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The lupus susceptibility allele DRB1*03:01 encodes a disease driving epitope [THP-1]

ABSTRACT: The lupus susceptibility allele DRB1*03:01 encodes a disease driving epitope [THP-1]

PROVIDER: PRJNA727352 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14423952.fastq.gz	Fastqsanger.gz
	SRR14423953.fastq.gz	Fastqsanger.gz
	SRR14423954.fastq.gz	Fastqsanger.gz
	SRR14423955.fastq.gz	Fastqsanger.gz
	SRR14423956.fastq.gz	Fastqsanger.gz

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The lupus susceptibility allele DRB1*03:01 encodes a disease driving epitope [THP-1]

Project description:We report RNA sequencing data that shows the differential effects of HLA-DRb1*0301 (LE), HLA-DRb1*0401 (SE) and HLA-DRb1*0402 (PE) on macrophage gene expression under IFNγ cell culture conditions.

2022-08-03 | GSE173876 | GEO

The lupus susceptibility allele DRB1*03:01 encodes a disease driving epitope

Project description:The lupus susceptibility allele DRB1*03:01 encodes a disease driving epitope

| PRJNA727339 | ENA

The lupus susceptibility allele DRB1*03:01 encodes a disease driving epitope [RAW264.7]

Project description:The lupus susceptibility allele DRB1*03:01 encodes a disease driving epitope [RAW264.7]

| PRJNA727351 | ENA

The lupus susceptibility allele DRB1*03:01 encodes a disease driving epitope [RAW264.7]

2022-08-03 | GSE173875 | GEO

The lupus susceptibility allele DRB1*03:01 encodes a disease driving epitope

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

2022-08-03 | GSE173877 | GEO

New Allele HLA-DRB1*03

Project description:Sample od DVMO Brasil, with new allele HLA-DRB1*03.

| PRJEB41331 | ENA

The HLA-DRB1*03:01 ligandome is highly conserved on N- and C-terminal residues outside the peptide-binding cleft

Project description:Human CD4+ T lymphocytes play an important role in inducing potent immune responses. They are activated and stimulated by peptides presented in Major Histocompatibility Complex Class II molecules. These MHC class II molecules typically present peptides of between 12 and 20 amino acids in length. The region that interacts with the MHC molecule, designated as the binding core, is highly conserved in the residues which anchor the peptide to the molecule. In addition, as these peptides are the product of proteolytic cleavages, certain conserved residues may be expected at the N- and C-termini outside the binding core. To study whether similar conserved residues are present in different types of cells , the ligandomes of HLA-DRB1*03:01 derived from two different cell types (dendritic cells and EBV-transformed B-cells) were identified with mass spectrometry and the binding core and N- and C-terminal residues were analysed using the frequencies of the amino acids in the human proteome. Similar binding motifs were found as well as comparable conservations in the N- and C-terminal residues. Furthermore, these terminal conservations of the HLA-DRB1*03:01 ligandome were compared to the N- and C-terminal conservations of the HLA-DRB1*04:01 ligandome acquired from dendritic cells. Again, comparable conservations were evident with only minor differences. Taken all together, these analyses show that there are conservations in the terminal residues of peptides, presumably the result of the activity of proteases involved in antigen processing.

2019-09-16 | PXD014253 | Pride

New Allele HLA-DRB1

Project description:HLA-DRB1*11:04 new

| PRJEB64134 | ENA

Direct quantification of viral epitope abundance reveals the importance of direct and cross-presentation in driving CTL responses during influenza infection

Project description:The magnitude of CD8+ T lymphocyte (CTL) responses to infection is a function of the available naïve T cell repertoire, combined with the context and duration of antigen presentation. Whilst T cell repertoires are relatively easily studied, the context and abundance of epitopes presented on infected cells and dendritic cells (DCs) and their subsequent impact on CTL responses are generally poorly understood. Using quantitative mass spectrometry, we identified and quantified the abundance of 21 class 1 Major Histocompatibility Complex molecule (MHCI)-restricted influenza A virus (IAV)-derived peptides following either direct presentation or cross-presentation. All identified peptides, including seven novel epitopes, elicited T cell responses in infected C57BL/6 mice. Quantitation of IAV epitopes displayed via direct presentation showed a maintenance of relative epitope abundance across distinct cell types, reflecting common antigen processing mechanisms. Comparison of epitope levels displayed via direct presentation and cross-presentation revealed a broad range of directly presented epitope abundances, which was normalised during cross-presentation. Further, we observed a clear disparity in the abundance of the two key immunodominant IAV antigens, wherein direct infection drove optimal nucleoprotein (NP)366-374 presentation, while cross-presentation was optimal for acid polymerase (PA)224-233 presentation. This study provides a detailed dissection of viral pMHCI abundance after infection and reveals the importance of both direct and cross-presentation in driving dominant CTL responses. The study also demonstrates how empirical assessment of epitope abundance in both modes of antigen presentation is necessary to fully understand the immunogenicity and response magnitude to T cell epitopes.

2019-07-02 | PXD012728 | Pride

Antigen Presentation-Independent Reciprocal Immune Modulation by HLA-DRB1 Allelic Epitopes that Associate with Autoimmune Disease Risk or Protection in Human Macrophages

Project description:We report RNA sequencing data that shows the the differential effects of HLA-DRb1*0401 (SE) and HLA-DRb1*0402 (PE) on marcophage gene expression under M1 polarizing cell culture conditions

2021-02-02 | GSE159279 | GEO

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