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

Serum uric acid is inversely associated with lung function in US adults

The relationship between serum uric acid and lung function has been controversial. This study aims to determine whether there is an independent relationship between serum uric acid and lung function in the National Health and Nutrition Examination Survey (NHANES) from 2007 to 2012. Serum uric acid was considered the exposure variable, and lung function (FEV1 and FVC) was the outcome variable. Multivariable linear regression was conducted with adjustments for potential confounders. The total number of participants from NHANES (2007-2012) was 30,442, of which 7514 were included in our analysis after applying exclusion criteria. We observed that serum uric acid was negatively associated with FEV1 and FVC after adjusting for confounders (β for FEV1 [- 24.77 (- 36.11, - 13.43)] and FVC [- 32.93 (- 47.42, - 18.45)]). Similarly, serum uric acid showed a negative correlation with FEV1 and FVC after adjusting for confounding variables both in male and female populations. The relationship between serum uric acid and FEV1 and FVC remained consistent and robust in various subgroups within both male and female populations, including age, race, BMI, alcohol consumption, smoking status, and income-poverty ratio. Serum uric acid is negatively associated with FEV1 and FVC in the US general healthy population. This negative relationship is significant in both the male and female populations.

Asthma and Chronic Obstructive Pulmonary Disease

In the United States, asthma and chronic obstructive pulmonary disease (COPD) disproportionately affect African Americans, Puerto Ricans, and other minority groups. Compared with non-Hispanic whites, minorities have been marginalized and more frequently exposed to environmental risk factors such as tobacco smoke and outdoor and indoor pollutants. Such divergent environmental exposures, alone or interacting with heredity, lead to disparities in the prevalence, morbidity, and mortality of asthma and COPD, which are worsened by lack of access to health care. In this article, we review the burden and risk factors for racial or ethnic disparities in asthma and COPD and discuss future directions in this field.

The creatinine-to-cystatin C ratio (a surrogate marker of muscle mass) as a predictor of lung function decline in older adults: A nationwide longitudinal study in China

BACKGROUND

Lung function decline is associated with sarcopenia, known as loss of skeletal muscle mass. The serum creatinine to cystatin C ratio (CCR) has been proposed as a biomarker of muscle mass. The associations between CCR and lung function decline are unknown.

METHODS

The study used two waves of data from China Health and Retirement Longitudinal Study (CHARLS) in 2011 and 2015. Serum creatinine and cystatin C were collected at baseline survey (2011). Lung function was assessed by peak expiratory flow (PEF) at 2011 and 2015. Linear regression models adjusted for potential confounders were conducted to analyze the cross-sectional association between CCR and PEF, and the longitudinal association between CCR and annual decline in PEF.

RESULTS

Totally, 5812 participants aged over 50 years (50.8% women; mean age 63.3 ± 6.5 years) were enrolled in a cross-sectional analysis in 2011, and further 4164 individuals were followed up in 2015. Serum CCR was positively associated with PEF and the PEF% pred. Per 1 SD higher of CCR was associated with 41.55 L/min increases in PEF (p < 0.001) and 10.77 (%) increase in PEF% pred (p < 0.001). Longitudinal analyses indicated that higher CCR level at baseline was related to slower annual decline in PEF and PEF% pred. And this relationship was significant only in women and in never smokers.

CONCLUSIONS

Higher CCR was associated with slower longitudinal PEF decline in women and never smokers. CCR may be a valuable marker to monitor and predict lung function decline in middle-aged and older adults.

Genetic association and causal inference between lung function and venous thromboembolism

BACKGROUND

Previous studies have indicated that lower lung function is related to a higher risk of venous thromboembolism (VTE). However, causal inferences may be affected by confounders, coheritability or reverse causality. We aimed to explore the causal association between lung function and VTE.

METHODS

Summary data from public genome-wide association studies (GWAS) for lung function and VTE were obtained from published meta-analysis studies and the FinnGen consortium, respectively. Independent genetic variables significantly related to exposure were filtered as proxy instruments. We adopted linkage disequilibrium score regression (LDSC) and two-sample Mendelian randomization (MR) analyses to infer the genetic backgrounds and causal associations between different lung functions and VTE events.

RESULTS

LDSC showed a genetic correlation between forced expiratory volume in one second (FEV1) and deep vein thrombosis (DVT) (rg = - 0.189, P = 0.005). In univariate MR (UVMR), there was suggestive evidence for causal associations of genetically predicted force vital capacity (FVC) with DVT (odds ratio (OR) 0.774; 95% confidence interval (CI) 0.641-0.934) via forwards analysis and genetically predicted pulmonary embolism (PE) with FVC (OR 0.989; 95% CI 0.979-0.999) via reverse analysis. Multivariate MR (MVMR) analyses of lung function-specific SNPs suggested no significant direct effects of lung function on VTE, and vice versa. Of note is the borderline causal effect of PE on FEV1 (OR 0.921; 95% CI 0.848-1.000).

