Citations

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

Introduction Asymptomatic individuals with negative Interferon-γ release assay (IGRA) and tuberculin skin test (TST) results are often labeled as tuberculosis-unexposed individuals. We hypothesize that flow cytometric (FC) detection of antigen-stimulated T-cells in peripheral blood can differentiate IGRA(-)/TST(-) individuals with and without prior potential M. tuberculosis (Mtb) exposure. Methods We used FC multiparameter profiling of T-cell activation markers in TST/IGRA-negative individuals at risk for Mtb exposure and in unexposed controls. Results We studied 54 IGRA(-)/TST(-) subjects, including 27 individuals at risk for prior Mtb exposure. While quantitative IGRA results were negative in all patients, FC profiling of CD3/CD4 + IFN-γ + HLA-DR + T-cells after stimulation with a pool of Mtb-specific region of difference-1 (RD1) peptides, mycobacterial (PPD and MTB300), or Candida antigens, statistically differentiated between unexposed and potentially exposed individuals (P<0.05). ROC analysis showed PPD and RD1 peptides responses had AUCs >0.7 (sensitivity of 55.5–74% and specificity of 66.6–85.1%). The presence of a polyfunctional RD1-reactive CD3/CD8 + IFN-γ + TNF-α + T-cell subset also significantly differentiated these groups (AUC 0.66). Other T-cell markers demonstrated no significant differences. Conclusions FC detection of antigen-specific IFN-γ + HLA-DR + CD4+T-cells and IFN-γ + TNF-α + CD8 + T-cells can differentiate IGRA(-)/TST(-) individuals at risk of Mtb exposure from unexposed controls. Further validation is needed to determine whether this immunoprofiling approach can improve detection of Mtb infections and identification of unexposed individuals for future biomarker studies and vaccine trails.

Abstract Background Research is limited on the impacts of menopause, defined as the permanent cessation of ovarian function and decline of reproductive hormones, on gastrointestinal symptom severity and disease progression in women with inflammatory bowel disease (IBD). This review synthesizes current evidence on the impact of menopause, menopause transition, and hormonal therapy (HT) on disease activity, IBD and menopause symptom severity, and disease progression among individuals with IBD. Methods A systematic literature review was reported following PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines and preregistered at PROSPERO (CRD42024564901). Five databases were searched without date restrictions. Data extraction and risk-of-bias assessment were performed independently by multiple reviewers. Results were qualitatively synthesized. Results Of 1667 records, 15 studies met inclusion criteria (5 cohort, 3 case-control, 7 cross-sectional) with IBD sample sizes from 37 to 1367. Evidence on HT and IBD risk was mixed: some studies linked HT to increased ulcerative colitis risk while others found no significant association after adjusting for confounders. Women with IBD experience earlier menopause than healthy control subjects. While most women reported no change in IBD symptoms postmenopause, a minority reported symptom worsening. HT may reduce flare severity. Women with IBD reported more severe vulvovaginal symptoms and had distinct vaginal microbiome profiles compared with healthy control subjects. Conclusions Few studies have explored the relationship between menopause and IBD. There is a need for continued research on the relationship between IBD disease activity and menopause symptoms to create tailored interventions to improve women’s health with IBD across the lifespan.

