Genetic ancestry-smoking interactions and lung function in African Americans: a cohort study

Health Disparities in Environmental and Occupational Lung Disease

Pulmonary health disparities disproportionately impact disadvantaged and vulnerable populations. This article focuses on disparities in disease prevalence, morbidity, and mortality for asthma, chronic obstructive pulmonary disease, pneumoconiosis, and lung cancer. Disparities are categorized by race, age, sex, socioeconomic status, and geographic region. Each category highlights differences in risk factors for the development and severity of lung disease. Risk factors include social, behavioral, economic, and biologic determinants of health (occupational/environmental exposures, psychosocial stressors, smoking, health literacy, health care provider bias, and health care access). Many of these risk factors are complex and inter-related; strategies proposed to decrease disparities require multilevel approaches.

Mixed-model admixture mapping identifies smoking-dependent loci of lung function in African Americans

Admixture mapping has led to the discovery of many genes associated with differential disease risk by ancestry, highlighting the importance of ancestry-based approaches to association studies. However, the potential of admixture mapping in deciphering the interplay between genes and environment exposures has been seldom explored. Here we performed a genome-wide screening of local ancestry-smoking interactions for five spirometric lung function phenotypes in 3300 African Americans from the COPDGene study. To account for population structure and outcome heterogeneity across exposure groups, we developed a multi-component linear mixed model for mapping gene-environment interactions and empirically showed its robustness and increased power. When applied to the COPDGene study, our approach identified two 11p15.2-3 and 2q37 loci, exhibiting local ancestry-smoking interactions at genome-wide significant level, which would have been missed by standard single-nucleotide polymorphism analyses. These two loci harbor the PARVA and RAB17 genes previously recognized to be involved in smoking behavior. Overall, our study provides the first evidence for potential synergistic effects between African ancestry and smoking on pulmonary function, and underlines the importance of ethnic diversity in genetic studies.

Maternal Black Race and Persistent Wheezing Illness in Former Extremely Low Gestational Age Newborns: Secondary Analysis of a Randomized Trial

OBJECTIVE

To evaluate the relationship between maternal self-reported race/ethnicity and persistent wheezing illness in former high-risk, extremely low gestational age newborns, and to quantify the contribution of socioeconomic, environmental, and biological factors on this relationship.

STUDY DESIGN

We assessed persistent wheezing illness determined at 18-24 months corrected (for prematurity) age in survivors of a randomized trial. Parents/caregivers were surveyed for wheeze and inhaled asthma medication use quarterly to 12 months, and at 18 and 24 months. We used multivariable analysis to evaluate the relationship of maternal race to persistent wheezing illness, and identified mediators for this relationship via formal mediation analysis.

RESULTS

Of 420 infants (25.2 ± 1.2 weeks of gestation and 714 ± 166 g at birth, 57% male, 34% maternal black race), 189 (45%) had persistent wheezing illness. After adjustment for gestational age, birth weight, and sex, infants of black mothers had increased odds of persistent wheeze compared with infants of nonblack mothers (OR = 2.9, 95% CI 1.9, 4.5). Only bronchopulmonary dysplasia, breast milk diet, and public insurance status were identified as mediators. In this model, the direct effect of race accounted for 69% of the relationship between maternal race and persistent wheeze, whereas breast milk diet, public insurance status, and bronchopulmonary dysplasia accounted for 8%, 12%, and 10%, respectively.

CONCLUSIONS

Among former high-risk extremely low gestational age newborns, infants of black mothers have increased odds of developing persistent wheeze. A substantial proportion of this effect is directly accounted for by race, which may reflect unmeasured environmental influences, and acquired and innate biological differences.

TRIAL REGISTRATION

ClinicalTrials.gov: NCT01022580.

