Christenson, S A

Abstract Rationale Mismatch of airway to lung size has been implicated in chronic obstructive pulmonary disease (COPD) pathophysiology, whether arising from disproportioned growth or from acquired pathologies over the life course. Lower airway-to-lung ratio (ALR), assessed reproducibly via computed tomography (CT) as the mean airway lumen diameters (trachea-to-subsegments) divided by the cubed root of lung volume, is associated with COPD risk and mortality (all-cause, respiratory, cardiovascular, lung cancer). We sought to characterize the airway biology associated with lower ALR by profiling bronchial gene expression across current and former smokers. Methods We leveraged clinical, radiologic, and bronchial epithelial RNA sequencing data from the SPIROMICS (SubPopulations and Intermediate Outcomes Measures in COPD Study) Phase 1 Bronchoscopy Sub-study (n = 161). To analyze transcriptional differential expression (DE) between participants based on CT-assessed ALR, we utilized DESeq2 and then identified impacted pathways by Ingenuity Pathway Analysis (IPA). Generating cell-type transcriptional signatures from lung and blood single cell sequencing atlases, we also assessed association of ALR with differences in airway cellular composition. Results Across all ever-smokers, after adjustment for age, sex, height, COPD status, smoking status, and pack-years, n = 1,324 genes from airway epithelial samples exhibited DE at a false discovery rate (FDR) <0.2. Per IPA, enriched pathways associated with lower ALR included neutrophilic degranulation and macrophage activity. In cell type analysis, lower ALR was associated with higher signatures of macrophages, neutrophils, dendritic cells, and B cells, and lower ciliated and club cell signatures. When we repeated DE analysis using the same covariate adjustments plus an interaction term for ALR and smoking, n = 713 DE genes were identified at FDR <0.2; the association of DE with lower ALR was overwhelmingly in current rather than former smokers (3699 vs. 2 genes). By pathway and cell type analyses, the association between lower ALR and heightened inflammation (greater macrophage and neutrophil signaling) and epithelial dysregulation (downregulated ciliated and club cell function) was primarily restricted to current smokers. Conclusions In adult ever-smokers, lower ALR is associated with transcriptomic evidence of heightened neutrophil- and macrophage-driven airway inflammation and reduced ciliated and club cell expression, associations that were most evident among current smokers. Whether these cross-sectional patterns, which suggest impaired mucociliary defense and a diminished capacity to clear inhaled particulates, are the result of pre-existing reduced ALR, its cause, or both, will require further investigation. This abstract is funded by: SPIROMICS was supported by contracts from the NIH/NHLBI (HHSN268200900013C, HHSN268200900014C, HHSN268200900015C, HHSN268200900016C, HHSN268200900017C, HHSN268200900018C, HHSN268200900019C, HHSN268200900020C, 75N92024D00012), grants from the NIH/NHLBI (U01HL137880, U24HL141762, R01HL182622, R01HL144718, and R01HL093081), and supplemented by contributions made through the Foundation for the NIH and the COPD Foundation from Amgen; AstraZeneca/MedImmune; Bayer; Bellerophon Therapeutics; Boehringer-Ingelheim Pharmaceuticals, Inc.; Bristol Myers Squibb; Chiesi Farmaceutici S.p.A.; Forest Research Institute, Inc.; Genentech; GlaxoSmithKline; Grifols Therapeutics, Inc.; Ikaria, Inc.; MGC Diagnostics; Novartis Pharmaceuticals Corporation; Nycomed GmbH; Polarean; ProterixBio; Regeneron Pharmaceuticals, Inc.; Sanofi; Sunovion; Takeda Pharmaceutical Company; Theravance Biopharma; Verona; and Mylan/Viatris.

