Project description:We profiled scRNA-seq of 284 samples collected from 196 individuals, including 22 patients with mild/moderate symptoms, 54 hospitalized patients with severe symptoms, and 95 recovered convalescent persons, as well as 25 healthy controls. The samples were obtained from various tissue types, including human peripheral blood mononuclear cells (249), bronchoalveolar lavage fluid (12) and pleural pleural effusion (1)/sputum (22).
Project description:A collection of constraint-based metabolic models of bronchoalveolar lavage fluid epithelia cells infected with SARS-CoV-2 based that were generated based on gene-expression data.
Project description:A collection of cell-type specific constraint-based metabolic models of human BALF2 cells (bronchoalveolar Lavage fluid cells) infected with SARS-CoV-2 based that were generated based on gene-expression data using a manually curated version of Recon 2 as base model.
Project description:Summary: Heart failure is frequently accompanied by pleural effusion, yet the biological impact of heart failure–associated pleural fluid on vascular endothelial function remains unclear. Here, we show that heart failure pleural fluid impairs endothelial barrier integrity and angiogenic capacity in human umbilical vein endothelial cells. Functional assays revealed increased permeability, reduced migration, and altered tube formation following treatment with patient-derived pleural fluid. Mechanistically, heart failure pleural fluid increased reactive oxygen species production and inflammatory signaling while downregulating tight junction protein ZO-1. Small RNA profiling identified miR 501 3p as a key mediator of these effects. Gain- and loss-of-function experiments demonstrated that miR 501 3p directly regulates ZO-1 expression and contributes to barrier disruption. These findings establish a microRNA-dependent mechanism linking heart failure pleural fluid to endothelial dysfunction and suggest a potential molecular pathway contributing to vascular complications in heart failure.
Project description:Transcriptional profile comparison of the pleural and ascites fluids in hydropic fetuses affected with chylothorax. Two-condition experiment, pleural fluid vs. ascites fluid. Comparison of the transcriptional profile between sample collected before and after OK-432 treatment and between fetuses with and without a G404S mutation in the ITGA9 gene
Project description:Purpose: Characterize the gene expression profile of of peritoneal mouse macrophages in Endotoxic shock and Tolerance through RNA sequencing Methods: RNA sequencing of RNA from peritoneal macrophages in Endotoxic shock and Tolerance isolated by peritoneal lavage and FACS sorting (F4/80+ CD11b+) Results: Endotoxic shock and Tolerance peritoneal mouse macrophages display differential gene expression. Conclusions: Endotoxic shock and Tolerance peritoneal mouse macrophages display differential gene expression.
Project description:Pleural infection is a severe and complicated disease with increasing incidence worldwide and is characterised by substantial associated morbidity and mortality.1,2 Although it is accepted that the disease is heterogeneous, and there is a validated clinical prediction score (RAPID)3,4, the biological endotypes of pleural infection remain elusive and pleural fluid specific criteria to assess the intrapleural response are not available. A better understanding of pleural infection subtypes could lead to improved treatment strategies and clinical outcomes. All patients with pleural infection follow the same clinical journey which focusses on hospital admission, pleural fluid drainage and administration of antibiotics however, their recovery progress and clinical outcomes differ significantly.1,2 A subgroup of patients exhibits ineffective or failed intrapleural fibrinolysis leading to the development of fibrous septations which further complicates treatment. Consequently, approximately 30% of patients do not respond to treatment and require invasive treatments including surgical drainage. Tandem mass spectrometry is a high-throughput proteomics assay which is a reliable, unbiased, and hypothesis-free analytical method for investigating the underlying biology of disease using clinical specimens.5 The pleural fluid proteome faithfully reflects the intrapleural environment and could be utilised to identify disease key mediators, biomarkers, and treatment targets. For instance, pleural fluid pH, glucose and lactate dehydrogenase are used as clinical biochemistry markers for diagnosing patients with pleural infection.1 Our study (The Oxford Pleural Infection Endotyping Study, TORPIDS 2) applied mass spectrometry to pleural fluid specimens (n=80) from the PILOT trial.4 Our primary aims were to discover endotypes in pleural infection, characterise the intrapleural immune response and investigate the association between patient endotypes and high-precision bacterial patterns. We assessed the association between pleural infection endotypes and important clinical outcomes (1-year survival and need for surgery)
Project description:We used the scRNA-seq to characterize disease-related heterogeneity within cell populations of macrophages/monocytes in the bronchoalveolar lavage fluid from West Highland white terriers either healthy or affected with canine idioapthic pulmonary fibrosis. The disease is still not well understood, occurs in old West Highland white terriers and results from deposition of fibrotic tissue in the lung parenchyma causing respiratory failure.