Genome-wide assessment of gene-by-smoking interactions in COPD

Cigarette smoke exposure is a major risk factor in chronic obstructive pulmonary disease (COPD) and its interactions with genetic variants could affect lung function. However, few gene-smoking interactions have been reported. In this report, we evaluated the effects of gene-smoking interactions on lung function using Korea Associated Resource (KARE) data with the spirometric variables—forced expiratory volume in 1 s (FEV₁). We found that variations in FEV₁ were different among smoking status. Thus, we considered a linear mixed model for association analysis under heteroscedasticity according to smoking status. We found a previously identified locus near SOX9 on chromosome 17 to be the most significant based on a joint test of the main and interaction effects of smoking. Smoking interactions were replicated with Gene-Environment of Interaction and phenotype (GENIE), Multi-Ethnic Study of Atherosclerosis-Lung (MESA-Lung), and COPDGene studies. We found that individuals with minor alleles, rs17765644, rs17178251, rs11870732, and rs4793541, tended to have lower FEV₁ values, and lung function decreased much faster with age for smokers. There have been very few reports to replicate a common variant gene-smoking interaction, and our results revealed that statistical models for gene-smoking interaction analyses should be carefully selected.

Choline Supplementation Normalizes Fetal Adiposity and Reduces Lipogenic Gene Expression in a Mouse Model of Maternal Obesity

Maternal obesity increases fetal adiposity which may adversely affect metabolic health of the offspring. Choline regulates lipid metabolism and thus may influence adiposity. This study investigates the effect of maternal choline supplementation on fetal adiposity in a mouse model of maternal obesity. C57BL/6J mice were fed either a high-fat (HF) diet or a control (NF) diet and received either 25 mM choline supplemented (CS) or control untreated (CO) drinking water for 6 weeks before timed-mating and throughout gestation. At embryonic day 17.5, HF feeding led to higher (p < 0.05) percent total body fat in fetuses from the HFCO group, while the choline supplemented HFCS group did not show significant difference versus the NFCO group. Similarly, HF feeding led to higher (p < 0.05) hepatic triglyceride accumulation in the HFCO but not the HFCS fetuses. mRNA levels of lipogenic genes such as Acc1, Fads1, and Elovl5, as well as the transcription factor Srebp1c that favors lipogenesis were downregulated (p < 0.05) by maternal choline supplementation in the HFCS group, which may serve as a mechanism to reduce fat accumulation in the fetal liver during maternal HF feeding. In summary, maternal choline supplementation improves indices of fetal adiposity in obese dams at late gestation.

What Ancestry Can Tell Us About the Genetic Origins of Inter-Ethnic Differences in Asthma Expression

Differences in asthma prevalence have been described across different populations, suggesting that genetic ancestry can play an important role in this disease. In fact, several studies have demonstrated an association between African ancestry with increased asthma susceptibility and severity, higher immunoglobulin E levels, and lower lung function. In contrast, Native American ancestry has been shown to have a protective role for this disease. Genome-wide association studies have allowed the identification of population-specific genetic variants with varying allele frequency among populations. Additionally, the correlation of genetic ancestry at the chromosomal level with asthma and related traits by means of admixture mapping has revealed regions of the genome where ancestry is correlated with the disease. In this review, we discuss the evidence supporting the association of genetic ancestry with asthma susceptibility and asthma-related traits, and highlight the regions of the genome harboring ancestry-specific genetic risk factors.

Leveraging local ancestry to detect gene-gene interactions in genome-wide data

BACKGROUND

Although genome-wide association studies have successfully identified thousands of variants associated to complex traits, these variants only explain a small amount of the entire heritability of the trait. Gene-gene interactions have been proposed as a source to explain a significant percentage of the missing heritability. However, detecting gene-gene interactions has proven to be very difficult due to computational and statistical challenges. The vast number of possible interactions that can be tested induces very stringent multiple hypotheses corrections that limit the power of detection. These issues have been mostly highlighted for the identification of pairwise effects and are even more challenging when addressing higher order interaction effects. In this work we explore the use of local ancestry in recently admixed individuals to find signals of gene-gene interaction on human traits and diseases.

