ArticleBMC pulmonary medicine2017
Unsupervised gene expression analyses identify IPF-severity correlated signatures, associated genes and biomarkers.
Article in BMC pulmonary medicine, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 48 citations in OpenAlex.
- Alveolar epithelial depletion of βPAK-interacting exchange factor drives spontaneous pulmonary fibrosis by impairing stemness.Signal transduction and targeted therapy · 2026Article
- A Multispecies, Modality-Agnostic Scalable In Vivo Mosaic Screening Platform for Therapeutic Target Discovery.bioRxiv : the preprint server for biology · 2026Article
- SEMA3B inhibits TGFβ-induced extracellular matrix protein production and its reduced levels are associated with a decline in lung function in IPF.American journal of physiology. Cell physiology · 2024Article
- Downregulation of HMGCS2 mediated AECIIs lipid metabolic alteration promotes pulmonary fibrosis by activating fibroblasts.Respiratory research · 2024Article
- New Insights via RNA Profiling of Formalin-Fixed Paraffin-Embedded Lung Tissue of Pulmonary Fibrosis Patients.International journal of molecular sciences · 2023Article
- Cluster analysis of transcriptomic datasets to identify endotypes of idiopathic pulmonary fibrosis.Thorax · 2023Article
- Wilms Tumor 1-Driven Fibroblast Activation and Subpleural Thickening in Idiopathic Pulmonary Fibrosis.International journal of molecular sciences · 2023Review
- Wild-type S100A3 and S100A13 restore calcium homeostasis and mitigate mitochondrial dysregulation in pulmonary fibrosis patient-derived cells.Frontiers in cell and developmental biology · 2023Article
- Pirfenidone exacerbates Th2-driven vasculopathy in a mouse model of systemic sclerosis-associated interstitial lung disease.The European respiratory journal · 2022Article
- Towards Treatable Traits for Pulmonary Fibrosis.Journal of personalized medicine · 2022Review
- Consensus Gene Co-Expression Network Analysis Identifies Novel Genes Associated with Severity of Fibrotic Lung Disease.International journal of molecular sciences · 2022Article
- Anti-Inflammatory and Anti-Fibrotic Effect of Immortalized Mesenchymal-Stem-Cell-Derived Conditioned Medium on Human Lung Myofibroblasts and Epithelial Cells.International journal of molecular sciences · 2022Article
- Dysregulated overexpression of Sox9 induces fibroblast activation in pulmonary fibrosis.JCI insight · 2021Article
- LncRNA CTD-2528L19.6 prevents the progression of IPF by alleviating fibroblast activation.Cell death & disease · 2021Article
- Article
- Identification of Hub Genes and Pathways Associated With Idiopathic Pulmonary FibrosisFrontiers in molecular biosciences · 2021Article
- Gene Expression Signatures Associated With Survival Times of Pediatric Patients With Biliary Atresia Identify Potential Therapeutic Agents.Gastroenterology · 2019Article
- Cleavage factor 25 deregulation contributes to pulmonary fibrosis through alternative polyadenylation.The Journal of clinical investigation · 2019Article
- Gene correlation network analysis to identify regulatory factors in idiopathic pulmonary fibrosis.Thorax · 2019Article
- Inflammatory pathways are upregulated in the nasal epithelium in patients with idiopathic pulmonary fibrosis.Respiratory research · 2018Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundIdiopathic Pulmonary Fibrosis (IPF) is a fatal fibrotic lung disease occurring predominantly in middle-aged and older adults. The traditional diagnostic classification of IPF is based on clinical, radiological, and histopathological features. However, the considerable heterogeneity in IPF presentation suggests that differences in gene expression profiles can help to characterize and distinguish disease severity.
methodsWe used data-driven unsupervised clustering analysis, combined with a knowledge-based approach to identify and characterize IPF subgroups.
resultsUsing transcriptional profiles on lung tissue from 131 patients with IPF/UIP and 12 non-diseased controls, we identified six subgroups of IPF that generally correlated with the disease severity and lung function decline. Network-informed clustering identified the most severe subgroup of IPF that was enriched with genes regulating inflammatory processes, blood pressure and branching morphogenesis of the lung. The differentially expressed genes in six subgroups of IPF compared to healthy control include transcripts of extracellular matrix, epithelial-mesenchymal cell cross-talk, calcium ion homeostasis, and oxygen transport. Further, we compiled differentially expressed gene signatures to identify unique gene clusters that can segregate IPF from normal, and severe from mild IPF. Additional validations of these signatures were carried out in three independent cohorts of IPF/UIP. Finally, using knowledge-based approaches, we identified several novel candidate genes which may also serve as potential biomarkers of IPF.
conclusionsDiscovery of unique and redundant gene signatures for subgroups in IPF can be greatly facilitated through unsupervised clustering. Findings derived from such gene signatures may provide insights into pathogenesis of IPF and facilitate the development of clinically useful biomarkers.
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