Genome-wide transcriptional profiling of M.TB–specific antigens stimulated peripheral blood mononuclear cells (PBMCs) for identification of potential signatures in discriminating active tuberculosis from latent infection
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE98461 | GEO | 2018/02/14
REPOSITORIES: GEO
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Project description:While blood transcriptional profiling has improved diagnosis and understanding of disease pathogenesis of adult tuberculosis (TB), no studies applying gene expression profiling of children with TB have been described so far. In this study, we have compared whole blood gene expression in childhood TB patients, as well as in healthy latently infected (LTBI) and uninfected (HC) children in a cohort of Warao Amerindians in the Delta Amacuro in Venezuela. We identified a 116-gene signature set by means of random forest analysis that showed an average prediction error of 11% for TB vs. LTBI and for TB vs. LTBI vs. HC in our dataset. Furthermore, a minimal set of only 9 genes showed a significant predictive value for all previously published adult studies using whole blood gene expression, with average prediction errors between 17% and 23%. Additionally, a minimal gene set of 42 genes with a comparable predictive value to the 116-gene set in both our dataset and the previously published literature cohorts for the comparsion of TB vs. LTBI vs. HC was identified. In order to identify a robust representative gene set that would hold stand among different ethnic populations, we selected ten genes that were highly discriminative between TB, LTBI and HC in all literature datasets as well as in our dataset. Functional annotation of these ten genes highlights a possible role for genes involved in calcium signaling and calcium metabolism as biomarkers for active TB. These ten genes were validated by quantitative real-time polymerase chain reaction in an additional cohort of 54 Warao Amerindian children with LTBI, HC and non-TB pneumonia. Decision tree analysis indicated that five of the ten genes were sufficient to diagnose 78% of the TB cases correctly with 100% specificity. We conclude that our data justify the further exploration of our signature set as biomarkers to diagnose childhood TB. Furthermore, as the identification of different biomarkers in ethnically distinct cohorts is apparent, it is important to cross-validate newly identified markers in all available cohorts. In this study, 27 children 1 to 15 years of age with TB (n=9), LTBI (n=9) and HC (n=9) were recruited between May 2010 and December 2010. Tuberculin skin test (TST) and QuantiFERON-TB Gold In-Tube assay (QFT-GIT) were performed on all children. A sputum sample was collected from all children with expectoration and a gastric aspirate was taken from all children under 6 years of age. Children with active TB were diagnosed based on culture of M. tuberculosis (n=2) or on the basis of clinical, epidemiological and radiological features (n=7). The latter group were children with a TST = 10 mm or a positive QFT-GIT result who presented all of: persistent fever >38M-BM-0C objectively recorded daily for at least two weeks, persistent cough for more than three weeks, weight loss (>5% reduction in weight compared with the highest weight recorded in last three months) or failure to thrive (documented crossing of percentile lines in the preceding three months), persistent lethargy or decrease in playfulness/activity reported by the parent and absence of clinical response on broad-spectrum antibiotics. Standard antero-posterior and lateral chest radiographs (CXRs) were taken from all children. Two independent experts, blinded to all clinical information, evaluated the CXRs and documented their findings on a standard report form. Where the two objective experts disagreed, a third expert was consulted and final consensus was achieved. A diagnosis of TB was only made when the CXR was consistent with TB9 and the child showed a positive clinical response to anti-TB treatment. Children were followed up clinically, radiologically and, in case of a negative TST at inclusion, by means of TST at six and 12 months after inclusion. LTBI was defined as a TST = 10mm and a positive QFT-GIT with a negative culture result on inclusion in the absence of radiological and clinical evidence of TB disease on inclusion as well as on t=6 and t=12 months. HC were children with a TST = 0 mm at inclusion and at t=6 and t=12 months. The HC had a negative QFT-GIT and a negative culture result at inclusion without radiological or clinical evidence of TB disease on inclusion nor on t=6 and t=12 months. TB patients were sampled before initiation of anti-TB treatment. Of three of the nine TB patients, a follow-up sample was taken when the patient was in anti-TB treatment for five months. All children were HIV-negative. 27 samples in total where analyzed, active TB infection (TB, n=9), Latent TB infection (LTBI, n=9) and healthy controls (HC, n=9) . Gene expression values were log2-transformed and differentially expressed genes were identified based on log2 fold changes (M-values). P values were calculated with a Bayes-regularized one-way ANOVA. Random Forest recursive feature elimination was used to find a signature geneset capable of discrimination active TB from latent TB and from non-infected individuals.