RESULTS

We introduce statistical methods that leverage the correlation between local ancestry and the hidden unknown causal variants to find distant gene-gene interactions. We show that the power of this test increases with the number of causal variants per locus and the degree of differentiation of these variants between the ancestral populations. Overall, our simulations confirm that local ancestry can be used to detect gene-gene interactions, solving the computational bottleneck. When compared to a single nucleotide polymorphism (SNP)-based interaction screening of the same sample size, the power of our test was lower on all settings we considered. However, accounting for the dramatic increase in sample size that can be achieve when genotyping only a set of ancestry informative markers instead of the whole genome, we observe substantial gain in power in several scenarios.

CONCLUSION

Local ancestry-based interaction tests offer a new path to the detection of gene-gene interaction effects. It would be particularly useful in scenarios where multiple differentiated variants at the interacting loci act in a synergistic manner.

The Effect of Ancestry and Genetic Variation on Lung Function Predictions: What Is "Normal" Lung Function in Diverse Human Populations?

Lung function measures are an invaluable screening test for respiratory health and have been associated with the morbidity and mortality related to different airway disease as well as all-cause mortality. Currently, reference values for spirometric measurements are obtained using equations derived from individual ethnic or racial groups. The rapid expansion of more racially and ethnically diverse populations will challenge current race-based lung function reference equations. Recent international general population studies and ancestry-based genetic studies have found that ancestry and genetic variation are determinants of lung function and have suggested a role for genetic ancestry or gene variants in future lung function reference equations. In this review, we discuss the potential limitations of current lung function reference equations in a global society which is becoming more ethnically, racially, and, thus, genetically diverse. We also focus on how an individual's ancestral background or genetic profile could provide the basis for more accurate, personalized predictions of an individual's baseline lung function.

A reconsideration of the role of self-identified races in epidemiology and biomedical research

A considerable number of studies in epidemiology and biomedicine investigate the etiology of complex diseases by considering (self-identified) race as a relevant variable and focusing on the differences in risk among racial groups in the United States; they extensively draw on a genetic hypothesis--viz. the hypothesis that differences in the risk of complex diseases among racial groups are largely due to genetic differences covarying with genetic ancestry--that appears highly problematic in the light of both current biological evidence and the theory of human genome evolution. Is this reason for dismissing self-identified races? No. An alternative promising use of self-identified races exists, and ironically is suggested by those studies that investigate the etiology of complex diseases without focusing on racial differences. These studies provide a large amount of empirical evidence supporting the primacy of the contribution of non-genetic as opposed to genetic factors to the risk of complex diseases. We show that differences in race--or, better, in racial self-identification--may be critically used as proxies for differences in risk-related exposomes and epigenomes in the context of the United States. Self-identified race is what we need to capture the complexity of the effects of present and past racism on people's health and investigate risk-related external and internal exposures, gene-environment interactions, and epigenetic events. In fact patterns of racial self-identifications on one side, and patterns of risk-related exposomes and epigenomes on the other side, constantly coevolve and tend to match each other. However, there is no guarantee that using self-identified races in epidemiology and biomedical research will be beneficial all things considered: special attention must be paid at balancing positive and negative consequences.

Self-reported race/ethnicity in the age of genomic research: its potential impact on understanding health disparities

