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1.  The Human Microbiome. Early Life Determinant of Health Outcomes 
Annals of the American Thoracic Society  2014;11(Suppl 1):S7-S12.
The development of new technologies to isolate and identify microbial genomes has markedly increased our understanding of the role of microbiomes in health and disease. The idea, first proposed as part of the hygiene hypothesis, that environmental microbes influence the developmental trajectories of the immune system in early life, has now been considerably extended and refined. The abundant microbiota present in mucosal surfaces, especially the gut, is actively selected by the host through complex receptor systems that respond differentially depending on the molecular patterns presented to mucosal cells. Germ-free mice are more likely to develop allergic airway inflammation and show alterations in normal motor control and anxiety. These effects can be reversed by neonatal microbial recolonization but remain unchanged if recolonization occurs in adults. What emerges from these recent studies is the discovery of a complex, major early environmental determinant of lifetime human phenotypes. To change the natural course of asthma, obesity, and other chronic inflammatory conditions, active manipulation of the extensive bacterial, phage, and fungal metagenomes present in mucosal surfaces may be required, specifically during the developing years. Domesticating the human microbiome and adapting it to our health needs may be a challenge akin to, but far more complex than, the one faced by humanity when a few dozen species of plants and animals were domesticated during the transition between hunter-gatherer and sedentary societies after the end of the Pleistocene era.
PMCID: PMC3972972  PMID: 24437411
2.  Ethnic-specific associations of rare and low-frequency DNA sequence variants with asthma 
Nature Communications  2015;6:5965.
Common variants at many loci have been robustly associated with asthma but explain little of the overall genetic risk. Here we investigate the role of rare (<1%) and low-frequency (1–5%) variants using the Illumina HumanExome BeadChip array in 4,794 asthma cases, 4,707 non-asthmatic controls and 590 case–parent trios representing European Americans, African Americans/African Caribbeans and Latinos. Our study reveals one low-frequency missense mutation in the GRASP gene that is associated with asthma in the Latino sample (P=4.31 × 10−6; OR=1.25; MAF=1.21%) and two genes harbouring functional variants that are associated with asthma in a gene-based analysis: GSDMB at the 17q12–21 asthma locus in the Latino and combined samples (P=7.81 × 10−8 and 4.09 × 10−8, respectively) and MTHFR in the African ancestry sample (P=1.72 × 10−6). Our results suggest that associations with rare and low-frequency variants are ethnic specific and not likely to explain a significant proportion of the ‘missing heritability’ of asthma.
Common variants account for only a small amount of the heritable risk for developing asthma. Using a meta-analysis approach, Igartua et al. identify one low-frequency missense mutation and two genes with functional variants that are associated with asthma, but only in specific ethnic groups.
PMCID: PMC4309441  PMID: 25591454
3.  The relation of circulating YKL-40 to levels and decline of lung function in adult life 
Respiratory medicine  2013;107(12):10.1016/j.rmed.2013.07.013.
YKL-40 is a chitinase-like protein that, in cross-sectional clinical studies, has been associated with severe asthma and COPD in smokers.
To determine the longitudinal relation of circulating YKL-40 to levels and lung function decline in the general population.
We used longitudinal data from up to 12 surveys from the population-based TESAOD study which was conducted in Tucson, Arizona between 1972-1996. In cross-sectional analyses, we also used data from 3 Spanish centers of the multicenter ECRHS study (ECRHS-Sp). Serum YKL-40 was measured at baseline in TESAOD and in survey 2 in ECRHS-Sp using ELISAs. Multivariate linear regression was used to test associations of serum YKL-40 to concomitant lung function. In TESAOD, random coefficients models were used to test associations of serum YKL-40 to subsequent decline of lung function.
Data on YKL-40 and lung function were available from 1088 TESAOD and 854 ECRHS-Sp adult participants (59% and 51% females; respectively). In adjusted multivariate meta-analyses, being in the highest YKL-40 quartile was associated cross-sectionally with significant deficits in FEV1 and FVC %predicted. In adjusted longitudinal analyses, TESAOD participants in the top YKL-40 quartile had an FEV1 decline that was 5 ml/yr (p=0.05) faster than subjects in the third quartile, 5 ml/yr (p=0.02) faster than subjects in the second quartile, and 10 ml/yr (p<0.001) faster than subjects in the lowest YKL-40 quartile. These longitudinal effects were particularly strong in smokers and absent in never smokers. After adjusting for covariates, as compared with the other three quartiles combined the top YKL-40 quartile was associated with a 9 ml/yr (p=0.001) faster FEV1 decline among smokers, while no significant effects were found among never smokers (2 ml/yr, p=0.35).
Circulating YKL-40 is associated with levels and decline of lung function in the general population and may be a biomarker of susceptibility to the long-term effects of cigarette smoking.