Abstract Background: Non-small cell lung cancer (NSCLC) makes up ~85% of lung cancers, and its major subtypes are adenocarcinoma (AD) and squamous cell carcinoma (SC). The histology classification of NSCLC has significant therapeutic and prognostic implications. As liquid biopsies are rapid and non-invasive, computational methods to classify NSCLC subtypes using cell-free DNA (cfDNA) are desired. Methods: Using The Cancer Genome Atlas (TCGA) NSCLC methylation data, we developed a method to classify AD and SC subtypes from cfDNA samples. We mapped TCGA methylation data to Guardant Infinity’s promoter regions and transformed them to allow for the transfer of the TCGA trained model to Infinity cfDNA epigenomic data. An advantage of this approach is that TCGA training data originates from the primary tumor, while cfDNA samples have low tumor fraction (TF) and may also contain signals from metastatic tumors. We trained a penalized Logistic Regression model with LASSO. To better fit the model to Infinity cfDNA data, we performed region filtering. Results: Our model effectively classified AD and SC subtypes from TCGA samples (AUC 0.97) (10-fold cross validation; Table 1). When evaluating on cfDNA samples with epigenomic TF ≥ 1%, the final model shows reasonable performance (AUC 0.94) (Table 1); the performance decreases when reduced to TF > 0.05% (AUC 0.89) as expected (Table 1). When evaluating cfDNA from uncategorized lung samples, the predicted AD probabilities have significant association with KRAS mutations (p-value = 0.027). Conclusion: Our results show that the penalized Logistic Regression model trained with tissue TCGA methylation data through mapping, transformation, and region selection can classify NSCLC subtypes from cfDNA samples. This method may offer a fast, non-invasive tool to inform subtype-based clinical decisions, especially in the setting of poorly-differentiated carcinomas, and to identify subtype switches upon resistance to targeted therapies. Table 1: Model evaluation on tissue TCGA samples and cfDNA Infinity samples (different TF cutoffs) Sample type N samples AUC Accuracy Sensitivity Specificity Precision F1 score tissue TCGA 907 0.97 0.93 0.94 +/- 0.02 0.93 +/- 0.02 0.94 +/- 0.02 0.94 +/- 0.01 cfDNA Infinity 17 (TF ≥ 1%) 0.94 0.88 0.83 +/- 0.3 0.91 +/- 0.17 0.83 +/- 0.3 0.83 +/- 0.21 cfDNA Infinity 29 (TF > 0.05%) 0.89 0.83 0.88 +/- 0.23 0.81 +/- 0.17 0.64 +/- 0.28 0.74 +/- 0.2 Citation Format: Laura Tung, Denis Tolkunov, Catalin Barbacioru, Deepika Kale, Scott Shell, Jill Tsai, Leylah Drusbosky, Kaushal Parikh, Han-Yu Chuang. Non-small cell lung cancer (NSCLC) histology classification using DNA methylation data captured from liquid biopsies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3499.

Abstract Aims HELIOS-A was a Phase 3, open-label study of vutrisiran, an RNA interference therapeutic, in patients with hereditary transthyretin (ATTRv) amyloidosis with polyneuropathy. This analysis evaluated vutrisiran's impact on exploratory cardiac endpoints in HELIOS-A patients. Methods and results Patients were randomized 3:1 to subcutaneous vutrisiran 25 mg every 3 months or intravenous patisiran 0.3 mg/kg every 3 weeks (reference group) for 18 months. Exploratory cardiac endpoints included change from baseline in N-terminal prohormone of brain-type natriuretic peptide (NT-proBNP) and echocardiographic parameters versus external placebo (APOLLO study). The modified intent-to-treat (mITT) population comprised randomized patients receiving any study drug (n = 122). A cardiac subpopulation with evidence of cardiac amyloid involvement (n = 40) was prespecified. 99mTc scintigraphy exploratory assessments in a planned vutrisiran-treated cohort at select sites were compared with baseline. At Month 18, vutrisiran demonstrated beneficial effects on NT-proBNP versus external placebo in the mITT and cardiac subpopulations (adjusted geometric mean fold change ratio [95% confidence interval] 0.480 [0.383–0.600], p = 9.606 × 10−10 and 0.491 [0.337–0.716], p = 0.0004, respectively). Benefits or trends towards benefit in echocardiographic parameters versus external placebo were observed for both populations. In 99mTc scintigraphy assessments, 32/47 (68.1%) and 31/48 (64.6%) patients exhibited reduced normalized left ventricular total uptake and heart-to-contralateral lung ratio, respectively. Perugini grade was reduced or unchanged versus baseline in 55/57 (96.5%) evaluable patients. No increase in cardiac adverse events was observed with vutrisiran versus external placebo. Conclusions Vutrisiran demonstrated evidence of potential benefit on cardiac manifestations in patients with ATTRv amyloidosis with polyneuropathy, with an acceptable safety profile.