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IPF AEx Series

ABSTRACT: Viruses in acute exacerbations of idiopathic pulmonary fibrosis Keywords: viral detection BAL from patients with acute exacerbations of IPF and stable IPF were hybridized to a pan-viral cDNA microarray to evaluate the presence of virus during these episodes

ORGANISM(S): Viruses

SUBMITTER: Sharon Wootton

PROVIDER: E-GEOD-27578 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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IPF AEx Series

Project description:Viruses in acute exacerbations of idiopathic pulmonary fibrosis Keywords: viral detection

2011-03-03 | GSE27578 | GEO

BAL proteomic signature of lung adenocarcinoma in IPF patients and its transposition in serum samples for less invasive diagnostic procedures

Project description:Idiopathic pulmonary fibrosis (IPF) is a form of chronic and irreversible fibrosing interstitial pneumonia of unknown aetiology, with an average survival time of 3-5 years after diagnosis. Emerging evidence suggests that IPF increases the risk of lung carcinogenesis. Both diseases show similarities in terms of risk factors, such as history of smoking, concomitant emphysema, and viral infections, besides sharing similar pathogenic pathways. Lung cancer diagnosis is often difficult in IPF patients because of the diffuse lung injuries and abnormalities due to the underlying fibrosis. This is reflected in the lack of optimal therapeutic strategies for patients with both diseases. For this purpose, we performed a proteomic study on bronchoalveolar lavage (BAL) samples from IPF, LC associated with IPF (LC-IPF) patients, and healthy controls (CTRL). Molecular pathways involved in inflammation, immune response, lipid metabolism and cell adhesion were found for the dysregulated proteins in LC-IPF, of which TTHY, APOA1, S10A9, RET4, GDRI1 and PROF1. The correlation test revealed a relationship between inflammation-related proteins and proteins associated with lipid metabolism. Also, the up-regulation of PROF1 in LC-IPF BAL and S10A9 in LC-IPF serum was validated. While APOA1 and APOE were validated as highly abundant in IPF BAL and low abundant in IPF serum. We evaluated nicotinamide phosphoribosyltransferase levels in serum highlighting its down-regulation in LC-IPF. Our retrospective analyses on BAL of IPF and LC-IPF patients extrapolate some potential biomarkers whose further evaluation at the serum level, permits the measurement of these potential biomarkers with a less invasive procedure.

2023-03-11 | PXD037720 | Pride

Assessment of Viral RNA in Idiopathic Pulmonary Fibrosis Using RNA-seq [poly(A) RNA]

Project description:We identified sporadic low-level evidence of viral infections in our lung tissue specimens, but did not find a statistical difference for expression of any virus, including EBV, herpesvirus saimiri and HERV-K, between IPF and control lungs. To the best of our knowledge, this is the first publication that employs RNA-seq to assess whether viral infections are linked to the pathogenesis of IPF. Our results do not address the role of viral infection in acute exacerbations of IPF, however, this analysis patently did not support an association between herpes virus detection and IPF. Conclusions: To the best of our knowledge, this is the first publication that employs RNA-seq to assess whether viral infections are linked to the pathogenesis of IPF. Our results do not address the role of viral infection in acute exacerbations of IPF, however, this analysis patently did not support an association between herpes virus detection and IPF.

2020-04-02 | GSE138239 | GEO

Assessment of Viral RNA in Idiopathic Pulmonary Fibrosis Using RNA-seq [nonPoly(A) RNA]

Project description:Results: We identified sporadic low-level evidence of viral infections in our lung tissue specimens, but did not find a statistical difference for expression of any virus, including EBV, herpesvirus saimiri and HERV-K, between IPF and control lungs. To the best of our knowledge, this is the first publication that employs RNA-seq to assess whether viral infections are linked to the pathogenesis of IPF. Our results do not address the role of viral infection in acute exacerbations of IPF, however, this analysis patently did not support an association between herpes virus detection and IPF. Conclusions: To the best of our knowledge, this is the first publication that employs RNA-seq to assess whether viral infections are linked to the pathogenesis of IPF. Our results do not address the role of viral infection in acute exacerbations of IPF, however, this analysis patently did not support an association between herpes virus detection and IPF.

2020-04-02 | GSE138283 | GEO

The soluble factor milieu in IPF and in COPD exacerbations dysregulates epithelial differentiation

Project description:In idiopathic pulmonary fibrosis (IPF) and chronic obstructive pulmonary disease (COPD), epithelial abnormalities are present including bronchiolization and alveolar cell death and dysfunction. As epithelial progenitor cells are directed by their microenvironment, we hypothesized that changes in the microenvironment disrupt normal epithelial growth and differentiation. We therefore mimicked the soluble factor microenvironment in IPF using an IPF cocktail (IPFc), composed of 9 factors which are increased in IPF lungs (CCL2, IL-1β, IL-4, IL-8, IL-13, IL-33, TGF-β, TNFα and TSLP) and in COPD exacerbations using an exacerbation cocktail (EC) composed of 4 factors that are increased during an exacerbation of COPD (TNFα, IL-1β, IL-6, IL-8). We asked whether the soluble factor milieu in IPF and COPD exacerbations affects epithelial growth and differentiation. Mouse lung organoids (primary EpCAM+ cells co-cultured with CCL206 fibroblasts) were used to study epithelial growth and differentiation. Organoids exposed to IPFc, EC or TGF-β (as a comparator) were resorted into EpCAM+ and CCL206 fractions, and subjected to RNA-sequencing.

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IPF Cell Atlas

Project description:IPF Cell Atlas

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Gene expression changes in IPF

Project description:To compare the gene expression changes in IPF and normal lung tissues. 4 IPF and 4 Normal samples

2012-06-29 | E-GEOD-35145 | biostudies-arrayexpress

IPF versus Control

Project description:Archived lung tissues of patients with IPF were obtained from the tissue bank of the Department of Pathology at the University of Pittsburgh. The diagnosis of IPF was confirmed by open lung biopsy. All patients fulfilled the criteria of the American Thoracic Society and European Respiratory Society for the diagnosis of IPF. Normal histology lung tissues resected from patients with lung cancer were used as controls. Keywords: parallel sample

2005-08-08 | GSE2052 | GEO

The soluble factor milieu in IPF and in COPD exacerbations dysregulates epithelial differentiation

Project description:The soluble factor milieu in IPF and in COPD exacerbations dysregulates epithelial differentiation

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Idiopathic pulmonary fibrosis (IPF)

Project description:Idiopathic pulmonary fibrosis (IPF)

| PRJNA802122 | ENA