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TCR beta chain sequencing of HLA-DP cross reactive CD4 T-cell clones

ABSTRACT: TCR beta chain sequencing of HLA-DP cross reactive CD4 T-cell clones

PROVIDER: PRJEB50041 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR8027900_1.fastq.gz	Fastqsanger.gz
	ERR8027900_2.fastq.gz	Fastqsanger.gz
	ERR8027901_1.fastq.gz	Fastqsanger.gz
	ERR8027901_2.fastq.gz	Fastqsanger.gz
	ERR8026773_1.fastq.gz	Fastqsanger.gz

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Promiscuity of peptides presented in HLA-DP molecules from different immunogenicity groups is associated with T-cell cross-reactivity

Project description:In the context of HLA-DP-mismatched allogeneic stem cell transplantation, mismatched HLA-DP alleles can provoke profound allo-HLA-DP-specific immune responses from the donor T-cell repertoire leading to graft-versus-leukemia effect and/or graft-versus-host disease in the patient. The magnitude of allo-HLA-DP-specific immune responses has been shown to depend on the specific HLA-DP disparity between donor and patient and the immunogenicity of the mismatched HLA-DP allele(s). HLA-DP peptidome clustering (DPC) was developed to classify the HLA-DP molecules based on similarities and differences in their peptide-binding motifs. To investigate a possible categorization of HLA-DP molecules based on overlap of presented peptides, we identified and compared the peptidomes of the thirteen most frequently expressed HLA-DP molecules. Our categorization based on shared peptides was in line with the DPC classification. We found that the HLA-DP molecules within the previously defined groups DPC-1 or DPC-3 shared the largest numbers of presented peptides. However, the HLA-DP molecules in DPC-2 segregated into two subgroups based on the overlap in presented peptides. Besides overlap in presented peptides within the DPC groups, a substantial number of peptides was also found to be shared between HLA-DP molecules from different DPC groups, especially for groups DPC-1 and -2. The functional relevance of these findings was illustrated by demonstration of cross-reactivity of allo-HLA-DP-reactive T-cell clones not only against HLA-DP molecules within one DPC group, but also across different DPC groups. The promiscuity of peptides presented in various HLA-DP molecules and the cross-reactivity against different HLA-DP molecules demonstrate that these molecules cannot be strictly categorized in immunogenicity groups.

2022-02-12 | PXD030591 | Pride

T-cell alloreactivity to HLA-DP is regulated by peptide repertoire divergence and HLA-DM mediated editing

Project description:Analysis of the peptide repertoires eluted from different HLA-DP molecules expressed in HeLa cells co-expressing Invariant chain either with or without HLA-DM as components of the HLA class II processing machinery. Divergence of the immunopeptidomes and the impact of HLA-DM were investigated in relation to the capacity of HLA-DP molecules to elicit alloreactive T-cell responses.

2022-11-21 | PXD017154 | Pride

HLA class II ligandome from HOM-2 and JY cell lines (HLA-DR an HLA-DP ligands)

Project description:A high-throughput mass spectrometry analysis was used to identify more than 16,000 cell peptides bound to several HLA-DR and -DP class II molecules isolated from large amounts of two human cell lines (HOM-2 and JY).

2021-11-03 | PXD028006 | Pride

Human HLA-DP RSV viral infection JY cell line mass spectrometry raws

Project description:49638 JY non-infected cells HLA-DP 49639 JY infected cells HLA-DP

2019-03-18 | MSV000083591 | MassIVE

HLA-II HOM2 and JY

Project description:49633 -> HOM2 HLA-DR 49637 -> HOM2 HLA-DP 49647 -> JY HLA-DR 49649 -> JY HLA-DP

2018-07-31 | MSV000082670 | MassIVE

HLA-DP, HLA-DQ, and HLA-DR have different requirements for invariant chain and HLA-DM.

Project description:The MHC is central to the adaptive immune response. The human MHC class II is encoded by three different isotypes, HLA-DR, -DQ, and -DP, each being highly polymorphic. In contrast to HLA-DR, the intracellular assembly and trafficking of HLA-DP molecules have not been studied extensively. However, different HLA-DP variants can be either protective or risk factors for infectious diseases (e.g. hepatitis B), immune dysfunction (e.g. berylliosis), and autoimmunity (e.g. myasthenia gravis). Here, we establish a system to analyze the chaperone requirements for HLA-DP and to compare the assembly and trafficking of HLA-DP, -DQ, and -DR directly. Unlike HLA-DR1, HLA-DQ5 and HLA-DP4 can form SDS-stable dimers supported by invariant chain (Ii) in the absence of HLA-DM. Uniquely, HLA-DP also forms dimers in the presence of HLA-DM alone. In model antigen-presenting cells, SDS-stable HLA-DP complexes are resistant to treatments that prevent formation of SDS-stable HLA-DR complexes. The unexpected properties of HLA-DP molecules may help explain why they bind to a more restricted range of peptides than other human MHC class II proteins and frequently present viral peptides.

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NKp44/HLA-DP-dependent regulation of CD8 T cell clonality by NK cells

Project description:NKp44/HLA-DP-dependent regulation of CD8 T cell clonality by NK cells

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Mtb HLA-E tetramer sorted CD8+ T-cells have a diverse TCR repertoire

Project description:HLA-E molecules can present self and pathogen-derived peptides to both NK-cells and T-cells. T-cells that recognize HLA-E peptides via their T-cell receptor (TCR) are termed donor-unrestricted T-cells due to restricted allelic variation of HLA-E. The composition and repertoire of HLA-E TCRs is not known so far. We performed TCR sequencing on CD8+ T-cells from 21 individuals recognizing HLA-E tetramers (TM) folded with 2 Mtb HLA-E restricted peptides. We sorted HLA-E Mtb TM+ and TMCD8+ T-cells directly ex vivo and performed bulk RNA-sequencing and single cell TCR sequencing. The identified TCR repertoire was diverse and showed no conservation between and within individuals. TCRs selected from our single cell TCR sequencing data could be activated upon HLA-E/peptide stimulation, although not robust, reflecting potentially weak interactions between HLA-E peptide complexes and TCRs. Thus, HLA-E Mtb specific T-cells have a highly diverse TCR repertoire.

2024-02-04 | GSE236154 | GEO

Diplodia sp. Dp 3 strain:Dp 3

Project description:Diplodia sp. Dp 3 transcriptome - Dp 3-C.2

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Diplodia sp. Dp 5 strain:Dp 5

Project description:Diplodia sp. Dp 5 transcriptome - Dp 5-B.2

| PRJNA584235 | ENA