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Altered binding of tumor antigenic peptides to MHC class I affects CD8 T cell effector responses

ABSTRACT: Altered binding of tumor antigenic peptides to MHC class I affects CD8 T cell effector responses

PROVIDER: PRJNA494845 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7969340.fastq.gz	Fastqsanger.gz
	SRR7969337.fastq.gz	Fastqsanger.gz
	SRR7969338.fastq.gz	Fastqsanger.gz
	SRR7969339.fastq.gz	Fastqsanger.gz

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Similar Datasets

Altered binding of tumor antigenic peptides to MHC class I affects CD8 T cell effector responses

Project description:T cell priming occurs when a naïve T cell recognizes cognate peptide-MHC complexes on an activated antigen presenting cell. The circumstances of this initial priming have dramatic ramifications on the fate of the newly primed T cell. Newly primed CD8 T cells can embark onto different trajectories, with some becoming short lived effector cells and others adopting a tissue resident or memory cell fate. To determine whether T cell priming influences the quality of the effector T cell response to tumors, we used transnuclear CD8 T cells that recognize the melanoma antigen TRP1 using TRP1high or TRP1low TCRs that differ in both affinity and fine specificity. From a series of altered peptide ligands, we identified a point mutation (K8) in a non-anchor residue that, when analyzed crystallographically and biophysically, destabilizes the peptide interaction with the MHC binding groove. We then compared the transcriptional profiles of TRP1-specific T cells activated in vitro with M9 peptide to those activated with K8 peptide.

2018-10-06 | GSE120892 | GEO

Proteogenomics-based identification of the repertoire of human MHC class I-associated peptides

Project description:We have develop a proteogenomics-based approach for identification of human MHC class I-associated peptides, including those deriving from polymorphisms, mutations and non-canonical reading frames

2016-12-22 | GSE67174 | GEO

Altered Binding of Tumor Antigenic Peptides to MHC Class I Affects CD8<sup>+</sup> T Cell-Effector Responses.

Project description:T-cell priming occurs when a naïve T cell recognizes cognate peptide-MHC complexes on an activated antigen-presenting cell. The circumstances of this initial priming have ramifications on the fate of the newly primed T cell. Newly primed CD8+ T cells can embark onto different trajectories, with some becoming short-lived effector cells and others adopting a tissue resident or memory cell fate. To determine whether T-cell priming influences the quality of the effector T-cell response to tumors, we used transnuclear CD8+ T cells that recognize the melanoma antigen TRP1 using TRP1high or TRP1low TCRs that differ in both affinity and fine specificity. From a series of altered peptide ligands, we identified a point mutation (K8) in a nonanchor residue that, when analyzed crystallographically and biophysically, destabilized the peptide interaction with the MHC binding groove. In vitro, the K8 peptide induced robust proliferation of both TRP1high and TRP1low CD8+ T cells but did not induce expression of PD-1. Cytokine production from K8-stimulated TRP1 cells was minimal, whereas cytotoxicity was increased. Upon transfer into B16 tumor-bearing mice, the reference peptide (TRP1-M9)- and K8-stimulated TRP1 cells were equally effective at controlling tumor growth but accomplished this through different mechanisms. TRP1-M9-stimulated cells produced more IFNγ, whereas K8-stimulated cells accumulated to higher numbers and were more cytotoxic. We, therefore, conclude that TCR recognition of weakly binding peptides during priming can skew the effector function of tumor-specific CD8+ T cells.

| S-EPMC6290996 | biostudies-literature

Impact of genomic polymorphisms on the repertoire of human MHC class I-associated peptides

Project description:We developed a novel approach combining next generation sequencing, bioinformatics and mass spectrometry to assess the impact of non-MHC polymorphisms on the repertoire of MHC I-associated peptides (MIPs). We compared the genomic landscape of MIPs eluted from B lymphoblasts of two MHC-identical siblings and determined that MIPs mirror the genomic frequency of non-synonymous polymorphisms but they behave as recessive traits at the surface level. Moreover, we showed that 11.7% of the MIP coding exome is polymorphic at the population level. Our method provides fundamental insights into the relation between the genomic self and the immune self and accelerates the discovery of polymorphic MIPs (also known as minor histocompatibility antigens), which play a major role in allo-immune responses. RNA-seq of human B lymphoblasts derived from peripheral blood mononuclear cells from 2 HLA-identical female siblings.