CONCLUSIONS

Our findings identified a coheritability of FEV1 (significant) and FVC (suggestive) with DVT. There was no convincing causal relationship between lung function and the risk of VTE events. The borderline causal effect of PE on FEV1 and the significant genetic correlation of FEV1 with DVT may have clinical implications for improving the quality of existing prevention and intervention strategies.

Causal Relationship Between Lung Function and Atrial Fibrillation: A Two Sample Univariable and Multivariable, Bidirectional Mendelian Randomization Study

Background: Observational studies have identified impaired lung function accessed by forced expiratory volume in one second (FEV1), forced vital capacity (FVC) or the ratio of FEV1 over FVC (FEV1/FVC) as an independent risk factor for atrial fibrillation (AF). However, the result may be affected by confounders or reverse causality.

Methods: We performed univariable MR (uvMR), multivariable MR (mvMR) and bidirectional two-sample MR to jointly estimate the causality of lung function with AF. Apart from the inverse variance weighted (IVW) approach as the main MR analysis, three complementary sensitive analyses approaches including MR-Egger regression, weighted median (WM) MR and Pleiotropy Residual Sum and Outlier (MR-PRESSO) in uvMR as well as mvMR-Egger and mvMR-PRESSO in mvMR were applied to control for pleiotropy. Linkage disequilibrium score (LDSC) regression was applied to estimate genetic correlation between lung function and AF.

Results: All forward and reverse uvMR analyses consistently suggested absent causal relations between lung function and AF risk [forward IVW: odds ratio (OR)_FEV1 = 1.031, 95% CI = 0.909–1.169, P = 0.630; OR_FVC = 1.002, 95% CI = 0.834–1.204, P = 0.982; OR_FEV1/FVC = 1.076, 95% CI = 0.966–1.199, P = 0.182; reverse IVW: OR_FEV1 = 0.986, 95% CI = 0.966–1.007, P = 0.187; OR_FVC = 0.985, 95% CI = 0.965–1.006, P = 0.158; OR_FEV1/FVC = 0.994, 95% CI = 0.973–1.015, P = 0.545]. The forward MR-Egger showed that each standard deviation (SD) increase in FEV1/FVC was related to a higher AF risk (OR = 1.502, 95% CI = 1.178–1.915, P = 0.006) without heterogeneity (Q_pval = 0.064), but pleiotropy effect exist (intercept = −0.017, P = 0.012). However, this significant effect disappeared after adjustment of FEV1 and FVC (OR = 1.523, 95% CI = 0.445–5.217, P = 0.503) in mvMR. No evidence was found for independent causal effects of FEV1 and FVC on AF in mvMR analysis by using mvIVW method (OR_FEV1 = 0.501, 95% CI = 0.056–4.457, P = 0.496; OR_FVC = 1.969, 95% CI = 0.288–13.474, P = 0.490). Notably, the association between lung function and AF were replicated using the FinnGen cohort data.

Conclusions: Our findings reported no coheritability between lung function and AF, and failed to find substantial causal relation between decreased lung function and risk of AF. However, lung function and AF were both associated with inflammation, which may be potential pathway, warranting further study.

Lung function decline is associated with serum uric acid in Korean health screening individuals

We performed a retrospective cohort study of 19,237 individuals who underwent at least three health screenings with follow-up periods of over 5 years to find a routinely checked serum marker that predicts lung function decline. Using linear regression models to analyze associations between the rate of decline in the forced expiratory volume in 1 s (FEV1) and the level of 10 serum markers (calcium, phosphorus, uric acid, total cholesterol, total protein, total bilirubin, alkaline phosphatase, aspartate aminotransferase, creatinine, and C-reactive protein) measured at two different times (at the first and third health screenings), we found that an increased uric acid level was significantly associated with an accelerated FEV1 decline (P = 0.0014 and P = 0.037, respectively) and reduced FEV1 predicted % (P = 0.0074 and P = 8.64 × 10^–7, respectively) at both visits only in non-smoking individuals. In addition, we confirmed that accelerated forced vital capacity (FVC) and FEV1/FVC ratio declines were observed in non-smoking individuals with increased serum uric acid levels using linear mixed models. The serum uric acid level thus potentially predicts an acceleration in lung function decline in a non-smoking general population.