PMCID: PMC3864627  PMID: 23920328
YKL-40; lung function; smoking
4.  Serum levels of club (Clara) cell secretory protein predict cancer mortality in adults 
The lancet. Respiratory medicine  2013;1(10):779-785.
Club (formerly Clara) cell secretory protein (CC16) is produced mainly by bronchiolar club cells and has been shown to have protective effects against airway inflammation and oxidative stress from cigarette smoking and related carcinogens. The goal of this study was to determine whether serum CC16 levels predict all-cause and cancer-specific mortality in adults.
We used data from the population-based TESAOD study, a prospective cohort study of respiratory health initiated in Tucson, AZ in 1972. At baseline, participants completed standardized respiratory questionnaires and lung function tests. Serum CC16 was measured in cryopreserved serum samples. A review of vital status of participants as of January 1st, 2011 was completed through contact with next of kin, collection of death certificates, and linkage with the National Death Index.
A total of 1086 participants who were 21 to 70 years old at enrollment were included. Of these, 653 (60%) died by 2011 and cause of death was ascertained for 649 (99%). In Cox proportional hazards models adjusted for sex, age, education, body mass index categories, smoking and pack-years, and baseline levels of lung function, serum CC16 levels at the baseline survey were inversely associated with mortality risk over the study follow-up. Mortality risk increased by 16% for each standard deviation (SD) decrease in CC16 (Hazard Ratio (HR), 95% CI: 1.16, 1.06 – 1.26; p = 0.0007). When data on cause-specific mortality were analyzed, each SD decrease in serum CC16 was associated with >40% increased risk of dying of cancer (adjusted HR=1.41, 1.19 – 1.67; p < 0.0001). Among smokers, the corresponding adjusted HRs for mortality by lung cancer were 1.52 (1.14 – 2.03; p = 0.004).
Serum CC16 levels predict mortality risk in the general adult population. The excess risk associated with lower CC16 is largely explained by cancer, particularly lung cancer.
PMCID: PMC3984132  PMID: 24461757
5.  Epidemiology of the Origins of Airflow Limitation in Asthma 
There is now conclusive evidence that, as a group, subjects with asthma have lower levels of lung function as compared with their peers and that a significant proportion of subjects with persistent asthma are at risk of developing non–fully reversible airflow limitation, the clinical hallmark of chronic obstructive pulmonary disease. Although at the population level the most conspicuous form of airflow limitation in asthma seems to be that of subjects who wheeze during the first years of life and whose symptoms persist into adult life, asthma-related lung deficits can be related to both acquired deficits in growth of lung function in childhood and steeper decline of lung function in adult life. These trajectories of lung function are likely to differ across subgroups of individuals with asthma, suggesting that different windows of opportunity may exist to modify the natural course of the disease before irreversible deficits are established. These observations indicate the importance of identifying biomarkers that can be used to target children and adults with asthma at increased risk for airflow limitation and determining whether pharmacological interventions can protect these patients from the development of chronic obstructive pulmonary disease.
PMCID: PMC2797072  PMID: 20008881
asthma; chronic obstructive pulmonary disease; lung function; airflow limitation; FEV1
6.  The Origins of Asthma and Chronic Obstructive Pulmonary Disease in Early Life 
Results from birth cohort and cross-sectional studies of young children with wheezing have uncovered strong associations between both lung function and immune responses in early life and the subsequent development of persistent wheezing and chronic airway obstruction up to mid-adulthood. It is now apparent that the pattern of bronchial hyperresponsiveness, deficits in lung function, and structural airway remodeling that are characteristic of asthma may be already established during the preschool years in most patients. Interactions between acute viral infections, especially those due to rhinovirus and respiratory syncytial virus, and exposure to perennial aeroallergens may induce persistent alterations in immune responses and airway function in susceptible subjects. Similarly, deficits in airway function present shortly after birth predict airflow limitation in early adult life, which in turn is a strong predisposing factor for chronic obstructive pulmonary disease. The fact that these alterations are more likely to occur during early life and even in utero than later during childhood suggests that there a developmental window of susceptibility during which exposures can disrupt normal growth trajectories. Novel strategies for primary prevention of chronic respiratory diseases will be based on the identification of the genetic and environmental factors that interactively cause these disruptions.
PMCID: PMC2677402  PMID: 19387029
asthma; COPD; infancy; spirometry
7.  Poor airway function in early infancy and lung function by age 22 years: a non-selective longitudinal cohort study 
Lancet  2007;370(9589):758-764.
Together with smoking, the level of lung function attained in early adulthood is among the strongest predictors of chronic obstructive pulmonary disease. Whether airway function measured shortly after birth is a determinant of this level is currently unknown.
