Bowler, Russell P.

Most genetic variants associated with complex traits are hypothesized to regulate gene expression. To understand the genetics underlying gene expression variability, we characterized 14,324 RNA-sequencing samples from the Trans-Omics for Precision Medicine program and performed expression and splicing quantitative trait locus (e/sQTL) analyses in six tissues and cell types, including whole blood ( n = 6454) and lung ( n = 1291). We detected tens of thousands of secondary cis-e/sQTLs, showing that secondary cis-e/sQTL discovery remains unsaturated. We fine-mapped UK Biobank–derived genome-wide association study (GWAS) signals from 164 traits and identified e/sQTL colocalizations for 10,611 GWAS signals, including 7096 that colocalize with secondary e/sQTLs. Our results suggest that even larger e/sQTL analyses will uncover additional secondary e/sQTLs, further benefiting GWAS interpretation.

BACKGROUND We constructed multi-trait polygenic risk scores (PRSs) predicting chronic obstructive pulmonary disease (COPD) and exacerbations, validated their performance in diverse cohorts, and identified PRS-related proteins for potential therapeutic targeting. METHODS PRSmix + , a multi-trait PRS framework, is used to train a composite PRS (PRS multi ) in COPDGene non-Hispanic White participants ( n = 6,647). Associations of PRS multi with COPD status (GOLD 2–4 vs. GOLD 0 or ICD) and exacerbation frequency were tested in COPDGene African American ( n = 2,466), ECLIPSE ( n = 1,858), Mass General Brigham Biobank ( n = 15,152), and All of Us ( n = 118,566). Protein prediction models were applied to GWAS summary statistics from traits contributing to PRS multi and were validated with proteomic data in COPDGene ( n = 5,173) and UK Biobank ( n = 5,012). RESULTS PRSmix + selected 7 traits for PRS multi . In multivariable models, PRS multi was associated with COPD status (meta-analysis random effects [RE] OR 1.58 [95% CI: 1.28–1.94]) and exacerbation frequency (meta-analysis RE β 0.21 [95% CI: 0.11–0.31]), with higher effect sizes observed in smoking-enriched cohorts. PRS multi outperformed traditional single-trait PRS in all tested cohorts. Using protein prediction models, we identified 73 proteins associated with the PRSs that were also validated with measured protein levels in COPDGene and UK Biobank. Of these proteins, 25 were linked to approved or investigational drugs. Notable targets include RAGE/sRAGE, IL1RL1, and SCARF2, all implicated in COPD pathogenesis and exacerbations. CONCLUSIONS Multi-trait PRS improves prediction of COPD and exacerbation risk. Integration with proteomic data identifies druggable protein targets, offering a promising avenue for precision medicine in COPD management. TRIAL REGISTRATION COPDGene: ClinicalTrials.gov NCT00608764; ECLIPSE: ClinicalTrials.gov NCT00292552.

Introduction There is an increased risk of chronic obstructive pulmonary disease (COPD) in heterozygotes for the alpha-1 antitrypsin (AAT) Z allele (PI*MZ), but there is significant variation in outcomes. Matrix metalloproteinases (MMPs) contribute to worse airway disease and emphysema. Given that the AAT protein is an antiprotease, we hypothesised that MMPs play a modifying role among AAT-deficient individuals. Methods We studied PI*MZ (n=39) and PI*ZZ (n=27) individuals from the Genomic Research in Alpha-1 Antitrypsin Deficiency and Sarcoidosis Study cohort. MMP (MMP3, MMP9, MMP10, MMP12 and MMP15) gene expression was assessed in bronchoalveolar lavage cells and peripheral blood mononuclear cells. Plasma protein MMP (MMP3, MMP9, MMP10 and MMP12) expression was assessed using SomaScan and BAL MMP15 protein using ELISA. MMP values were log-transformed, and linear regression analyses were used to assess lung function, patient-reported outcomes and CT emphysema adjusted for age, body mass index, sex and duration of smoking. Results Alveolar MMP3 and MMP15 were uniquely associated with worse lung function, patient-reported outcomes and emphysema among PI*MZ individuals. MMP10 was associated with less disease severity among PI*MZ individuals. Discussion Our study shows that alveolar MMP3 and MMP15 may uniquely contribute to disease among PI*MZ individuals, raising the possibility that they could serve as biomarkers or therapeutic targets in this highly prevalent COPD phenotype. Furthermore, we show that MMP10 may serve a protective effect. In aggregate, these data support further studies of the MMP pathway among lung-affected PI*MZ individuals, as they may serve as biomarkers or pharmacological targets in future studies.

