Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1243056 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR32904560_1.fastq.gz | Fastqsanger.gz | |||
| SRR32904560_2.fastq.gz | Fastqsanger.gz | |||
| SRR32904561_1.fastq.gz | Fastqsanger.gz | |||
| SRR32904561_2.fastq.gz | Fastqsanger.gz | |||
| SRR32904562_1.fastq.gz | Fastqsanger.gz |
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Project description:Cystic Fibrosis (CF) is the most common life limiting genetic disorder, characterized by chronic respiratory failure secondary to inflammation and chronic bacterial lung infection. Pseudomonas aeruginosa lung infection is associated with more severe lung disease and rapid progression of respiratory failure when compared to Staphylococcus aureus infection. We hypothesized that a specific signature of epigenetic factors targeting specific gene transcripts contributes to the increased morbidity seen in CF patients with chronic Pseudomonas infection. We collected exhaled breath condensate (EBC) from 27 subjects and evaluated miRNA signatures in these samples using commercial PCR array. We identified predicted mRNA targets and associated signaling pathways using Ingenuity Pathway Analysis. We found 11 differentially expressed miRNAs in EBC of patients infected with Pseudomonas aeruginosa compared to EBC from CF patients who were not chronically infected with Pseudomonas aeruginosa.
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Project description:Novel exhaled breath condensate device tests 4 times. Each test generated a single saliva sample and a corresponding exhaled breath condensate sample
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Project description:We analyzed expression of miRNAs in Exhaled Breath Condensates from pediatric patients with sickle cell disease, asthma, sickle cell disease and asthma, and controls
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Project description:To analyze expression of inflammatory cytokines in Exhaled Breath Condensates from pediatric patients with sickle cell disease, asthma, sickle cell disease and asthma, and controls
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Project description:<p>Real-time breath analysis using secondary electrospray ionization coupled with high-resolution mass spectrometry is a fast and noninvasive method to access the metabolic state of a person. However, it lacks the ability to unequivocally assign mass spectral features to compounds due to the absence of chromatographic separation. This can be overcomed by using exhaled breath condensate and conventional liquid chromatography-mass spectrometry (LC-MS) systems. In this study, to the best of our knowledge, we confirm for the first time the presence of six amino acids (GABA, Oxo-Pro, Asp, Gln, Glu, and Tyr) previously reported to be involved in response to and side effects from antiseizure medications in exhaled breath condensate and by extension in exhaled human breath.</p>
2023-01-26 | MTBLS6760 | MetaboLights
Project description:The present study explored whether the proteomic analysis of exhaled breath condensate (EBC) may provide potential biomarkers for their use in non-invasive screening strategies for the early detection of lung cancer (LC). EBC was collected from 192 individuals (49 control volunteers, 49 risk factor-smoking volunteers, 46 chronic obstructive pulmonary disease patients and 48 LC patients). Using LC-MS/MS a total of 348 different proteins with a different pattern among the four groups were identified in EBC samples. Despite the great variability observed among individuals, significantly more proteins were identified in the EBC from LC patients compared to other groups. Furthermore, the average number of proteins identified per sample was significantly higher in LC patients and Receiver Operating Characteristic curve analysis showed an area under the curve of 0.8, indicating diagnostic value. Proteins frequently detected in EBC, such as dermcidin and hornerin, along with others much less frequently detected, such as hemoglobin and histone isoforms, were identified. Cytokeratins (KRTs) were the most abundant proteins in EBC samples and levels of KRT6A, KRT6B and KRT6C isoforms were significantly higher in samples from LC patients. Moreover, the amount of most KRTs in EBC samples from LC patients showed a significant positive correlation with tumor size. Finally, we used a random forest algorithm to generate a robust model using EBC protein data for the diagnosis of patients with LC. Thus, this study demonstrates that the proteomic analysis of EBC samples is an appropriated approach to develop biomarkers for the diagnosis of lung cancer.
