Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA298417 | ENA |
REPOSITORIES: ENA
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Project description:Although extensive studies have demonstrated the gene expression patterns of antigen-specific CD4+ and CD8+ T-cells during chronic hepatitis C virus (HCV) infection, the transcriptional profiles of global CD4+ and CD8+ T-cells remains unclear. In this report, we recruited 10 long-term (~20 years) treatment-naM-CM-/ve chronic HCV (CHC) patients and 5 healthy donors (HDs) to investigate differences in global CD4+ and CD8+ T-cells gene expression profile. Global CD4+ and CD8+ T-cells showed unique transcriptional profiles in the expression of apoptosis-related genes. We identified BCL2, PMAIP1, and CASP1 in CD4+ T-cells and IER3 and BCL2A1 in CD8+ T-cells from CHC patients as HCV-specific gene signatures. The unique apoptosis-related gene expression profilesin global CD4+ and CD8+ T-cells programmed by chronic HCV infection seemed to enhance activation-induced apoptosis, which was suffered by global CD4+ and CD8+ T-cells. We obtained 15 blood samples to identify the gene expression signatures of global CD4+ and CD8+ T-cells due to chronic HCV infection. The samples included: 5 samples from high HCV viral load patients (HCV-h), 5 samples from low HCV viral load (HCV-l) and 5 samples from healthy donors (HD). HCV patients were all Ab+ and treatment-naive prior to the study. Samples were taken once from each individual. Global CD4+ and CD8+ T-cells were enriched by microbeads, and total RNA were used in gene chip analysis.
2013-08-19 | E-GEOD-49954 | biostudies-arrayexpress
Project description:MicroRNAs (miRNAs) have emerged as important players in the regulation of T-cell functionality. However, comprehensive insight into the extent of age-related miRNA changes in T cells is lacking. We established miRNA expression patterns of CD45RO- naïve and CD45RO+ memory T-cell subsets isolated from peripheral blood cells from young and elderly individuals. Unsupervised clustering of the miRNA expression data revealed an age-related clustering in the CD45RO- T cells, while CD45RO+ T cells clustered based on expression of CD4 and CD8. Seventeen miRNAs showed an at least 2-fold up- or downregulation in CD45RO- T cells obtained from young as compared to old donors. Validation on the same and independent samples revealed a statistically significant age-related upregulation of miR-21, miR-223 and miR-15a. In a T-cell subset analysis focusing on known age-related phenotypic changes, we showed significantly higher miR-21 and miR-223 levels in CD8+CD45RO-CCR7- TEMRA compared to CD45RO-CCR7+ TNAIVE-cells. Moreover, miR-21 but not miR-223 levels were significantly increased in CD45RO-CD31- post-thymic TNAIVE cells as compared to thymic CD45RO-CD31+ TNAIVE cells. Upon activation of CD45RO- TNAIVE cells we observed a significant induction of miR-21 especially in CD4+ T cells, while miR-223 levels significantly decreased only in CD4+ T cells. Besides composition and activation, we showed a borderline significant increase in miR-21 levels upon an increasing number of population doublings in CD4+ T-cell clones. Together, our results show that ageing related changes in miRNA expression are dominant in the CD45RO- T-cell compartment. The differential expression patterns can be explained by age related changes in T-cell composition, i.e. accumulation of CD8+ TEMRA and CD4+ post thymic expanded CD31- T cells and by cellular ageing, as demonstrated in a longitudinal clonal culture model. MicroRNA profiling was performed in eight T cell subsets: CD4 naive (CD3+CD4+CD45RO-), CD8 naive (CD3+CD4-CD45RO-), CD4 memory (CD3+CD4+CD45RO+) and CD8 memory (CD3+CD4-CD45RO+) T cells derived from 5 healthy young and 5 healthy old participants.
2015-05-23 | E-GEOD-69191 | biostudies-arrayexpress
Project description:Mature B cells, CD4+ T cells and CD8+ T cells were isolated from the peripheral blood of two human donors. Naive CD4+ and CD8+ T cells were cultured for three days to induce activation. The B cells and naive and activated T cells were profiled by RNA-seq, ATAC-seq and Hi-C.