Abstract Rationale Inflammation is central to chronic obstructive pulmonary disease (COPD) pathogenesis but incompletely represented in COPD prognostic models. The neutrophil-to-lymphocyte ratio (NLR) is a readily available inflammatory biomarker. Objectives To explore the associations of NLR with smoking status, clinical features of COPD, and future adverse outcomes. Methods We analyzed NLR calculated from the complete blood count of participants who currently or formerly smoked (n = 2,624) and tobacco-naive control subjects (n = 187) in the SPIROMICS multicenter observational cohort study. We assessed the stability of NLR at 6 weeks and 1 year, the association with select blood biomarkers, and the impact of smoking on NLR and cell counts. We stratified participants by NLR quartiles to compare cross-sectional clinical features at enrollment, prospectively observed exacerbations at 1 year, and mortality during longitudinal follow up. Results Higher NLR quartiles were broadly associated with more severe clinical features of COPD. NLR values were repeatable at 6 weeks (intraclass correlation coefficient, 0.74) and 1 year (intraclass correlation coefficient, 0.62). The impact of smoking on NLR varied with the severity of airflow limitation, mediated by an interaction between smoking, forced expiratory volume in 1 second percent predicted, and neutrophil counts but not lymphocyte counts. The highest NLR quartile (>3.11) was associated with an increased risk of exacerbation over 1 year (adjusted odds ratio, 1.51; 95% confidence interval, 1.18, 1.92) and increased risk of mortality (adjusted hazard ratio, 1.41; 95% confidence interval, 1.20, 1.66) compared with quartiles 1–3. Conclusions Elevated NLR in stable COPD is a widely available biomarker associated with increased risk for exacerbation and death. The impact of cigarette smoking on NLR varies with disease severity.

Abstract Rationale High-attenuation area (HAA) is a computed tomography (CT) tool that correlates with lung inflammation and fibrosis. Systemic molecular correlates of HAA (e.g., plasma proteins) may inform biological processes involved in interstitial lung disease. Objectives To identify plasma proteins that associate with HAA and correlate with a higher probability of developing new-onset fibrotic or subpleural interstitial lung abnormalities (ILAs). Methods Plasma protein levels were measured using a semiquantitative aptamer-based platform in MESA (the Multi-Ethnic Study of Atherosclerosis; N = 5,486) and SPIROMICS (Subpopulations and Intermediate Outcome Measures in COPD Study; N = 1,781). Linear regression models identified HAA-associated proteins after adjustment for demographic and socioeconomic factors, CT scanner parameters, study center, and batch. Associations of HAA-related proteins with new-onset fibrotic or subpleural ILAs were examined in MESA participants with ILA assessments on full-lung CT 10 years later. Immunohistochemical staining of select proteins was performed in lung tissue from pulmonary fibrosis cases. Measurements and Main Results There were 75 proteins detected that were significantly associated with HAA in MESA and SPIROMICS. Gene Ontology analysis of these proteins identified processes involved in immune cell chemotaxis and cellular growth and apoptosis. Seven proteins were associated with a higher probability of new-onset fibrotic or subpleural ILAs in MESA, and two of these, junctional adhesion molecule-like protein and GTP cyclohydrolase 1 feedback regulatory protein, stained in areas of fibrosis in lung tissue from patients with interstitial lung disease. Conclusions Plasma proteins associated with more HAA are involved in immune and cellular processes and associate with new-onset fibrotic-subpleural ILA.

