Metatranscriptomes of Tuberculous Sputum
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB10919 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR1022500.fastq.gz | Fastqsanger.gz | |||
| ERR1022510.fastq.gz | Fastqsanger.gz | |||
| ERR1022501.fastq.gz | Fastqsanger.gz | |||
| ERR1022511.fastq.gz | Fastqsanger.gz | |||
| ERR1022502.fastq.gz | Fastqsanger.gz |
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Project description:In this study we profiled sputum samples of active and non tuberculosis patients for a comparative proteomics study to identify deregulated important molecules as markers.
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Project description:Sputum expectorated by the pulmonary tuberculosis patients still remains a primary diagnostic specimen. The expression pattern of mycobacteria in sputum will lead to an insight of bacterial adaptation at the most highly transmissible stage of infection and can also help in identifying newer diagnostic as well as drug targets. Further, the identification of crossreactive gene targets from the sputum samples of other lung diseases will help to find the diagnostic candidates which will be highly specific to pulmonary tuberculosis.
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Project description:Purpose: Accurate diagnosis of complete inactivation of tuberculosis lesions is still a challenge with respect to sputum-negative tuberculosis. RNA-sequencing was conducted to uncover potential lncRNA indicators of metabolic activity in tuberculosis lesions. Methods: Lung tissues with high metabolic activity (PET-high) and low metabolic activity (PET-low) demonstrated by fluorine-18-fluorodeoxyglucose positron emission tomography/computed tomography (FDG-PET/CT) were collected from five sputum-negative tuberculosis patients for RNA-sequencing. Differentially expressed mRNAs and lncRNAs were identified, and their correlations were evaluated to constructed lncRNA-mRNA co-expression network. Afterwards, cis- or trans-targets of differentially expressed lncRNAs were predicted, followed by establishing lncRNA-target-pathway network, in which lncRNAs and mRNAs with high degrees were measured by quantitative real-time PCR using samples collected from 11 patients. Prediction efficiencies of lncRNA indicators were assessed by receiver operating characteristic curve analysis, Bioinformatics analysis was performed for potential lncRNAs. Results: In total, 386 mRNAs and 44 lncRNAs were identified to be differentially expressed. Differentially expressed mRNAs in lncRNA-mRNA co-expression network were significantly associated with the fibrillar collagen, platelet-derived growth factor binding, and leukocyte migration involved in inflammatory response. One cis-target gene and 440 trans-target genes were predicted for differentially expressed lncRNAs. Seven genes (C1QB, CD68, CCL5, CCL19, MMP7, HLA-DMB, and CYBB) and two lncRNAs (ENST00000429730.1 and MSTRG.93125.4) were validated to be significantly up-regulated. The area under the curve of ENST00000429730.1 and MSTRG.93125.4 was 0.750 and 0.813, respectively. Conclusion: Two lncRNAs ENST00000429730.1 and MSTRG.93125.4 might be considered as potential indicators of metabolic activity in tuberculosis lesions for sputum-negative tuberculosis.
