Citations

Abstract Rationale Alpha-1 antitrypsin (AAT) deficiency, primarily caused by homozygous SERPINA1 Z mutation, increases the risk of COPD. Individuals carrying one Z and one normal M allele (MZ) have higher COPD risk than MM individuals, although many never develop disease. COPD is a polygenic condition influenced by numerous genetic factors across the genome and by environmental exposures such as smoking. We aimed to examine how polygenic factors and smoking modify risk of airflow obstruction in MZ compared with MM. Methods We included participants with the MZ and MM genotypes from the Framingham Heart Study. We first tested the association between AAT genotype (MZ coded as 1 and MM as 0) and FEV1/FVC, stratified by ever-smoking status, and further evaluated interactions between AAT genotype and smoking pack-years. Next, for each participant we calculated a polygenic risk score (PRS) for FEV1/FVC, which was derived from external genome-wide association studies in the UK Biobank and SpiroMeta Consortium. To reflect risk for airflow limitation, higher PRSs correspond to lower FEV1/FVC. We then tested the interaction between the PRS and AAT genotype, stratified by ever-smoking. Models were adjusted for age, sex, height, current smoking, pack-years (among ever-smokers), familial relatedness, and in PRS models, principal components of genetic ancestry. Results Among 4,220 participants (mean age 53.7 years, 54.2% female, 50.2% ever-smokers, mean FEV1/FVC 74.6%), 133 (3.2%) had MZ genotype. In never-smokers, MZ individuals had 1.72% higher FEV1/FVC compared with MM (P = 0.032), whereas no difference was observed among ever-smokers (β= -0.39%; P = 0.65). Cumulative smoking modified the effect of MZ genotype on FEV1/FVC (interaction β= -0.13% per pack-year; P = 0.003); this interaction persisted among ever-smokers (β= -0.11% per pack-year; P = 0.044). A one-standard-deviation increase in the FEV1/FVC PRS was associated with lower FEV1/FVC in both never- (β= -2.37%; P < 0.0001) and ever-smokers (β= -2.46%; P < 0.0001). A higher PRS was disproportionately associated with reduced FEV1/FVC in MZ compared to MM (interaction β= -1.87% per standard-deviation PRS increase, P = 0.027) among ever-smokers, but not in never-smokers (P = 0.15). Conclusions In this community-based cohort, the AAT MZ genotype was associated with higher FEV1/FVC among non-smokers compared to MM. The interaction between MZ genotype and pack-years suggested a dose-dependent modifying effect of smoking on the MZ-related COPD risk. Among ever-smokers, higher polygenic risk further amplified susceptibility to airflow obstruction in MZ compared with MM. These findings highlight the roles of both polygenic and environmental risk factors in COPD susceptibility in MZ. Replication of the results is needed. This abstract is funded by: This work is supported by an Alpha-1 Foundation Grant and a Boston University Department of Medicine Career Investment Award

Abstract Background Muscle loss in COPD results from both disuse atrophy and systemic inflammation. We sought to identify inflammatory biomarkers associated with loss of pectoralis muscle area in COPD using serial CT scans and peripheral blood proteomics. Design We analyzed five-year longitudinal data from COPDGene, an ongoing observational cohort of current and former tobacco smokers with or without airflow obstruction. We quantified pectoralis major muscle (PMM) area on chest CT scans using a 3D convolutional neural network (CNN) trained on CT volumes and annotations provided by the TotalSegmentator project. We compared participants with CT PMM data and plasma proteins by SOMAScan (1K platform) from Phase 2 and 3 (paired n = 1,191). The correlation coefficient (r) between longitudinal changes in protein and in PMM area was plotted against the false discovery rate (FDR)-adjusted p-values. Proteins significantly associated with muscle loss (blue) or gain (red) were visualized using volcano plots. We then analyzed a subset (paired n = 500) of individuals with BMI>25 in Phase 2 whose BMI declined in Phase 3. Proteomic models were adjusted for age and clinical center. Pathway analysis utilized G:Profiler. Results Of the participants with paired proteomic and PMM data, mean PMM area was 21.7 ± 17.3 cm² at Phase 2 and 21.3 ± 17.9 cm² at Phase 3, with an annual change in PMM area of -0.31 + 0.99 cm². Multiple proteins were associated with muscle loss from Phase 2 to 3 (including leptin, FABP, and growth hormone receptor) and muscle gain (including F172A, GMEB2, and RNF41) (Fig 1a). Significant pathways were related to cancer, growth factor receptor dysregulation, and PI3K/AKT signaling. When restricting to those with BMI>25 who experienced BMI decline at Phase 3, muscle loss was associated with increased leptin and PACAP, versus association of gain with increased GDF118, EF1β, and FJF6 (Fig 1b). In the entire group, leptin declined between Phase 2 to Phase 3 in n = 571 participants and increased or was unchanged in n = 620. Compared with leptin decline, unchanged or increased leptin was associated with significantly greater interval PMM loss (−2.25 ± 9.75 cm² vs + 0.98 ± 9.43 cm²; p < 0.001) (Fig 1c). Conclusion Loss of PMM over five years was associated with several plasma proteins, including FABP and growth hormone receptor. The top biomarker, leptin, is a pleiotropic adipokine that regulates energy balance and inflammation. Integrating imaging and proteomics may identify future therapeutic targets to mitigate skeletal muscle loss in COPD. This abstract is funded by: This work was supported by NHLBI grants U01 HL089897 and U01 HL089856 and by NIH contract 75N92023D00011

