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Comparison of young and aged mouse CD8 TN, TVM and TMEM cells directly ex vivo and after polyclonal stimulation

ABSTRACT: Comparison of young and aged mouse CD8 TN, TVM and TMEM cells directly ex vivo and after polyclonal stimulation

PROVIDER: PRJNA445598 | ENA |

REPOSITORIES: ENA

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Comparison of young and aged mouse CD8 TN, TVM and TMEM cells directly ex vivo and after polyclonal stimulation

Project description:The overall study (Quinn et al. Cell Reports, 2018) aimed to understand why CD8 virtual memory T (TVM) cells become markedly less proliferative in response to TCR-driven signals with increasing age, whereas CD8 true naive (TN) cells maintain their proliferative capacity. Age-associated decreases in primary CD8+ T cell responses occur, in part, due to direct effects on naïve CD8++ T cells to reduce intrinsic functionality, but the precise nature of this defect remains undefined. Ageing also causes accumulation of antigen-naïve but semi-differentiated “virtual memory” (TVM) cells but their contribution to age-related functional decline is unclear. Here, we show that TVM cells are poorly proliferative in aged mice and humans, despite being highly proliferative in young individuals, while conventional naïve T cells (TN cells) retain proliferative capacity in both aged mice and humans. Adoptive transfer experiments in mice illustrated that naïve CD8 T cells can acquire a proliferative defect imposed by the aged environment but age-related proliferative dysfunction could not be rescued by a young environment. Molecular analyses demonstrate that aged TVM cells exhibit a profile consistent with senescence, marking the first description of senescence in an antigenically naïve T cell population.

2018-06-19 | GSE112304 | GEO

EXoO-Tn: Tag-n-Map the Tn Antigen in the Human Proteome

Project description:Tn antigen (Tn), a single N-acetylgalactosamine (GalNAc) monosaccharide attached to protein Ser and Thr residues, is found on most solid tumors yet rarely detected in adult tissues: featuring it one of the most distinctive signatures of cancers. Although it is prevalent in cancers, Tn-glycosylation sites are not entirely clear owing to the lack of suitable technology. Knowing the Tn-glycosylation sites will spur the development of the new vaccines, diagnostics, and therapeutics of cancers. Here, we report a novel technology named EXoO-Tn for large-scale mapping of Tn-glycosylation sites. EXoO-Tn utilizes glycosyltransferase C1GalT1 and isotopically-labeled UDP-Gal(13C6) to tag and convert Tn to Gal(13C6)-Tn. This exquisite Gal(13C6)-Tn structure is recognized by a human-gut-bacterial enzyme, called OpeRATOR, that specifically cleaves N-termini of the Gal(13C6)-Tn-occupied Ser and Thr residues to yield site-containing glycopeptides. The enzymes C1GalT1 and OpeRATOR could be used concurrently in one-pot. The effectiveness of EXoO-Tn was evaluated by analyzing Jurkat cells, where 947 Tn-glycosylation sites from 480 glycoproteins were mapped. Bioinformatic analysis of the identified site-specific Tn-glycoproteins revealed conserved motif, cellular localization, relative position in proteins, and mapped site-specific Tn-glycoproteome in different studies. Given the significance of Tn in cancers, EXoO-Tn is anticipated to have broad utilities in clinical study of cancers.

2022-02-15 | PXD014390 | Pride

Elucidation of the effects of tonic TCR stimulation and tissue environments of the chromatin status of naive CD4 T (TN) cells

Project description:Naive CD4 T (TN) cells show some degree of heterogeneity. However, mechanisms that alter TN cells are still largely unknown, and physiological importance in the phenotypic alteration of TN cells is unclear. Thus, to reveal the mechanisms that alter TN cell characteristics, we performed transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) on TN cells from different secondary lymphoid organs with different strength of tonic TCR stimulation.

