Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq of human CD8low and CD8high cytotoxic T lymphocytes upon in vitro starvation

ABSTRACT: RNA-seq of human CD8low and CD8high cytotoxic T lymphocytes upon in vitro starvation

PROVIDER: PRJNA856332 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR20007116.fastq.gz	Fastqsanger.gz
	SRR20007117.fastq.gz	Fastqsanger.gz
	SRR20007118.fastq.gz	Fastqsanger.gz
	SRR20007119.fastq.gz	Fastqsanger.gz
	SRR20007120.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 12

Similar Datasets

RNA-seq of human CD8low and CD8high cytotoxic T lymphocytes upon in vitro starvation

Project description:The mechanistic target of rapamycin (mTOR) signaling, which is an essential metabolic pathway that influences T cell differentiation, can be limited under conditions of metabolic stress e.g. during the cell starvation. As we observed reduced CD8 expression upon cell starvation in vitro, we sorted human cytotoxic T lymphocytes derived from six donors into low CD8 expression and high CD8 expressing T lymphocytes using flow cytometry. Their transcriptome was analyzed in order to investigate the two CD8 subsets. Our data suggests a functional diversity of CD8low and CD8high T cells with regard to cytotoxic effector function that might be useful to study these cells also in tumor sections or under conditions when cytotoxic T cells need to adapt to a changing microenvironment.

2022-09-30 | GSE207621 | GEO

Transcriptome analysis of MAZR and/or Runx3-deficient cytotoxic T lymphocytes

Project description:We investigated transcriptional changes in MAZR-, Runx3- and MAZR/Runx3-deficient cytotoxic T lymphocytes (CTLs). This analysis revealed that MAZR plays a compensatory role in the Runx3-dependent transcriptional program of CTL differentiation.

2021-03-11 | GSE129772 | GEO

RNA-seq of murine cytotoxic T lymphocytes unstimulated and stimulated with anti-CD3 for 10, 20, 40 and 60 minutes

Project description:We wished to examine early transcriptional changes that occur after TCR engagement in CD8+ cytotoxic T lymphocytes (CTLs). To this end, we differentiated effector CTLs from OTI TCR transgenic mice for 7 days in vitro and then stimulated them with anti-CD3 for various times before lysing for RNA-seq. Results demonstrated significant transcriptional changes starting from 20 minutes. After 60 minutes, upregulated genes were most enriched for cytokines and transcriptional machinery.

2023-10-15 | E-MTAB-12083 | biostudies-arrayexpress

Personalized neoantigen-based T cell therapy triggers cytotoxic lymphocytes expressing polyclonal TCR against metastatic ovarian cancer

Project description:Neoantigen-reactive cytotoxic T lymphocytes play a vital role in precise cancer cell elimination. In this study, we demonstrate the effectiveness of personalized neoantigen-based T cell therapy in inducing tumor regression in two patients suffering from heavily-burdened metastatic ovarian cancer. Our approach involved the development of a robust pipeline for ex vivo expansion of neoantigen-reactive T lymphocytes. Neoantigen peptides were designed and synthesized based on the somatic mutations of the tumors and their predicted HLA binding affinities. These peptides were then presented to T lymphocytes through co-culture with neoantigen-loaded dendritic cells for ex vivo expansion. Subsequent to cell therapy, both patients exhibited significant reductions in tumor marker levels and experienced substantial tumor regression. One patient achieved repeated cancer regression through infusions of T cell products generated from newly identified neoantigens. Transcriptomic analyses revealed a remarkable increase in neoantigen-reactive cytotoxic lymphocytes in the peripheral blood of the patients following cell therapy. These cytotoxic T lymphocytes expressed polyclonal T cell receptors (TCR) against neoantigens, along with abundant cytotoxic proteins and pro-inflammatory cytokines. The efficacy of neoantigen targeting was significantly associated with the immunogenicity and TCR polyclonality. Notably, the neoantigen-specific TCR clonotypes persisted in the peripheral blood after cell therapy. Our findings indicate that personalized neoantigen-based T cell therapy triggers cytotoxic lymphocytes expressing polyclonal TCR against ovarian cancer, suggesting its promising potential in cancer immunotherapy.