2019-08-16 | PXD006436 | Pride
Project description:Obtaining multiple sample types from the same exhaled breath condensate (EBC) sample can reduce the number of samples needed for diagnostics purposes, allowing for sampling to be completed quicker and making it even easier to collect breath from patients. In this study, we performed analysis for volatile organic compounds (VOCs) and proteins from the same EBC sample. Pooled EBC samples were split into two groups: three samples that utilized immersion thin film-solid phase microextraction (TF-SPME) sampling for VOCs analysis and three samples that did not undergo TF-SPME sampling (non-TF-SPME). All six EBC samples were analyzed using liquid chromatography with tandem mass spectrometry (LC-MS/MS) for proteomics analysis. VOCs were analyzed via two-dimensional gas chromatography-mass spectrometry (GC x GC-MS). One hundred and eighty-four VOCs were found to be more abundant in EBC samples compared to blank or controls. There was no significant difference in the number of proteins detected in the TF-SPME samples compared to the non-TF-SPME samples and 144 of the 206 total unique proteins detected were found in both sample groups. These results indicate that TF-SPME sampling does not negatively affect the number of proteins that can be detected in EBC. This work is a step towards linking VOC and protein data together to obtain multi-omics breath data from a single breath sample.
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Project description:Background: Primary graft dysfunction (PGD) remains a challenge to lung transplantation (LTx) recipients as a leading cause of poor early outcomes. New methods are needed for the rapid detection of PGD and the measurement of particle flow rate (PFR) from exhaled breath is a novel means to monitor disease. Methods: 22 recipient pigs underwent orthotopic left LTx and were evaluated for PGD on the third post-operative day. Exhaled breath particles (EBPs) and PFR were measured on mechanical ventilation. EBPs were evaluated with mass spectrometry and the proteome was compared to tissue biopsies and bronchoalveolar lavage fluid (BALF). Findings were confirmed in EBPs from 11 human transplant recipients. Results: 9 recipients developed PGD and had significantly higher PFR (686.4 (449.7-8824.0) particles per minute (ppm)) compared to recipients without PGD (116.6 (79.7-307.4) ppm, p=0.0005). From proteomic analysis, porcine and human EBP proteins recapitulated the BAL and adherens and tight junction proteins were underexpressed in PGD tissue. Conclusions: Histological and proteomic analysis found significant changes to the alveolar-capillary barrier to explain the increased PFR in recipients with PGD. Combined with the similarity of proteomic profiles between EBPs and BALF, exhaled breath measurement is proposed as a rapid and non-invasive bedside measurement of PGD.
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Project description:The establishment and public sharing of comprehensive proteome maps of human tissues and biofluids are essential to improve biomedical knowledge and to support biomarker discovery studies. In this study, we performed an in-depth proteomics characterization of the exhaled breath condensate (EBC), a non-invasive sample obtained from the condensation of the airway lining fluid. Two pooled samples of EBC, each combined from 10 healthy donors, were lyophilized and their protein content analyzed by high-resolution tandem mass spectrometry-based proteomics. Two “technical” negative control samples were processed in parallel with the pooled samples to correct for exogenous protein contamination and avoid erroneous identifications.
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Project description:Tuberculosis (TB) is one of the top ten causes of death worldwide and the leading cause of death from a single infectious agent. Globally, an estimated of 10 million people developed TB in 2018 according to WHO report. An estimated one third of all TB cases are not diagnosed or notified, partly due to the major limitations of current diagnostic tools. To achieve the goals of the WHO’s End TB Strategy, which targets for 2030 a 90% reduction in the number of TB deaths and an 80% reduction in the TB incidence rate compared with levels in 2015, diagnostic tools are critically important. Among the three diagnostic priorities identified by the WHO and the TB community is the development of a point-of-care biomarker-based non-sputum-based test to diagnose pulmonary TB, and ideally also extrapulmonary TB. To be successfully implemented at point-of-cares, a new test should use an easily accessible sample, such as urine, blood or breath condensate. Here, we explored whether bacilli-derived molecules released in the extracellular milieu during infection could be detected in the exhaled breath condensate, allowing a specific diagnosis of TB. Interestingly, we detected by proteomic analysis a set of Mycobacterium tuberculosis proteins in all smear-positive and smear-negative adult patients, as well as of children with TB
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