Ontology highlight
ABSTRACT:
PROVIDER: PRJNA524922 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8653290.fastq.gz | Fastqsanger.gz | |||
| SRR8653290_1.fastq.gz | Fastqsanger.gz | |||
| SRR8653290_2.fastq.gz | Fastqsanger.gz | |||
| SRR8653300.fastq.gz | Fastqsanger.gz | |||
| SRR8653300_1.fastq.gz | Fastqsanger.gz |
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Project description:A novel modified HLA-B*57:01-restricted epitope was identified in one of the reversed-phase fractions following immunoaffinity purification of HLA-peptide complexes from C1R cells expressing HIV envelope protein. Also includes six immunopeptidome datasets from several B57 and env transfected cell lysates.
2018-02-19 | PXD004471 | Pride
Project description:The purpose of this study is to evaluate the safety and time to progression of HLA-A*0201 restricted epitope peptides VEGFR1 and VEGFR2 emulsified with Montanide ISA 51 in combination with Tegafur/Uracil/Folinate chemotherapy.
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Project description:The purpose of this study is to evaluate the safety and time to progression of HLA-A*2402 restricted epitope peptides RNF43, TOMM34, VEGFR1 and VEGFR2 emulsified with Montanide ISA 51 in combination with Tegafur/Uracil/Folinate chemotherapy.
| 2055342 | ecrin-mdr-crc
Project description:Peptides generated by proteasome-catalyzed splicing of non-contiguous amino acid sequences have been shown to constitute a source of non-templated human leukocyte antigen class I (HLA-I) epitopes, but their role in pathogen-specific immunity remains unknown. CD8+ T cells are key mediators of human immunodeficiency virus type 1 (HIV-1) control, and identification of novel epitopes to enhance targeting of infected cells is a priority for prophylactic and therapeutic strategies. To explore the contribution of proteasome-catalyzed peptide splicing (PCPS) to HIV-1 epitope generation, we developed a broadly-applicable mass spectrometry-based discovery workflow that we employed to identify spliced HLA-I-bound peptides on HIV-infected cells. We demonstrate that HIV-1-derived spliced peptides comprise a novel, but relatively minor, component of the HLA-I-bound viral immunopeptidome. Although spliced HIV-1 peptides may elicit CD8+ T cell responses relatively infrequently during infection, CD8+ T cells primed by partially-overlapping contiguous epitopes in HIV-infected individuals were able to cross-recognize spliced viral peptides, suggesting a potential role for PCPS in restricting HIV-1 escape pathways. Vaccine-mediated priming of responses to spliced HIV-1 epitopes could thus provide a novel means of exploiting epitope targets typically under-utilized during natural infection.
2019-11-25 | PXD015489 | Pride
Project description:Human leukocyte antigen (HLA) class I restricted neo-epitopes play a key role in inducing an adaptive cytotoxic T lymphocyte response against cancer. To enhance therapeutic and personalized cancer vaccination strategies, the identification of these cancer-specific neo-epitopes is essential. Current workflows for the neo-epitope identification are often laborious and still require computational deconvolution to determine the correct peptide sequence and its corresponding restriction element. In this study, we evaluated the use of an mRNA-based workflow, which allows for more precise purification of HLA-I/peptide (pHLA) complexes and potentially facilitates peptide identification by liquid chromatography-tandem mass spectrometry (LC-MS/MS). The approach uses mRNA encoding a specific HLA-I molecule linked with a Twin-Strep-Tag (HLA-TST), allowing affinity-based purification and downstream analysis of pHLA. We delivered a proof-of-concept for this approach by co-delivering mRNA encoding a TST-coupled HLA-A*0201 with mRNA encoding the HLA-A*0201-restricted p53 epitope via electroporation in HLA-A*0201- K562 cells. The findings of this study show the promise of the mRNA-based strategy in neo-epitope research. However, further studies are necessary to fully understand the technical factors that can affect the peptides identified by LC-MS/MS.
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Project description:In this study we investigate the potential of targeting citrullinated GRP78 for cancer therapy. We select five peptides and show the identification CD4 T cell responses to one citrullinated GRP78 epitope that is restricted through HLA DP*0401 and HLA-DR*0101 alleles. This peptide is detected by mass spectrometry in B16 melanoma grown in vivo and citrulline specific CD4 responses to this epitope mediate efficient therapy of established B16 melanoma tumours in HHDII/DP4 transgenic mouse model. We demonstrate the existence of a repertoire of responses to the citrullinated GRP78 peptide in healthy individuals.
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Project description:Sanjuan2013 - Evolution of HIV T-cell epitope, immune activation model
Model of cellular immune response against HIV.
This model is described in the article:
Immune activation promotes evolutionary conservation of T-cell epitopes in HIV-1.
Sanjuán R, Nebot MR, Peris JB, Alcamí J.