2021-01-21 | GSE126117 | GEO
Project description:Analysis of the naive and antigen experienced B-cell receptor repertoire in healthy donors of different ages
| PRJEB15348 | ENA
Project description:Disturbed expression of microRNAs (miRNAs) in regulatory T-cells (Tregs) leads to development of autoimmunity in experimental mouse models. However, the miRNA expression signature characterizing Tregs of autoimmune diseases, such as rheumatoid arthritis (RA) has not been determined yet. Moreover, the technical limitations prevented the analysis of such minute T-cell population as naive and memory Tregs. In this study we have used a microarray approach to comprehensively analyze miRNA expression signatures of naive Tregs (CD4+CD45RO-CD25++), memory Tregs (CD4+CD45RO+CD25+++), as well as conventional naive (CD4+CD45RO-CD25-) and memory (CD4+CD45RO+CD25-) T-cells (Tconvs) derived from peripheral blood of RA patients, and matched healthy controls. Differential expression of selected miRNAs was validated by TaqMan-based qRT-PCR. We found a positive correlation between increased expression of miR-451 in T-cells of RA patients and disease activity score (DAS28), ESR levels, and serum levels of IL-6. Moreover, we found characteristic, disease and treatment independent, global miRNA expression signatures defining naive Tregs, memory Tregs, naive Tconvs and memory Tconvs. The analysis allowed us to define miRNAs characteristic for a general naive phenotype (e.g. miR-92a), a general memory phenotype (e.g. miR-21, miR-155), and most importantly miRNAs specifically expressed in both naive and memory Tregs, defining as such the Treg phenotype (i.e. miR-146a, miR-3162, miR-1202, miR-1246a, and miR-4281). MicroRNA profiling was performed in four CD4+ T-cell subsets: naive Tconventional (CD3+CD8-CD45RO-CD25-), naive Tregulatory (CD3+CD8-CD45RO-CD25+), memory Tconventional (CD3+CD8-CD45RO+CD25-), and memory Tregulatory (CD3+CD8-CD45RO+CD25+) derived from 2 healthy controls, and 6 rheumatoid arthritis patients (total n=8).
2014-01-22 | E-GEOD-50646 | biostudies-arrayexpress
Project description:Gene expression data of primary human naive and memory CD4+T lymphocytes purified from peripheral blood are generated to be analyzed in different ways such as for traditional searching of differentially expressed genes between the two cell subsets or in combination to in-silico data of microRNAs target prediction for microRNAs known to be characteristically expressed in the two cell subsets. Two cell subsets (cell types) FACS purified from peripheral blood of six samples/healthy donors (samples #3,5,6,7,026,065). Naive CD4+ T cells were extracted from all 6 samples and 6 biological replicas were obtained (3N, 5N, 6N, 7N, 026N, 065N), while memory CD4+T cells were extracted from 4 samples and 4 biological replicas were obtained (3m, 5m, 6m, 7m). Both naive and memory replicas from samples 3, 5, 6 and 7 were hybridized onto two beadsarrays each while those from samples 026 and 065 were hybridized on 1 beadsarray each (for a total of 18 beadsarrays used). For analysis purposes naive cells samples 3N, 5N, 6N and 7N can be considered paired with memory samples 3m, 5m, 6m and 7m respectively, since they are obtained from the same blood samples/healthy donors.
2011-06-26 | E-GEOD-22880 | biostudies-arrayexpress
Project description:Comparison of mRNA expression showed widespread changes in the circulating CD8+ but not CD4+ T-cells from patients with severe asthma. No changes were observed in the CD4+ and CD8+ T-cells in non-severe asthmatics versus healthy controls. Bioinformatics analysis showed that the changes in CD8+ T-cell mRNA expression were associated with multiple pathways involved in T-cell activation. As with mRNAs, we also observed widespread changes in expression of non-coding RNA species including natural antisense, pseudogenes, intronic long ncRNAs and long intergenic long ncRNAs in CD8+ T-cells from severe asthmatics. Measurement of the miRNA expression profile showed selective down-regulation of miR-28-5p in CD8+ T-cells and reduction of miR-146a and miR-146b in both CD4+ and CD8+ T-cells. mRNA samples were collected from circulating CD4+ and CD8+ T-cells from healthy donors as well as donors with severe and non-severe asthma.
2011-08-31 | E-GEOD-31773 | biostudies-arrayexpress
Project description:We introduced single-chain trimer (SCT) technologies into a high throughput platform for pMHC library generation that can be used for screening antigen specific CD8+ T cells. We compared the diversity of T cell receptor repertoire captured by SCT and folded peptide-MHC multimer presenting HLA-A02:01 restricted CMV peptide. We then constructed SCT libraries designed to capture SARS-CoV-2 spike specific CD8+ T cells from COVID-19 participants and healthy donors. TCR sequencing with antigen specificity was analyzed. The immunogenicity of these epitopes was validated by functional assays of T cells with cloned TCRs captured using SCT libraries.
2022-01-01 | E-MTAB-11229 | biostudies-arrayexpress
Project description:Mature B cells, CD4+ T cells and CD8+ T cells were isolated from the peripheral blood of two human donors. Naive CD4+ and CD8+ T cells were cultured for three days in the presence of Dynabeads Human T-Activator CD3/CD28 beads (Life Technologies, cat. no. 111.31D) to induce activation. The B cells and naive and activated T cells were profiled by whole transcriptome RNA-seq.
2021-01-21 | GSE126116 | GEO