Proteomic biomarkers of progressive fibrosing interstitial lung disease: a multicentre cohort analysis (PF-ILD Proteomics-BioLINCC)
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PROVIDER: PRJNA1231611 | ENA |
REPOSITORIES: ENA
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Project description:Proteomic biomarkers of progressive fibrosing interstitial lung disease: a multicentre cohort analysis (PF-ILD Proteomics-BioLINCC)
| PRJNA1231612 | ENA
Project description:Progressive fibrosing interstitial lung disease (PF-ILD) describes a phenotypic subset of interstitial lung diseases characterized by progressive, intractable lung fibrosis. PF-ILD is separate from, but has radiographic, histopathologic, and clinical similarities to idiopathic pulmonary fibrosis. Two antifibrotic medications, nintedanib and pirfenidone, have been approved for use in patients with idiopathic pulmonary fibrosis. Recently completed randomized controlled trials have demonstrated the clinical efficacy of antifibrotic therapy in patients with PF-ILD. The validation of efficacy of antifibrotic therapy in PF-ILD has changed the treatment landscape for all of the fibrotic lung diseases, providing a new treatment pathway and opening the door for combined antifibrotic and immunosuppressant drug therapy to address both the fibrotic and inflammatory components of ILD characterized by mixed pathophysiologic pathways.
| S-EPMC8197477 | biostudies-literature
Project description:ObjectivesProgressive fibrosing interstitial lung disease (PF-ILD) is characterised by increased pulmonary fibrosis, lung function decline, acute exacerbations, decreased quality of life and increased mortality. Nintedanib may slow down disease progression, but long-term outcomes are unknown. We aimed to assess the cost-effectiveness of nintedanib in comparison to placebo, both on top of usual care in patients with PF-ILD.MethodsAn individual PF-ILD patient simulation model was created, using data and extrapolations from the nintedanib and placebo arms of the INBUILD trial. Clinical outcomes (mortality, exacerbations, lung transplants), economic outcomes (direct and indirect costs) and the cost-effectiveness of nintedanib over a 10-year time horizon were forecasted using the Netherlands as a case example. Disease progression was driven by lung function decline, with forced vital capacity (FVC) health states ranging from < 40 to ≥ 110 FVC of % predicted. Sensitivity and scenario analyses were performed to assess the impact of parameter assumptions on the cost-effectiveness and to test model robustness.ResultsOver a 10-year follow-up, nintedanib gained an average of 1.31 discounted life years and an average of 0.87 discounted quality-adjusted life years (QALYs), resulting in an incremental cost-effectiveness ratio (ICER) of €60,690 per QALY. Sensitivity analyses showed cost variations had a minor impact on the ICER. Results were mainly driven by mortality probabilities and disease-related utilities. Scenario analyses indicated most sensitivity to the time horizon and lung transplantation costs.ConclusionLong-term treatment with nintedanib could result in considerable health gains for patients with PF-ILD and can be considered cost-effective under the common willingness-to-pay threshold.
| S-EPMC9440187 | biostudies-literature
Project description:Fibrosing interstitial lung diseases (ILDs) encompass a diverse range of scarring disorders that lead to progressive lung failure. Previous gene expression profiling studies focused on idiopathic pulmonary fibrosis (IPF) and bulk tissue samples. We employed digital spatial profiling to gain new insights into the spatial resolution of gene expression across distinct lung microenvironments (LMEs) in IPF, chronic hypersensitivity pneumonitis (CHP) and non-specific interstitial pneumonia (NSIP). We identified differentially expressed genes between LMEs within each condition, and across histologically similar regions between conditions. Uninvolved areas in IPF and CHP were remarkably distinct from normal controls, and displayed potential therapeutic targets. Hallmarks LMEs of each condition retained a distinct gene signature, but these could not be reproduced in matched lung tissue samples. Based on these gene expression signatures and unsupervised clustering, we grouped previously unclassified ILD cases into NSIP or CHP. Lastly, we characterized a gene expression pattern associated with poor outcome . Overall, our work uniquely dissects gene expression profiles between LMEs within and across different types of fibrosing ILDs. This new spatial transcriptomics approach has the potential to reclassify unclassifiable cases, to qualify the transcriptional relevance of smaller biopsies for clinical use, and to predict outcome at the time of diagnosis.
2024-09-30 | GSE255174 | GEO
Project description:Transcriptional comparison of alveolar macrophages from patients with RA-ILD. IIM-ILD and DI-ILD.
| PRJNA597348 | ENA
Project description:Fibrosing interstitial lung diseases (ILDs) encompass a diverse range of scarring disorders that lead to progressive lung failure. Previous gene expression profiling studies focused on idiopathic pulmonary fibrosis (IPF) and bulk tissue samples. We employed digital spatial profiling to gain new insights into the spatial resolution of gene expression across distinct lung microenvironments (LMEs) in IPF, chronic hypersensitivity pneumonitis (CHP) and non-specific interstitial pneumonia (NSIP). We identified differentially expressed genes between LMEs within each condition, and across histologically similar regions between conditions. Uninvolved areas in IPF and CHP were remarkably distinct from normal controls, and displayed potential therapeutic targets. Hallmarks LMEs of each condition retained a distinct gene signature, but these could not be reproduced in matched lung tissue samples. Based on these gene expression signatures and unsupervised clustering, we grouped previously unclassified ILD cases into NSIP or CHP. Lastly, we characterized a gene expression pattern associated with poor outcome . Overall, our work uniquely dissects gene expression profiles between LMEs within and across different types of fibrosing ILDs. This new spatial transcriptomics approach has the potential to reclassify unclassifiable cases, to qualify the transcriptional relevance of smaller biopsies for clinical use, and to predict outcome at the time of diagnosis.
