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The immunopeptidome of HLA-DR from PBMC

ABSTRACT: Quantifiying the impact of initial cell counts on the identified HLA-DR immunopeptidome of PBMC.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Blood Cell, Blood

DISEASE(S): Disease Free

SUBMITTER: Hesham ElAbd

LAB HEAD: Prof. Dr. Andreas Tholey

PROVIDER: PXD023032 | Pride | 2021-08-23

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	08102020_0.5_all_ids_merged_psm_perc_filtered.mzTab.gz	Mztab
	08102020_1_all_ids_merged_psm_perc_filtered.mzTab.gz	Mztab
	08102020_HLA_0_5.mzML	Mzml
	08102020_HLA_0_5.raw	Raw
	08102020_HLA_1.mzML	Mzml

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1 - 5 of 13

Publications

Immunopeptidomics toolkit library (IPTK): a python-based modular toolbox for analyzing immunopeptidomics data.

ElAbd Hesham H Degenhardt Frauke F Koudelka Tomas T Kamps Ann-Kristin AK Tholey Andreas A Bacher Petra P Lenz Tobias L TL Franke Andre A Wendorff Mareike M

BMC bioinformatics 20210817 1

<h4>Background</h4>The human leukocyte antigen (HLA) proteins play a fundamental role in the adaptive immune system as they present peptides to T cells. Mass-spectrometry-based immunopeptidomics is a promising and powerful tool for characterizing the immunopeptidomic landscape of HLA proteins, that is the peptides presented on HLA proteins. Despite the growing interest in the technology, and the recent rise of immunopeptidomics-specific identification pipelines, there is still a gap in data-anal ...[more]

PMID: 34404349

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HLA class II ligandome from HOM-2 and JY cell lines (HLA-DR an HLA-DP ligands)

Project description:A high-throughput mass spectrometry analysis was used to identify more than 16,000 cell peptides bound to several HLA-DR and -DP class II molecules isolated from large amounts of two human cell lines (HOM-2 and JY).

2021-11-03 | PXD028006 | Pride

FACS-sorted cells from Young Adults Vaccinated with Influenza TIV or LAIV Vaccines during 2008/09 Flu Season

Project description:Systems vaccinology has emerged as an interdisciplinary field that combines systems wide measurements and network and predictive modeling applied to vaccinology. Here we used the systems vaccinology approach to study the molecular mechanisms underlying the innate responses to the trivalent inactivated influenza (TIV) and live attenuated influenza (LAIV) vaccination in humans, and to identify early gene signatures that predict the magnitude of the antibody responses to influenza vaccination. During the 2008 influenza season, healthy adults were vaccinated with TIV (6 vaccinees) or LAIV (6 vaccinees), and blood samples isolated at day 0 and at day 7 post-vaccination. Cell subsets (B cells, Monocytes, mDCs and pDCs) were FACS-sorted from frozen PBMCs. Microarrays were performed using amplified total RNA.

2011-07-10 | E-GEOD-29618 | biostudies-arrayexpress

LC-MS of PBMC in SLE and healthy control

Project description:Systemic Lupus Erythematosus (SLE) is a systemic autoimmune disease that displays a significant gender difference in terms of incidence and severity. However, the underlying mechanisms accounting for sexual dimorphism remain unclear. To reveal the heterogeneity in the pathogenesis of SLE between male and female patients. PBMC were collected from 15 patients with SLE (7 males, 8 females) and 15 age-matched healthy controls (7 males, 8 females) for proteomic analysis. Enrichment analysis of proteomic data revealed that type I interferon signaling and neutrophil activation networks mapped to both male and female SLE, while male SLE has a higher level of neutrophil activation compared with female SLE. Our findings define gender heterogeneity in the pathogenesis of SLE and may facilitate the development of gender-specific treatments.

2022-08-12 | PXD033144 | Pride

Mapping naturally presented T-cell antigens in medulloblastoma based on integrative multi-omics

Project description:Medulloblastoma is the most frequent malignant primary brain tumor in children. Despite recent advances in integrated genomics, the prognosis in children with high-risk medulloblastoma remains devastating, and new tumor-specific therapeutic approaches are needed. Here, we present an atlas of naturally presented T-cell antigens in medulloblastoma. We mapped the human leukocyte antigen (HLA)-presented peptidomes of 28 tumors and performed comparative immunopeptidome profiling against an in-house benign database. Medulloblastoma proved to be a rich source of novel tumor-associated antigens, naturally presented on HLA class I and II molecules. Remarkably, most tumor-associated peptides and proteins were subgroup-specific, whereas shared presentation among all subgroups of medulloblastoma (WNT, SHH, Group 3 and Group 4) was rare. Functional testing of top-ranking novel candidate antigens demonstrated the induction of peptide-specific T-cell responses, supporting their potential for T-cell immunotherapy. This study is an in-depth mapping of naturally presented T-cell antigens in medulloblastoma. Integration of immunopeptidomics, transcriptomics, and epigenetic data led to the identification of a large set of actionable targets that can be further used for the translation into the clinical setting by facilitating the informed design of immunotherapeutic approaches to children with medulloblastoma.

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Expression data from iPSCs, iPSC-derived neurons, PBMC-derived Monocytes, PBMC-derived Macrophages, PBMC-derived induced microglia

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2023-02-27 | PXD033383 | Pride

Systems biology of vaccination for seasonal influenza in humans

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Natural and cryptic peptides dominate the immunopeptidome of atypical teratoid rhabdoid tumors.

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The HLA-Ligand-Atlas. A resource of natural HLA ligands presented on benign tissues

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