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TCR affinity defines tumor-specific CD8 T cell differentiation and dysfunction [RNA-seq]

ABSTRACT: TCR affinity defines tumor-specific CD8 T cell differentiation and dysfunction [RNA-seq]

PROVIDER: PRJNA594911 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10668700_1.fastq.gz	Fastqsanger.gz
	SRR10668700_2.fastq.gz	Fastqsanger.gz
	SRR10668701_1.fastq.gz	Fastqsanger.gz
	SRR10668701_2.fastq.gz	Fastqsanger.gz
	SRR10668702_1.fastq.gz	Fastqsanger.gz

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TCR affinity defines tumor-specific CD8 T cell differentiation and dysfunction

Project description:TCR affinity defines tumor-specific CD8 T cell differentiation and dysfunction

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TCR affinity defines tumor-specific CD8 T cell differentiation and dysfunction [ATAC-seq]

Project description:TCR affinity defines tumor-specific CD8 T cell differentiation and dysfunction [ATAC-seq]

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TCR affinity defines tumor-specific CD8 T cell differentiation and dysfunction [RNA-seq]

Project description:RNA-seq analysis of tumor-specific CD8 T cells encountering tumor antigens with varying TCR/pMHC affinity.

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TCR affinity defines tumor-specific CD8 T cell differentiation and dysfunction [ATAC-seq]

Project description:ATACseq analysis of tumor-infiltrating CD8 T cells encountering high (F6) or low (D4) affinity tumor antigen.

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Single-cell RNA sequencing of OT-I CD8+ T cells after stimulation with different affinity ligands

Project description:Activation of CD8+ T cells depends exquisitely on the affinity of the T cell receptor (TCR) for a peptide MHC (pMHC) ligand complex. Here, we activated OT-I transgenic CD8+ T cells with pure peptide and examined early activation responses by single-cell RNA-sequencing. T cells were activated with the high affinity OT-I cognate peptide (N4=SIINFEKL) for 1, 3 or 6 hours, or with reduced affinity peptides (T4=SIITFEKL and G4=SIIGFEKL) or the non-binding peptide (NP68=ASNENMDAM) for 6 hours. Cells were then sorted into 96-well plates by FACS and RNA was sequenced following an adapted Smart-Seq2 protocol.

2018-06-25 | E-MTAB-6051 | biostudies-arrayexpress

T cell receptor signal strength and antigen affinity differentially regulate memory CD8+ T cell development

Project description:IL-2 inducible tyrosine kinase (Itk) is a Tec family non-receptor tyrosine kinase that is known to regulate T cell receptor signal strength (TcR) and T cell development and differentiation. TcR signal strength and antigen affinity are parameters known to regulate the development of CD8+ T cell memory. However, the intersection between TcR signal strength and antigen affinity on CD8+ memory T cell development remains unclear. Therefore, we compared the transcriptomes of WT and Itk-/- OT-1/Rag-/- CD8+ T cells at day 0 and day 7 following infection with Listeria monocytogenes expressing the SIINFEKL (N4) or SIITFEKL (T4) OVA peptide variant (different affinities for TcR) by RNA sequencing.

2020-09-30 | GSE137406 | GEO

TCR affinity defines tumor-specific CD8 T cell differentiation and dysfunction

Project description:This SuperSeries is composed of the SubSeries listed below.

