Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

HLA class I ligandome of colon cancer tissues for lncRNA antigen identification

ABSTRACT: MS data of HLA class I ligandome of human colon cancer tissues

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Takayuki Kanaseki

PROVIDER: PXD024533 | JPOST Repository | Mon Sep 27 00:00:00 BST 2021

REPOSITORIES: jPOST

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ST419_CRC71_A24.raw	Raw
	ST419_CRC71_A24_PD.mgf	Mgf
	ST503_Colo320_A24.raw	Raw
	ST503_Colo320_A24_PD.mgf	Mgf
	ST544_CRC117_A24.raw	Raw

Items per page:

1 - 5 of 20

Publications

CD8+ T-cell Immune Surveillance against a Tumor Antigen Encoded by the Oncogenic Long Noncoding RNA PVT1.

Kikuchi Yasuhiro Y Tokita Serina S Hirama Tomomi T Kochin Vitaly V Nakatsugawa Munehide M Shinkawa Tomoyo T Hirohashi Yoshihiko Y Tsukahara Tomohide T Hata Fumitake F Takemasa Ichiro I Sato Noriyuki N Kanaseki Takayuki T Torigoe Toshihiko T

Cancer immunology research 20210825 11

CD8+ T cells recognize peptides displayed by HLA class I molecules on cell surfaces, monitoring pathologic conditions such as cancer. Advances in proteogenomic analysis of HLA ligandomes have demonstrated that cells present a subset of cryptic peptides derived from noncoding regions of the genome; however, the roles of cryptic HLA ligands in tumor immunity remain unknown. In the current study, we comprehensively and quantitatively investigated the HLA class I ligandome of a set of hum ...[more]

PMID: 34433589

Similar Datasets

HLA class II ligandome of colon cancer tissues for neoantigen identification

Project description:MS data of HLA class II ligandome of human colon cancer tissues

2024-09-25 | PXD054060 | JPOST Repository

HLA class I ligandome of colon cancer tissues for neoantigen identification

Project description:MS data of HLA class I ligandome of human colon cancer tissues

2021-07-26 | PXD026573 | JPOST Repository

HLA class I ligandome of renal cancer tissues for hERV antigen identification

Project description:MS data of HLA class I ligandome of human renal cancer tissues

2023-11-15 | PXD038140 | JPOST Repository

Mapping the HLA ligandome of Colorectal Cancer Reveals an Imprint of Malignant Cell Transformation

Project description:Immunopeptidome analysis of colorectal adenocarcinoma tissues as well as adjacent benign tissues was performed to characterize the natural HLA class I and class II presented ligandome represented in the context of malignancy as well as in benign tissue of the colon.

2019-03-12 | PXD009602 | Pride

Pre-fractionation extends, but creates a bias in the detectable HLA class Ι ligandome

Project description:HLA class Ι molecules on the cell surface enable CD8+ T lymphocytes to recognize cellular alterations in the form of antigens, including mutations, protein copy number alterations, aberrant post-translational modifications or pathogen proteins. At any given moment, tens of thousands of different self and foreign HLA class Ι peptide ligands may be presented on the cell surface by MHC class Ι complexes. Analysis of the HLA ligandome thrusts therefore unique challenges due to their enormous biochemical diversity and inherently wide range of abundances. Despite advances in enrichment, separation, MS instrumentation and fragmentation, it is still not achievable to cover the HLA class Ι ligandome in sufficient depth to support routine identification of e.g. viral pathogens or immuno-therapeutically important tumor neo-antigens. In this study, we evaluate two pre-fractionation techniques, high pH reversed phase and strong cation exchange for complementary analysis of HLA class Ι peptide ligands, benchmarking them against analyses circumventing pre-fractionation. We observe that pre-fractionation substantially extends the detectable HLA class Ι ligandome, but also creates an identification bias. We advocate a rational choice between no-fractionation, high pH reversed phase or strong cation exchange pre-fractionation for deeper HLA class Ι ligandome analysis depending on the targeted HLA locus, allele or peptide ligand modification

2019-02-25 | PXD011257 | Pride

Tumour-associated antigenic peptides are present in the HLA class I ligandome of cancer cell line derived extracellular vesicles.