2023-12-01 | GSE248401 | GEO

Actinomycin D treated cytotoxic T lymphocytes

Project description:Effector cytotoxic T lymphocytes (CTLs) are critical for ridding the body of infected or cancerous cells. Recognition of an antigenic ligand by the CTL’s T cell receptor (TCR) triggers a signalling cascade that ultimately results in the targeted release of cytolytic granules and/or secretion of cytokines and chemokines to alert and recruit additional immune cells. These signalling cascades are capable of initiating transcription, translation, and cytoskeletal rearrangements. While previous work has demonstrated how translation and intracellular reorganisation contribute to CTL effector responses, the role of transcription is less well studied. To address this, we examined the impact of blocking transcription on the CTL proteome during TCR stimulation. These data demonstrated a strong transcriptional requirement for expression of cytokines and chemokines but not cytolytic molecules. Together with functional studies, these data reveal differential molecular control of the cell-cell communication and cytolytic functions of effector CTLs. CTLs exhibit complete and persistent priming for cytolytic activity prior to target cell encounter, but they require de novo transcription to recruit additional immune cells that amplify the response.

2023-10-16 | PXD034920 | Pride

Cytotoxic lymphocytes use mechanosurveillance to target biophysical vulnerabilities in cancer

Project description:Cytotoxic lymphocytes use mechanosurveillance to target biophysical vulnerabilities in cancer

| PRJNA692218 | ENA

Bulk RNA sequencing of cytotoxic T lymphocytes of OT1 mice

Project description:Bulk RNA sequencing of cytotoxic T lymphocytes of OT1 mice

| PRJNA788127 | ENA

ILC2s directly activate anti-tumor cytotoxic CD8+ T lymphocytes by internalizing, processing, and presenting exogenous antigens

Project description:Type-2 innate-lymphoid cells (ILC2s) associate with both tumor promotion and inhibition. We found that ILC2s may induce anti-tumor immunity by a hitherto-unrealized mechanism: they may internalize, process, and present exogenous tumor antigen on major-histocompatibility-complex class-I (MHCI) molecules with costimulatory molecules to CD8+ T cells. This converts the T cells into cytotoxic-T-lymphocytes (CTLs). Specifically, transferring ILC2s into tumor-bearing mice inhibited tumor growth in a CD8+ T cell-dependent manner. Moreover, co-culturing human or murine CD8+ T cells with ILC2s upregulated T-cell expression of cytotoxic molecules. The resulting CTLs efficiently killed tumor cells in vitro and upon transfer into tumor-bearing mice. ILC2s were found to internalize exogenous antigens via clathrin-dependent endocytosis and to process/present them as efficiently as professional antigen-presenting cells for CD8+ T cells (type-1 conventional dendritic cells). Thus, ILC2s can present antigen to CD8+ T cells and induce their tumor-killing activity. This novel finding has promising implications for anti-tumor strategies.

2024-08-31 | GSE241945 | GEO

In-depth analysis of the phosphoprotein landscape of cytotoxic T lymphocytes and its regulation by cytokines

Project description:Here we present high-resolution mass spectrometry analysis of changes to the phosphoproteome of cytotoxic T lymphocytes (CTL) induced by the cytokine, Interleukin 12 (IL-12). We treated CTL with a short and long IL-12 stimulation and mapped the changes to the phosphoproteome using quantitative SILAC-based phosphoproteomics.

2016-08-24 | PXD004644 | Pride

Physiologic expression and function of the MDR1 transporter in cytotoxic T lymphocytes

Project description:Multidrug resistance (MDR)-1 acts as a chemotherapeutic drug efflux pump in tumor cells, although its physiologic functions remain enigmatic. Using a recently-developed MDR1-knockin reporter allele (Abcb1aAME/+), we found that constitutive MDR1 expression amongst hematopoietic cells was observed mainly in cytolytic lymphocytes—including CD8+ cytotoxic T lymphocytes (CTL) and natural killer cells—and regulated by Runt-related (Runx) transcription factors. Although MDR1 was dispensable for naïve CD8+ T cell development, it was required for both normal accumulation of effector CTL following acute viral infection and protective function of memory CTL upon challenge with an intracellular bacterium. MDR1 acted early after naïve CD8+ T cell activation to suppress oxidative stress, enforce survival and safeguard mitochondrial function in developing CTL. Together, these data highlight an important endogenous function of MDR1 in cell-mediated immune responses, and suggest that ongoing efforts to intentionally inhibit MDR1 in cancer patients could be counter-productive. This SuperSeries is composed of the SubSeries listed below.

2020-02-27 | GSE143141 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data