2013-02-05 | E-GEOD-41055 | biostudies-arrayexpress
Project description:While blood transcriptional profiling has improved diagnosis and understanding of disease pathogenesis of adult tuberculosis (TB), no studies applying gene expression profiling of children with TB have been described so far. In this study, we have compared whole blood gene expression in childhood TB patients, as well as in healthy latently infected (LTBI) and uninfected (HC) children in a cohort of Warao Amerindians in the Delta Amacuro in Venezuela. We identified a 116-gene signature set by means of random forest analysis that showed an average prediction error of 11% for TB vs. LTBI and for TB vs. LTBI vs. HC in our dataset. Furthermore, a minimal set of only 9 genes showed a significant predictive value for all previously published adult studies using whole blood gene expression, with average prediction errors between 17% and 23%. Additionally, a minimal gene set of 42 genes with a comparable predictive value to the 116-gene set in both our dataset and the previously published literature cohorts for the comparsion of TB vs. LTBI vs. HC was identified. In order to identify a robust representative gene set that would hold stand among different ethnic populations, we selected ten genes that were highly discriminative between TB, LTBI and HC in all literature datasets as well as in our dataset. Functional annotation of these ten genes highlights a possible role for genes involved in calcium signaling and calcium metabolism as biomarkers for active TB. These ten genes were validated by quantitative real-time polymerase chain reaction in an additional cohort of 54 Warao Amerindian children with LTBI, HC and non-TB pneumonia. Decision tree analysis indicated that five of the ten genes were sufficient to diagnose 78% of the TB cases correctly with 100% specificity. We conclude that our data justify the further exploration of our signature set as biomarkers to diagnose childhood TB. Furthermore, as the identification of different biomarkers in ethnically distinct cohorts is apparent, it is important to cross-validate newly identified markers in all available cohorts. In this study, 27 children 1 to 15 years of age with TB (n=9), LTBI (n=9) and HC (n=9) were recruited between May 2010 and December 2010. Tuberculin skin test (TST) and QuantiFERON-TB Gold In-Tube assay (QFT-GIT) were performed on all children. A sputum sample was collected from all children with expectoration and a gastric aspirate was taken from all children under 6 years of age. Children with active TB were diagnosed based on culture of M. tuberculosis (n=2) or on the basis of clinical, epidemiological and radiological features (n=7). The latter group were children with a TST = 10 mm or a positive QFT-GIT result who presented all of: persistent fever >38°C objectively recorded daily for at least two weeks, persistent cough for more than three weeks, weight loss (>5% reduction in weight compared with the highest weight recorded in last three months) or failure to thrive (documented crossing of percentile lines in the preceding three months), persistent lethargy or decrease in playfulness/activity reported by the parent and absence of clinical response on broad-spectrum antibiotics. Standard antero-posterior and lateral chest radiographs (CXRs) were taken from all children. Two independent experts, blinded to all clinical information, evaluated the CXRs and documented their findings on a standard report form. Where the two objective experts disagreed, a third expert was consulted and final consensus was achieved. A diagnosis of TB was only made when the CXR was consistent with TB9 and the child showed a positive clinical response to anti-TB treatment. Children were followed up clinically, radiologically and, in case of a negative TST at inclusion, by means of TST at six and 12 months after inclusion. LTBI was defined as a TST = 10mm and a positive QFT-GIT with a negative culture result on inclusion in the absence of radiological and clinical evidence of TB disease on inclusion as well as on t=6 and t=12 months. HC were children with a TST = 0 mm at inclusion and at t=6 and t=12 months. The HC had a negative QFT-GIT and a negative culture result at inclusion without radiological or clinical evidence of TB disease on inclusion nor on t=6 and t=12 months. TB patients were sampled before initiation of anti-TB treatment. Of three of the nine TB patients, a follow-up sample was taken when the patient was in anti-TB treatment for five months. All children were HIV-negative.