2024-03-01 | GSE215773 | GEO

Light dependent gene expression in D. shibae wildtype compared to the gene expression in the transposonmutants D. shibae Dshi_1135::Tn, D. shibae ppaA::Tn and D. shibae ppsR::Tn

Project description:Light dependent gene expression in D. shibae wildtype compared to the gene expression in the transposonmutants D. shibae Dshi_1135::Tn, D. shibae ppaA::Tn and D. shibae ppsR::Tn. Dinoroseobacter shibae DFL12T (DSM 16493T) and the transposonmutants D. shibae Dshi_1135::Tn, D. shibae ppaA::Tn and D. shibae ppsR::Tn were grown in artificial saltwater minimal medium (SWM) in baffled flasks shaking at 180 rpm and 30 °C and incubation was performed under light, dark and bluelight conditions. D. shibae wild type and mutant strain were grown under aerobic conditions up to the mid exponential growth phase (OD578 nM 0.5).

2023-10-01 | GSE244289 | GEO

Tn-Seq of Benzalkonium Chloride Treated and Untreated Acinetobacter baumannii

Project description:The goal of this Tn-Seq study was to determine important determinants of Acinetobacter baumannii tolerance of sub-MIC concentrations of benzalkonium chloride. This Tn-seq data was then utilized to aide in the determination of the sub-MIC mechanism of action for benzalkonium chloride.

2018-01-23 | GSE96745 | GEO

Observation of the effects of the product Tn on the expression of A. thaliana genes - Project TN 2014: effect on Arabidopsis thaliana

Project description:au14-01_tn - Observation of the effects of the product Tn on the expression of genes of A. thaliana. - Observation of the effects of the product Tn on the expression of genes of Arabidopsis thaliana related to nutrition and development. - Each plant is sprayed with a product. 24h or 48h after treatment, a leaf is removed for RNA extraction and analysis.

2017-02-01 | GSE93095 | GEO

Comparison of mRNA expression between naive CD4+ T (TN) cells treated or not treated with IL-1b

Project description:To analyze effects of IL-1b on TN cells, RNA-seq analysis was performed on freshly prepared TN cells (0 h) and TN cells cultured with or without recombinamt IL-1b.

2024-03-01 | GSE215776 | GEO

Comparison of Tn-seq of Escherichia coli using B-2163 and MFDpir as donor strains.

Project description:To perform Tn-seq experiments random distribution of the transposon in the genome of the recipient cells is essential. In case transposon is delivered into the host cell by conjugation, donor may affect the distribution of the transposon in the genome of the recipient cell. Here, we provide two Tn-seq performed with two different donor strains. FX371 corresponds the Tn-seq using E. coli B-2163 as donor strain. FX442 corresponds to the Tn-seq using E. coli MFDpir as donor strain.

2020-11-12 | E-MTAB-9713 | biostudies-arrayexpress

RNA expression data of Tn/mem-iPSC derived T/ CAR T cells, PBMC derived T/CAR T cells, PBMC derived NK cells and Tn/mem-iPSC cells

Project description:T and CAR T cells were generated from mock or CD19CAR+ Tn/mem-derived induced pluripotent stem cells (Tn/mem-iPS) by 3D-organoid culture system. We performed RNA deep sequencing analysis to better elucidate their phenotype and compare their gene expression profiles among groups of Tn/mem-iPSC derived T/ CAR T cells, PBMC derived T/CAR T cells, PBMC derived NK cells and T-iPSC cells, as well as CD4 and CD8 subsets of iPSC derived or PBMC derived CAR T cells.

2022-02-01 | GSE193422 | GEO

Effects of mTOR inhibition on the phenotypes of spleen naive CD4+ T (TN) cells.

Project description:To analyze the influence of mTOR activity on TN cells, RNA-seq analysis was performed on splenic TN cells from mice treated or not treated with the mTOR inhibitor Rapamycin.

2024-02-26 | GSE232385 | GEO

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