2021-12-09 | GSE141818 | GEO

Analysis of the interactomes of ZAP70, CD247 and SLP76 upon stimulation of murine CD8+ T cells with ligands of different affinity to the TCR

Project description:T cells have the remarkable ability to sense and discriminate between a wide range of antigenic peptides bound to major histocompatibility complex molecules (pMHC). Here, we use interactomics to monitor in a time dependent manner the early molecular events taking place upon stimulation of murine CD8+ T cells with ligands of different affinity to the TCR. We used the mouse OT-I model in which T cells specifically recognize the ovalbumin OVA 257-264 peptide (SIINFEKL, also named N4) bound to the MHC-I molecule H-2Kb (pMHC). The OT-I TCR also recognizes altered peptide ligands amongst which SIITFEKL (T4) and SIIGFEKL (G4) with sub-optimal binding capacities (ligand affinity N4>T4>G4). For affinity purification (AP) of signalling complexes, we crossed OT-I TCR transgenic mice onto mice expressing an endogenous tagged (One-Strep-Tag: OST) version of the CD3z (also called CD247), ZAP70 or SLP76 molecules. CD8+ T cells were purified from pooled lymph nodes and spleens, shortly expanded, and were left unstimulated or stimulated with N4, T4 and G4 soluble pMHC tetramers for 30, 120 or 300 s. Complexes formed around either CD247, ZAP70 or SLP76 were then purified and analysed by mass spectrometry. Each AP-MS purification is associated with a corresponding control (purification from OT-I CD8+ T cells expressing only the endogenous version of each bait, cultured and stimulated in the same conditions). The number of replicate biological experiments was n=3 for all time-points, and each sample was analyzed twice by single-run nano LC-MS. In addition, the whole proteome of OT-I cell was analyzed by label-free shotgun proteomics in order to calculate cellular protein abundances for each interactor.

2022-07-05 | PXD029974 | Pride

Time-resolved phosphoproteomic analysis of murine CD8+ T cells upon stimulation with ligands of different affinity to the TCR

Project description:T cells have the remarkable ability to sense and discriminate between a wide range of antigenic peptides bound to major histocompatibility complex molecules (pMHC). Here, we use phosphoproteomics to monitor in a time dependent manner the signalling cascade taking place upon stimulation of murine CD8+ T cells with ligands of different affinity to the TCR. We used the mouse OT-I model in which T cells specifically recognize the ovalbumin OVA257-264 peptide (SIINFEKL, also named N4) bound to the MHC-I molecule H-2Kb (pMHC). The OT-I TCR also recognizes altered peptide ligands amongst which SIITFEKL (T4) and SIIGFEKL (G4) with sub-optimal binding capacities (ligand affinity N4>T4>G4). CD8+ T cells were purified from pooled lymph nodes and spleens, shortly expanded, and were left unstimulated or stimulated with N4, T4 and G4 soluble pMHC tetramers for 30, 120, 300 or 600s. We conducted six independent multiplexed experiments, each containing either independent stimulations with the N4 and T4 peptides (N4-T4 experiments, 3 replicates) or with the N4 and G4 peptides (N4-G4 experiments, 3 replicates). Samples from each experiment were labeled by TMT10plex, pooled and subjected to phospho-enrichment using first TiO2 beads and then phospho-Tyrosine (pY) immuno-precipitation (IP). Samples were injected before TiO2 enrichment, after TiO2 and after TiO2 followed by pY IP for analysis of the proteome, serine/threonine phospho-proteome and tyrosine phospho-proteome, respectively.

2022-07-05 | PXD030080 | Pride

Zfp36l1 establishes the high affinity CD8 T cell response by directly linking TCR affinity to cytokine sensing

Project description:The T cell effector phase is dominated by few T cells with high affinity TCR for the respective immunodominant antigen. During priming T cells have to process multiple cues in form of antigen, costimulation and cytokines, thus a plethora of T cells with different specificities and affinities has to compete for these cues. IL2 has been suggested to be a pivotal pleiotropic molecule which organizes the quantity, quality and clonal composition of T cells contributing to the effector response. How individual T cells compete for and respond to IL2 and other key cytokines at the molecular level and as a consequence, how this competition shapes population dynamics is still poorly understood. Here we describe how the RNA binding protein ZFP36L1 acts as a sensor of antigen affinity and establishes dominance of high affinity T cells by promoting the response to IL2.

2023-04-24 | GSE230373 | GEO

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