Homo sapiens
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ABSTRACT:
PROVIDER: PRJNA352062 | ENA |
REPOSITORIES: ENA
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Project description:Globally, the anti-tuberculosis (TB) treatment success rate is approximately 85%, with treatment failure, relapse and death occurring in a significant proportion of pulmonary TB patients. Treatment success rates are lower among people with diabetes mellitus (DM). Predicting treatment failure early after diagnosis would allow early treatment adaptation and may improve global TB control. Methods Samples were collected in a longitudinal cohort study of adult TB patients with or without concomitant DM from South Africa and Indonesia to characterize whole blood transcriptional profiles before and during anti-TB treatment, using unbiased RNA-Seq and targeted gene dcRT-MLPA. Findings We report differences in whole blood transcriptome profiles between patients with a good versus poor anti-TB treatment outcome, which were observed before initiation of treatment and throughout treatment. An eight-gene and 22-gene blood transcriptional signatures distinguished patients with a good treatment outcome from patients with a poor treatment outcome at diagnosis (AUC=0·815) or two weeks (AUC=0·834) after initiation of anti-TB treatment, respectively. Importantly, high accuracy was obtained by cross-validating this signature in an external cohort (AUC=0·749). Interpretation These findings suggest that transcriptional profiles can be used as a prognostic biomarker for treatment failure and success, even in patients with concomitant DM.
2022-08-02 | GSE193979 | GEO
Project description:A blood RNA signature for tuberculosis disease risk: a prospective cohort study
| PRJNA315611 | ENA
Project description:A blood RNA signature for tuberculosis disease risk in household contact study - GC6 cohort.
| PRJNA369684 | ENA
Project description:Identification of blood biomarkers that prospectively predict progression of Mycobacterium tuberculosis infection to tuberculosis disease might lead to interventions that combat the tuberculosis epidemic. We aimed to assess whether global gene expression measured in whole blood of healthy people allowed identification of prospective signatures of risk of active tuberculosis disease. RESULTS:Between July 6, 2005, and April 23, 2007, we enrolled 6363 from the ACS study and 4466 from independent South African and Gambian cohorts. 46 progressors and 107 matched controls were identified in the ACS cohort. A 16 gene signature of risk was identified. The signature predicted tuberculosis progression with a sensitivity of 66·1% (95% CI 63·2â68·9) and a specificity of 80·6% (79·2â82·0) in the 12 months preceding tuberculosis diagnosis. The risk signature was validated in an untouched group of adolescents (p=0·018 for RNA sequencing and p=0·0095 for qRT-PCR) and in the independent South African and Gambian cohorts (p values <0·0001 by qRT-PCR) with a sensitivity of 53·7% (42·6â64·3) and a specificity of 82·8% (76·7â86) in 12 months preceding tuberculosis. Interpretation: The whole blood tuberculosis risk signature prospectively identified people at risk of developing active tuberculosis, opening the possibility for targeted intervention to prevent the disease. In this prospective cohort study, we followed up healthy, South African adolescents aged 12â18 years from the adolescent cohort study (ACS) who were infected with M tuberculosis for 2 years. We collected blood samples from study participants every 6 months and monitored the adolescents for progression to tuberculosis disease. A prospective signature of risk was derived from whole blood RNA sequencing data by comparing participants who developed active tuberculosis disease (progressors) with those who remained healthy (matched controls). After adaptation to multiplex qRT-PCR, the signature was used to predict tuberculosis disease in untouched adolescent samples and in samples from independent cohorts of South African and Gambian adult progressors and controls. Participants of the independent cohorts were household contacts of adults with active pulmonary tuberculosis disease.
2016-03-22 | E-GEOD-79362 | biostudies-arrayexpress
Project description:A total of 156 LARC patients (training cohort n = 60; validation cohort n = 96) were included in the study who underwent surgical resection post PCRT. By using univariate and multivariate logistic regression, we identified a 9-gene signature that differentiated between responders and non-responders. ; The novel 9-gene signature is robust in predicting response to PCRT in LARC patients. Tailored treatment approaches in good and poor responders to PCRT may improve the oncologic outcomes of patients with LARC.
2019-10-23 | GSE139255 | GEO
Project description:Identification of blood biomarkers that prospectively predict progression of Mycobacterium tuberculosis infection to tuberculosis disease might lead to interventions that combat the tuberculosis epidemic. We aimed to assess whether global gene expression measured in whole blood of healthy people allowed identification of prospective signatures of risk of active tuberculosis disease. RESULTS:Between July 6, 2005, and April 23, 2007, we enrolled 6363 from the ACS study and 4466 from independent South African and Gambian cohorts. 46 progressors and 107 matched controls were identified in the ACS cohort. A 16 gene signature of risk was identified. The signature predicted tuberculosis progression with a sensitivity of 66·1% (95% CI 63·2–68·9) and a specificity of 80·6% (79·2–82·0) in the 12 months preceding tuberculosis diagnosis. The risk signature was validated in an untouched group of adolescents (p=0·018 for RNA sequencing and p=0·0095 for qRT-PCR) and in the independent South African and Gambian cohorts (p values <0·0001 by qRT-PCR) with a sensitivity of 53·7% (42·6–64·3) and a specificity of 82·8% (76·7–86) in 12 months preceding tuberculosis. Interpretation: The whole blood tuberculosis risk signature prospectively identified people at risk of developing active tuberculosis, opening the possibility for targeted intervention to prevent the disease.
2016-03-22 | GSE79362 | GEO
Project description:Develop an EGFR mutation gene expression signature to aid in predicting response and clinical outcome and to identify genes associated with the EGFR-dependent phenotype
2011-09-06 | GSE31548 | GEO
Project description:Develop an EGFR mutation gene expression signature to aid in predicting response and clinical outcome and to identify genes associated with the EGFR-dependent phenotype
2011-09-06 | GSE31546 | GEO
Project description:Develop an EGFR mutation gene expression signature to aid in predicting response and clinical outcome and to identify genes associated with the EGFR-dependent phenotype
2011-09-06 | GSE31547 | GEO
Project description:Changes in the blood transcriptome upon treatment were studied in a cohort of 42 latent tuberculosis (TB) subjects and 8 active TB subiects. Samples were collected at diagnosis (prior the start of treatment) and post treatment and gene expression studied with Illumina microarrays. We hypothesize that individuals with latent TB at risk of developing active disease are immunologically closer to those with active TB and will thus display a blood transcriptomic signature similar to active TB subjects upon treatment. This signature should significantly differ from the one mounted by latent TB individuals at low risk of progression. Thus, monitoring blood transcriptomic changes following anti-TB therapy might inform on which latent TB subjects should be prioritized for receiving therapeutic intervention in order to prevent further transmission.
2021-12-08 | GSE152532 | GEO