Naive CD4+ T cell activation transcriptome
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ABSTRACT:
PROVIDER: PRJNA171178 | ENA |
REPOSITORIES: ENA
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Project description:Naive CD4+ T cells are the common precursors of multiple effector and memory T cell subsets and possess a high plasticity in terms of differentiation potential. This stem-cell like character is important for cell therapies aiming at regeneration of specific immunity. Cell surface proteins are crucial for recognition and response to signals mediated by other cells or environmental changes. Knowledge of cell surface proteins of human naive CD4+ T cells and their changes during the early phase of T cell activation is urgently needed for a guided differentiation of naive T cells and may support the selection of pluripotent cells for cell therapy.<br>Periodate oxidation and aniline-catalyzed oxime ligation (PAL) technology was applied with subsequent quantitative LC-MS/MS (PAL-qLC-MS/MS) to generate a dataset describing the surface proteome of human naive CD4+ T cells and to monitor dynamic changes during the early phase of activation. This led to the identification of 173 N-glycosylated surface proteins, of which 24 were previously not known to be expressed on human naive CD4+ T cells or have no defined role within T cell activation. To independently confirm the proteomic dataset and to analyse the cell surface by an alternative technique a systematic phenotypic expression analysis of surface antigens via flow cytometry was performed. This screening expanded the previous dataset, resulting in 229 surface proteins which are expressed on naive unstimulated and activated CD4+ T cells. Furthermore, we generated a surface expression atlas based on transcriptome data, experimental annotation and predicted subcellular localization, and correlated the proteomics result with this transcriptional dataset.<br>This extensive surface atlas provides an overall naive CD4+ T cell surface resource and will enable future studies aiming at a deeper understanding of mechanisms of T cell biology allowing the identification of novel immune targets usable for the development of therapeutic treatments.
2015-05-27 | PXD001432 | Pride
Project description:We used microarrays to detail the global gene transcription underlying T cells activation during the first 24 hours after stimulation. CD4+CD45RA+ T cells were sorted and cultured with different stimulatory conditions (Non-stimulated, anti-CD3 and anti-CD3 plus anti-CD28) for different times (0 hours, 4 hours and 24 hours). 3 replicates for each condition were analyzed.
2013-07-03 | E-GEOD-39594 | biostudies-arrayexpress
Project description:CD4+ T cells are critical components in the human immune system. They produce cytokines to fight against pathogens and abnormal cells and stimulate other cells, such as B cells, macrophages, and neutrophils, to generate an immune response.
Naive CD4+ T cells are precursor cells that can differentiate into T helper - 1, - 2, - 17 (Th1, Th2, Th17) and regulatory T cells (Tregs) subtypes based on the type of pathogens or disease. The naive CD4+ T cell model consists of 5179 reactions, 3153 metabolites, and 1055 genes. Together with Th1, Th2, and Th17 models, the naive CD4+ T cell model helped identify drug targets and repurposable drugs against autoimmune diseases.
2023-11-27 | MODEL1909260003 | BioModels
Project description:RNA sequencing of the chromatin associated RNA and nucleoplasm associated RNA of Naive CD4+ T cells to identify novel chromatin associated RNAs containing TEs. RNA sequencing of Naive CD4+ T cells or Activated Naive CD4+ T cells treated with Scr or LINE1 antisense oligonucleotides (ASO).
2021-10-20 | E-MTAB-9574 | biostudies-arrayexpress
Project description:Cell activation is a vital step for T cell memory/effector differentiation as well as for productive HIV infection. To identify novel regulators of this process, we used next generation sequencing to profile changes in microRNA expression occurring in purified human naive CD4 T cells in response to TCR stimulation and HIV infection. HIV infection had no significant impact on global miR expression in quiescent nave CD4 T cells. We identified miR-34c-5p as a novel miR strongly induced by TCR stimulation of nave CD4 T cells, and found that it was consistently down-regulated in response to viral infection. Over-expression of miR-34c-5p had a positive effect on HIV-1 replication. Finally, we demonstrated that miR-34c-5p alters the expression of several genes involved in TCR signaling and cell activation, identifying it as a novel regulator of nave CD4 T cell activation potentially targeted by HIV infection.
2016-12-21 | E-MTAB-4214 | biostudies-arrayexpress
Project description:We used microarrays to detail the global gene transcription effect of Dec1 underlying T cells activation during the first 24 hours after stimulation. CD4+CD62LhiCD25- T cells were sorted and cultured with different stimulatory conditions (anti-CD3 and anti-CD3 plus anti-CD28) for 24 hours. 4 replicates for each condition were analyzed.
2013-07-03 | E-GEOD-39595 | biostudies-arrayexpress
Project description:In order investigate the control of genes encoding cytoskeletal motor proteins and their interaction partners in primary T-cells, we performed whole transcriptome microarray profiling of cell activation for memory and naïve T-cells isolated from three anonymous blood donors. CD4+CD25- naïve or memory T-cells were cultured in medium alone or stimulated ex vivo and harvested for total RNA isolation and whole transcriptome microarray analysis.
2013-01-23 | E-GEOD-33272 | biostudies-arrayexpress
Project description:<p>We use next generation sequencing to investigate the different transcriptomes of closely related CD4+ T-cells from healthy human donors to elucidate the genetic programs that underlie their specialized immune functions. Six cell types were included: Regulatory T-cells (CD25hiCD127low/neg with >95% FOXP3+ purity), regulatory T-cells activated using PMA/ionomycin, CD25-CD45RA+ ('naive' helper T-cells), CD25-CD45RO+ ('memory' helper T-cells), activated Th17 cells (>98% IL17A+ purity) and activated IL17-CD4+ T-cells (called 'ThPI'). Poly-T capture beads were used to isolate mRNA from total RNA, and fragment sizes of ~200 were sequenced from both ends on Illumina's genome analyzer. We confirm many of the canonical signature genes of T-cell populations, but also discover new genes whose expression is limited to specific CD4 T-cell lineages, including long non-coding RNAs. Additionally, we find that genes encoded at loci linked to multiple human autoimmune diseases are enriched for preferential expression upon T-cell activation, suggesting that an aberrant response to T-cell activation is fundamental to pathogenesis.</p>
| phs000626 | dbGaP
Project description:BLUEPRINT EpiVar RNA-seq for Naive naive CD4+ T-cells
| EGAS00001000752 | EGA
Project description:H3K36me3 ChIP sequencing performed on circulating ex vivo isolated CD4+ Naive T cells and Activated CD4+ Naive T cells
2021-10-20 | E-MTAB-9572 | biostudies-arrayexpress