma.

On the Replication of Genetic Associations: Timing Can Be Everything!

The failure of researchers to replicate genetic-association findings is most commonly attributed to insufficient statistical power, population stratification, or various forms of between-study heterogeneity or environmental influences.(1) Here, we illustrate another potential cause for nonreplications that has so far not received much attention in the literature. We illustrate that the strength of a genetic effect can vary by age, causing age-varying associations. If not taken into account during the design and the analysis of a study, age-varying genetic associations can cause nonreplication. By using the 100K SNP scan of the Framingham Heart Study, we identified an age-varying association between a SNP in ROBO1 and obesity and hypothesized an age-gene interaction. This finding was followed up in eight independent samples comprising 13,584 individuals. The association was replicated in five of the eight studies, showing an age-dependent relationship (one-sided combined p = 3.92 x 10(-9), combined p value from pediatric cohorts = 2.21 x 10(-8), combined p value from adult cohorts = 0.00422). Furthermore, this study illustrates that it is difficult for cross-sectional study designs to detect age-varying associations. If the specifics of age- or time-varying genetic effects are not considered in the selection of both the follow-up samples and in the statistical analysis, important genetic associations may be missed.

Birth by cesarean section, allergic rhinitis, and allergic sensitization among children with a parental history of atopy

BACKGROUNDnCesarean delivery can alter neonatal immune responses and increase the risk of atopy. Studies of the relation between cesarean delivery and allergic diseases in children not selected on the basis of a family history of atopy have yielded inconsistent findings.nnnOBJECTIVEnWe sought to examine the relation between birth by cesarean delivery and atopy and allergic diseases in children at risk for atopy.nnnMETHODSnWe examined the relation between mode of delivery and the development of atopy and allergic diseases among 432 children with a parental history of atopy followed from birth to age 9 years. Asthma was defined as physician-diagnosed asthma and wheeze in the previous year, and allergic rhinitis was defined as physician-diagnosed allergic rhinitis and naso-ocular symptoms apart from colds in the previous year. Atopy was considered present at school age if there was 1 or more positive skin test response or specific IgE to common allergens. Stepwise logistic regression was used to study the relation between cesarean delivery and the outcomes of interest.nnnRESULTSnAfter adjustment for other covariates, children born by cesarean section had 2-fold higher odds of atopy than those born by vaginal delivery (odds ratio, 2.1; 95% CI, 1.1-3.9). In multivariate analyses birth by cesarean section was significantly associated with increased odds of allergic rhinitis (odds ratio, 1.8; 95% CI, 1.0-3.1) but not with asthma.nnnCONCLUSIONSnOur findings suggest that cesarean delivery is associated with allergic rhinitis and atopy among children with a parental history of asthma or allergies. This could be explained by lack of contact with the maternal vaginal/fecal flora or reduced/absent labor during cesarean delivery.

Assessing the Reproducibility of Asthma Candidate Gene Associations, Using Genome-wide Data

RATIONALEnAssociation studies have implicated many genes in asthma pathogenesis, with replicated associations between single-nucleotide polymorphisms (SNPs) and asthma reported for more than 30 genes. Genome-wide genotyping enables simultaneous evaluation of most of this variation, and facilitates more comprehensive analysis of other common genetic variation around these candidate genes for association with asthma.nnnOBJECTIVESnTo use available genome-wide genotypic data to assess the reproducibility of previously reported associations with asthma and to evaluate the contribution of additional common genetic variation surrounding these loci to asthma susceptibility.nnnMETHODSnIllumina Human Hap 550Kv3 BeadChip (Illumina, San Diego, CA) SNP arrays were genotyped in 422 nuclear families participating in the Childhood Asthma Management Program. Genes with at least one SNP demonstrating prior association with asthma in two or more populations were tested for evidence of association with asthma, using family-based association testing.nnnMEASUREMENTS AND MAIN RESULTSnWe identified 39 candidate genes from the literature, using prespecified criteria. Of the 160 SNPs previously genotyped in these 39 genes, 10 SNPs in 6 genes were significantly associated with asthma (including the first independent replication for asthma-associated integrin beta(3) [ITGB3]). Evaluation of 619 additional common variants included in the Illumina 550K array revealed additional evidence of asthma association for 15 genes, although none were significant after adjustment for multiple comparisons.nnnCONCLUSIONSnWe replicated asthma associations for a minority of candidate genes. Pooling genome-wide association study results from multiple studies will increase the power to appreciate marginal effects of genes and further clarify which candidates are true asthma genes.