2020-09-30 | GSE158767 | GEO
Project description:Mycobacterium tuberculosis strain:sputum | isolate:sputum Genome sequencing
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Project description:Background: Assessments of airways inflammation in patients with chronic obstructive pulmonary diseases (COPD) require semi-invasive procedures and specialized sample processing know-how. In this study we aimed to set up and validate a novel non-invasive processing-free method for RNA sequencing (RNAseq) of spontaneous sputum samples collected from COPD patients. Methods: Spontaneous sputum samples were collected and stabilized, with or without selection of plugs and with or without the use of a stabilizer specifically formulated for downstream diagnostic testing (PrimeStore® Molecular Transport Medium). After 8-day storage at ambient temperature RNA was isolated according to an optimized RNAzol® method. An average percentage of fragments longer than 200 nucleotides (DV200) >30% and an individual yield >50ng were required for progression of samples to sequencing. Finally, to assess if the transcriptome generated would reflect a true endotype of COPD inflammation, the outcome of single-sample gene-set enrichment analysis (ssGSEA) was validated using an independent set of processed induced sputum samples Results: RNA extracted from spontaneous sputum using a stabilizer showed an average DV200 higher than 30%. 70% of the samples had a yield >50ng and were submitted to downstream analysis. There was a straightforward correlation in terms of gene expression between samples handled with or without separation of plugs. This was also confirmed by principal component analysis and ssGSEA. The top ten enriched pathways resulting from spontaneous sputum ssGSEA were associated to features of COPD, namely, inflammation, immune responses and oxidative stress; up to 70% of these were in common within the top ten enriched pathways resulting from induced sputum ssGSEA. Conclusion: This analysis confirmed that the typical COPD endotype was represented within spontaneous sputum and supported the current method as a non-invasive processing-free procedure to assess the level of sputum cell inflammation in COPD patients by RNAseq analysis.
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Project description:Three complete TMTs for saliva and three complete TMTs for sputum samples from active tuberculosis patients (TB) and their household infected (LTI) and uninfected (nonLTI) contacts.
Parallel Reaction Monitoring (PRM) analysis in sputum samples of infected and uninfected contacts to measure levels of MUC7, CYST, CAH6 and PERL.
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Project description:Several microRNAs (miRs) have been described as potential biomarkers in liquid biopsies and in the context of allergic asthma, while therapeutic effects on the airway expression of miRs remain elusive. In this study, we investigated epigenetic miR-associated mechanisms in the sputum of grass pollen allergic patients with and without allergen specific immunotherapy (AIT). Induced sputum samples of healthy controls (HC), AIT treated and untreated grass pollen allergic rhinitis patients with (AA) and without asthma (AR) were profiled using miR microarray and transcriptome microarray analysis of the same samples. miR targets were predicted in silico and used to identify inverse regulation. Local PGE2 levels were measured using ELISA. Two Hundred and fifty nine miRs were upregulated in the sputum of AA patients compared with HC, while only one was downregulated. The inverse picture was observed in induced sputum of AIT-treated patients: while 21 miRs were downregulated, only 4 miRs were upregulated in asthmatics upon AIT. Of these 4 miRs, miR3935 stood out, as its predicted target PTGER3, the prostaglandin EP3 receptor, was downregulated in treated AA patients compared with untreated. The levels of its ligand PGE2 in the sputum supernatants of these samples were increased in allergic patients, especially asthmatics, and downregulated after AIT. Finally, local PGE2 levels correlated with ILC2 frequencies, secreted sputum IL13 levels, inflammatory cell load, sputum eosinophils and symptom burden.While profiling the sputum of allergic patients for novel miR expression patterns, we uncovered an association between miR3935 and its predicted target gene, the prostaglandin E3 receptor, which might mediate AIT effects through suppression of the PGE2-PTGER3 axis.
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Project description:There is a need for better tools to evaluate new or repurposed TB drugs. The whole blood bactericidal activity (WBA) assay has been advocated for this purpose. We investigated whether transcriptional responses in the WBA assay resemble TB responses in vivo, and whether the approach might additionally reveal mechanisms of response. Microarray analysis was performed on Mycobacterium tuberculosis (Mtb) RNA extracted from whole blood cultures, sputum from TB patients on combination treatment, and drug-free broth cultures
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Project description:Transcriptome analysis of mycobacteria in sputum samples of pulmonary tuberculosis patients
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Project description:Sputum cells collected before (visit 2) and after (visit 4) allergen challenge in asthma patients were isolated and RNA purified for analysis on gene expression arrays. Human subject recruitment part of NIH sponsored protocol as part of the Eosinophil Program Project Grant (PI: Dr. Nizar Jarjour) Sputum cell RNA collected from induced sputum cells before and 48 hours after whole-lung allergen challenge.
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