A Between Ethnicities Comparison of Chronic Obstructive Pulmonary Disease Genetic Risk

RARB genetic variants might contribute to the risk of chronic obstructive pulmonary disease based on a case-control study

BACKGROUND

Chronic obstructive pulmonary disease (COPD) is a progressive respiratory disease that severely impairs patients' respiratory function and quality of life. RARB is involved in COPD progression by affecting inflammatory reactions, cell proliferation, and apoptosis. The impact of single nucleotide polymorphisms (SNPs) within RARB on COPD susceptibility remains unclear. Here, we aimed to evaluate the association between RARB SNPs and COPD risk.

METHODS

A total of 270 COPD patients and 271 healthy controls were enrolled. The MassARRAY iPLEX platform tested the genotype of the SNPs. The association was analyzed using logistic regression analysis. The false-positive report probability (FPRP) analysis was performed to validate the significant findings. The relationship between SNPs and RARB expression was evaluated using the GTEx database.

RESULTS

Our study found a significant association between rs6799734 and COPD susceptibility (OR 1.88, p = 0.008, p (FDR) = 0.047). The stratified analysis revealed that this association was particularly pronounced among individuals aged ≤ 71 years (OR 2.34, p = 0.011, p (FDR) = 0.045), males (OR 2.60, p = 0.002, p (FDR) = 0.013), those with a BMI ≥ 24 (OR 3.95, p = 0.018, p (FDR) = 0.108), and smokers (OR 2.48, p = 0.020, p (FDR) = 0.120). Additionally, rs1286641 and rs1881706 showed significant associations with COPD risk in females and smokers. These associations were further validated by FPRP analysis. Preliminary mechanism studies indicated that rs1286641 and rs1881706 were related to RARB expression.

CONCLUSION

Our findings suggest a potential role of RARB SNPs in influencing COPD risk.

Much Lower Prevalence and Mortality of Chronic Obstructive Pulmonary Disease in Japan Than in the United States Despite Higher Smoking Rates: A Meta-Analysis/Systematic Review

BACKGROUND

A recent systematic review showed Japan's mortality from chronic obstructive pulmonary disease (COPD) is the lowest among 204 countries, despite notably higher smoking rates in men in Japan than in the United States. This study aims to compare (1) trends in smoking rates, (2) trends in COPD mortality, and (3) the spirometry-based COPD prevalence in the general adult population between Japan and the United States.

METHODS

Age- and sex-specific smoking rates from the 1980s through 2010s and COPD mortality from 1999 through 2019 were obtained from national surveys and official statistics (International Classification of Diseases-10th codes J40-44), respectively. A systematic review and meta-analysis was performed to estimate COPD prevalence in Japan, while the National Health and Nutrition Examination Survey 2007-2012 was used for the United States. A fixed ratio of 0.7 of forced expiratory volume in the first second of forced vital capacity was used to define COPD.

RESULTS

Over the past 4 decades, men in Japan consistently had 20-30% higher smoking rates than their United States counterparts. From 1999-2019, age-adjusted COPD mortality in men in Japan was only a third of the United States, whereas that in women was less than a tenth in 2019. Synthesizing data from 11 studies, involving 89,955 participants, Japan's COPD prevalence was more than 10% lower than in the United States in almost all age groups for both sexes.

CONCLUSION

This study showed markedly lower rates of COPD in Japan than in the United States. Investigating factors contributing to the paradoxical observations could lead to advancing COPD risk reduction strategies.

Screening the Best Risk Model and Susceptibility SNPs for Chronic Obstructive Pulmonary Disease (COPD) Based on Machine Learning Algorithms

Background and Purpose

Chronic obstructive pulmonary disease (COPD) is a common and progressive disease that is influenced by both genetic and environmental factors, and genetic factors are important determinants of COPD. This study focuses on screening the best predictive models for assessing COPD-associated SNPs and then using the best models to predict potential risk factors for COPD.