Non-selected infants were enrolled at birth in the Tucson Children's Respiratory Study in 1980-84. Infant maximal expiratory flows at functional residual capacity (V'maxFRC) were measured by the chest compression technique at 2 months (mean±SD: 2.3±1.9m); values were logarithmically transformed and adjusted for length. Forced expiratory volume in one second (FEV1), forced vital capacity (FVC) and forced expiratory flow between 25% and 75% of FVC (FEF25-75) were measured at ages 11, 16 and 22 years before and after 180μg of albuterol. Participant characteristics were determined at enrollment and at each time of testing.
Airway function was available for 123 participants in infancy and at least once at ages 11, 16 or 22 years. Using a random effects model, participants in the lowest quartile for infant V'maxFRC had persistently lower values for FEV1/FVC ratio (-5.2%, p<0.001), FEF25-75 (-663ml/s, p<0.001) and FEV1 (-233ml, p=0.001) through age 22 compared to the upper three quartiles, after adjusting for height, weight, age and sex. The magnitude and significance of the effect did not change appreciably after additionally adjusting for current wheeze, smoking, atopy and parental asthma.
Diminished airway function present shortly after birth is a risk factor for airflow obstruction in early adult life.
PMCID: PMC2831283  PMID: 17765525
8.  Wheezing and bronchial hyper-responsiveness in early childhood as predictors of newly diagnosed asthma in early adulthood: a longitudinal birth-cohort study 
Lancet  2008;372(9643):1058-1064.
Incidence of asthma increases during the early adult years, but the relative influence of sex and early life factors in determining newly diagnosed asthma in young adults is unknown.
Healthy newborns (n=1246) were enrolled in the Tucson Children's Respiratory Study. Parental characteristics early life wheezing phenotypes, airway function and bronchial hyperresponsiveness to cold dry air and sensitization to Alternaria were determined by age 6 years. Physician diagnosed asthma, both chronic and newly diagnosed, and airway function were determined at age 22 years.
Average incidence of asthma between 16 and 22 years was 12.6 per thousand person-years. One fourth of all cases of active asthma at age 22 were newly diagnosed, of which 71% were females. Asthma remittance by age 22 was higher among males (p=0.008). Age at diagnosis was linearly associated with FEV1/FVC ratio at age 22. Late-onset (multinomial odds ratio [M-OR]= 7.4 [95% CI:3.9,14]) and persistent wheezing (M-OR=14.0 [6.8,28]) in early life, sensitization to Alternaria (M-OR=3.6 [2.1,6.4]), low airway function at age 6 (M-OR=2.1 [1.1,3.9]) and bronchial hyperresponsiveness at age 6 (M-OR=4.5 [1.9,10]) were independently associated with chronic asthma at age 22. Bronchial hyperresponsiveness (M-OR=6.9 [2.3,21]), low airway function at age 6 (M-OR=2.8 [1.1,6.9]), late-onset (M-OR=4.6 [1.7,12]) and persistent wheezing (M-OR=4.0 [1.2,14]) predicted newly diagnosed asthma at age 22.
Among young adults, females preferentially develop newly diagnosed asthma, but most had already wheezed in early life and had bronchial hyperresponsiveness by age 6. The roots of early adult onset asthma can be found in the preschool years.
PMCID: PMC2831297  PMID: 18805334
9.  Integrated genome-wide association, coexpression network, and expression single nucleotide polymorphism analysis identifies novel pathway in allergic rhinitis 
BMC Medical Genomics  2014;7:48.
Allergic rhinitis is a common disease whose genetic basis is incompletely explained. We report an integrated genomic analysis of allergic rhinitis.
We performed genome wide association studies (GWAS) of allergic rhinitis in 5633 ethnically diverse North American subjects. Next, we profiled gene expression in disease-relevant tissue (peripheral blood CD4+ lymphocytes) collected from subjects who had been genotyped. We then integrated the GWAS and gene expression data using expression single nucleotide (eSNP), coexpression network, and pathway approaches to identify the biologic relevance of our GWAS.
GWAS revealed ethnicity-specific findings, with 4 genome-wide significant loci among Latinos and 1 genome-wide significant locus in the GWAS meta-analysis across ethnic groups. To identify biologic context for these results, we constructed a coexpression network to define modules of genes with similar patterns of CD4+ gene expression (coexpression modules) that could serve as constructs of broader gene expression. 6 of the 22 GWAS loci with P-value ≤ 1x10−6 tagged one particular coexpression module (4.0-fold enrichment, P-value 0.0029), and this module also had the greatest enrichment (3.4-fold enrichment, P-value 2.6 × 10−24) for allergic rhinitis-associated eSNPs (genetic variants associated with both gene expression and allergic rhinitis). The integrated GWAS, coexpression network, and eSNP results therefore supported this coexpression module as an allergic rhinitis module. Pathway analysis revealed that the module was enriched for mitochondrial pathways (8.6-fold enrichment, P-value 4.5 × 10−72).