This review explores the limitations of self-reported race, ethnicity, and genetic ancestry in biomedical research. Various terminologies are used to classify human differences in genomic research including race, ethnicity, and ancestry. Although race and ethnicity are related, race refers to a person's physical appearance, such as skin color and eye color. Ethnicity, on the other hand, refers to communality in cultural heritage, language, social practice, traditions, and geopolitical factors. Genetic ancestry inferred using ancestry informative markers (AIMs) is based on genetic/genomic data. Phenotype-based race/ethnicity information and data computed using AIMs often disagree. For example, self-reporting African Americans can have drastically different levels of African or European ancestry. Genetic analysis of individual ancestry shows that some self-identified African Americans have up to 99% of European ancestry, whereas some self-identified European Americans have substantial admixture from African ancestry. Similarly, African ancestry in the Latino population varies between 3% in Mexican Americans to 16% in Puerto Ricans. The implication of this is that, in African American or Latino populations, self-reported ancestry may not be as accurate as direct assessment of individual genomic information in predicting treatment outcomes. To better understand human genetic variation in the context of health disparities, we suggest using "ancestry" (or biogeographical ancestry) to describe actual genetic variation, "race" to describe health disparity in societies characterized by racial categories, and "ethnicity" to describe traditions, lifestyle, diet, and values. We also suggest using ancestry informative markers for precise characterization of individuals' biological ancestry. Understanding the sources of human genetic variation and the causes of health disparities could lead to interventions that would improve the health of all individuals.

Second and third trimester amniotic fluid mesenchymal stem cells can repopulate a de-cellularized lung scaffold and express lung markers

BACKGROUND/PURPOSE

This study examined the potential of amniotic fluid mesenchymal stem cells (AF-MSCs) to generate lung precursor cells in vitro and on a xenologous three-dimensional de-cellularized lung scaffold.

METHODS

AF-MSCs were isolated from human amniotic fluid obtained from 17-37 weeks gestation. Lung differentiation was induced on Matrigel or on de-cellularized rat lungs intra-tracheally injected with AF-MSCs by culturing with a modification of small airway growth medium (mSAGM) lacking retinoic acid (RA) and triodothyronine (T3) with addition of fibroblast growth factor-10 (FGF10). Cells and scaffolds were characterized by immunofluorescence and RT-PCR for markers of viability, proliferation, and lung distal airway differentiation (TTF-1(+) and SPC(+)) in the absence of markers of brain (TuJ1(-)) and thyroid (Pax8(-)).

RESULTS

After culture in mSAGM on either Matrigel or lung scaffolds, there were TTF-1(+)/TuJ1(-)/Pax8(-) cells, indicating a lung precursor phenotype. In addition, SPC(+) cells also evolved suggesting a more mature lung phenotype.

CONCLUSIONS

We demonstrate that mid- to late-trimester AF-MSCs can be induced to develop into lung precursor cells when cultured on the appropriate extracellular matrix (ECM), making them a viable source for use in cell therapy or development of an ex vivo tissue engineered lung.

Obstructive airway disease in urban populations

PURPOSE OF REVIEW

Obstructive lung disease (OLD), including asthma and chronic obstructive pulmonary disease, has a more substantial prevalence and morbidity in urban populations. This review highlights recent publications examining the epidemiology, risk factors and interventions concerning OLD in urban populations.

RECENT FINDINGS

Using a variety of approaches, estimates of asthma prevalence in urban populations range from 5 to 25%. Early life exposures including in-utero cigarette smoke, postnatal bisphenol A, home and school particulates, and environmental air pollution contribute to increased OLD prevalence and symptom manifestations. Individuals with increased exposure to traffic-related pollution demonstrate abnormal inflammatory and lung function profiles. Obesity, more common in urban populations, is likely both a risk factor for asthma as well as contributor to poor control. Interventions targeted at home-based education and assessments are efficacious and cost-effective in improving outcomes of OLD in urban settings.

SUMMARY

The burden of OLD in urban populations is driven by maternal, environmental and acquired factors. There are few recent data regarding risk factors and interventions for urban cohorts with chronic obstructive pulmonary disease. The complex interplay of race, socioeconomic status, environmental exposures and healthcare access in the urban population requires continued research efforts.

