Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

HLA class II ligandome of colon cancer tissues for neoantigen identification

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

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Takayuki Kanaseki

PROVIDER: PXD054060 | JPOST Repository | Wed Sep 25 00:00:00 BST 2024

REPOSITORIES: jPOST

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SA029_CRC41_classII.mgf	Mgf
	SA029_CRC41_classII.raw	Raw
	SA029_CRC41_classII_gencode_v31_pc_translations_sequest.mzTab	Mztab
	SA050_CRC72_classII.mgf	Mgf
	SA050_CRC72_classII_WES_missense%20plus%20gencode_v31_pc_translations_sequest.mzTab	Mztab

Items per page:

1 - 5 of 20

Publications

HLA class II neoantigen presentation for CD4+ T cell surveillance in HLA class II-negative colorectal cancer.

Matsumoto Satoru S Tsujikawa Takahiro T Tokita Serina S Mohamed Bedeir Mai M Matsuo Kazuhiko K Hata Fumitake F Hirohashi Yoshihiko Y Kanaseki Takayuki T Torigoe Toshihiko T

Oncoimmunology 20240919 1

Neoantigen-reactive CD4+ T cells play a key role in the anti-tumor immune response. However, the majority of epithelial tumors are negative for HLA class II (HLA-II) surface expression, and less is known about the processing of HLA-II antigens. Here, we directly identified naturally presented HLA-II neoantigens in HLA-II negative colorectal cancer (CRC) tissue using a proteogenomic approach. The neoantigens were immunogenic and induced patient CD4+ T cells with a Th1-like m ...[more]

PMID: 39508845

Similar Datasets

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 colon cancer tissues for lncRNA antigen identification

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

2021-09-27 | PXD024533 | JPOST Repository

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

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

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

HLA-I and HLA-II peptidomes of endometrial cancer

Project description:MS data of HLA class I and HLA class II ligandome of human endometrial cancer

2024-10-31 | PXD050576 | JPOST Repository

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

HLA class II subs

Project description:HLA class II full-length submissions 30/08/2022

| PRJEB55642 | ENA

Tuning DO:DM ratios modulates HLA class II immunopeptidomes

Project description:Major Histocompatibility Complex Class II antigen presentation underlies a wide range of immune responses in health and disease. Although peptide ligand binding affinity has been the major focus for explaining and predicting class II antigens, we know that the levels and activities of accessory molecules, HLA-DM (DM) and HLA-DO (DO) can have strong effects on peptide repertoires. However, the extent to which these antagonistic proteins’ levels relative to one another shape the identities and properties of peptides selected for presentation remains unclear. Hence, after creating cell line panel with varying DO:DM ratios, of we set out to measure the effects these ratios can have on peptide presentation. Using a combined immunopeptidomic and proteomic discovery strategy, we profiled ligandome differences across this panel. By surveying over 10,000 unique HLA-DR4-presented peptides, we found marked increases in repertoire diversity and altered physical properties of presented peptides that corresponded with increasing DO:DM ratios.

2023-10-24 | PXD024392 | Pride

Sampling from proteome to HLA-DR ligandome

2018-08-24 | MSV000082848 | MassIVE