Abstract Introduction Resilient smokers, who maintain respiratory health despite smoking, remain poorly characterized. Airway epithelial cell gene expression in resilient smokers can provide insight into mechanisms and pathways that may protect smokers from developing smoking-related lung disease. The objective of this study is to identify genes and potential pathways associated with lung-related resilience. Methods Resilient smokers were defined based on a previously published multi-dimensional definition which includes the absence of: 1) spirometric airflow limitation, 2) symptoms (cough/sputum, dyspnea), 3) radiographic (HRCT) abnormalities, 4) exacerbations, and 5) an accelerated FEV1 decline. “Non-resilient” smokers had preserved spirometry but showed abnormalities in at least one domain of resilience. We analyzed airway epithelial brush samples from 21 resilient and 34 non-resilient smokers from SPIROMICS. Differential gene expression was performed using DESeq2 package in R, which estimates differential expression using generalized linear models. We adjusted for sequencing batch, age (continuous), race, gender, and current smoking status. While controlling for these covariates we evaluated differential gene expression between resilient and non-resilient smokers, the interaction between resilience and smoking status, and in each sub-category of resilient (absence of symptoms, radiographic abnormalities, exacerbations, and accelerated decline in FEV1). Results We identified 98 genes that were differentially expressed (FDR ≤0.1) when comparing resilient to non-resilient smokers, 20 of those genes were up regulated in resilient smokers (Figure 1). Notable genes included cadherin-12 (CDH12), aspartate beta-hydroxylase (ASPH), and protein kinase AMP-activated alpha 2 (PRKAA2). CDH12 is involved in cell adhesion and epithelial integrity. ASPH influences cell adhesion and signaling. PRKAA2 plays role in cellular homeostasis and stress response, which may be altered in non-resilient smokers, affecting cellular metabolism and inflammation. BPI folding containing family A member (BPIFA1) was significantly associated with smoking status in the interaction analysis, suggesting its role in modulating the impact of smoking on resilience. BPIFA1 has anti-microbial properties, regulates immune responses, and contributes mucosal surface protection. Sub-category analysis identified 17 genes associated with resilience to symptoms and 2 genes related to physiologic resilience (FEV1 decline), though no significant genes were associated with radiographic or exacerbation resilience. Conclusion Differential gene expression of airway epithelial cells identified distinct expression patterns between resilient and non-resilient smokers. Specifically, genes associated with epithelial cell adhesion, signaling, and cellular homeostasis were up regulated in resilient smokers. These findings suggest that resilient smokers may have transcriptomic profiles and potential mechanisms that mitigate the effects of cigarette smoke.

Abstract Chronic obstructive pulmonary disease (COPD) and pulmonary emphysema were the third-leading cause of death globally in 2019. Besides alpha-1 antitrypsin deficiency, emphysema lacks disease-modifying medications due to its heterogeneity and there remains a need to further investigate emphysema subtypes to advance its diagnosis and treatment. Recent unsupervised machine learning of the texture and anatomical location of emphysema on computed tomography (CT) images of the lung defined six quantitative CT emphysema subtypes uniquely associated with specific gene variants, environmental exposures, symptoms, physiology and clinical events. We aim to identify associations of plasma proteins with each CT emphysema subtype cross-sectionally in a multi-ethnic general population sample. MESA is a prospective cohort study that recruited 6,814 participants from six communities who self-identified as White, Black, Hispanic, or Asian race/ethnicity, ages 45-84 years old and free of clinical cardiovascular disease in 2000-02. The MESA Lung Study performed CT scans among 3,137 participants in 2010-12, which were labeled with previously described (PMID: 37268414) CT emphysema subtypes. Proteomics was assessed using SomaScan version 4.1 assay (7,596 plasma proteins). Linear regression models were adjusted for age, height, weight, sex, race, educational attainment, smoking status, pack years, urine cotinine level, body-mass index (BMI), estimated glomerular filtration rate (eGFR), CT scanner manufacturer and other CT emphysema subtypes. Results were adjusted to reflect a False Discovery Rate (FDR) p-value of less than 5% using the Benjamini-Hochberg method. Among 2,343 participants with both CT and proteomic data (mean age 69.5 years, 52.3% women, 23.7% with COPD), we identified statistically significant associations of proteins with the vanishing lung subtype (42 proteins; top hit Natural cytotoxicity triggering receptor 3 ligand 1, q = 2.9[asterisk]10-9), restrictive combined pulmonary fibrosis/emphysema (CPFE) subtype (11 proteins; top hit Integrin alpha-2/b1, q=1.0[asterisk]10-5), the combined bronchitis-apical emphysema subtype (9 proteins; top hit Desmoglein-2, q=8.8[asterisk]10-13), and the diffuse emphysema subtype (4 proteins; top hit Pulmonary surfactant-associated protein D, q=5.7[asterisk]10-3). No significant proteins were associated with the obstructive CPFE or senile subtypes after FDR correction. Most proteins were uniquely associated with one CT emphysema subtype, while a few proteins were associated with more than one subtype. This study identified specific proteins for different CT emphysema subtypes, many of which have been related less specifically to emphysema, including pulmonary surfactant production, anti-inflammatory pathways, and mitochondrial deregulation, amongst others. Validation of these proteomic associations can provide insight into further pathway assessment, clinical biomarker discovery, and targeted prevention of emphysema in the general population.

