Pulmonary tuberculosis metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA664352 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12964900.fastq.gz | Fastqsanger.gz | |||
| SRR12964900_1.fastq.gz | Fastqsanger.gz | |||
| SRR12964900_2.fastq.gz | Fastqsanger.gz | |||
| SRR12965000_1.fastq.gz | Fastqsanger.gz | |||
| SRR12965000_2.fastq.gz | Fastqsanger.gz |
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Project description:: Pulmonary tuberculosis (TB) generates chronic systemic inflammation and metabolic dysregulation. The liver is the master regulator of metabolism and to determine the impact of pulmonary TB on this organ we undertook unbiased mRNA and protein analyses of the liver in mice with TB.
2024-09-19 | PXD055781 | Pride
Project description:Pulmonary tuberculosis is a multigene disease, and some of the genes affect the development of Pulmonary tuberculosis. The study wants to find different expression genes in blood from Pulmonary tuberculosis patient and normal people who have genetic relationship wtih each other. We used microarrays to detail the global programme of gene expression in the blood between Pulmonary tuberculosis patient's and normal people's who have genetic relationship wtih each other.
2017-12-06 | GSE107731 | GEO
Project description:Background: Mycobacterium tuberculosis infection is a leading cause of infectious death worldwide. Gene-expression microarray studies profiling the blood transcriptional response of tuberculosis (TB) patients have been undertaken in order to better understand the host immune response as well as to identify potential biomarkers of disease. To date most of these studies have focused on pulmonary TB patients with gene-expression profiles of extra-pulmonary TB patients yet to be compared to those of patients with pulmonary TB or sarcoidosis. Methods A novel cohort of patients with extra-pulmonary TB and sarcoidosis was recruited and the transcriptional response of these patients compared to those with pulmonary TB using a variety of transcriptomic approaches including testing a previously defined 380 gene meta-signature of active TB. Results The 380 meta-signature broadly differentiated active TB from healthy controls in this new dataset consisting of pulmonary and extra-pulmonary TB. The top 15 genes from this meta-signature had a lower sensitivity for differentiating extra-pulmonary TB from healthy controls as compared to pulmonary TB. We found the blood transcriptional responses in pulmonary and extra-pulmonary TB to be heterogeneous and to reflect the extent of symptoms of disease. Conclusions The transcriptional signature in extra-pulmonary TB demonstrated heterogeneity of gene expression reflective of symptom status, while the signature of pulmonary TB was distinct, based on a higher proportion of symptomatic individuals. These findings are of importance for the rational design and implementation of mRNA based TB diagnostics.
2016-11-04 | GSE83456 | GEO
Project description:Genome wide DNA methylation profiling in the blood between Pulmonary tuberculosis patient's and normal people's who have genetic relationship wtih each other.
2017-12-12 | GSE107917 | GEO
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.
2017-04-18 | GSE93316 | GEO
Project description:<p>Pulmonary tuberculosis (PTB) and diabetes mellitus (DM) are common chronic diseases that threaten human health. Patients with DM are susceptible to PTB, an important factor that aggravates the complications of diabetes. However, the molecular regulatory mechanism underlying the susceptibility of patients with DM to PTB infection remains unknown. Healthy subjects, patients with primary PTB and patients with primary PTB complicated by DM were recruited according to inclusion and exclusion criteria. Peripheral whole blood was collected, and alteration profiles and potential molecular mechanisms were further analyzed using integrated bioinformatics analysis of metabolomics and transcriptomics. In this study, transcriptional data revealed that lipocalin 2 (LCN2), defensin alpha 1 (DEFA1), peptidoglycan recognition protein 1 (PGLYRP1) and integrin subunit alpha 2b (ITGA2B) were significantly upregulated, while chloride intracellular channel 3 (CLIC3) significantly down-regulated in PTB-DM by contrast to HC group. Additionally, the IL-17, PI3K-AKT and PPAR signaling pathways are important for PTB infection and regulation of PTB-complicated diabetes. Metabolomic data showed that glycerophospholipid metabolism, carbon metabolism and fat digestion and absorption processes were enriched in the differential metabolic analysis. Finally, integrated analysis of both metabolomic and transcriptomic data indicated that the NOTCH1/JAK/STAT signaling pathway is important in PTB complicated by DM. In conclusion, PTB infection altered the transcriptional and metabolic profiles of patients with DM. Metabolomic and transcriptomic changes were highly correlated in PTB-infected patients with DM. Peripheral metabolite levels may be used as biomarkers for PTB management in patients with DM.