Trachoma_GWAS_Unscarred_Controls
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ABSTRACT:
PROVIDER: EGAD00010000940 | EGA |
REPOSITORIES: EGA
Publications
Conjunctival fibrosis and the innate barriers to Chlamydia trachomatis intracellular infection: a genome wide association study.
Roberts Chrissy h Ch Franklin Christopher S CS Makalo Pateh P Joof Hassan H Sarr Isatou I Mahdi Olaimatu S OS Sillah Ansumana A Bah Momodou M Payne Felicity F Jeffreys Anna E AE Bottomley William W Natividad Angels A Molina-Gonzalez Sandra S Burr Sarah E SE Preston Mark M Kwiatkowski Dominic D Rockett Kirk A KA Clark Taane G TG Burton Matthew J MJ Mabey David C W DC Bailey Robin R Barroso Inês I Holland Martin J MJ
Scientific reports 20151130
Chlamydia trachomatis causes both trachoma and sexually transmitted infections. These diseases have similar pathology and potentially similar genetic predisposing factors. We aimed to identify polymorphisms and pathways associated with pathological sequelae of ocular Chlamydia trachomatis infections in The Gambia. We report a discovery phase genome-wide association study (GWAS) of scarring trachoma (1090 cases, 1531 controls) that identified 27 SNPs with strong, but not genome-wide significant, ...[more]
Similar Datasets
Project description:Triple-negative (TN) breast cancers need to be refined in order to identify therapeutic subgroups of patients. We conducted an unsupervised analysis of microarray gene-expression profiles of 107 TN breast cancer patients and undertook robust functional annotation of the molecular entities found by means of numerous approaches including immunohistochemistry and gene-expression signatures. An 87 TN external cohort was used for validation. Fuzzy clustering separated TN tumours into three clusters: C1 (22.4%), C2 (44.9%) and C3 (32.7%). C1 patients were older (mean = 64.6 years) than C2 (mean = 56.8 years; P = 0.03) and C3 patients (mean = 51.9 years; P = 0.0004). Histological grade and Nottingham prognostic index were higher in C2 and C3 than in C1 (P < 0.0001 for both comparisons). Significant event-free survival (EFS) (P = 0.03) was found according to cluster membership: patients belonging to C3 had a better outcome than patients in C1 (P = 0.01) and C2 (P = 0.02). EFS analysis results were confirmed when our cohort was pooled with external cohort (n = 194; P = 0.01). Functional annotation showed that 22% of TN patients were not basal-like (C1). C1 was enriched in luminal subtypes and positive androgen receptor (luminal androgen receptor [LAR]). C2 could be considered as an almost pure basal-like cluster. C3, enriched in basal-like subtypes, but to a lesser extent, included 26% of claudin-low subtypes. Dissection of immune response showed that high immune response (HIR) and low M2-like macrophages were a hallmark of C3, and that these patients had a better EFS than C2 patients, characterized by low immune response (LIR) and high M2-like macrophages: P = 0.02 for our cohort, and P = 0.03 for pooled cohorts. We identified 3 subtypes of TN patients: LAR (22%), basal-like with LIR and high M2-like macrophages (45%) and basal-enriched with HIR and low M2-like macrophages (33%). We pointed out that macrophages and other immune effectors offer a variety of therapeutic targets in breast cancer, and particularly in TN basal-like tumours. Furthermore, we showed that CK5 antibody was better suited than CK5/6 antibody to subtype TN patients.