Our results highlight mitochondrial pathways as a target for further investigation of allergic rhinitis mechanism and treatment. Our integrated approach can be applied to provide biologic context for GWAS of other diseases.
PMCID: PMC4127082  PMID: 25085501
Genome-wide association study; Allergic rhinitis; Coexpression network; Expression single-nucleotide polymorphism; Coexpression module; Pathway; Mitochondria; Hay fever; Allergy
10.  A genome-wide association study of bronchodilator response in asthmatics 
The pharmacogenomics journal  2013;14(1):41-47.
Reversibility of airway obstruction in response to β2-agonists is highly variable among asthmatics, which is partially attributed to genetic factors. In a genome-wide association study of acute bronchodilator response (BDR) to inhaled albuterol, 534,290 single nucleotide polymorphisms (SNPs) were tested in 403 white trios from the Childhood Asthma Management Program using five statistical models to determine the most robust genetic associations. The primary replication phase included 1397 polymorphisms in three asthma trials (pooled n=764). The second replication phase tested 13 SNPs in three additional asthma populations (n=241, n=215, and n=592). An intergenic SNP on chromosome 10, rs11252394, proximal to several excellent biological candidates, significantly replicated (p=1.98×10−7) in the primary replication trials. An intronic SNP (rs6988229) in the collagen (COL22A1) locus also provided strong replication signals (p=8.51×10−6). This study applied a robust approach for testing the genetic basis of BDR and identified novel loci associated with this drug response in asthmatics.
PMCID: PMC3706515  PMID: 23508266
pharmacogenetics; asthma; bronchodilator response; genome-wide association study; albuterol
11.  CD14, Endotoxin, and Asthma Risk 
A functional single nucleotide polymorphism in the 5 genomic region of CD14 (CD14/−159) is one of the most widely tested genetic variations in relation to asthma and associated traits. The results of these studies have shown a remarkable, statistically significant heterogeneity, with some studies indicating the T-allele as a risk factor, others the C-allele, and others finding no association. Recent studies in which exposure to house-dust endotoxin or to domestic sources of microbial exposure were assessed concomitantly with CD14/−159 have shown a consistent, replicable gene-environment interaction. Specifically, results suggest that the C-allele is a risk factor for allergic phenotypes at low levels of exposure, whereas the T-allele is a risk factor at high levels of exposure. This finding seems to be explained by a genetically-determined heterogeneity for the protective effect of microbial exposure on allergic phenotypes, with homozygotes for the C-allele showing a much stronger negative association between exposure and allergic outcomes than carries of the other two genotypes. These results suggest that the often encountered, limited replicability of genetic associations may, at least in part, be due to complex interactions between genes and environment in determining asthma-related outcomes.
PMCID: PMC2647622  PMID: 17607003
asthma; CD14; gene–environment interaction
12.  Maternal microchimerism protects against the development of asthma 
Maternal asthma and child’s sex are among the most significant and reproducible risk factors for the development of asthma. Although the mechanisms for these effects are unknown, they likely involve non-classical genetic mechanisms. One such mechanism could involve the transfer and persistence of maternal cells to her offspring, a common occurrence known as maternal microchimerism (MMc). MMc has been associated with many autoimmune diseases, but has not been investigated for a role in asthma or allergic disease.
We hypothesized that some of the observed risks for asthma may be due to different rates of transmission or persistence of maternal cells to children of mothers with asthma compared to children of mothers without asthma, or to sons compared to daughters. We further hypothesized that rates of MMc differ between children with and without asthma.
We tested these hypotheses in 317 subjects from three independent cohorts using a real-time quantitative PCR assay to detect a non-inherited HLA allele in the child.
MMc was detected in 20.5% of subjects (range 16.8% – 27.1% in the three cohorts). We observed lower rates of asthma among MMc positive subjects compared to MMc negative subjects (odds ratio [OR] 0.38, 95% CI 0.19, 0.79; P=0.029). Neither maternal asthma nor sex of the child was a significant predictor of MMc in the child (P = 0.81 and 0.15, respectively).
Our results suggest for the first time that MMc may protect against the development of asthma.
PMCID: PMC3700564  PMID: 23434286
Microchimerism; maternal; asthma
13.  Gene–Environment Interactions in Asthma 
Many environmental factors and a large number of genetic polymorphisms have been reported to be associated with asthma risk in different locales and at different ages. It seems that what we call asthma is a heterogeneous set of conditions for which the only common feature is recurrent airway obstruction that is at least partially responsive to usual asthma therapy. Recent studies in which environmental factors and genetic variants were studied concomitantly have suggested a potential unifying concept for the disease. It seems that asthma is a genetically mediated development dysregulation of diverse immune and airway responses to a variety of specific and nonspecific exposures. It thus seems improbable that most genetic variants associated with asthma influence the disease regardless of which environmental factors trigger it and at which lifetime phase they are present. More likely, the most important gene variants for asthma are polymorphisms that exert their influence on the network system controlling biological responses to asthma-related exposures.