</p><p><strong>IMPORTANCE:</strong> The comorbidity of diabetes mellitus (DM) significantly increases the risk of tuberculosis infection and adverse tuberculosis treatment outcomes. Most previous studies have focused on the relationship between the effect of blood glucose control and the outcome of anti-tuberculosis treatment in pulmonary tuberculosis (PTB)-DM; however, early prediction and the underlying molecular mechanism of susceptibility to PTB infection in patients with DM remain unclear. Here, transcriptome sequencing and untargeted metabolomics were performed to elucidatethe key molecules and signaling pathways involved in PTB infection and the susceptibility of patients with diabetes to PTB. Our findings contribute to the development of vital diagnostic biomarkers for PTB or PTB-DM and provide acomprehensive understanding of molecular regulation during disease progression.</p>
2023-07-26 | MTBLS7623 | MetaboLights
Project description:Novel biomarkers to identify infectious patients transmitting Mycobacterium tuberculosis are urgently needed to control the global tuberculosis (TB) pandemic. We hypothesized that proteins released into the plasma in active pulmonary TB are clinically useful biomarkers to distinguish TB cases from healthy individuals and patients with other respiratory infections. We applied a highly sensitive non-depletion tandem mass spectrometry discovery approach to investigate plasma protein expression in pulmonary TB cases compared to healthy controls in South African and Peruvian cohorts. . Plasma samples were analysed from 11 untreated male patients with active pulmonary TB and 10 male healthy control samples. Each plasma sample was initially separated into four segments by size exclusion chromatography, and each segment was processed individually. Analyses of plasma segments were performed in twelve iTRAQ (isobaric tags for relative and absolute quantification) 8-plex experimental sets in a block randomised design comprising three experimental sets. Each iTRAQ experiment contained a bridging master-pool plasma sample run in every experiment. Healthy controls were matched to TB samples by age, ethnicity, and smoking status within each iTRAQ set. Protein abundances from the plasma segments and multi-consensus reports were combined and adjusted for experimental batch effects. Protein abundances from the remaining combined plasma segment proteomes between experimental sets and the combined multi-consensus proteomes were analysed by complementary bioinformatic approaches to identify candidate diagnostic protein biomarkers. In total, 4,696 protein identifications were made across all iTRAQ experiments, at 5% FDR (false discovery rate). This comprised 2,332 unique host-derived proteins and 22 Mtb-derived proteins. Of these, 594 host proteins had a quantification result for every sample analysed and therefore comprised the complete quantified proteome. Subsequent bioinformatic analysis identified 118 differentially expressed proteins by three complementary bioinformatic pipelines and were taken forward in subsequent validation work as strong candidate biomarkers of pulmonary TB.
2024-06-22 | PXD051070 | Pride
Project description:In this study, differentially abundant plasma metabolites were screened by using the ultra-high performance liquid chromatography coupled with Q Exactive mass spectrometry in pulmonary tuberculosis(TB) patients and normal controls(NC) or patients with other pulmonary diseases such as, community-acquired pneumonia(CAP) and lung cancer(LC).
2019-08-05 | ST001231 | MetabolomicsWorkbench
Project description:The critical role of type I IFN (IFN I ) in viral disease is thoroughly documented while their function in bacterial infection remains ambiguous. General interest in biological functions of IFN I in Mycobacterium tuberculosis (Mtb) infection was raised by the identification of a distinct IFN I gene expression signature in tuberculosis (TB) patients. Here we demonstrate that TB-susceptible mice lacking the receptor for IFN I (IFNAR1) were protected from death upon aerogenic infection with Mtb. Increased survival was accompanied by reduced bacterial burden and ameliorated lung pathology as well as diminished production of proinflammatory IL-1?, among other cytokines. IFNAR1 signaling did not affect T cell responses, but markedly altered migration of inflammatory monocytes and neutrophils to the lung during pulmonary TB. This process was orchestrated by presence of IFNAR1 in both immune and tissue-resident radioresistant cells. IFNAR1-driven TB susceptibility was initiated by CXCL5/CXCL1-driven accumulation of neutrophils into alveoli and subsequently a distinct compartmentalization of Mtb in lung phagocytes. We conclude that IFN I alters early innate events at the site of Mtb invasion leading to unleashed inflammation. Hence, our data furnish a mechanistic explanation for the detrimental role of IFN I in pulmonary TB. dual-color color-swap
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Project description:We used human miRNA arrays to explore the miRNA expression profile in pulmonary tuberculosis patients (PTB), pulmonary with pleural tuberculosis patients (PPLTB) and non-tuberculous pleurisy patients (NTP).
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