2015-05-19 | GSE58812 | GEO
Project description:Triple-negative (TN) breast cancers need to be refined in order to identify therapeutic subgroups of patients. We conducted an unsupervised analysis of microarray gene-expression profiles of 107 TN breast cancer patients and undertook robust functional annotation of the molecular entities found by means of numerous approaches including immunohistochemistry and gene-expression signatures. An 87 TN external cohort was used for validation. Fuzzy clustering separated TN tumours into three clusters: C1 (22.4%), C2 (44.9%) and C3 (32.7%). C1 patients were older (mean = 64.6 years) than C2 (mean = 56.8 years; P = 0.03) and C3 patients (mean = 51.9 years; P = 0.0004). Histological grade and Nottingham prognostic index were higher in C2 and C3 than in C1 (P < 0.0001 for both comparisons). Significant event-free survival (EFS) (P = 0.03) was found according to cluster membership: patients belonging to C3 had a better outcome than patients in C1 (P = 0.01) and C2 (P = 0.02). EFS analysis results were confirmed when our cohort was pooled with external cohort (n = 194; P = 0.01). Functional annotation showed that 22% of TN patients were not basal-like (C1). C1 was enriched in luminal subtypes and positive androgen receptor (luminal androgen receptor [LAR]). C2 could be considered as an almost pure basal-like cluster. C3, enriched in basal-like subtypes, but to a lesser extent, included 26% of claudin-low subtypes. Dissection of immune response showed that high immune response (HIR) and low M2-like macrophages were a hallmark of C3, and that these patients had a better EFS than C2 patients, characterized by low immune response (LIR) and high M2-like macrophages: P = 0.02 for our cohort, and P = 0.03 for pooled cohorts. We identified 3 subtypes of TN patients: LAR (22%), basal-like with LIR and high M2-like macrophages (45%) and basal-enriched with HIR and low M2-like macrophages (33%). We pointed out that macrophages and other immune effectors offer a variety of therapeutic targets in breast cancer, and particularly in TN basal-like tumours. Furthermore, we showed that CK5 antibody was better suited than CK5/6 antibody to subtype TN patients. Subtyping molecular characterization within a cohort of 107 TN-IHC by means of gene expression profiling
2015-05-19 | E-GEOD-58812 | biostudies-arrayexpress
Project description:Transcriptional analysis upon the overexpression of the folate gene cluster on a high copy plasmid when compared to an empty vector in the lactic acid bacterium L. plantarum. The transcriptional response was determined for both strains in the presence and absence of pABA thereby using the hybridisation sceme as described in the data processing section. Keywords: response to folate gene cluster overexpression and pABA treatment The batch experiment with and without pABA scheme consisted of a loop design with 21 microarrays with the following samples hybridized on one array and labeled with Cy3 and Cy5, respectively: C1+P and F1+P, F1+P and C2+P, C2+P and F3+P, F3+P and C3+P, C3+P and F2+P, F2+P and C1+P, C1+P and C2+P, F2+P and F3+P, C1-P and F1-P, F1-P and C2-P, C2-P and F3-P, F3-P and C3-P, C3-P and F2-P, F2-P and C1-P, C1-P and C2-P, F2-P and F3-P, C3-P and F1+P, F2+P and C1-P, C2+P and F3-P, F1-P and C3+P, and F2+P and F1-P. Here, C1+P, C2+P, C3+P, F1+P, F2+P, and F3+P represent biological triplicates of the L. plantarum harboring pNZ7021 and pNZ7026, respectively, when grown in batch in the presence of pABA. The C1-P, C2-P, C3-P, F1-P, F2-P, and F3-P, represents the L. plantarum harboring pNZ7021 and pNZ7026, respectively, when grown in batch in the absence of pABA.
2008-05-31 | E-GEOD-8956 | biostudies-arrayexpress
Project description:In this dataset, we include the expression data obtained from gastric cancer tissues and gastric normal tissues to determine the differentially expressed genes in gastric cancer tissues 10 tissues (5 paired of gastric cancer vs.normal tissues) were analysed. We generated the following pairwise comparisons:C1 VS.N1;C2 VS.N2;C3 VS.N3;C4 VS.N4;C5 VS.N5; genes with a fold-change ≥2 were selected
2014-04-16 | E-GEOD-56807 | biostudies-arrayexpress
Project description:C2- and C3-sulfonates were quantified in marine plankton particulate samples.