PMCID: PMC2647610  PMID: 17202288
asthma; genetics; environment; interaction
14.  Do oral corticosteroids reduce the severity of acute lower respiratory tract illnesses in preschool children with recurrent wheezing? 
The Journal of allergy and clinical immunology  2013;131(6):10.1016/j.jaci.2013.01.034.
Oral corticosteroids (OCSs) are recommended for severe wheezing episodes in children. However, limited evidence supports this intervention in preschool children with outpatient wheezing illnesses.
We sought to investigate whether OCSs reduce symptom scores during acute lower respiratory tract illnesses (LRTIs) in preschool children with recurrent wheeze
We performed post hoc and replication analyses in 2 outpatient cohorts of children aged 1 to 5 years with episodic wheezing participating in clinical trials. We compared symptom scores during LRTIs that were or were not treated with OCSs, adjusting for differences in disease and episode severity covariates.We stratified episodes by severity by using a propensity model. The primary outcome was the area under the curve (AUC) of total symptom scores among the more severe episodes.
Two hundred fifteen participants from the Acute Intervention Management Strategies trial experienced 798 acute LRTIs, 112 of which were defined as severe based on propensity scores. The AUCs of total symptom scores did not differ between the episodes that were (n = 70) and were not (n = 42) treated with OCSs (P = .46) nor was there an OCS treatment effect on individual symptom scores. Similar analyses of the Maintenance Versus Intermittent Inhaled Corticosteroids in Wheezing Toddlers trial, involving 278 participants with 133 severe LRTIs, confirmed the above findings (P =.46 for AUC of total symptoms score comparison).
In 2 separate cohorts of preschool children with episodic wheezing, OCS treatment during clinically significant LRTIs did not reduce symptom severity during acute LRTIs, despite asthma controller medication use during most episodes. These findings need to be confirmed in a prospective randomized controlled trial.
PMCID: PMC3810170  PMID: 23498594
Oral corticosteroids; episodic wheezing; preschool children
15.  Outcome of Asthma and Wheezing in the First 6 Years of Life 
Rationale: The effect of early life wheezing on respiratory function and continued symptoms through adolescence has not been fully described. Using data from a population-based birth cohort in Tucson, Arizona, we previously described four phenotypes based on the occurrence of wheezing lower respiratory illnesses before age 3 yr and active wheeze at age 6 yr: never wheezers (n = 425), transient early wheezers (n = 164), persistent wheezers (n = 113), and late-onset wheezers (n = 124).
Objective: We sought to determine the prognosis for these phenotypes, with reference to lung function and symptoms, through adolescence.
Methods: Current wheeze was assessed by questionnaire, lung function was measured by conventional spirometry, and atopy was determined by skin prick tests.
Results: The prevalence of atopy and wheeze by age 16 yr was similar for never and transient wheezers and for persistent and late-onset wheezers. Both transient early, and persistent wheezers had significantly lower FEF25–75 (–259 ml/s, p < 0.001, and –260 ml/s, p = 0.001, respectively), FEV1 (–75 ml, p = 0.02, and –87 ml, p = 0.03, respectively), and FEV1:FVC ratio (–1.9%, p = 0.002, and –2.5%, p = 0.001, respectively) through age 16 yr compared with never wheezers. Late-onset wheezers had levels of lung function similar to those of never wheezers through age 16 yr. There was no significant change in lung function among subjects with any of the four phenotypes, relative to their peers, from age 6 to 16 yr.
Conclusion: Patterns of wheezing prevalence and levels of lung function are established by age 6 yr and do not appear to change significantly by age 16 yr in children who start having asthmalike symptoms during the preschool years.
PMCID: PMC2718414  PMID: 16109980
adolescent; preschool child; respiratory function tests
16.  A Meta-analysis of Genome-wide Association Studies for Serum Total IgE in Diverse Study Populations 
Immunoglobulin E (IgE) is both a marker and mediator of allergic inflammation. Despite reported differences in serum total IgE levels by race-ethnicity, African American and Latino individuals have not been well represented in genetic studies of total IgE.
To identify the genetic predictors of serum total IgE levels.
We used genome wide association (GWA) data from 4,292 individuals (2,469 African Americans, 1,564 European Americans, and 259 Latinos) in the EVE Asthma Genetics Consortium. Tests for association were performed within each cohort by race-ethnic group (i.e., African American, Latino, and European American) and asthma status. The resulting p-values were meta-analyzed accounting for sample size and direction of effect. Top single nucleotide polymorphism (SNP) associations from the meta-analysis were reassessed in six additional cohorts comprising 5,767 individuals.