Methods

Healthy subjects (n=290) and COPD patients (n=233) were included in this study, the Agena MassARRAY platform was applied to genotype the subjects for SNPs. The selected sample loci were first screened by logistic regression analysis, based on which the key SNPs were further screened by LASSO regression, RFE algorithm and Random Forest algorithm, and the ROC curves were plotted to assess the discriminative performance of the models to screen the best prediction model. Finally, the best prediction model was used for the prediction of risk factors for COPD.

Results

One-way logistic regression analysis screened 44 candidate SNPs from 146 SNPs, on the basis of which 44 SNPs were screened or feature ranked using LASSO model, RFE-Caret, RFE-Lda, RFE-lr, RFE-nb, RFE-rf, RFE-treebag algorithms and random forest model, respectively, and obtained ROC curve values of 0.809, 0.769, 0.798, 0.743, 0.686, 0.766, 0.743, 0.719, respectively, so we selected the lasso model as the best model, and then constructed a column-line graph model for the 25 SNPs screened in it, and found that rs12479210 might be the potential risk factors for COPD.

Conclusion

The LASSO model is the best predictive model for COPD and rs12479210 may be a potential risk locus for COPD.

The genomic landscape of chronic obstructive pulmonary disease: Insights from nutrigenomics

Chronic obstructivе pulmonary disеasе (COPD), a rеspiratory disеasе, is influenced by a combination of gеnеtic and еnvironmеntal factors. Thе fiеld of nutrigеnomics, which studiеs thе intеrplay bеtwееn diеt and gеnеs, provides valuable insights into thе gеnomic landscapе of COPD and its implications for production and managеmеnt. This rеviеw providеs a comprеhеnsivе ovеrviеw of thе gеnеtic aspеcts of COPD and thе rolе of nutrigеnomics in advancing our undеrstanding of thе undеrlying mеchanisms. Through studies of gеnomе-widе associations, researchers have identified gеnеtic factors that contribute to suscеptibility to COPD. Thеsе gеnеs arе associatеd with oxidativе strеss, inflammation, and antioxidant dеfеnsе mеchanisms. Nutrigеnomics rеsеarch is currеntly invеstigating how diеtary componеnts interact with gеnеtic variations to modulatе thе dеvеlopmеnt of COPD. Antioxidants, omеga-3 fatty acids and vitamin D havе dеmonstratеd potеntial bеnеfits in rеducing inflammation, improving lung function, and minimizing еxacеrbations in patients with COPD. Therefore, there are sеvеral challеngеs that must be added to the nutrigеnomic rеsеarch. The challenges include thе nееd for largеr clinical trials, adding hеtеrogеnеity and validating biomarkеrs. In the tеrms of futurе dirеctions, prеcision nutrition, gеnе-basеd thеrapiеs, biomarkеr dеvеlopmеnt, intеgration of multi-omics data, systеms biology analysis, longitudinal studiеs, and public hеalth implications arе important arеas to еxplorе. Pеrsonalizеd nutritional intеrvеntions based on an individual's gеnеtic profilе hold grеat promisе for optimizing COPD managеmеnt. In conclusion, nutrigеnomics provides valuable insights into the gеnomic landscapе of COPD and its intеraction with the disease. This knowlеdgе can guidе thе dеvеlopmеnt of pеrsonalizеd diеtary stratеgiеs and gеnе-basеd thеrapiеs for thе prеvеntion and managеmеnt of COPD. Howеvеr, morе rеsеarch is nееdеd to validatе thеsе findings, dеvеlop еffеctivе intеrvеntions, and implеmеnt thеm еffеctivеly in clinical practicе to improvе thе quality of lifе for pеoplе with COPD.