2019-03-29 | ST001184 | MetabolomicsWorkbench
Project description:The Streptomyces coelicolor system SCO4596/4597/4598 (AbrC1/C2/C3), composed of two histidine kinases and one response regulator, had positive effects both on morphological development and antibiotic production. This represents the microarray analyses of the deltaabrC1/C2/C3 and wild-type transcriptomes from 50 hours cultures grown on solid plates
2010-09-30 | E-MEXP-2841 | biostudies-arrayexpress
Project description:Introduction: Neoadjuvant chemoradiotherapy (nCRT) was the foundation treatment for locally advanced rectal cancer (LARC). The nCRT can improve the efficacy of immunotherapy on account of its in-situ vaccine effect. Objective: The aim is to identify stable and reliable transcriptome signatures to predict the efficacy of immune checkpoint blockade (ICB) in patients with LARC. Methods: Immunophenotyping was established by using xCell immune cell infiltration abundance and consistent clustering in GSE39582 and verified in several data sets. The effects of immunophenotyping, follicular regulatory T cells, tumor associated fibroblasts (CAF) and tertiary lymphoid structures (TLS) signatures on the efficacy of ICB were analyzed by using IMvigor210, GSE91061 and an independent Daping Hospital (DPH) cohort. Results: There are four stable and repeatable immune subtypes in rectal cancer, among which C1 is low immune infiltration type, C2 is high interstitial infiltration type, C3 is high immune infiltration type and C4 is ion channel type. C2 is mainly characterized by high infiltration CAF, C3 is characterized by high infiltration of cytotoxic T lymphocytes, high expression of PD-L1 and TLS. In rectal cancer patients receiving nCRT, immunophenotyping was not significantly associated with pathological remission rate, but immunophenotyping was an independent prognostic factor of RFS. In IMvigor210 patients treatment with atezolizumab, the pathological remission rates of C1, C2, C3 and C4 were 23.86%, 10.94%, 33.33% and 23.08% respectively (χ2 = 8.981, P = 0.029), which were 11.76%, 50.00%, 42.86% and 0.0% respectively in the GSE91061 patients treatment with nivolumab (Fisher's exact probability, P = 0.018). Both follicular regulatory T cells and CAF showed a further impact on the ICB therapeutic efficacy of C2 and C3 subtype. In addition, both GSE91404 and DPH cohorts showed that nCRT treatment induced a significant increase in the expression of TNFRSF9 and abundance of macrophages in C3 subtype. Conclusion: Our data suggest that there are four immune types of rectal cancer, which are related to the prognosis of patients. Among them, C3 and some C2 subtypes represents the patients who may benefit from ICB after nCRT treatment.
2022-09-17 | GSE213331 | GEO
Project description:Gambian specimens without trachomatous scarring
| EGAD00010000941 | EGA
Project description:We tested a genome-scale artificial transcription factor (ATF) library in reprogramming mouse embryonic fibroblasts to induced pluripotent stem (iPS) cells. Three combinations of ATFs (C2, C3, and C4) could induce pluripotency when expressed with Sox2, Klf4, and c-Myc. The transcriptional profiles of ATF-induced iPS cells are similar to that of iPS cells induced with Oct4, Sox2, Klf4, and c-Myc and mouse embryonic stem cells, exhibiting up-regulation of pluripotency markers and down-regulation of fibroblast markers. We performed ChIP-seq on the active histone mark H3K27ac and the repressive histone mark H3K9me3 in C2+SKM iPS cells, C3+SKM iPS cells, in Oct4+SKM to validate the total transcriptome results. In addition, the ATFs from C2 were chromatin immunoprecipitated to determine where they are bound in the genome at an intermediate stage before being fully reprogrammed to iPS cells. This study provides a proof-of-principle that a gene-activating ATF library can be used to identify cell fate-defining transcriptional networks in an unbiased manner.
2016-12-05 | GSE89220 | GEO
Project description:We report epigenetic changes in the chromatin accessibility landscape of retinal myeloid cells from mice preconditioned with 4xLPS injections persist after the initial inflammation has subsided. We compared the data of scATAC-seq performed on nuclei extracted from sorted CX3CR1+ retinal cells from mice 3 days after CNV induction, preconditioned with either PBS or 4xLPS 1 month before, or Naïve retinas without CNV induction, preconditioned with PBS. After quality control, filtering and dimension reduction, a two-dimensional UMAP was performed on the remaining 835, 821, and 588 cells in the PBS, 4xLPS, and Naive groups respectively. Unbiased clustering was applied using Leiden algorithm, which partitioned CX3CR1+ myeloid cells into 8 distinct clusters (C1–C8). Based on previously described cell-specific gene signatures, we identified microglia (clusters C1, C2 and C3), monocytes (clusters C4 and C5), and macrophages (cluster C6). Gene expression scores identified C4 as circulating monocytes and C5 as a mixture of classical and inflammatory monocytes. The three microglial populations (C1, C2, and C3), harbor the greatest epigenetic diversity following induction of CNV or preconditioning. GSEA analysis revealed that the C2 subpopulation was characterized by considerable enrichment in opened chromatin regions corresponding to genes coding for inflammation-related pathways. In contrast, the C1 subpopulation showed higher numbers of closed chromatin in genes coding for inflammatory processes. Moreover, when compared to the C1 and C2 subpopulations, C3 had open chromatin regions only in two gene sets coding for inflammation-related pathways, and three gene sets with closed chromatin regions. Together, these data demonstrate that the chromatin landscape of retina-resident microglia is impacted differently by both the prior systemic exposure to LPS and by CNV.
2023-02-22 | GSE194226 | GEO