We identified 10 unique regions where the combined association statistic was associated with total serum IgE levels (P-value <5.0×10−6) and the minor allele frequency was ≥5% in two or more population groups. Variant rs9469220, corresponding to HLA-DQB1, was the most significantly associated SNP with serum total IgE levels when assessed in both the replication cohorts and the discovery and replication sets combined (P-value = 0.007 and 2.45×10−7, respectively). In addition, findings from earlier GWA studies were also validated in the current meta-analysis.
This meta-analysis independently identified a variant near HLA-DQB1 as a predictor of total serum IgE in multiple race-ethnic groups. This study also extends and confirms the findings of earlier GWA analyses in African American and Latino individuals.
PMCID: PMC3596497  PMID: 23146381
meta-analysis; genome wide association study; total immunoglobulin E; race-ethnicity; continental population groups
17.  New Insights into the Natural History of Asthma: Primary Prevention on the Horizon 
Recent studies of the natural history of asthma have shifted attention towards viral respiratory illness in early life as a major risk factor associated with the development of the most persistent forms of the disease. Although early aeroallergen sensitization is strongly associated with chronic asthma, several trials in which single aeroallergen exposure in pregnancy and early childhood was successfully accomplished and compared with sham avoidance have failed to show any decrease in asthma incidence. New evidence suggests that complex interactions occur between viral infection and aeroallergen sensitization in genetically susceptible subjects, which trigger the immune responses and airway changes that are characteristic of persistent asthma. The finding that exposure to bacterial products among children raised on farms is associated with diminished asthma prevalence during the school years has now been replicated, and experimental studies have suggested that these effects are mediated by the activation of T-regulatory cells in the airway. It is thus plausible to hypothesize that primary prevention of asthma could be attained through surrogate therapeutic interventions that activate similar mechanisms in young children at high risk for asthma.
PMCID: PMC3963825  PMID: 22036094
Nature materials  2013;12(3):10.1038/nmat3574.
The cytoplasm of living cells responds to deformation in much the same way as a water-filled sponge does. This behaviour, although intuitive, is connected to long-standing and unsolved fundamental questions in cell mechanics.
PMCID: PMC3882307  PMID: 23422717
19.  Further Replication Studies of the EVE Consortium Meta-Analysis Identifies Two Asthma Risk Loci in European Americans 
Genome-wide association studies of asthma have implicated many genetic risk factors, with well-replicated associations at approximately 10 loci that account for only a small proportion of the genetic risk.
We aimed to identify additional asthma risk loci by performing an extensive replication study of the results from the EVE Consortium meta-analysis.
We selected 3186 SNPs for replication based on the p-values from the EVE Consortium meta-analysis. These SNPs were genotyped in ethnically diverse replication samples from nine different studies, totaling to 7202 cases, 6426 controls, and 507 case-parent trios. Association analyses were conducted within each participating study and the resulting test statistics were combined in a meta-analysis.
Two novel associations were replicated in European Americans: rs1061477 in the KLK3 gene on chromosome 19 (combined OR = 1.18; 95% CI 1.10 – 1.25) and rs9570077 (combined OR =1.20 95% CI 1.12–1.29) on chromosome 13q21. We could not replicate any additional associations in the African American or Latino individuals.
This extended replication study identified two additional asthma risk loci in populations of European descent. The absence of additional loci for African Americans and Latino individuals highlights the difficulty in replicating associations in admixed populations.
PMCID: PMC3666859  PMID: 23040885
Asthma; genetic risk factors; meta-analysis; KLK3
20.  ITGB5 and AGFG1 variants are associated with severity of airway responsiveness 
BMC Medical Genetics  2013;14:86.
Airway hyperresponsiveness (AHR), a primary characteristic of asthma, involves increased airway smooth muscle contractility in response to certain exposures. We sought to determine whether common genetic variants were associated with AHR severity.
A genome-wide association study (GWAS) of AHR, quantified as the natural log of the dosage of methacholine causing a 20% drop in FEV1, was performed with 994 non-Hispanic white asthmatic subjects from three drug clinical trials: CAMP, CARE, and ACRN. Genotyping was performed on Affymetrix 6.0 arrays, and imputed data based on HapMap Phase 2, was used to measure the association of SNPs with AHR using a linear regression model. Replication of primary findings was attempted in 650 white subjects from DAG, and 3,354 white subjects from LHS. Evidence that the top SNPs were eQTL of their respective genes was sought using expression data available for 419 white CAMP subjects.
The top primary GWAS associations were in rs848788 (P-value 7.2E-07) and rs6731443 (P-value 2.5E-06), located within the ITGB5 and AGFG1 genes, respectively. The AGFG1 result replicated at a nominally significant level in one independent population (LHS P-value 0.012), and the SNP had a nominally significant unadjusted P-value (0.0067) for being an eQTL of AGFG1.