Prediction and stratification of longitudinal risk for chronic obstructive pulmonary disease across smoking behaviors

Smoking is the leading risk factor for chronic obstructive pulmonary disease (COPD) worldwide, yet many people who never smoke develop COPD. We perform a longitudinal analysis of COPD in the UK Biobank to derive and validate the Socioeconomic and Environmental Risk Score which captures additive and cumulative environmental, behavioral, and socioeconomic exposure risks beyond tobacco smoking. The Socioeconomic and Environmental Risk Score is more predictive of COPD than smoking status and pack-years. Individuals in the highest decile of the risk score have a greater risk for incident COPD compared to the remaining population. Never smokers in the highest decile of exposure risk are more likely to develop COPD than previous and current smokers in the lowest decile. In general, the prediction accuracy of the Social and Environmental Risk Score is lower in non-European populations. While smoking status is often considered in screening COPD, our finding highlights the importance of other non-smoking environmental and socioeconomic variables.

Prediction and stratification of longitudinal risk for chronic obstructive pulmonary disease across smoking behaviors

Smoking is the leading risk factor for chronic obstructive pulmonary disease (COPD) worldwide, yet many people who never smoke develop COPD. We hypothesize that considering other socioeconomic and environmental factors can better predict and stratify the risk of COPD in both non-smokers and smokers. We performed longitudinal analysis of COPD in the UK Biobank to develop the Socioeconomic and Environmental Risk Score (SERS) which captures additive and cumulative environmental, behavioral, and socioeconomic exposure risks beyond tobacco smoking. We tested the ability of SERS to predict and stratify the risk of COPD in current, previous, and never smokers of European and non-European ancestries in comparison to a composite genome-wide polygenic risk score (PGS). We tested associations using Cox regression models and assessed the predictive performance of models using Harrell's C index. SERS (C index = 0.770, 95% CI 0.756 to 0.784) was more predictive of COPD than smoking status (C index = 0.738, 95% CI 0.724 to 0.752), pack-years (C index = 0.742, 95% CI 0.727 to 0.756). Compared to the remaining population, individuals in the highest decile of the SERS had hazard ratios (HR) = 7.24 (95% CI 6.51 to 8.05, P < 0.0001) for incident COPD. Never smokers in the highest decile of exposure risk were more likely to develop COPD than previous and current smokers in the lowest decile with HR=4.95 (95% CI 1.56 to 15.69, P=6.65×10-3) and 2.92 (95%CI 1.51 to 5.61, P=1.38×10-3), respectively. In general, the prediction accuracy of SERS was lower in the non-European populations compared to the European evaluation set. In addition to genetic factors, socioeconomic and environmental factors beyond smoking can predict and stratify COPD risk for both non- and smoking individuals. Smoking status is often considered in screening; other non-smoking environmental and non-genetic variables should be evaluated prospectively for their clinical utility.

De novo discovery of traits co-occurring with chronic obstructive pulmonary disease

Chronic obstructive pulmonary disease (COPD) is a heterogeneous group of chronic lung conditions. Genome-wide association studies have identified single-nucleotide polymorphisms (SNPs) associated with COPD and the co-occurring conditions, suggesting common biological mechanisms underlying COPD and these co-occurring conditions. To identify them, we have integrated information across different biological levels (i.e., genetic variants, lung-specific 3D genome structure, gene expression and protein-protein interactions) to build lung-specific gene regulatory and protein-protein interaction networks. We have queried these networks using disease-associated SNPs for COPD, unipolar depression and coronary artery disease. COPD-associated SNPs can control genes involved in the regulation of lung or pulmonary function, asthma, brain region volumes, cortical surface area, depressed affect, neuroticism, Parkinson's disease, white matter microstructure and smoking behaviour. We describe the regulatory connections, genes and biochemical pathways that underlay these co-occurring trait-SNP-gene associations. Collectively, our findings provide new avenues for the investigation of the underlying biology and diverse clinical presentations of COPD. In so doing, we identify a collection of genetic variants and genes that may aid COPD patient stratification and treatment.

Particle radioactivity from radon decay products and reduced pulmonary function among chronic obstructive pulmonary disease patients

BACKGROUND

Radon (222Rn) decay products can attach to particles in the air, be inhaled, and potentially cause airway damage.