Abstract RATIONALE The best described endotype of COPD is alpha-1 antitrypsin (AAT) deficiency, which is due to a genetic abnormality in the SERPINA1 gene. Homozygotes for the Z allele (PI[asterisk]ZZ individuals) carry the genotype most commonly associated with severe AAT deficiency, but a highly prevalent endotype is the heterozygous state (PI[asterisk]MZ individuals). Here we test the hypothesis that individuals with PI[asterisk]MZ genotype are at higher risk for COPD exacerbation and healthcare utilization compared to those with no pathogenic variants in the SERPINA1 gene (PI[asterisk]MM individuals). METHODS Real-world data on 4,456 individuals with available AAT genotyping were extracted from the Cleveland Clinic Health System (CCHS) electronic health records (EHR) and analyzed to compare the risk of moderate COPD exacerbation (defined as a short-term steroid prescription), all-cause emergent care (defined as an express care visit, urgent care visit, or emergency department visit), and all-cause hospitalization between individuals with PI[asterisk]MZ vs. PI[asterisk]MM genotypes. Cox proportional hazards models were used to adjust for age, sex, race, BMI, smoking status, comorbidity count, liver disease diagnosis, and median income by zip code.To assess the effect of AAT levels on outcomes, we categorized participants into three groups based on AAT level and used 90 mg/dL as a threshold given it is the lower limit of the normal reference range and genotype: MM individuals with an AAT level >90 mg/dL, MZ >90 mg/dL and MZ <90 mg/dL. To assess the effect of PI[asterisk]MZ genotype among individuals with pre-existing lung disease, we performed a subgroup analysis of individuals with at least a six-month inhaler prescription. RESULTS In this cohort, 308 individuals had a PI[asterisk]MZ genotype. PI[asterisk]MZ was associated with increased risk for moderate COPD exacerbations (adjusted HR [95% CI]: 1.66 [1.27, 2.17]) and hospitalizations (adjusted HR [95% CI]: 1.44 [1.19, 1.75]) compared to PI[asterisk]MM. The risk of hospitalization was higher among PI[asterisk]MZ individuals with AAT levels <90 mg/dL (adjusted HR [95% CI]: 1.59 [1.14, 2.23]) but not in those with AAT levels >90 mg/dL, as compared to PI[asterisk]MM. Sensitivity analysis in those treated with inhaler therapy showed overall similar results. CONCLUSIONS Increased hospitalizations and moderate COPD exacerbations among PI[asterisk]MZ individuals compared to PI[asterisk]MM individuals merit future prospective studies to better characterize the longitudinal course and healthcare utilization among those with an PI[asterisk]MZ genotype. Given the high prevalence of these carriers globally, PI[asterisk]MZ represents a COPD phenotype that invites additional investigation to identify biomarkers of worse disease and treatable traits.