2013-02-05 | GSE41055 | GEO
Project description:Superbugs such as drug-resistant Mycobacterium tuberculosis (DR-M.tb) poses a serious global health threat. Upon infection, M.tb reaches the alveolar space and comes in close contact with soluble components of the human alveolar lining fluid (ALF) for an uncertain period of time prior to and following its encounter with alveolar compartment cells. Homeostatic ALF hydrolases, which main function is maintaining lung health, modify the M.tb cell envelope, driving M.tb-host cell interactions. Still, the contribution of human ALF to M.tb adaptation to the host during infection is poorly understood. Here, we exposed 4 M.tb strains (H37Rv, HN878, CDC1551, W-7642) with different levels of virulence, transmissibility, and drug resistance to human ALF for shorter (15 min) and longer (12 h) periods of time. RNA sequencing was performed to determine the strains’ transcriptional profiles in response to ALF exposure. Gene expression analysis showed a clear temporal and strain-specific adaptation to human ALF. When comparing ALF-exposed vs. unexposed bacteria for each M.tb strain, differential expression (DE) analysis revealed a total of 397 DE genes associated with lipid metabolism, cell envelope and processes, intermediary metabolism and respiration, and regulatory proteins, among others. Most DE was detected at 12 h post-ALF exposure, with DR-M.tb strain W-7642 having the highest number of DE genes. Interestingly, genes from the KstR2 regulon, which controls the degradation of cholesterol C and D rings, were significantly upregulated early in all strains post-ALF exposure. These results indicate that M.tb-ALF contact (15 min to 12 h prior to M.tb recognition by host cells in the alveolar space) drives global metabolic and physiologic changes in M.tb during the initial stages of the infection, with potential implications in infection outcome.
2024-02-20 | GSE228998 | GEO
Project description:A subset of individuals with a high probability of exposure to M. tuberculosis (M.tb) appears to ‘resist’ established M.tb infection, as demonstrated by serially negative tuberculin skin test (TST) or IFN-γ release assay (IGRA) results. While these ‘resisters’ (RSTR) display IFN-γ-independent T cell responses to the M.tb-specific antigens ESAT-6 and CFP-10, it is currently unknown whether unique T cell functional programs are associated with this clinical outcome. We used multi-modal single-cell RNA, TCR sequencing, multi-parameter flow cytometry, and cytokine analysis in a discovery and validation format to compare the phenotypes and functions of M.tb-specific T cells between RSTRs and matched controls with ‘latent’ M.tb infection (LTBI). M.tb-specific T cells were clonally expanded in both RSTRs and LTBIs, confirming the priming of adaptive immune responses after M.tb exposure. However, M.tb-specific T cells derived from RSTRs showed enrichment of T regulatory as well as Th17-like functional programs compared to LTBIs, which were characterized by Th1*-like effector programs. Th17-like functional programs were also associated with a lack of progression to active TB among South African adolescents with LTBI, as well as bacterial control in published non-human primate studies. Together, these data suggest that ‘resisters’ may successfully control M.tb after exposure and immune priming and establish a set of T cell biomarkers to facilitate further study of this important clinical phenotype.
2024-06-01 | GSE267774 | GEO
Project description:Efforts to eradicate TB are largely threatened by drug-resistant tuberculosis, particularly, multidrug-resistant tuberculosis (MDR-TB). It is imperative to find one or more specific biomarkers for diagnosing MDR-TB earlier and declining the incidence. Growing evidences have showed lncRNAs are widely expressed and take part in the genesis and development of many diseases, including tuberculosis. Therefore, to screen the differential lncRNAs among MDR-TB, drug-sensitive tuberculosis(DS-TB) and healthy controls(HCs) is a good strategy to acquire potential biomarkers for MDR-TB diagnosis and partly describe the mechanism of MDR-TB. Here, the present study aimed to investigate the differential expression profile of lncRNAs in serum among patients with MDR-TB ,DS-TB and HCs using lncRNA microarray
2021-09-10 | GSE183787 | GEO
Project description:Effect of Thiol reductive stress (DTT 1mM) on M.tb Rv was studied. DTT reduced at 1 mM concentration was added to log pahse culture of M.tb H37Rv. After Three hours RNA was isolated and hybridization was done on HRI-UMNDJ Mycobacterium tuberculosis 4.8K CAG_Mtb microarrays.