Project description:The recent success of monoclonal antibody checkpoint inhibitor therapies that enhance the ability of CD8+ T cells to detect cancer-related antigenic peptides has refocused the need to fully understand the repertoire of peptides being presented to the immune system. Whilst the peptide ligandome presented by cell surface HLA class I molecules on cancer cells has been studied extensively, the ligandome of extracellular vesicles remains poorly defined. Here we report the HLA class I ligandome of both cell surface and extracellular vesicles from eight breast cancer cell lines (MCF7, MDA-MB-231, MDA-MB-361, MDA-MB-415, MDA-MB-453, HCC 1806, HCC 1395, and HCC 1954), and additionally the melanoma cell line ESTDAB-056 and the multiple myeloma line RPMI 8226. Utilising HLA class I immunoisolation and mass spectrometry we detected a total of 6574 peptides from the cell surface and 2461 peptides from the extracellular vesicles of the cell lines studied. Within the extracellular vesicle HLA class I ligandome we identified 150 peptides derived from tumour associated antigenic proteins, of which 19 peptides have been shown to elicit T cell responses in previous studies. Our data thus confirms for the first time the presence of clinically relevant tumour-associated antigenic peptides in the HLA class I ligandome present on EV.

2022-04-01 | PXD025345 | Pride

HLA-I and HLA-II peptidomes for NESSIE

Project description:MS data of HLA class I and HLA class II ligandome of human colon tissue and LCLs

2024-08-08 | PXD047303 | JPOST Repository

Gene and protein sequence features augment HLA class I ligand predictions (mRNA sequencing)

Project description:The sensitivity of malignant tissues to T cell-based cancer immunotherapies is dependent on the presence of targetable HLA class I ligands on the tumor cell surface. Peptide intrinsic factors, such as HLA class I affinity, likelihood of proteasomal processing, and transport into the ER lumen have all been established as determinants of HLA ligand presentation. However, the role of sequence features at the gene and protein level as determinants of epitope presentation has not been systematically evaluated. To address this, we performed HLA ligandome mass spectrometry on patient-derived melanoma lines and used this data-set to evaluate the contribution of 7,124 gene and protein sequence features to HLA sampling. This analysis reveals that a number of predicted modifiers of mRNA and protein abundance and turn-over, including predicted mRNA methylation and protein ubiquitination sites, inform on the presence of HLA ligands. Importantly, integration of gene and protein sequence features into a machine learning approach augments HLA ligand predictions to a comparable degree as predictive models that include experimental measures of gene expression. Our study highlights the value of gene and protein features to HLA ligand predictions.

2023-01-08 | GSE210999 | GEO

Gene and protein sequence features augment HLA class I ligand predictions (ribosome profiling)

2023-01-08 | GSE210998 | GEO

Sampling from proteome to HLA-DR ligandome

Project description:Comprehensive analysis of the complex nature of the Human Leukocyte Antigen (HLA) class II ligandome is of utmost importance to understand the basis for CD4+ T cell mediated immunity and tolerance. Here, we implemented important improvements in the analysis of the repertoire of HLA-DR-presented peptides, using hybrid mass spectrometry-based peptide fragmentation techniques on a ligandome sample isolated from matured human monocyte-derived dendritic cells (DC). The reported data set constitutes nearly 14 thousand unique high-confident peptides, i.e. the largest single inventory of human DC derived HLA-DR ligands to date. From a technical viewpoint the most prominent finding is that no single peptide fragmentation technique could elucidate the majority of HLA-DR ligands, due to the wide range of physical chemical properties displayed by the HLA-DR ligandome. Our in-depth profiling allowed us to reveal a strikingly modest correlation between the abundance levels of surface-presented peptides and the cellular expression of their source proteins. Important selective sieving from the sampled proteome to the ligandome, was evidenced by specificity in the sequences of the core regions both at their N- and C- termini, hence not only reflecting binding motifs but also dominant protease activity associated to the endolysosomal compartments. Moreover, we demonstrate that the HLA-DR ligandome reflects a surface representation of cell-compartments specific for biological events linked to the maturation of monocytes into antigen presenting cells. Our results present new perspectives into the complex nature of the HLA class II system and will aid future immunological studies in characterizing the full breadth of potential CD4+ T cell epitopes relevant in health and disease.

2016-01-25 | PXD002951 | Pride