Abstract Rationale: Individuals with chronic obstructive pulmonary disease (COPD) have different clinical trajectories, some with minimal symptom burden, others experiencing recurrent exacerbations, the most severe of which require hospitalization. Existing diagnostics, including spirometry and symptom assessments, lack the precision to identify high-risk patients who may benefit from timely preventive therapies. Nuclear cell-free DNA (ncfDNA) is a well-established marker of systemic tissue injury, implicated in amplifying inflammation by triggering type 1 interferon release by activating DNA-sensing pathways. Because COPD is accompanied by inflammation and tissue injury systemically, we hypothesized that ncfDNA is associated with increased risk of severe exacerbations requiring hospitalization. Methods: Design: We utilized baseline plasma samples randomly selected from 672 individuals with COPD from the Subpopulations and Intermediate Outcomes Measures in COPD Study (SPIROMICS) cohort, which prospectively collected exacerbation numbers and type. The primary endpoint was exacerbation requiring hospitalization. Secondary endpoints included total number of exacerbations (defined as use of oral steroids, antibiotics, or healthcare utilization) and severe exacerbations (defined as requiring emergency room care or hospitalization). Measure: We measured plasma ncfDNA using digital droplet PCR. Analysis: We assessed the association of ncfDNA with exacerbation outcomes using negative binomial regression or Cox regression, adjusting for age, percent post-bronchodilator forced expiratory volume in one second (FEV1), supplemental oxygen use, and smoking status. Results: In total, 57% (n=383) of COPD participants experienced exacerbations, 29% (n=197) at least one severe, and 22% (n=145) requiring hospitalization, the latter at a median of 622 days from enrollment (IQR=287-997). Higher ncfDNA levels at enrollment correlated with measures of COPD severity, including baseline FEV1 (beta = -0.12, 95% CI -0.18 to -0.049, p <0.001). Higher ncfDNA associated with increased risk of COPD exacerbation requiring hospitalization (incidence rate ratio (IRR) 1.40, 95% CI 1.12-1.75, p =0.003) and severe exacerbations (IRR 1.36, 95% CI 1.11-1.67, p=0.002) and a trend towards total exacerbations (IRR 1.11, 95% CI 0.98-1.26, p= 0.09). The primary outcome, risk of time-to-first hospitalization, correlated significantly with higher ncfDNA with hazard ratio (HR) 1.23, 95% CI 1.01-1.49, p=0.037. Conclusion: These results suggest that ncfDNA may serve as a predictor for severe and hospitalization-associated COPD exacerbations. To better understand the relationship between ncfDNA and COPD pathophysiology, follow-up studies should explore longitudinal trends and cfDNA tissue sources, and their link to COPD exacerbations.

Background: Thrombo-inflammation is a hallmark of acute Covid-19, with higher thrombo-inflammatory markers during infection associated with adverse outcomes. We hypothesized that higher pre-pandemic biomarkers, reflecting a higher thrombo-inflammatory setpoint, might identify people at greater risk of severe manifestations of Covid-19. Hypothesis: Pre-pandemic inflammation markers are associated with risk of hospitalized or fatal (hereafter, “severe”) Covid-19 in a multi-ethnic US sample. Methods: From 2020-2023, C4R harmonized pre-pandemic measures and ascertained Covid-19 across 14 longstanding cohort studies. In 12 cohorts, we assessed biomarker data and covariates from the study visit closest to the pandemic for 6 analytes shown in the Table. HRs of severe Covid-19 by pre-pandemic biomarkers were estimated using cause-specific Cox regression, treating non-severe Covid-19 as a competing risk, and adjusting for pre-pandemic sociodemographic and clinical characteristics. Results: Biomarkers were measured a mean of 20 years before the pandemic with different sample sizes for each (Table footnote). Mean age at the start of the pandemic was in the 60s or 70s depending on the biomarker. The most represented race or ethnic groups were White and Black. The largest sample was for C-reactive protein, and there were 1,001 severe Covid-19 cases among 38,784 participants. In the adjusted models, considered individually, higher CRP, leukocyte count, factor VIII and fibrinogen, but not other markers, were associated with greater risk of severe Covid-19 (Table).Associations were robust across subgroups and time since biomarker measurement (example for C-reactive protein in Figure). Conclusions: In this prospective multi-study analysis of a multi-ethnic population, higher basal levels of thrombo-inflammation markers were associated with greater risk of severe Covid-19. Since we considered non-severe Covid-19 as a competing risk, associations may reflect factors related to progression to more serious Covid-19 illness.