Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ARTEMIS: a novel mass-spec platform for HLA-restricted self and disease-associated peptide discovery

ABSTRACT: Data are associated with the development of a platform for the simple and robust detection of MHC class I peptides.

INSTRUMENT(S): Orbitrap Fusion ETD, LTQ Orbitrap Elite

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Roland Strong

PROVIDER: MSV000087172 | MassIVE | Fri Apr 09 12:07:00 BST 2021

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

ARTEMIS: A Novel Mass-Spec Platform for HLA-Restricted Self and Disease-Associated Peptide Discovery.

Project description:Conventional immunoprecipitation/mass spectroscopy identification of HLA-restricted peptides remains the purview of specializing laboratories, due to the complexity of the methodology, and requires computational post-analysis to assign peptides to individual alleles when using pan-HLA antibodies. We have addressed these limitations with ARTEMIS: a simple, robust, and flexible platform for peptide discovery across ligandomes, optionally including specific proteins-of-interest, that combines novel, secreted HLA-I discovery reagents spanning multiple alleles, optimized lentiviral transduction, and streamlined affinity-tag purification to improve upon conventional methods. This platform fills a middle ground between existing techniques: sensitive and adaptable, but easy and affordable enough to be widely employed by general laboratories. We used ARTEMIS to catalog allele-specific ligandomes from HEK293 cells for seven classical HLA alleles and compared results across replicates, against computational predictions, and against high-quality conventional datasets. We also applied ARTEMIS to identify potentially useful, novel HLA-restricted peptide targets from oncovirus oncoproteins and tumor-associated antigens.

| S-EPMC8111693 | biostudies-literature

Critical residues within the TAPBPR scoop loop for HLA-A2 binding and peptide loading are determined by deep mutational scanning

Project description:The loading of high affinity peptides onto nascent class I MHC (MHC-I) molecules is facilitated by chaperones, including the class I-specific chaperone TAP-binding protein-related (TAPBPR). TAPBPR features a loop (amino acids 24-35) that projects towards the empty MHC-I peptide binding groove and rests above the F pocket. The 24-35 loop is much shorter in the closely related homologue tapasin, and therefore may be partly responsible for the unique antigen editing properties of TAPBPR. Previously we reported a deep mutational scan of human TAPBPR focused on the 24-35 loop, and determined the relative effects of single amino acid mutations on binding and peptide-mediated release of the murine H2-Dd MHC-I allomorph. Here, we extend our studies to determine the mutational landscape of the 24-35 loop when TAPBPR binds a human MHC-I allomorph, HLA-A*02:01. The data highlights how TAPBPR affinity can be increased or decreased for different MHC-I allomorphs by tuning the electrostatic complementarity of the 24-35 loop for surfaces on the rim of the peptide-binding groove. By changing the selection pressure from HLA-A2 binding to HLA-A2 loading and processing, we find that TAPBPR is reasonably tolerant of mutations in the 24-35 loop for efficient peptide-MHC-I processing and surface trafficking.

2019-09-01 | GSE126206 | GEO

Expression data from self-deprived regulatory CD4 T cells

Project description:Disruption of TCR /MHC class II interactions leads rapidly to alterations of the common CD4 Treg transcriptional signature Self-deprived, non-functional Tregs were compare to fully functional Tregs by microarrays. Total T cells from the periphery of WT mice were adoptively transferred into CD3ε-/- recipient mice lacking or not MHC class II molecule expression (MHC II- or MHC II+ recipient mice, respectively). Five days later, peripheral Tregs transferred in MHC II - competent (CD4CD25B6) or - deficient (CD4CD25IIko) recipient were purified for RNA extraction and hybridization on Affymetrix microarrays.

2011-01-20 | E-GEOD-26714 | biostudies-arrayexpress

Impact of abacavir and abacavir analogues on HLA-B*57:01 peptide presentation

Project description:Characterisation of peptide ligands of the Major histocompatibility class (MHC) I allele, HLA-B*57:01, expressed in the C1R (Class I reduced) B-lymphoblastoid cell line, after exposure to the anti-retroviral abacavir or abacavir analogues.

2019-10-03 | PXD015398 | Pride

Impacts of HLA-B57 micropolymorphism (MRM)

Project description:Comparison of peptide ligands of major histocompatibility class (MHC) I isolated by immunoaffinity purification from the C1R (Class I reduced) B-lymphoblastoid cell line, transfected with the MHC class I alleles HLA-B*57:01, HLA-B*57:03 and HLA-B*58:01.

2018-10-24 | PXD009850 | Pride

Expression data from young and adult mice after over expression of self MHC class l protein in skeletal muscle.

Project description:Over expression of MHC Class l protein in skeletal muscle causes myositis. Phenotype after expression in young mice is more severe. We performed gene expression profiling on young and adult mice after over expression of self MHC class l protein in skeletal muscle Muscle from young ( early) , adult (Late) and cntrol (control) mice , n=3 each group, was used for gene expression profiling

2009-06-02 | E-GEOD-14997 | biostudies-arrayexpress

The self-peptide repertoire plays a critical role in transplant tolerance induction

Project description:While direct allorecognition underpins both solid organ allograft rejection and tolerance induction, the specific molecular targets of most directly-alloreactive CD8+ T cells have not been defined. In this study, we used a combination of genetically-engineered MHC I constructs, mice with a hepatocyte-specific mutation in the class I antigen-presentation pathway and immunopeptidomic analysis to provide definitive evidence for the contribution of the peptide cargo of allogeneic MHC I molecules to transplant tolerance induction. We established a systematic approach for the discovery of directly-recognised pMHC epitopes, and identified 17 strongly immunogenic H-2Kb-associated peptides recognised by CD8+ T cells from B10.BR (H-2k) mice, 13 of which were also recognised by BALB/c (H-2d) mice. As few as five different tetramers used together were able to identify almost 40% of alloreactive T cells within a polyclonal population. To our knowledge, this represents the first example of such an approach in the context of direct allorecognition.

2021-12-06 | PXD022695 | Pride

The self-peptide repertoire plays a critical role in transplant tolerance induction

2021-12-06 | PXD023015 | Pride

Expression data from young and adult mice after over expression of self MHC class l protein in skeletal muscle.

2009-06-02 | GSE14997 | GEO