RESEARCH QUESTION

Is short-term exposure to particle radioactivity (PR) attributable to radon decay products emitted from particulate matter ≤2.5 μm in diameter (PM2.5) associated with pulmonary function in chronic obstructive pulmonary disease (COPD) patients?

STUDY DESIGN AND METHODS

In this cohort study, 142 elderly, predominantly male patients with COPD from Eastern Massachusetts each had up to 4 one-week long seasonal assessments of indoor (home) and ambient (central site) PR and PM2.5 over the course of a year (467 assessments). Ambient and indoor PR were measured as α-activity on archived PM2.5 filter samples. Ratios of indoor/ambient PR were calculated, with higher ratios representing PR from an indoor source of radon decay. We also considered a measure of outside air infiltration that could dilute the concentrations of indoor radon decay products, the indoor/ambient ratio of sulfur concentrations in PM2.5 filter samples. Spirometry pre- and post-bronchodilator (BD) forced expiratory volume in 1 s (FEV1) and forced vital capacity (FVC) were conducted following sampling. Generalized additive mixed models were adjusted for meteorologic variables, seasonality, and individual-level determinants of pulmonary function. We additionally adjusted for indoor PM2.5 and black carbon (BC).

RESULTS

PR exposure metrics indicating radon decay product exposure from an indoor source were associated with a reduction in FEV1 and FVC. Patients in homes with high indoor PR (≥median) and low air infiltration (

INTERPRETATION

Our findings raise concern about the harmful effects of PR exposures attributable to residential radon on pulmonary function in patients with COPD.

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Key Words

• Chronic obstructive pulmonary disease
• Particle radioactivity
• Pulmonary function
• Radiation
• Radon
• Spirometry

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MESH Headings

• Humans
• Male
• Aged
• Female
• Radon Daughters
• Air Pollutants/analysis
• Radioactivity
• Cohort Studies
• Particulate Matter/analysis
• Pulmonary Disease, Chronic Obstructive
• Soot
• Radon
• Environmental Exposure/analysis

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Grants

• R01 ES019853 NIEHS NIH HHS
• R21 ES029637 NIEHS NIH HHS

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Affiliation(s)

Veronica A Wang Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
Petros Koutrakis Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
Longxiang Li Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
Man Liu Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
Carolina L Z Vieira Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
Brent A Coull Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
Edward F Maher Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
Choong-Min Kang Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
Eric Garshick Pulmonary, Allergy, Sleep and Critical Care Medicine Section, Veterans Affairs Boston Healthcare System, Boston, MA, USA; Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA.

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Polygenic scores for low lung function and the future risk of adverse health outcomes

Aims

Reduced lung function and adverse health outcomes are often observed. This study characterizes genetic susceptibility for reduced lung function and risk of developing a range of adverse health outcomes.

Methods

We studied 27,438 middle-aged adults from the Malmö Diet and Cancer study (MDCS), followed up to 28.8 years. Trait-specific Polygenic scores (PGS) for forced expiratory volume in 1 s (FEV₁) and forced vital capacity (FVC) were constructed for each participant using MDCS genetic data and summary statistics from the latest GWAS of lung function. Linear regression models and cox proportional hazards regression models were used to assess associations between adverse health outcomes and lung function-PGS.

Results

FEV₁-PGS and FVC-PGS were significantly associated with mean sBP at baseline after adjustments (FEV₁-PGS Q1 (highest PGS = highest lung function): 140.7mmHg vs. Q4: 141.5mmHg, p-value 0.008). A low FVC-PGS was significantly associated with the risk of future diabetic events after adjustments (Q4 vs. Q1 HR: 1.22 (CI 1.12–1.32), p-trend < 0.001) and had added value to risk prediction models for diabetes. Low FEV₁-PGS was significantly associated with future coronary events (Q4 vs. Q1 HR: 1.13 (CI: 1.04–1.22), p-trend 0.008). No significant association was found between PGS and sudden cardiac death, chronic kidney disease or all-cause mortality. Results remained largely unchanged in a subgroup of subjects when further adjusted for apolipoproteins.