2015-04-28 | E-GEOD-68350 | biostudies-arrayexpress
Project description:When exposed to M. tuberculosis, 25-50% become infected, of which 10-20% having several symptoms. Currently, there is no marker for judging the efficacy of M tuberculosis (Mtb) treatment, and it is judged based on the appearance of subjective symptoms and radiological findings. In this study, we attempted to establish a marker to distinguish patients who relapsed after TB treatment from patients who had recurrence after TB treatment using the information of circulating miRNA expression. Thirty two patients with tuberculosis infection aged 18 years or older were enrolled. 16 patients had onset or recurrence of TB and 16 patients with latent tuberculosis infection (LTBI) with positive test for Interferon gamma release assays (IGRA) and no chest X-ray examination. Total RNA from serum in exosome-rich fraction was extracted and then miRNA expression analysis was performed using a next-generation sequencer and NGS data analyzed using miRDeep2. Using expression information of nine miRNAs, TB and LTBI could be separated with 71.8% accuracy. The odds ratio also was 6.16, and the p-value was 3.20e-02, respectively. The expression of hsa-miR-122-5p was significantly different between TB and LTBI (p <0.05). Here we established a novel method to efficiently differentiate LTBI from patients with tuberculosis infection. Since this method can be performed in a low invasive manner such as blood sampling, it is promising tool for utilizing follow-up of TB treatment.
2021-03-18 | GSE149645 | GEO
Project description:we studied the role of exosomes isolated from M.tb infected macrophages in modulating the macrophage response to IFN-γ. Nimblegen microarray gene expression studies were used to compare the suppression of IFN-γ inducible genes by exosomes relative to the virulent strain of M.tuberculosis. Overall our study suggest that exosomes, as carriers of M.tb pathogen associated molecular patterns (PAMPs), may provide a mechanistic link by which M.tb may exert its suppression of host immune response beyond the infected cell, and implies a physiological role for exosomes in immune surveillance of TB.
2011-06-05 | GSE29731 | GEO
Project description:we studied the role of exosomes isolated from M.tb infected macrophages in modulating the macrophage response to IFN-γ. Nimblegen microarray gene expression studies were used to compare the suppression of IFN-γ inducible genes by exosomes relative to the virulent strain of M.tuberculosis. Overall our study suggest that exosomes, as carriers of M.tb pathogen associated molecular patterns (PAMPs), may provide a mechanistic link by which M.tb may exert its suppression of host immune response beyond the infected cell, and implies a physiological role for exosomes in immune surveillance of TB. Macrophages were treated with exosomes, infected with M.tb H37Rv or left untreated for 18 hours followed by +/- IFN-γ for an additional 18 hours. Cells were harvested and RNA was isolated and converted to double stranded cDNA and subsequently labeled and hybridized onto Mus musculus 4×72 Nimblegen microarray using Nimblegen Hybridization system 4 according to manufacturer’s instructions (Roche)
2011-06-05 | E-GEOD-29731 | biostudies-arrayexpress
Project description:Tuberculosis (TB) remains a major public health problem and we lack a comprehensive understanding of how Mycobacterium tuberculosis (M. tb) infection impacts host immune responses. We compared, at two timepoints, the induced immune response to TB antigen, BCG and IL-1β stimulation between latently M. tb infected individuals (LTBI) and active TB patients. The immune response was stimulated using the TruCulture system with the corresponding stimulations: TB antigen, BCG, 1L1b, and the Luminex xMAP array was used to assess the cytokines expression profile of the samples.
2022-11-05 | E-MTAB-12380 | biostudies-arrayexpress