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

Abstract Rationale Asthma and obesity are common comorbidities, both driven by inflammation and oxidative stress. Oxylipins are derivatives of polyunsaturated fatty acids that regulate the onset and resolution of inflammation. Oxylipin profiles are altered in obesity and have been shown to differentiate asthma from non-asthma; however, the association between oxylipins and asthma outcomes and the impact of obesity is not known. This study aims to identify differences in serum oxylipins associated with asthma morbidity and evaluate the effect modification by BMI. Methods We analyzed 150 participants in the Best African American Response to Asthma Drugs (BARD) clinical trial. Ninety oxylipins were quantified using liquid chromatography tandem mass spectroscopy from serum obtained at the time of randomization. Oxylipins found to be above the limit of detection in > 80% of samples were log-transformed and included in the analysis. Asthma severity measures included past 12-month systemic corticosteroid use for asthma exacerbation, spirometry, asthma control and asthma quality of life questionnaires (AQLQ). The associations between oxylipins and asthma outcomes were tested using multivariable regression models adjusted for sex, age, BMI, absolute eosinophil count, percent African ancestry, and child vs adult/adolescent cohort. A false discovery rate (FDR) of < 0.1 is used to determine statistical significance. Results Of the 90 oxylipins measured, 42 (46.7%) were detected in > 80% of all samples and included in the analysis. In multivariable models, the pro-inflammatory arachidonic acid (AA) derivative 5,6-DiHETrE was associated with decreased odds of past 12-month systemic corticosteroid use (FDR-adjusted p-value 0.0628). AA derivatives TXB2, PGF2a, and 6-α-prostaglandin were associated with increased FEV1/FVC (FDR-adjusted p-values=0.0925). Thirteen oxylipins were associated with decreased asthma-related quality of life in multivariable models, including AA metabolites 5S-HETE, 5-KETE, 14,15-EET, LTB4, and Lipoxin A4; dihomo-gamma-linoleic acid metabolites 5-HETrE and 15-HETrE; linoleic acid metabolites 3-OxoODE and 9-OxoODE; and eicosapentaenoic acid metabolites 15-HEPE and 17,18-EpETE, all with FDR-adjusted p-values<0.05. Oxylipin-BMI interaction was significant only in the AQLQ models. In all but LTE4, increased concentrations of oxylipins were associated with a decreased quality of life in individuals with higher BMI (Figure). Six of these oxylipins are products of lipoxygenase activity. Conclusions In this study, we find decreased quality of life with increasing concentrations of pro-inflammatory and resolving oxylipins among those with obesity. These oxylipins are primarily produced via lipoxygenases and may represent an important inflammatory pathway in obesity-associated asthma. Quantification of sputum oxylipins and correlation with serum levels will be important in understanding potential mechanisms and is forthcoming. This abstract is funded by: K12TR004412, R01HL123385, U10HL098075, Parker B. Francis Fellowship, 2L30HL159725