Based on current knowledge of ITGB5 and AGFG1, our results suggest that variants within these genes may be involved in modulating AHR. Future functional studies are required to confirm that our associations represent true biologically significant findings.
PMCID: PMC3765944  PMID: 23984888
Asthma; Airway hyperresponsiveness; Genome-wide association study; ITGB5; AGFG1
21.  Genetic Variation in Vascular Endothelial Growth Factor-A and Lung Function 
Rationale: Given the role of vascular endothelial growth factor (VEGF) in lung development, we hypothesized that polymorphisms in VEGF-A may be associated with lung function.
Objectives: The current study was designed to assess the role of genetic variants in VEGF-A as determinants of airway function from infancy through early adulthood.
Methods: Association between five single-nucleotide polymorphisms (SNPs) in VEGF-A and lung function were assessed longitudinally in two unselected birth cohorts and cross-sectionally among infants. Replication with two SNPs was conducted in adults and children with asthma. We investigated the functionality of the SNP most consistently associated with lung function (rs3025028) using Western blotting to measure the ratio of plasma VEGF-A165b/panVEGF-A165 among homozygotes.
Measurements and Main Results: In two populations in infancy, C-allele homozygotes of rs3025028 had significantly higher VmaxFRC, forced expiratory flow50, and forced expiratory flow25–75 compared with other genotype groups. Among preschool children (age 3 yr), C allele of rs3025028 was associated with significantly higher specific airway conductance, with similar findings observed for lung function in school-age children. For FEV1/FVC ratio similar findings were observed among adolescents and young adults (birth cohort), and then replicated in adults and schoolchildren with asthma (cross-sectional studies). For rs3025038, plasma VEGF-A165b/panVEGF-A165 was significantly higher among CC versus GG homozygotes (P ≤ 0.02) at birth, in school-age children, and in adults.
Conclusions: We report significant associations between VEGF-A SNP rs3025028 and parameters of airway function measured throughout childhood, with the effect persisting into adulthood. We propose that the mechanism may be mediated through the ratios of active and inhibitory isoforms of VEGF-A165, which may be determined by alternative splicing.
PMCID: PMC3373065  PMID: 22461367
lung function; vascular endothelial growth factor-A; genetics
22.  Genomewide Association between GLCCI1 and Response to Glucocorticoid Therapy in Asthma 
The New England journal of medicine  2011;365(13):1173-1183.
The response to treatment for asthma is characterized by wide interindividual variability, with a significant number of patients who have no response. We hypothesized that a genomewide association study would reveal novel pharmacogenetic determinants of the response to inhaled glucocorticoids.
We analyzed a small number of statistically powerful variants selected on the basis of a family-based screening algorithm from among 534,290 single-nucleotide polymorphisms (SNPs) to determine changes in lung function in response to inhaled glucocorticoids. A significant, replicated association was found, and we characterized its functional effects.
We identified a significant pharmacogenetic association at SNP rs37972, replicated in four independent populations totaling 935 persons (P = 0.0007), which maps to the glucocorticoid-induced transcript 1 gene (GLCCI1) and is in complete linkage disequilibrium (i.e., perfectly correlated) with rs37973. Both rs37972 and rs37973 are associated with decrements in GLCCI1 expression. In isolated cell systems, the rs37973 variant is associated with significantly decreased luciferase reporter activity. Pooled data from treatment trials indicate reduced lung function in response to inhaled glucocorticoids in subjects with the variant allele (P = 0.0007 for pooled data). Overall, the mean (± SE) increase in forced expiratory volume in 1 second in the treated subjects who were homozygous for the mutant rs37973 allele was only about one third of that seen in similarly treated subjects who were homozygous for the wild-type allele (3.2 ± 1.6% vs. 9.4 ± 1.1%), and their risk of a poor response was significantly higher (odds ratio, 2.36; 95% confidence interval, 1.27 to 4.41), with genotype accounting for about 6.6% of overall inhaled glucocorticoid response variability.
A functional GLCCI1 variant is associated with substantial decrements in the response to inhaled glucocorticoids in patients with asthma. (Funded by the National Institutes of Health and others; number, NCT00000575.)
PMCID: PMC3667396  PMID: 21991891
23.  Asthma Outcomes: Exacerbations 
The goals of asthma treatment include preventing recurrent exacerbations. Yet there is no consensus about the terminology for describing or defining “exacerbation,” or about how to characterize an episode’s severity.
National Institutes of Health (NIH) institutes and other federal agencies convened an expert group to propose how asthma exacerbation should be assessed as a standardized asthma outcome in future asthma clinical research studies.