Abstract Rationale Eosinophilic airway inflammation in COPD is associated with more frequent exacerbations,lower lung function,and corticosteroid responsiveness.DNA methylation captures information about genetic factors and environmental exposures, but is under-studied in eosinophilic COPD.We hypothesized that sputum cell methylation patterns reflect genomic regulation of inflammatory endotypes in COPD by DNA sequence variation. Methods We analyzed DNA previously extracted from induced sputum cells for a prior study(PMID38261629) for which sufficient quantity DNA remained for methylation arrays.For this analysis,we focused on n = 132 SPIROMICS participants with ≥20 pack-years smoking history.Samples were stratified into tertiles based on sputum eosinophil proportions,previously determined from sputum cell differential analysis by the centralized sputum analysis core for SPIROMICS(Univ of North Carolina).We assessed proportion of DNA methylation (β values) spanning 936,866 CpG sites using the Illumina Infinium Methylation EPICv2.0 BeadChip Array,which we transformed into M values(meffil R package). To identify differentially methylated regions (DMRs)(FDR<0.05 in minimum of 2 CpG sites per gene region),we contrasted CpG β values between the high-eosinophil and low-eosinophil tertiles(N = 44 each),using the DMRcate package.We tested for enrichment of genes overlapping with significant DMRs using Enrichr (GWAS Catalog 2025 gene set library).To identify genetic variants associated with DNA methylation levels,we performed Methylation Quantitative Trait Loci (meQTL) analysis using TensorQTL.For each CpG site,we tested associations with SNPs within a ± 500 kb window (cis-meQTL).The linear regression model included age,sex,BMI,smoking status,smoking pack-years,study site,inhaled corticosteroid use, the first two genetic principal components, cell-type proportions (macrophages/monocytes, neutrophils, squamous epithelial cells, lymphocytes), and eosinophil tertile . Significant meQTLs were identified at an FDR<0.05 using Benjamini-Hochberg correction. Results A total of 532 eosinophil-associated DMRs (FDR < 0.05) were identified between the high- and low-eosinophil groups,encompassing 446 unique genes.The top enriched pathways related to counts of eosinophils (adjusted p = 0. 00002464), lymphocytes (adjusted p = 0.0001860), and the sum of eosinophils-plus-basophils (adjusted p = 0.0001860).We identified 18,432 significant SNP-CpG/meQTL pairs (FDR < 0.05),suggesting extensive genetic influence on airway DNA methylation patterns.Among the n = 521 eosinophil-associated CpGs that overlapped with meQTLs,rs55687040 (TENT2,a gene involved in mRNA and miRNA processing) is a GWAS locus for FEV1/FVC ratio (PMID: 26634245), suggesting possible genetic control of airway eosinophilic methylation signatures. Conclusions Our findings disclose distinct DNA methylation signatures associated with sputum eosinophil proportion in COPD.A subset of these CpGs are regulated by genetic variants,suggesting an integrated genetic-epigenetic mechanism underlying airway eosinophilic inflammation with the potential to influence COPD risk and severity. This abstract is funded by: SPIROMICS was supported by contracts from the NIH/NHLBI (HHSN268200900013C, HHSN268200900014C, HHSN268200900015C, HHSN268200900016C, HHSN268200900017C, HHSN268200900018C, HHSN268200900019C, HHSN268200900020C), grants from the NIH/NHLBI (U01 HL137880, U24 HL141762, R01 HL182622, and R01 HL144718), and supplemented by contributions made through the Foundation for the NIH and the COPD Foundation from Amgen; AstraZeneca/MedImmune; Bayer; Bellerophon Therapeutics; Boehringer-Ingelheim Pharmaceuticals, Inc.; Chiesi Farmaceutici S.p.A.; Forest Research Institute, Inc.; Genentech; GlaxoSmithKline; Grifols Therapeutics, Inc.; Ikaria, Inc.; MGC Diagnostics; Novartis Pharmaceuticals Corporation; Nycomed GmbH; Polarean; ProterixBio; Regeneron Pharmaceuticals, Inc.; Sanofi; Sunovion; Takeda Pharmaceutical Company; and Theravance Biopharma and Mylan/Viatris.