Abstract Rationale Higher African genetic ancestry has been associated with lower lung function, among individuals from specific racial-ethnic groups. The influence and interactions of genetic variation and ancestry in lung function is poorly understood. This study investigates ancestry-associated loci influencing lung function via admixture mapping and fine-scale allelic association. Methods 512 African American patients with asthma (≥12 years) from the Severe Asthma Research Program and Collaborative Study on the Genetics of Asthma (SARP/CSGA) cohorts were genotyped on the OmniExpress and HumanHap1M arrays or had whole-genome sequencing (WGS). For admixture mapping, global ancestry was inferred using ADMIXTURE and local ancestry estimated using RFMix v1.5.4 with CEU (N = 99) and YRI (N = 108) references across 15,095 local ancestry segments. Peak regions and contiguous segments (p < 10-3) were fine mapped in SARP using local ancestry estimated from WGS with MAF ≥0.03. The Local Ancestry Adjusted Allelic Association (LAAA) model was used to fine map local genetic effect, local ancestry effect, and the interaction between the two, adjusted for age, sex, height, BMI, cohort, and percentage global African ancestry. SNPs with local genetic or interaction p < 10⁻³ were tested for replication in 282 adolescent/adult participants from the Best African Response to Asthma Drugs (BARD) cohort genotyped with the MEGA array imputed to TOPMed (MAF ≥0.03). Results Mean African genetic ancestry was 81.3% in SARP and 80.1% in BARD. In SARP, African genetic ancestry was inversely associated with lung function (FEV₁:β = −7.9, p = 0.005; FVC:β = −9.0, p = 0.004), with stronger effects in females (FEV₁: β = −9.3, p = 0.003; FVC: β = −11.4, p = 0.001) than males (FEV₁:β = −6.4, p = 0.237; FVC:β = −5.7, p = 0.340). Similar total and sex-specific associations were identified in BARD. Admixture mapping in SARP/CSGA identified significant peaks for maximum FVC (p < 1.87 × 10⁻4) on chromosomes 8 and 17 near RP1 and RBFOX3, and near-significant peaks on chromosome 5 near IQGAP2, SNRPCP2, SV2C and for the maximum FEV₁/FVC ratio on chromosome 10 near PCDH15. Fine mapping identified the top SNP on chromosome 8 (rs73587686; p-allele-dose=9.0x10-5; RGS20; q11.23), with 62 additional SNPs overlapping RGS20. SNP rs7825816 was also identified in SARP (β = 2.35, p-allele-dose =1.03 × 10⁻4) and replicated in BARD (β = 1.15, p-allele-dose =0.03). In BARD, LAAA also identified eight additional SNPs (p ≤ 0.05) in the same LD block (chr8:53914976-53918297) overlapping with RGS20, ATP6V1H, and TCEA1. Conclusions We identified multiple chromosomal regions associated with lung function in asthma patients of predominantly African genetic ancestry. Lung function associations were strongest at genetic variation near a key that was replicated in an independent asthma cohort. This abstract is funded by: R01 K08 HL118128, R01 HL142992, R01 NR013700, R01 HL69167, R01 HL161674, HL69116, HL69167, HL69170, HL69174, U10 HL109164, U10 HL109257, U10 HL109146, U10 HL109172, U10 HL109250, U10 HL109250, U10 HL109250, U10 HL109168, U10 HL109152, U10 HL109086-04, U10 HL098115, HL098102, HL098096, HL098075, HL098090, HL098177, HL098098, HL098107, HL098112, HL098103, and K12 HL89992

