Isolate samples (BAL and UA)
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA688510 | ENA |
REPOSITORIES: ENA
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Project description:Clinical bronchoalveolar lavage (BAL) samples Targeted loci
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Project description:BAL samples raw sequence reads from lung transplant recipients
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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
Project description:Bronchoalveolar lavage samples collected from lung transplant recipients. Numeric portion of sample name is an arbitrary patient ID and AxBx number indicates the perivascular (A) and bronchiolar (B) scores from biopsies collected on the same day as the BAL fluid was collected. Several patients have more than one sample in this series and can be determined by patient number followed by a lower case letter. Acute rejection state is determined by the combined A and B score - specifically, a combined AB score of 2 or greater is considered an acute rejection. Keywords = Bronchoalveolar lavage Keywords = lung transplant Keywords: other
2004-11-30 | GSE2018 | GEO
Project description:Optimization of the protocols for isolation HLA-DR (MHCII) peptides from human BAL.
2016-08-08 | PXD002439 | Pride
Project description:Brachypodium hybridum Bal-P1 Resequencing genome sequencing
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Project description:We performed high-throughput single-cell RNA sequence using mouse BAL cells to identify subpopulations of airway cells.
2023-01-21 | GSE166290 | GEO
Project description:Background: A subset of asthmatics does not respond to steroid therapy and therefore is at risk for escalation of disease severity. The cause of corticosteroid resistant (CR) asthma is unknown. Gene microarray technologies have the potential to substantiate new hypotheses regarding the etiology of corticosteroid resistance. Methods: Gene microarray analysis was performed with bronchoalveolar lavage (BAL) cells of CR and corticosteroid sensitive (CS) asthmatics. Increased gene expression was verified with real time PCR and at the protein level by ELISA. Findings: Microarray analyses demonstrated significantly higher levels (over two-fold increase, p<0.05) of TNF-alpha, IL-1alpha, IL-1beta, IL-6, CXCL1, CXCL2, CXCL3, CXCL8 (IL-8), CCL3, CCL4, CCL20 gene expression in BAL cells of CR than CS asthmatics. These findings, confirmed by RT-PCR in additional BAL samples, were consistent with classical macrophage activation by bacterial products. In contrast, markers of alternatively-activated macrophages, Arginase I and CCL24, were decreased in CR asthmatics. Genes associated with activation of the LPS signaling pathway (EGR1, DUSP2, MAIL, TNFAIP3) were significantly elevated in CR BAL samples (p<0.05). CR asthmatics had significantly higher amounts (1444.0±457.3 pg per mg of total protein) of LPS in BAL fluid than CS asthmatics (270.5±216.0 pg; p<0.05). Prolonged exposure to LPS induced functional steroid resistance to dexamethasone (DEX) in normal monocytes, demonstrated by persistently elevated IL-6 levels in the presence of DEX. Interpretation: Classical macrophage activation and induction of LPS signaling pathways along with high endotoxin levels detected in BAL fluid from CR asthmatics suggest that LPS exposure may contribute to CR asthma. Experiment Overall Design: Patients with a diagnosis of asthma according to American Thoracic Society criteria were selected for evaluation. Asthmatics had a baseline FEV1% predicted of 55% to 85% of predicted, a beta2-adrenergic response of â¥12% of baseline FEV1% predicted and/or a methacholine PC20 value of â¤8 mg/ml. Asthma patients were further subdivided in CR and CS groups, based on their response to steroids. The definition was based on change in FEV1 % predicted over a one-week course of 40 mg/day of oral prednisone. Asthmatic patients were defined as CS if they had an increase in FEV1% predicted of greater than 15% after a one-week course of prednisone, and as CR if less than 12% change in FEV1% predicted was observed. None of the asthmatic subjects recruited for this study had evidence for other types of lung diseases. None of the subjects had received systemic corticosteroid therapy for at least one month prior to bronchoscopy. All subjects provided written informed consent to participate in the study. The study was approved by the Institutional Review Board at National Jewish Medical and Research Center, Denver, CO. Gene array studies of BAL macrophages were performed in 3 CR and 3 CS asthmatics.
2009-07-01 | E-GEOD-7368 | biostudies-arrayexpress
Project description:This study describes a circulating miRNA signature of unstable angina (UA), which may be used as a novel biomarker for unstable coronary artery disease (CAD). The Taqman low-density miRNA array were used to identify distinct miRNA expression profiles in the plasma of patients with typical UA and angiographically documented CAD (UA group, n = 13) compared to individuals with non-cardiac chest pain (control group, n = 13).
2013-08-13 | GSE49823 | GEO
Project description:Next-generation sequencing of human BAL cells obtained from human patients with differing degrees of asthma in a search for variations in gene expressions.
2021-04-01 | GSE136587 | GEO