A Genetic Risk Score Associated with Chronic Obstructive Pulmonary Disease Susceptibility and Lung Structure on Computed Tomography

Rationale: Chronic obstructive pulmonary disease (COPD) has been associated with numerous genetic variants, yet the extent to which its genetic risk is mediated by variation in lung structure remains unknown.Objectives: To characterize associations between a genetic risk score (GRS) associated with COPD susceptibility and lung structure on computed tomography (CT).Methods: We analyzed data from MESA Lung (Multi-Ethnic Study of Atherosclerosis Lung Study), a U.S. general population-based cohort, and SPIROMICS (Subpopulations and Intermediate Outcome Measures in COPD Study). A weighted GRS was calculated from 83 SNPs that were previously associated with lung function. Lung density, spatially matched airway dimensions, and airway counts were assessed on full-lung CT. Generalized linear models were adjusted for age, age squared, sex, height, principal components of genetic ancestry, smoking status, pack-years, CT model, milliamperes, and total lung volume.Measurements and Main Results: MESA Lung and SPIROMICS contributed 2,517 and 2,339 participants, respectively. Higher GRS was associated with lower lung function and increased COPD risk, as well as lower lung density, smaller airway lumens, and fewer small airways, without effect modification by smoking. Adjustment for CT lung structure, particularly small airway measures, attenuated associations between the GRS and FEV₁/FVC by 100% and 60% in MESA and SPIROMICS, respectively. Lung structure (P < 0.0001), but not the GRS (P > 0.10), improved discrimination of moderate-to-severe COPD cases relative to clinical factors alone.Conclusions: A GRS associated with COPD susceptibility was associated with CT lung structure. Lung structure may be an important mediator of heritability and determinant of personalized COPD risk.

UMAP reveals cryptic population structure and phenotype heterogeneity in large genomic cohorts

Human populations feature both discrete and continuous patterns of variation. Current analysis approaches struggle to jointly identify these patterns because of modelling assumptions, mathematical constraints, or numerical challenges. Here we apply uniform manifold approximation and projection (UMAP), a non-linear dimension reduction tool, to three well-studied genotype datasets and discover overlooked subpopulations within the American Hispanic population, fine-scale relationships between geography, genotypes, and phenotypes in the UK population, and cryptic structure in the Thousand Genomes Project data. This approach is well-suited to the influx of large and diverse data and opens new lines of inquiry in population-scale datasets.

The demographic history of human populations features varying geographic and social barriers to mating. Over time, these barriers have led to varying levels of genetic relatedness among individuals. This population structure is informative about human history, and can have a significant impact on studies of medical genetics. Because population structure depends on myriad demographic, ecological, and social forces, a priori visualization is useful to identify subtle patterns of population structure. We use a dimension reduction method—UMAP—to visualize population structure in three genomic datasets and find previously unobserved patterns, revealing fine-scale population structure and illustrating differences between groups in traits such as white blood cell count, height, and FEV1, a measure of lung function. Using UMAP is computationally efficient and can identify fine-scale population structure in large population datasets. We find it particularly useful to reveal phenotypic variation among genetically related populations, and recommend it is a complement to principal component analysis in primary data visualization.

Exacerbation-prone asthma in the context of race and ancestry in Asthma Clinical Research Network trials

BACKGROUND

Minority groups of African descent experience disproportionately greater asthma morbidity compared with other racial groups, suggesting that genetic variation from a common ancestry could influence exacerbation risk.

OBJECTIVE

We evaluated clinical trial measures in the context of self-reported race and genetic ancestry to identify risk factors for asthma exacerbations.

METHODS

One thousand eight hundred forty multiethnic subjects from 12 Asthma Clinical Research Network and AsthmaNet trials were analyzed for incident asthma exacerbations with Poisson regression models that included clinical measures, self-reported race (black, non-Hispanic white, and other), and estimates of global genetic African ancestry in a subgroup (n = 760).

RESULTS

Twenty-four percent of 1840 subjects self-identified as black. Black and white subjects had common risk factors for exacerbations, including a history of 2 or more exacerbations in the previous year and FEV₁ percent predicted values, whereas chronic sinusitis, allergic rhinitis, and gastroesophageal reflux disease were only associated with increased exacerbation risk in black subjects. In the combined multiethnic cohort, neither race (P = .30) nor percentage of genetic African ancestry as a continuous variable associated with exacerbation risk (adjusted rate ratio [RR], 1.26 [95% CI, 0.94-1.70; P = .13]; RR per 1-SD change [32% ancestry], 0.97 [95% CI, 0.78-1.19; P = .74]). However, in 161 black subjects with genetic data, those with African ancestry greater than the median (≥82%) had a significantly greater risk of exacerbation (RR, 3.06 [95% CI, 1.09-8.6; P = .03]).