PLoS Biol. 2013 Apr;11(4):e1001523
Abstract:
The immune system should constitute a strong selective pressure promoting viral genetic diversity and evolution. However, HIV shows lower sequence variability at T-cell epitopes than elsewhere in the genome, in contrast with other human RNA viruses. Here, we propose that epitope conservation is a consequence of the particular interactions established between HIV and the immune system. On one hand, epitope recognition triggers an anti-HIV response mediated by cytotoxic T-lymphocytes (CTLs), but on the other hand, activation of CD4(+) helper T lymphocytes (TH cells) promotes HIV replication. Mathematical modeling of these opposite selective forces revealed that selection at the intrapatient level can promote either T-cell epitope conservation or escape. We predict greater conservation for epitopes contributing significantly to total immune activation levels (immunodominance), and when TH cell infection is concomitant to epitope recognition (trans-infection). We suggest that HIV-driven immune activation in the lymph nodes during the chronic stage of the disease may offer a favorable scenario for epitope conservation. Our results also support the view that some pathogens draw benefits from the immune response and suggest that vaccination strategies based on conserved TH epitopes may be counterproductive.
Note from the author:
this version of the model is more general that the one described in the paper. This is because: (i) it can consider simultaneously Th-epitope escape mutants, CTL-epitope escape mutants and full T-cell (Th and CTL) escape mutants, by setting the mutation rate of Th and CTL escape mutants to zero. (ii) It allows for back mutations, which were ignored in all the simulations shown in the paper. (iii) It allows for a fitness cost of escape mutants, which was set to zero in the article. (iv) pAPCs can be infected and produce viruses (the rate of viral production for pAPCs was set to zero in the paper).
This model is hosted on BioModels Database
and identified
by: MODEL1302180001
.
To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource
for published quantitative kinetic models
.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to the public
domain worldwide. Please refer to CC0 Public Domain
Dedication
for more information.
2005-01-01 | MODEL1302180001 | BioModels
Project description:Sanjuan2013 - Evolution of HIV T-cell epitope, control model
Control model in which the virus targets a nonimmune cell type C (e.g., hepatocytes, epithelial cells, etc.), instead of T H
cells.
This model is described in the article:
Immune activation promotes evolutionary conservation of T-cell epitopes in HIV-1.
Sanjuán R, Nebot MR, Peris JB, Alcamí J.
PLoS Biol. 2013 Apr;11(4):e1001523
Abstract:
The immune system should constitute a strong selective pressure promoting viral genetic diversity and evolution. However, HIV shows lower sequence variability at T-cell epitopes than elsewhere in the genome, in contrast with other human RNA viruses. Here, we propose that epitope conservation is a consequence of the particular interactions established between HIV and the immune system. On one hand, epitope recognition triggers an anti-HIV response mediated by cytotoxic T-lymphocytes (CTLs), but on the other hand, activation of CD4(+) helper T lymphocytes (TH cells) promotes HIV replication. Mathematical modeling of these opposite selective forces revealed that selection at the intrapatient level can promote either T-cell epitope conservation or escape. We predict greater conservation for epitopes contributing significantly to total immune activation levels (immunodominance), and when TH cell infection is concomitant to epitope recognition (trans-infection). We suggest that HIV-driven immune activation in the lymph nodes during the chronic stage of the disease may offer a favorable scenario for epitope conservation. Our results also support the view that some pathogens draw benefits from the immune response and suggest that vaccination strategies based on conserved TH epitopes may be counterproductive.
This model is hosted on BioModels Database
and identified
by: MODEL1302180002
.
To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource
for published quantitative kinetic models
.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain
Dedication
for more information.
2005-01-01 | MODEL1302180002 | BioModels
Project description:Human CD8+ T cells are the final mediators of autoimmune β-cell destruction in type 1 diabetes. However, their target epitopes have not been demonstrated to be naturally processed and presented by β cells. We therefore performed an epitope discovery study combining HLA Class I peptidomics and transcriptomics strategies. Inflammatory cytokines increased β-cell peptide presentation in vitro, paralleling upregulation of HLA Class I expression. Peptide sources included known β-cell antigens and several insulin granule proteins. Preproinsulin yielded multiple previously described HLA-A2-restricted epitopes. Secretogranin V (SCG5/7B2), proconvertase-2, urocortin-3 and the insulin gene enhancer protein ISL-1 were identified as novel β-cell antigens, which were processed into HLA-A2-restricted epitopes recognized by circulating naïve CD8+ T cells in type 1 diabetic and healthy donors. HLA-A2-bound neo-epitopes were also represented and originated from an alternative mRNA splice isoform (SCG5-009) and from an islet amyloid polypeptide transpeptidation product. This first description of the β-cell HLA peptidome opens new avenues to understand the antigen processing pathways employed by β cells and provides a valuable tool for developing T-cell biomarkers and tolerogenic vaccination strategies.
2018-08-02 | GSE108413 | GEO
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