2024-09-30 | GSE255173 | GEO
Project description:Antifibrotic therapy with nintedanib is the clinical mainstay in the treatment of progressive fibrosing interstitial lung disease (ILD). High-dimensional medical image analysis, known as radiomics, provides quantitative insights into organ-scale pathophysiology, generating digital disease fingerprints. Here, we used an integrative analysis of radiomic and proteomic profiles (radioproteomics) to assess whether changes in radiomic signatures can stratify the degree of antifibrotic response to nintedanib in (experimental) fibrosing ILD. Unsupervised clustering of delta radiomic profiles revealed two distinct imaging phenotypes in mice treated with nintedanib, contrary to conventional densitometry readouts, which showed a more uniform response. Integrative analysis of delta radiomics and proteomics demonstrated that these phenotypes reflected different treatment response states, as further evidenced on transcriptional and cellular levels. Importantly, radioproteomics signatures paralleled disease- and drug related biological pathway activity with high specificity, including extracellular matrix (ECM) remodeling, cell cycle activity, wound healing, and metabolic activity. Evaluation of the preclinical molecular response-defining features, particularly those linked to ECM remodeling, in a cohort of nintedanib-treated fibrosing ILD patients, accurately stratified patients based on their extent of lung function decline. In conclusion, delta radiomics has great potential to serve as a non-invasive and readily accessible surrogate of molecular response phenotypes in fibrosing ILD. This could pave the way for personalized treatment strategies and improved patient outcomes. References: Hallal, Mahmoud, Sophie Braga-Lagache, Jovana Jankovic, Cedric Simillion, Rémy Bruggmann, Anne-Christine Uldry, Ramanjaneyulu Allam, Manfred Heller, and Nicolas Bonadies. 2021. “Inference of Kinase-Signaling Networks in Human Myeloid Cell Line Models by Phosphoproteomics Using Kinase Activity Enrichment Analysis (KAEA).” BMC Cancer 21 (1): 789.
2024-10-17 | PXD052594 | Pride
Project description:Fibrotic interstitial lung disease (ILD) are lung disorders characterized by the accumulation of extracellular matrix, ultimately resulting in the destruction of the pulmonary scaffold. Continuous pro-fibrotic signaling perpetuates the remodeling process, specifically targeting the epithelial cell compartment, thereby destroying the gas exchange area. Studies that address this detrimental crosstalk between lung epithelial cells and fibroblasts are key to understanding ILD. With the aim of identifying functionally relevant targets that drive mesenchymal-epithelial crosstalk and their potential as new avenues to therapeutic strategies, we developed an organoid co-culture system based on human induced pluripotent stem cell-derived alveolar epithelial type 2 cells and lung fibroblasts from ILD patients as well as IMR-90 controls. While organoid formation capacity and organoid size was comparable in the presence of ILD or control lung fibroblasts, metabolic activity was significantly increased in ILD co-cultures. Alveolar organoids cultured with ILD fibroblasts further demonstrated reduced stem cell function supported by reduced Surfactant Protein C gene expression together with an aberrant basaloid-prone differentiation program indicated by elevated Cadherin 2, Bone Morphogenic Protein 4 and Vimentin transcription. In order to identify key mediators of the misguided mesenchymal-to-epithelial crosstalk with a focus on disease-relevant inflammatory processes, we used secretome mass spectrometry to identify key signals secreted by end stage ILD lung fibroblasts. Over 2000 proteins were detected in a single-shot experiment with 47 differentially upregulated proteins when comparing ILD and non-chronic lung disease control fibroblasts. The secretome profile was dominated by chemokines of the C-X-C motif family, including CXCL1, -3, and -8, all interfering with (epithelial) growth factor signaling orchestrated by Interleukin 11 (IL11), steering fibrogenic cell-cell communication, and proteins regulating extracellular matrix remodeling including epithelial-to-mesenchymal transition. When in turn treating 3D monocultures of iAT2s with IL11 we recapitulated the co-culture results obtained with primary ILD fibroblasts including changes in metabolic activity as well as organoid formation capacity and size. In summary, our analysis identified mesenchyme-derived mediators likely contributing to the disease-perpetuating mesenchymal-to-epithelial crosstalk in ILD by using sophisticated alveolar organoid co-cultures indicating the importance of cytokine-driven aberrant epithelial differentiation and confirmed IL11 as a key player in ILD using an unbiased approach.
2023-04-19 | PXD039554 | Pride
Project description:GWAS in Fibrosing Interstitial Lung Disease
| PRJNA248931 | ENA