Conclusion

Genetic susceptibility for reduced lung function is associated with higher sBP, increased risk of diabetes and to a lesser extent, future coronary events, suggesting etiological roles of lung function on these outcomes. Using PGS, high-risk groups could be early detected to implement early lifestyle changes to mitigate the risk.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12933-022-01661-y.

Role of an unclassified Lachnospiraceae in the pathogenesis of type 2 diabetes: a longitudinal study of the urine microbiome and metabolites

Recent investigations have revealed that the human microbiome plays an essential role in the occurrence of type 2 diabetes (T2D). However, despite the importance of understanding the involvement of the microbiota throughout the body in T2D, most studies have focused specifically on the intestinal microbiota. Extracellular vesicles (EVs) have been recently found to provide important evidence regarding the mechanisms of T2D pathogenesis, as they act as key messengers between intestinal microorganisms and the host. Herein, we explored microorganisms potentially associated with T2D by tracking changes in microbiota-derived EVs from patient urine samples collected three times over four years. Mendelian randomization analysis was conducted to evaluate the causal relationships among microbial organisms, metabolites, and clinical measurements to provide a comprehensive view of how microbiota can influence T2D. We also analyzed EV-derived metagenomic (N = 393), clinical (N = 5032), genomic (N = 8842), and metabolite (N = 574) data from a prospective longitudinal Korean community-based cohort. Our data revealed that GU174097_g, an unclassified Lachnospiraceae, was associated with T2D (β = −189.13; p = 0.00006), and it was associated with the ketone bodies acetoacetate and 3-hydroxybutyrate (r = −0.0938 and −0.0829, respectively; p = 0.0022 and 0.0069, respectively). Furthermore, a causal relationship was identified between acetoacetate and HbA1c levels (β = 0.0002; p = 0.0154). GU174097_g reduced ketone body levels, thus decreasing HbA1c levels and the risk of T2D. Taken together, our findings indicate that GU174097_g may lower the risk of T2D by reducing ketone body levels.

A microbe that may help protect against type II diabetes has been detected by examining extracellular vesicles (EVs), tiny membrane-wrapped packages secreted by human cells and by the bacteria making up the microbiome. Examining EVs allows researchers to sample microbial populations other than the intensively studied intestinal microbiome. Sungho Won, Seoul National University, and Geum-Sook Hwang, Korea Basic Science Institute, Seoul, and coworkers studied the microbial EVs in urine samples collected from South Korean subjects over four years. They identified a previously unclassified bacterial species in the family Lachnospiraceae that was associated with lower risk of developing type II diabetes. Further investigation showed that these bacteria may break down ketone bodies, metabolic byproducts that signal disrupted sugar metabolism leading to diabetes. These results contribute to understanding how the microbiome contributes to metabolic health and disease.

Genetic Factors Associated with COPD Depend on the Ancestral Caucasian/Amerindian Component in the Mexican Population

Genetic variability influences the susceptibility to and severity of complex diseases; there is a lower risk of COPD in Hispanics than in non-Hispanic Caucasians. In this study, we included 830 Mexican-Mestizo subjects; 299 were patients with COPD secondary to tobacco smoking, and 531 were smokers without COPD. We employed a customized genotyping array of single nucleotide polymorphisms (SNPs). The population structure was evaluated by principal component analysis and allele association through a logistic regression model and haplotype identification. In this study, 118 individuals were identified with a high Caucasian component and 712 with a high Amerindian component. Independent of the ancestral contribution, two SNPs were associated with a reduced risk (p ≤ 0.01) of developing COPD in the CYP2A6 (rs4105144) and CYP2B6 (rs10426235) genes; however, a haplotype was associated with an increased risk of COPD (p = 0.007, OR = 2.47) in the CHRNA5-CHRNA3 loci among smokers with a high Caucasian component. In Mexican-Mestizo smokers, there are SNPs in genes that encode proteins responsible for the metabolism of nicotine associated with a lower risk of COPD; individuals with a high Caucasian component harboring a haplotype in the CHRNA5-CHRNA3 loci have a higher risk of suffering from COPD.