Importance Standard adjuvant therapy for human papillomavirus–associated oropharyngeal squamous cell carcinoma (HPV-OPSCC) is radiation therapy 60 Gy with or without cisplatin delivered in 30 fractions during 6 weeks. A phase 3 randomized clinical trial demonstrated decreased toxic effects and improved patient-reported outcomes with de-escalated adjuvant radiation therapy (DART) compared with standard therapy; however, outcomes for patients treated in the clinical practice setting following trial adoption remain unknown. Objective To compare characteristics and oncologic outcomes of patients treated with DART during clinical trials (on study) and in clinical practice settings (off study) and report progression-free survival (PFS) by risk category. Design, Setting, and Participants This retrospective cohort study included patients treated with DART in the MC1273 and MC1675 trials and in clinical practice after study completion at a multisite tertiary care center. Patients with surgically resectable HPV-OPSCC who underwent margin-negative resection between August 20, 2013, and March 21, 2023, and were treated with DART were included in the analysis. Those with prior head and neck cancer, pT0 or pT4 disease, unknown HPV status, metastatic disease at presentation, synchronous primary tumors, induction chemotherapy, or treatment at an outside institution were excluded. Data were analyzed from July 1, 2024, to July 18, 2025. Interventions DART consisting of 30 to 36 Gy in 1.5- to 1.8-Gy fractions twice daily with docetaxel 15 mg/m 2 on days 1 and 8. Main Outcomes and Measures Progression-free survival as measured via Kaplan-Meier analysis. Results A total of 282 patients were included in the analysis: 176 (62.4%) in the on-study group and 106 (37.6%) in the off-study group (252 [89.4%] male; mean [SD] age, 59.1 [9.3] years). Both groups were predominantly male (157 [89.2%] and 95 [89.6%], respectively) and consisted mostly of never smokers (118 [67.0%] and 62 [58.5%], respectively). Pathologic features were similar between groups except for nodal stage (pN1: 155 [88.1%] on study vs 102 [96.2%] off study; pN2: 21 [11.9%] on study vs 4 [3.8%] off study; P = .02). The median follow-up times were 5.2 years (95% CI, 5.2-5.8 years) in the on-study group and 2.2 years (95% CI, 1.9-2.4 years) in the off-study group. Two-year PFS was similar (93% [95% CI, 88%-97%] on study vs 93% [95% CI, 88%-99%] off study). For patients with pN1 and no extranodal extension (ENE), 2- and 5-year PFS were 97% (95% CI, 93%-100%) and 96% (95% CI, 92%-100%), respectively. Patients with pN1 and ENE had a 2- and 5-year PFS of 93% (95% CI, 89%-98%) and 87% (95% CI, 81%-94%), respectively. Conclusions and Relevance In this retrospective cohort study of patients receiving DART on and off study, oncologic outcomes were similar between the 2 groups. Fewer patients with pN2 received DART off study, given the interim results of MC1675. Patients with pN1 and no ENE treated with DART had excellent 2- and 5-year PFS, supporting DART as a compelling treatment option in well-selected patients. An additional study that is currently underway will evaluate biomarker risk-stratified treatment of patients with pN1 and ENE receiving DART.

Background/Objectives: Locoregional anal squamous cell carcinoma (ASCC) is usually cured with chemoradiotherapy; however, some patients relapse, require salvage abdominoperineal resection or develop metastatic disease. Approximately 90% of cases are driven by high-risk human papillomavirus, most commonly HPV16. Conventional surveillance using clinical examination and imaging may have limited sensitivity and specificity and is not individualized by recurrence risk. Circulating biomarkers (CBs), particularly circulating tumor DNA (ctDNA), have emerged as promising methods for real-time disease monitoring. We systematically reviewed available evidence evaluating CBs across treatment timepoints in localized ASCC. Methods: A PROSPERO-registered review (ID: 1133987) was conducted according to PRISMA guidelines. PubMed, EMBASE, Cochrane CENTRAL, Web of Science, and major conference proceedings (ASCO, ESMO, ASTRO) were searched on 30 November 2025. We included prospective or retrospective studies (≥10 patients) with stage I–III disease treated with curative-intent chemoradiotherapy that reported CBs, assay characteristics, and at least one clinical outcome. Studies with predominantly localized cohorts were included even if small proportions of metastatic patients were present, provided results relevant to curative-intent populations could be interpreted. Data were synthesized narratively by timepoint (baseline, mid-treatment, end of treatment, post-treatment/surveillance) and assay type given methodological heterogeneity. Results: Fifteen studies were included. CB assays comprised four categories: viral HPV ctDNA assays, tumor-informed ctDNA assays, non-specific total cell-free DNA (cfDNA) quantification, and circulating tumor cell (CTC)-based assays. Baseline detection rates varied by assay type. Viral HPV ctDNA assays demonstrated detection rates of 59–100%, while tumor-informed ctDNA assays showed rates of 79–89%. Across studies, higher CB detection rates and levels were generally associated with greater tumor burden, including more advanced T and N stage disease. Mid-treatment ctDNA clearance identified patients with excellent locoregional control and progression-free survival, whereas persistent ctDNA was associated with treatment failure. End-of-treatment and surveillance ctDNA positivity predicted recurrence within individual cohorts, with reported sensitivities of 80–90%, specificities of 95–99%, and molecular lead times preceding clinical or radiographic detection. In contrast, non-tumor-specific cfDNA dynamics showed more variable prognostic associations and were less consistently linked to tumor burden. Conclusions: Across heterogeneous assays, CB dynamics provide clinically meaningful prognostic information in localized ASCC, particularly when measured during treatment and early surveillance. Viral HPV and tumor-informed ctDNA may have the potential to guide follow-up intensity and inform future escalation or de-escalation strategies; however, prospective, standardized trials are needed to define actionable thresholds and test ctDNA-guided management.