CONCLUSION

Black subjects have unique risk factors for asthma exacerbations, of which global African genetic ancestry had the strongest effect.

Spirometry reference values for Black adults in Brazil

Objective:

To derive reference equations for spirometry in healthy Black adult never smokers in Brazil, comparing them with those published in 2007 for White adults in the country.

Methods:

The examinations followed the standards recommended by the Brazilian Thoracic Association, and the spirometers employed met the technical requirements set forth in the guidelines of the American Thoracic Society/European Respiratory Society. The lower limits were defined as the 5th percentile of the residuals.

Results:

Reference equations and limits were derived from a sample of 120 men and 124 women, inhabitants of eight Brazilian cities, all of whom were evaluated with a flow spirometer. The predicted values for FVC, FEV₁, FEV₁/FVC ratio, and PEF were better described by linear equations, whereas the flows were better described by logarithmic equations. The FEV₁ and FVC reference values derived for Black adults were significantly lower than were those previously derived for White adults, regardless of gender.

Conclusions:

The fact that the predicted spirometry values derived for the population of Black adults in Brazil were lower than those previously derived for White adults in the country justifies the use of an equation specific to the former population.

A candidate gene identification strategy utilizing mouse to human big-data mining: "3R-tenet" in COPD genetic research

Background

Early life impairments leading to lower lung function by adulthood are considered as risk factors for chronic obstructive pulmonary disease (COPD). Recently, we compared the lung transcriptomic profile between two mouse strains with extreme total lung capacities to identify plausible pulmonary function determining genes using microarray analysis (GSE80078). Advancement of high-throughput techniques like deep sequencing (eg. RNA-seq) and microarray have resulted in an explosion of genomic data in the online public repositories which however remains under-exploited. Strategic curation of publicly available genomic data with a mouse-human translational approach can effectively implement “3R- Tenet” by reducing screening experiments with animals and performing mechanistic studies using physiologically relevant in vitro model systems. Therefore, we sought to analyze the association of functional variations within human orthologs of mouse lung function candidate genes in a publicly available COPD lung RNA-seq data-set.

Methods

Association of missense single nucleotide polymorphisms, insertions, deletions, and splice junction variants were analyzed for susceptibility to COPD using RNA-seq data of a Korean population (GSE57148). Expression of the associated genes were studied using the Gene Paint (mouse embryo) and Human Protein Atlas (normal adult human lung) databases. The genes were also assessed for replication of the associations and expression in COPD−/mouse cigarette smoke exposed lung tissues using other datasets.

Results

Significant association (p <  0.05) of variations in 20 genes to higher COPD susceptibility have been detected within the investigated cohort. Association of HJURP, MCRS1 and TLR8 are novel in relation to COPD. The associated ADAM19 and KIT loci have been reported earlier. The remaining 15 genes have also been previously associated to COPD. Differential transcript expression levels of the associated genes in COPD- and/ or mouse emphysematous lung tissues have been detected.

Conclusion

Our findings suggest strategic mouse-human datamining approaches can identify novel COPD candidate genes using existing datasets in the online repositories. The candidates can be further evaluated for mechanistic role through in vitro studies using appropriate primary cells/cell lines. Functional studies can be limited to transgenic animal models of only well supported candidate genes. This approach will lead to a significant reduction of animal experimentation in respiratory research.

Electronic supplementary material

The online version of this article (10.1186/s12931-018-0795-y) contains supplementary material, which is available to authorized users.

African ancestry is associated with cluster-based childhood asthma subphenotypes

BACKGROUND

Childhood asthma is a syndrome composed of heterogeneous phenotypes; furthermore, intrinsic biologic variation among racial/ethnic populations suggests possible genetic ancestry variation in childhood asthma. The objective of the study is to identify clinically homogeneous asthma subphenotypes in a diverse sample of asthmatic children and to assess subphenotype-specific genetic ancestry in African-American asthmatic children.

METHODS

A total of 1211 asthmatic children including 813 in the Childhood Asthma Management Program and 398 in the Childhood Asthma Research and Education program were studied. Unsupervised cluster analysis on clinical phenotypes was conducted to identify homogeneous subphenotypes. Subphenotype-specific genetic ancestry was estimated for 167 African-American asthmatic children. Genetic ancestry association with subphenotypes/clinical phenotypes were determined.