We utilized comprehensive literature reviews and expert opinion to compile a list of asthma exacerbation outcomes, and classified them as either core (required in future studies), supplemental (used according to study aims and standardized), or emerging (requiring validation and standardization). This work was discussed at an NIH-organized workshop in March 2010 and finalized in September 2011.
No dominant definition of “exacerbation” was found. The most widely used definitions included 3 components, all related to treatment, rather than symptoms: (1) systemic use of corticosteroids, (2) asthma-specific emergency department visits or hospitalization, and (3) use of short-acting β-agonists (SABAs) as quick-relief (sometimes referred to as “rescue” or “reliever”) medications.
The working group participants propose that the definition of “asthma exacerbation” be “a worsening of asthma requiring the use of systemic corticosteroids to prevent a serious outcome.” As core outcomes, they propose inclusion and separate reporting of several essential variables of an exacerbation. Further, they propose the development of a standardized, component-based definition of “exacerbation” with clear thresholds of severity for each component.
PMCID: PMC3595577  PMID: 22386508
Asthma exacerbations; severity of acute asthma; asthma outcomes; urgent asthma care
24.  Integration of Mouse and Human Genome-Wide Association Data Identifies KCNIP4 as an Asthma Gene 
PLoS ONE  2013;8(2):e56179.
Asthma is a common chronic respiratory disease characterized by airway hyperresponsiveness (AHR). The genetics of asthma have been widely studied in mouse and human, and homologous genomic regions have been associated with mouse AHR and human asthma-related phenotypes. Our goal was to identify asthma-related genes by integrating AHR associations in mouse with human genome-wide association study (GWAS) data. We used Efficient Mixed Model Association (EMMA) analysis to conduct a GWAS of baseline AHR measures from males and females of 31 mouse strains. Genes near or containing SNPs with EMMA p-values <0.001 were selected for further study in human GWAS. The results of the previously reported EVE consortium asthma GWAS meta-analysis consisting of 12,958 diverse North American subjects from 9 study centers were used to select a subset of homologous genes with evidence of association with asthma in humans. Following validation attempts in three human asthma GWAS (i.e., Sepracor/LOCCS/LODO/Illumina, GABRIEL, DAG) and two human AHR GWAS (i.e., SHARP, DAG), the Kv channel interacting protein 4 (KCNIP4) gene was identified as nominally associated with both asthma and AHR at a gene- and SNP-level. In EVE, the smallest KCNIP4 association was at rs6833065 (P-value 2.9e-04), while the strongest associations for Sepracor/LOCCS/LODO/Illumina, GABRIEL, DAG were 1.5e-03, 1.0e-03, 3.1e-03 at rs7664617, rs4697177, rs4696975, respectively. At a SNP level, the strongest association across all asthma GWAS was at rs4697177 (P-value 1.1e-04). The smallest P-values for association with AHR were 2.3e-03 at rs11947661 in SHARP and 2.1e-03 at rs402802 in DAG. Functional studies are required to validate the potential involvement of KCNIP4 in modulating asthma susceptibility and/or AHR. Our results suggest that a useful approach to identify genes associated with human asthma is to leverage mouse AHR association data.
PMCID: PMC3572953  PMID: 23457522
25.  Familial aggregation of allergen-specific sensitization and asthma 
Familial aggregation of specific response to allergens and asthma adjusted for age and sensitization to multiple allergens was assessed in two large population cohorts. Allergen skin prick tests (SPTs) were administered to 1151 families in the Tucson Children’s Respiratory Study (CRS) and 435 families in the Tucson Epidemiological Study of Airway Obstructive Disease (TESAOD). Sensitization was defined by wheal size ≥ 3 mm; physician-diagnosed asthma at age ≥ 8 years was based on questionnaires. Using S.A.G.E. 6.1 software ASSOC and FCOR, familial correlations of crude and adjusted phenotypes were evaluated. Crude estimates of parent-offspring (P-O) and sibling correlations were statistically significant for most allergens, ranging from 0.03 to 0.29. After adjusting for age of assessment and “other atopy” (SPT-positive response to additional allergens), correlations were reduced by14–71%. Sibling correlations for specific response to allergens were consistently higher than P-O correlations, but this difference was significant only for dust mite and weed mix in the TESAOD population. Familial correlation for atopic status (any positive SPTs versus none) tended to be higher than for specific allergens. Asthma, with and without adjustment, showed greater familial correlation than either specific or general SPT response and significantly higher sibling correlation in TESAOD than in CRS, probably due to the older age of the siblings and the longer period of ascertainment. In conclusion, significant familial aggregation of specific response to allergen after adjustment for other atopy appears to reflect a genetic propensity toward atopy, dependent on shared familial exposures. Results also suggest that inheritance of asthma is independent of atopic sensitization.
PMCID: PMC3267008  PMID: 22017397
familial aggregation; specific response to allergens; atopy; asthma

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