2013-12-08 | E-GEOD-48918 | biostudies-arrayexpress

Chicken MHC class II presented Marek's disease virus (MDV) and infectious bursal disease virus (IBDV) antigenic peptides

Project description:Viral diseases pose major threats to humans and other animals, including the billions of chickens that are an important food source as well as a public health concern due to zoonotic pathogens. Unlike humans and other typical mammals, the major histocompatibility complex (MHC) of chickens can confer decisive resistance or susceptibility to many viruses. Examples are Marek's disease virus (MDV) and Infectious bursal disease virus (IBDV). We used a new in vitro infection system and immunopeptidomics to identify peptides presented to T lymphocytes via classical MHC class II molecules.

2021-09-10 | PXD023954 | Pride

A deep mutational scan of the MHC class I-specific chaperone TAPBPR for sites important for peptide editing

Project description:TAP-binding protein-related (TAPBPR) is an endoplasmic reticulum-resident chaperone that facilitates class I MHC (MHC-I) processing and peptide loading. TAPBPR has (1) chaperone function to stabilize misfolded or partially folded nascent MHC-I substrates, and (2) editing function, in which it catalyzes the exchange of low affinity for high affinity antigenic peptides in the MHC-I peptide-binding groove. TAPBPR-TM is a chimera of the TAPBPR ectodomain and a canonical TM domain, which escapes the endoplasmic reticulum to reach the cell surface. We reasoned that at the cell surface, TAPBPR-TM is more likely to interact with folded MHC-I and thus surface interactions will be more representative of editing function. When tapasin, a homolog of TAPBPR and the main MHC-I-specific chaperone, is knocked out, surface trafficking of HLA-A2 (a human MHC-I allele) is severely diminished, but surface HLA-A2 levels are rescued by over-expression of TAPBPR-TM. Using this assay as the foundation for a fluorescence-based selection, we deep mutationally scanned 104 positions on TAPBPR-TM to identify sites critical for engaging folded MHC-I.

2023-03-09 | GSE218828 | GEO

HLA-DP(84Gly) constitutively presents endogenous peptides generated by the class I antigen processing pathway

Project description:Classical antigen processing/presentation mechanisms lead to the presentation of antigenic peptides derived from endogenous and exogenous sources for MHC class I and class II molecules, respectively. We show here that, unlike other class II, prevalent HLA-DP molecules whose chains encode Gly84 (DP84Gly) constitutively present endogenous peptides.

2016-10-04 | MSV000080228 | MassIVE

Impact of genomic polymorphisms on the repertoire of human MHC class I-associated peptides

2013-12-08 | GSE48918 | GEO

Identification of blood MHC-binding peptides in mice after Brucella infection

Project description:We infected mice with Brucella, took mouse blood 6 days after infection, MHC binding antigenic peptides were collected by immunoprecipitation method and verified by mass spectrometry

2022-03-27 | PXD032855 |

A deep mutational scan of the MHC class I-specific chaperone tapasin

Project description:Tapasin acts as the principal MHC-I-specific chaperone for facilitating folding and antigenic peptide loading of nascent MHC class I substrates in the cell. In cells where tapasin has been knocked out, the processing and surface trafficking of the human MHC-I allele HLA-A2 is substantially reduced. Over-expression of tapasin rescues HLA-A2 surface expression. Using this assay as the basis for a fluorescence-based selection, tapasin was deep mutationally scanned at 108 positions in the core, at the interface with MHC-I, and on the ‘backside’ distal from where MHC-I binds. Critical residues of tapasin for rescue of HLA-A2 processing map to sites that contact the underside of the MHC-I alpha-2 domain, to the surface contacting the MHC-1 beta2m and alpha-3 domains, and to the base of a protruding loop that rests above the peptide-binding groove (but not to the tip of the loop itself).

2020-10-09 | GSE159247 | GEO

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