Abstract Background For many evidence criteria within v3.0 of the ACMG/AMP guidelines, methodologies have been developed to empower their use outside the stipulated evidence strengths. However, no such methodology has been established for case-control data (PS4). With the release of large-scale unselected case-control datasets and expansion of nationally-collected laboratory datasets enriched for pathogenic variant carriers, there is potential to combine datasets across ascertainment contexts in a more quantitative manner using novel likelihood ratio tools. Methods Using our published PS4-LR-Calculator, we calculated a combined log likelihood ratio (PS4-LLR) across five datasets (three unselected, and two enriched), and estimated enrichment of pathogenic variants in clinically-ascertained laboratory data using truncating variant prevalence. Results Data were combined for 10,817 missense variants from 325,345 female breast cancer patients and 671,006 controls of Western European ancestry for five breast cancer susceptibility genes ( BRCA1, BRCA2, PALB2, ATM, CHEK2 ). A combined LLR was produced for 4,690 missense variants; 927 variants received evidence towards pathogenicity (LLR≥ 1), and 3,242 received evidence towards benignity (LLR≤ -1). Conclusion This flexible, variant-level methodology combines nationally-collected ‘enriched’ datasets with unselected case-control cohorts, expanding the available information for case-control analysis, boosting power, enabling exploration of atypical penetrance and empowering variant classification.

OBJECTIVE The aim of this study was to evaluate freedom from tumor progression and clinical outcomes in older adults with small- to medium-sized vestibular schwannoma (VS) managed by observation versus stereotactic radiosurgery (SRS) to better inform optimal management in this patient population. METHODS In this international multicenter study, patients aged ≥ 60 years with Koos grade I or II VS managed by observation or SRS were retrospectively reviewed. Propensity score matching was conducted using patient characteristics, tumor size, and hearing assessments. Outcome measures of freedom from tumor progression, serviceable hearing preservation (SHP), and neurological function (tinnitus, vestibulopathy, House-Brackmann grade, and trigeminal nerve function) were assessed for both groups. RESULTS The observation and SRS groups each comprised 51 matched patients (median age 68 years for both). Ipsilateral serviceable hearing was observed at presentation for 35 patients in each group. The median follow-up duration was 39 months in the observation group versus 27 months in the SRS group (p = 0.5). Tumor progression was significantly lower with SRS than with observation (2% vs 52.9%, p < 0.001). The rate of 5-year freedom from tumor progression was 100% in the SRS group versus 43% (95% CI 29%–64%) in the observation group. The rate of 10-year freedom from tumor progression was 90% (95% CI 73%–100%) in the SRS group versus 20% (95% CI 8.5%–49%) in the observation group. At the last follow-up, hearing loss occurred in 42.9% of the observation group and 51.4% of those who underwent SRS (p = 0.5). The 3-year SHP rate was 68% (95% CI 53%–88%) versus 65% (95% CI 49%–85%) (p = 0.8), and the 5-year SHP rate was 53% in both groups (95% CI 36%–78% in the observation group and 95% CI 35%–79% in the SRS group, p = 0.8). The composite endpoint of tumor progression and/or worsened neurological outcome, including hearing loss, tinnitus, vestibulopathy, facial nerve dysfunction (House-Brackmann grade), or trigeminal dysfunction, demonstrated a significantly lower rate in the SRS group (17.6%) compared with the observation group (66.7%) (p < 0.001). CONCLUSIONS SRS in older patients for management of Koos grade I or II VS resulted in significantly superior rates of freedom from tumor progression, comparable hearing preservation rates, and significantly higher rates of favorable overall radiographic and neurological outcomes than observation alone. Compared with observation, SRS might be the preferred management option in this patient population.