Admixture mapping identifies a quantitative trait locus associated with FEV1/FVC in the COPDGene Study

African Americans are admixed with genetic contributions from European and African ancestral populations. Admixture mapping leverages this information to map genes influencing differential disease risk across populations. We performed admixture and association mapping in 3,300 African American current or former smokers from the COPDGene Study. We analyzed estimated local ancestry and SNP genotype information to identify regions associated with FEV1 /FVC, the ratio of forced expiratory volume in one second to forced vital capacity, measured by spirometry performed after bronchodilator administration. Global African ancestry inversely associated with FEV1 /FVC (P = 0.035). Genome-wide admixture analysis, controlling for age, gender, body mass index, current smoking status, pack-years smoked, and four principal components summarizing the genetic background of African Americans in the COPDGene Study, identified a region on chromosome 12q14.1 associated with FEV1 /FVC (P = 2.1 × 10(-6) ) when regressed on local ancestry. Allelic association in this region of chromosome 12 identified an intronic variant in FAM19A2 (rs348644) as associated with FEV1 /FVC (P = 1.76 × 10(-6) ). By combining admixture and association mapping, a marker on chromosome 12q14.1 was identified as being associated with reduced FEV1 /FVC ratio among African Americans in the COPDGene Study.

Mitochondrial DNA sequence associations with dementia and amyloid-β in elderly African Americans

Mitochondrial dysfunction occurs early in the course of several neurodegenerative diseases, and is potentially related to increased oxidative damage and amyloid-β (Aβ) formation in Alzheimer's disease. The goals of this study were to assess mtDNA sequence associations with dementia risk, 10-year cognitive change, and markers of oxidative stress and Aβ among 1089 African-Americans in the population-based Health, Aging, and Body Composition Study. Participants were free of dementia at baseline, and incidence was determined in 187 (18%) cases over 10 to 12 follow-up years. Haplogroup L1 participants were at increased risk for developing dementia (odds ratio = 1.88, 95% confidence interval = 1.23-2.88, p = 0.004), lower plasma Aβ42 levels (p = 0.03), and greater 10-year decline on the Digit Symbol Substitution Test (p = 0.04) when compared with common haplogroup L3. The p.V193I, ND2 substitution was associated with significantly higher Aβ42 levels (p = 0.0012), and this association was present in haplogroup L3 (p = 0.018) but not L1 (p = 0.90) participants. All associations were independent of potential confounders, including APOEε4 status and nuclear genetic ancestry. Identification of mtDNA sequence variation associated with dementia risk and cognitive decline may contribute to the development of new treatment targets and diagnostic tests that identify responders to interventions targeting mitochondria.

Biomarkers of tobacco smoke exposure and asthma severity in adults

BACKGROUND

Tobacco biomarkers including serum cotinine and urinary 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol (NNAL) have been used in research settings.

PURPOSE

The goal of the study was to examine the association of cotinine and NNAL with asthma outcomes in the U.S. adult population.

METHODS

A cross-sectional design was used, using data from the National Health and Nutrition Examination Survey, 2007-2008, with participants aged >20 years with self-reported asthma (N=456). Past-year asthma exacerbations and emergency room/urgent care visits for asthma were examined. Analyses were conducted in 2013.

RESULTS

Among adult asthmatics, 50.3% reported a past-year asthma attack (61.8% smokers, 46.6% nonsmokers, p=0.029). Among these, 24.7% reported a past-year emergency/urgent visit for asthma (34.7% smokers, 20.1% nonsmokers, p=0.034). Median concentrations of cotinine and creatinine-adjusted NNAL (NNAL/Cr) were significantly higher in those with a past-year asthma attack (0.43 ng/mL and 7.28 pg/mL) than in those without (0.06 ng/mL and 2.26 pg/mL), and highest in those with past-year emergency/urgent visits (0.93 ng/mL and 28.14 pg/mL). Among nonsmokers, increasing levels of log cotinine or log NNAL/Cr, adjusted for demographics, were significantly associated with past-year asthma exacerbation (log cotinine OR=1.46 [95% CI=1.1, 1.92]; log NNAL/Cr OR=1.42 [95% CI=1.07, 1.88]) and past-year emergency/urgent visit (log cotinine OR=1.95 [95% CI=1.32, 2.88]; log NNAL/Cr OR=1.58 [95% CI=1.23, 2.02]). Among smokers, increasing biomarker levels were not significantly associated with either outcome.