RESULTS

Three distinct subphenotypes were identified: a moderate atopic dermatitis (AD) group with negative skin prick test (SPT) and preserved lung function; a high AD group with positive SPT and airway hyperresponsiveness; and a low AD group with positive SPT and lower lung function. African ancestry at asthma genome-wide association study (GWAS) SNPs differed between subphenotypes (64, 89, and 94% for the three subphenotypes, respectively) and was inversely correlated with AD; each additional 10% increase in African ancestry was associated with 1.5 fold higher in IgE and 6.3 higher odds of positive SPT (all p-values < 0.0001).

CONCLUSIONS

By conducting phenotype-based cluster analysis and assessing subphenotype-specific genetic ancestry, we were able to identify homogeneous subphenotypes for childhood asthma that showed significant variation in genetic ancestry of African-American asthmatic children. This finding demonstrates the utility of these complementary approaches to understand and refine childhood asthma subphenotypes and enable more targeted therapy.

Effect of altering breathing frequency on maximum voluntary ventilation in healthy adults

Background

Compared to other pulmonary function tests, there is a lack of standardization regarding how a maximum voluntary ventilation (MVV) maneuver is performed. Specifically, little is known about the variation in breathing frequency (f_R) and its potential impact on the accuracy of test results. This study examines the effect of several preselected values for f_R and one self-selected f_R (f_Rself) on MVV.

Methods

Ten participants performed MVV maneuvers at various f_R values, ranging from 50 to 130 breaths·min^− 1 in 10 breaths·min^− 1 intervals and at one f_Rself. Three identical trials with 2-min rest periods were conducted at each f_R, and the sequence in which f_R was tested was randomized. Ventilation and related parameters were measured directly by gas exchange analysis via a metabolic measurement system.

Results

A third-order polynomial regression analysis showed that MVV = − 0.0001(f_R)³ + 0.0258(f_R)²–1.38(f_R) + 96.9 at preselected f_R and increased up to approximately 100 breaths·min^− 1 (r² = 0.982, P < 0.001). Paired t-tests indicated that average MVV values obtained at all preselected f_R values, but not f_Rself, were significantly lower than the average maximum value across all participants. A linear regression analysis revealed that tidal volume (V_T) = − 2.63(MVV) + 300.4 at preselected f_R (r² = 0.846, P < 0.001); however, this inverse relationship between V_T and MVV did not remain true for the self-selected f_R. The V_T obtained at this f_R (90.9 ± 19.1% of maximum) was significantly greater than the V_T associated with the most similar MVV value (at a preselected f_R of 100 breaths·min^− 1, 62.0 ± 10.4% of maximum; 95% confidence interval of difference: (17.5, 40.4%), P < 0.001).

Conclusions

This study demonstrates the shortcomings of the current lack of standardization in MVV testing and establishes data-driven recommendations for optimal f_R. The true MVV was obtained with a self-selected f_R (mean ± SD: 69.9 ± 22.3 breaths·min^− 1) or within a preselected f_R range of 110–120 breaths·min^− 1. Until a comprehensive reference equation is established, it is advised that MVV be measured directly using these guidelines. If an individual is unable to perform or performs the maneuver poorly at a self-selected f_R, ventilating within a mandated f_R range of 110–120 breaths·min^− 1 may also be acceptable.

Fluoroscopic Estimation of Thoracic Dimensional Changes in Healthy Dogs

Background

Current methods available for assessing alterations in lung mechanics require sophisticated equipment and are of limited availability. A method that could assess lung area change with respiration might be a clinically useful surrogate for assessing lung compliance.

Objective

To use fluoroscopy to determine percent change in thoracic and lung areas in healthy dogs.

Animals

Forty‐four client‐owned dogs with no evidence of respiratory disease.

Methods

Prospective study. Resting respiration was recorded fluoroscopically, and peak inspiratory and expiratory frames were captured for 3 typical respiratory cycles. The number of intrathoracic pixels in the entire thoracic cavity was measured for both inspiration and expiration, and the average percent change in intrathoracic area was determined for each dog. This process was repeated by a hemithorax measurement of lung area that excluded the mediastinum and cardiac silhouette. Proposed reference ranges (and 95% confidence intervals [CI]) were computed by a nonparametric percentile distribution.

Results

Median percent change in thoracic dimension for the total thorax measurement was 12.5% (CI, 8.9–24.0%). Median percent change for the hemithorax measurement was significantly (P < 0.001) larger (20.8%, CI, 14.3–37.6%). Both measurement techniques were correlated with body weight but not with age, sex, thoracic conformation, body condition score (BCS), or breed.

Conclusions and Clinical Importance

Fluoroscopy allows a noninvasive and repeatable measure of lung area changes during respiration that must be corrected for body weight. Additional studies in dogs with respiratory diseases are needed to determine its utility in detecting clinically useful alterations in lung area changes.

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.