Understanding racial differences of COPD patients with an ecological model: two large cohort studies in the US and Korea

Background

There are limited data about the racial difference in the characteristics of chronic obstructive pulmonary disease (COPD) patients who are treated at clinics. We aimed to compare sociodemographic and clinical characteristics between US and Korean COPD patients using large-scale nationwide COPD cohorts.

Methods

We used the baseline demographic and clinical data of COPD patients aged 45 years or older with at least a 10 pack-per year smoking history from the Korean COPD Subtype Study (KOCOSS, n = 1686) cohort (2012-2018) and phase I (2008-2011) of the US Genetic Epidemiology of COPD (COPDGene) study (n = 4477, 3461 were non-Hispanic whites [NHW], and 1016 were African Americans [AA]).

Results

Compared to NHW, AA had a significantly lower adjusted prevalence ratio (aPR) of cough >3 months (aPR: 0.67; 95% CI [confidence interval]: 0.60-0.75) and phlegm >3 months (aPR: 0.78, 95% CI: 0.70-0.86), but higher aPR of dyspnea (modified Medical Round Council scale ⩾2) (aPR: 1.22; 95% CI: 1.15-1.29), short six-minute walk distance (<350 m) (aPR: 1.98; 95% CI: 1.81-2.14), and poor quality of life (aPR: 1.10; 95% CI: 1.05-1.15). Compared to NHW, Koreans had a significantly lower aPR of cough >3 months (aPR: 0.53; 95% CI: 0.47-0.59), phlegm >3 months (aPR: 0.75; 95% CI: 0.67-0.82), dyspnea (aPR: 0.72; 95% CI: 0.66-0.79), and moderate-to-severe acute exacerbation in the previous year (aPR: 0.73; 95% CI: 0.65-0.82). NHW had the highest burden related to chronic bronchitis symptoms and cardiovascular diseases related to comorbidities.

Conclusion

There are substantial differences in sociodemographic characteristics, clinical presentation, and comorbidities between COPD patients from the KOCOSS and COPDGene, which might be caused by interactions between various intrapersonal, interpersonal, and environmental factors of the ecological model. Thus, a broader and more comprehensive approach would be necessary to understand the racial differences of COPD patients.

Integrated genetic and epigenetic analyses uncover MSI2 association with allergic inflammation

BACKGROUND

The relationship between allergic and eosinophilic inflammation, either systemic or local, in allergic diseases remains unclear.

OBJECTIVE

We performed combined genome-wide association study (GWAS) and epigenome-wide (EWAS) for atopy and tissue eosinophilia to identify both genetic and epigenetic signatures between systemic and local allergic inflammation, and to capture global patterns of gene regulation.

METHODS

We included 126 subjects for atopy analysis and 147 for tissue eosinophilia analysis, as well as 18 normal nasal tissue samples. We identified differentially methylated positions (DMPs) and genes associated with atopy and tissue eosinophilia. Furthermore, we performed mendelian randomization analysis and penalized regression along with replication in an independent cohort.

RESULTS

EWAS identified genes, including Musashi RNA binding protein 2 (MSI2), associated with atopy, which contained enriched DMPs that genetically affect atopy. A direct association was observed between MSI2 single-nucleotide polymorphisms and atopy, as was a causal effect of changes in MSI2 expression and methylation on atopy, which was replicated in a Costa Rican population. Regarding tissue eosinophilia, EWAS identified genes with enriched DMPs directly contributing to tissue eosinophilia at the gene level, including CAMK1D. The gene ontology terms of the identified genes for both phenotypes encompassed immune-related terms.

CONCLUSION

EWAS combined with GWAS identified novel candidate genes, especially the methylation of MSI2, contributing to systemic allergic inflammation. Certain genes displayed a greater association with either systemic or local allergic inflammation; however, it is expected that a harmonized effect of these genes influences immune responses.