Abstract Rationale Thymic stromal lymphopoietin (TSLP) is an epithelial alarmin chiefly implicated in T2 airway inflammation, though it may also participate in broader (non-T2) inflammatory processes. The utility of airway epithelial gene expression of TSLP and its specific receptor subunit, cytokine receptor-like factor 2 (CRLF2), as biomarkers of downstream inflammation and clinical outcomes remains unclear. Methods We analyzed RNA sequencing data from bronchial airway brushing obtained in phase 1 of the SPIROMICS bronchoscopy sub-study (N = 161: 23 never-smokers, 67 ever-smokers with COPD, 71 ever-smokers without COPD). We related airway TSLP and CRLF2 expression to clinical, hematologic/sputum measures, and gene-expression signatures of T2/eosinophilic and neutrophilic inflammation, including to our published T2 signature and to eosinophil and neutrophil signatures derived from single-cell atlas data. Associations used Spearman correlations and linear models adjusted for age, sex, race/ethnicity, COPD status, smoking status, and pack-years. Results CRLF2 expression correlated with gene-expression evidence of both T2/eosinophilic and neutrophilic inflammation: T2 signature (ρ = 0.26, p < 0.001), eosinophil signature (ρ = 0.44, p < 0.001), and neutrophil signature (ρ = 0.39, p < 0.001). CRLF2 was positively associated with log sputum neutrophil count (ρ = 0.24, p = 0.024) and blood neutrophil count (ρ = 0.036, p < 0.001), but not with sputum or blood eosinophil counts. Higher CRLF2 related to worse baseline lung function, particularly among current smokers, (lower post-bronchodilator FEV1: ρ = −0.21, p = 0.008), as well as greater 5-year FEV1 decline across current and former smokers (ρ = −0.22, p = 0.007). Significant findings persisted after covariate adjustment. In contrast, TSLP expression, although strongly correlated with expression of the epithelial alarmin IL33 (ρ = 0.53, p < 0.001), was negatively correlated with CRLF2 (ρ = −0.24, p = 0.002) and with eosinophil and neutrophil gene-expression signatures (ρ = −0.26 and −0.33, both p < 0.001). TSLP expression showed no association with sputum or blood cell counts. Conclusions In bronchial epithelium from SPIROMICS, gene expression of CRLF2, but not of TSLP, tracked with downstream alarmin-relevant inflammatory programs, consistent with a regulatory role in TSLP signaling through TSLPR, as well as with clinically meaningful outcomes. CRLF2 expression was associated with evidence of both T2/eosinophilic and neutrophilic inflammation, and with lower baseline FEV1 and accelerated FEV1 decline, suggesting engagement of a broader, clinically relevant inflammatory milieu. By contrast, epithelial TSLP transcript levels mirrored IL33 gene expression but were not associated with cellular or transcriptomic inflammation. These findings position CRLF2, rather than TSLP expression itself, as a potential airway biomarker of TSLP-axis activity and disease impact with potential implications for patient stratification as well as strategic approaches for TSLP-pathway-targeted therapies. This abstract is funded by: SPIROMICS was supported by contracts from the NIH/NHLBI (HHSN268200900013C, HHSN268200900014C, HHSN268200900015C, HHSN268200900016C, HHSN268200900017C, HHSN268200900018C, HHSN268200900019C, HHSN268200900020C, 75N92024D00012), grants from the NIH/NHLBI (U01HL137880, U24HL141762, R01HL182622, R01HL144718, and R01HL093081), and supplemented by contributions made through the Foundation for the NIH and the COPD Foundation from Amgen; AstraZeneca/MedImmune; Bayer; Bellerophon Therapeutics; Boehringer-Ingelheim Pharmaceuticals, Inc.; Bristol Myers Squibb; Chiesi Farmaceutici S.p.A.; Forest Research Institute, Inc.; Genentech; GlaxoSmithKline; Grifols Therapeutics, Inc.; Ikaria, Inc.; MGC Diagnostics; Novartis Pharmaceuticals Corporation; Nycomed GmbH; Polarean; ProterixBio; Regeneron Pharmaceuticals, Inc.; Sanofi; Sunovion; Takeda Pharmaceutical Company; Theravance Biopharma; Verona; and Mylan/Viatris.

Abstract Background Prostaglandin E2 (PGE2) exerts paradoxical effects in asthma, acting as both a protective mediator and a contributor to pathology depending on context. Its role is shaped by type 2 (T2)-status, eosinophilia, and exacerbation frequency. In epithelial cell cultures from asthmatic and healthy individuals, interleukin (IL)-13 suppresses PGE2 synthesis genes (PTGS2 and PGES) while upregulating HPGD, which encodes for the PGE2 catabolic enzyme 15-prostaglandin dehydrogenase (15-PGDH) (PMID:16751012), suggesting diminished PGE2 availability during T2 inflammation. Similarly, in aspirin-exacerbated respiratory disease (AERD), impaired cyclooxygenase disrupts PGE2 biosynthesis, fueling unchecked leukotriene production and eosinophilic inflammation (PMID: 30516547), underscoring PGE2’s protective role in limiting disease progression. Conversely, in nasal polyps, tuft cells are activated by IL-13 to produce PGE2 (PMID: 35608904), highlighting PGE2’s potential