CONCLUSIONS

In a population-based cross-sectional analysis, increased cotinine and NNAL were found to be associated with asthma exacerbation and healthcare use in nonsmokers with asthma. If these findings are confirmed in prospective studies, these biomarkers might be candidates for clinical indicators of risk of asthma.

Socioeconomic status and lung cancer: unraveling the contribution of genetic admixture

OBJECTIVES

We examined the relationship between genetic ancestry, socioeconomic status (SES), and lung cancer among African Americans and Latinos.

METHODS

We evaluated SES and genetic ancestry in a Northern California lung cancer case-control study (1998-2003) of African Americans and Latinos. Lung cancer case and control participants were frequency matched on age, gender, and race/ethnicity. We assessed case-control differences in individual admixture proportions using the 2-sample t test and analysis of covariance. Logistic regression models examined associations among genetic ancestry, socioeconomic characteristics, and lung cancer.

RESULTS

Decreased Amerindian ancestry was associated with higher education among Latino control participants and greater African ancestry was associated with decreased education among African lung cancer case participants. Education was associated with lung cancer among both Latinos and African Americans, independent of smoking, ancestry, age, and gender. Genetic ancestry was not associated with lung cancer among African Americans.

CONCLUSIONS

Findings suggest that socioeconomic factors may have a greater impact than genetic ancestry on lung cancer among African Americans. The genetic heterogeneity and recent dynamic migration and acculturation of Latinos complicate recruitment; thus, epidemiological analyses and findings should be interpreted cautiously.

Genetic ancestry and the relationship of cigarette smoking to lung function and per cent emphysema in four race/ethnic groups: a cross-sectional study

BACKGROUND

Cigarette smoking is the major cause of chronic obstructive pulmonary disease and emphysema. Recent studies suggest that susceptibility to cigarette smoke may vary by race/ethnicity; however, they were generally small and relied on self-reported race/ethnicity.

OBJECTIVE

To test the hypothesis that relationships of smoking to lung function and per cent emphysema differ by genetic ancestry and self-reported race/ethnicity among Caucasians, African-Americans, Hispanics and Chinese-Americans.

DESIGN

Cross-sectional population-based study of adults age 45-84 years in the USA.

MEASUREMENTS

Principal components of genetic ancestry and continental ancestry estimated from one million genome-wide single nucleotide polymorphisms; pack-years of smoking; spirometry measured for 3344 participants; and per cent emphysema on computed tomography for 8224 participants.

RESULTS

The prevalence of ever-smoking was: Caucasians, 57.6%; African-Americans, 56.4%; Hispanics, 46.7%; and Chinese-Americans, 26.8%. Every 10 pack-years was associated with -0.73% (95% CI -0.90% to -0.56%) decrement in the forced expiratory volume in 1 s to forced vital capacity (FEV1 to FVC) and a 0.23% (95% CI 0.08% to 0.38%) increase in per cent emphysema. There was no evidence that relationships of pack-years to the FEV1 to FVC, airflow obstruction and per cent emphysema varied by genetic ancestry (all p>0.10), self-reported race/ethnicity (all p>0.10) or, among African-Americans, African ancestry. There were small differences in relationships of pack-years to the FEV1 among male Chinese-Americans and to the FEV1 to FVC ratio with African and Native American ancestry among male Hispanics only.

CONCLUSIONS

In this large cohort, there was little to no evidence that the associations of smoking to lung function and per cent emphysema differed by genetic ancestry or self-reported race/ethnicity.