pathogenicity. Objective To assess associations between PGE2-pathway gene expression in bronchial brushings and asthma severity, and to determine how nasal polyp history modifies these relationships. Methods We analyzed bronchial epithelial brushings from 109 adults with asthma (mean age 42.4±12.1, 64% female, 52% severe asthma, 18% nasal polyps) using normalized and batch-corrected RNA-seq data from the baseline visit in the Severe Asthma Research Program (SARP)3 (PMID: 36796454). Age-adjusted and nasal polyp-adjusted relationships were calculated between ratios of PGE2 synthesis and metabolism genes and clinical outcomes (ASSESS score, FEV1 %predicted). The composite PGE2 score (PMID: 35608904), derived from nasal polyp analysis, was calculated from the average scaled log-normalized expression of six PGE2-responsive genes. All data were analyzed using a linear regression mixed model with a random effect for site. Results Ratios of PGE2 synthesis genes (PTGS1/2, PTGES2) to HPGD were significantly associated with greater disease severity (change in ASSESS Score) (Fig.1A, solid lines) and lower lung function (change in FEV1 %predicted) (Fig.1B, solid lines). These relationships persisted after adjusting for nasal polyps (Fig.1, dashed lines). The composite PGE2 score was also related to disease severity (Fig.1A, black solid line) but attenuated when nasal polyps were accounted for (Fig.1A, black dashed lines). Interestingly, lower lung function remained associated with the PGE2 score even after nasal polyp adjustment (Fig.1B, dashed black lines). Conclusions Our analysis demonstrates that the balance between PGE2 synthesis and degradation in the bronchial epithelium is closely linked to asthma severity and lung function, independent of nasal polyp status. Future work will integrate transcriptomic and clinical data longitudinally to establish whether PGE2 could serve as a biomarker for asthma trajectory. This abstract is funded by: HL115118 (LCD), U10HL109152 (S.E.W.), U10HL109172 (to E.I. and B.D.L), U10HL109168 (N.N.J.), U10HL109250 (S.C.E), U10HL109164 (W.C.M), U10HL109257 (M.C), and U10HL109146 (to P.G.W. and S.A.C.)

Abstract Rationale Type-1 inflammation in asthma leads to significant airway level changes independent of Type-2 inflammation and may underlie the severity seen in combined Type1/2 high disease. As IFNs can cause airway epithelial injury and impaired repair, we applied a novel interpretable machine learning algorithm, SLIDE, to analyze the transcriptome of airway epithelial brushings of mild-moderate (MMA) and severe asthma (SA) participants in the Immune Mechanisms in Severe Asthma (IMSA) cohort to identify latent/hidden factors of disease that associate with disease severity. Methods The expression of genes identified by SLIDE as part of a co-expression program was assessed in the full IMSA cohort by severity and in an independent cohort of the NHLBI Severe Asthma Research Program (SARP). We also examined associations of these genes with clinical asthma outcomes in both cohorts. Results SLIDE identified aberrant increased expression of membrane-tethered mucin genes, MUC1 and MUC4. MUC1 appeared in each of 5 significant latent factors associated with greater severity and MUC4 in 2/5. Standard DGE analysis also identified the gene CEACAM5 as a predictor of severity. Pathway analysis of latent factor genes revealed airway keratinization which may contribute to airway remodeling and worsening obstruction over time. Expression of MUC1, MUC4, and CEACAM5 were increased in SA compared to HC in both the full IMSA and separate SARP cohorts (p < 0.001 for all genes in both cohorts). Expression in MMA was consistently lower than in SA in both cohorts, reaching significance in IMSA (p < 0.01) but not consistently in SARP (MUC1 p = 0.04, MUC4 p = 0.27, CEACAM5 p = 0.27). Protein analysis of endobronchial biopsies by immunofluorescence staining showed a trend towards increased MUC1 protein content with evidence of secretion. MUC1, MUC4 and CEACAM5 were negatively correlated with FEV1 % predicted in both cohorts (IMSA: MUC1 r=-0.47, p < 0.01, MUC4 r=-0.47, p < 0.01, CEACAM5 r=-0.62, p < 0.01; SARP: MUC1 r=-0.19, p = 0.05, MUC4 r=-0.29, p < 0.01, CEACAM5 r=-0.51, p < 0.01). All three genes positively correlated with prospective exacerbations in both cohorts (IMSA: MUC1 r = 0.345, p = 0.01, MUC4 r = 0.216, p = 0.08, CEACAM5 r = 0.368, p < 0.01; SARP: MUC1 r = 0.22, p = 0.02, MUC4 r = 0.32, p < 0.01, CEACAM5 r = 0.38, p < 0.01). Conclusions The expression of MUC1, MUC4 and CEACAM5 increased with asthma severity in the airway epithelium and correlated with both prospective exacerbations and obstruction. As pathway analysis of genes in the significant latent factors were associated with airway keratinization aberrant expression of these mucins (with known signaling functions) may contribute to maladaptive repair and airway remodeling that drives obstruction over time, contributing to worse asthma outcomes. This abstract is funded by: NIH