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Pancreatic beta cell HLA class I peptidome

ABSTRACT: Immunopeptidomics of pancreatic beta cells and detection of peptide sequences from canonical and novel open reading frames and aberant translation events.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Type B Pancreatic Cell, Pancreatic Islet Beta Cell

DISEASE(S): Type 1 Diabetes Mellitus

SUBMITTER: Tim Fugmann

LAB HEAD: Prof. Tim Fugmann

PROVIDER: PXD056070 | Pride | 2025-12-01

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	20200626_HomoSapiens_UniProt_Ref_iRT_NuORF_24.fasta	Fasta
	20220411_HLA9-1_DDA_iRT.mzXML	Mzxml
	20220411_HLA9-1_DDA_iRT.percolator.decoy.pep.xml	Pepxml
	20220411_HLA9-1_DDA_iRT.percolator.target.pep.xml	Pepxml
	20220411_HLA9-1_DDA_iRT.raw	Raw

Items per page:

1 - 5 of 45

Publications

Proteogenomic Discovery of Novel Open Reading Frames With HLA Immune Presentation on Human β-Cells.

Walters Kathryn K Castro-Gutierrez Roberto R Sarkar Soumyadeep S Baldwin Amber A Baker Alexandra S AS Shilleh Ali H AH Anderson Amanda M AM Nakayama Maki M Fugman Tim T Nakayasu Ernesto S ES Mukherjee Neelanjan N Russ Holger A HA

Diabetes 20251201 12

Ribosome profiling (Ribo-seq) measures translational regulation and reveals novel or unannotated open reading frames (nuORFs) otherwise difficult to identify. Recent reports demonstrate that nuORFs regulate gene expression and immune recognition, highlighting their emerging biological roles. Pancreatic β-cells are critical for maintaining euglycemic conditions, and β-cell impairment contributes to diabetes development. Identification of nuORF and protein/peptide products in human β-cells could r ...[more]

PMID: 40896833

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MHC-I peptidome analysis of human foreskin fibroblasts

Project description:Ribosome profiling (Ribo-seq) recently revealed the expression of thousands of short open reading frames (sORFs) in eukaryotic cells. They encode for a class of instable peptides, which evade experimental validation by whole-proteome mass spectrometry. Here, we show that computational elimination of experimental noise from Ribo-seq data unravels fundamental new aspects of sORF biology. Based on the revised annotation of cellular sORFs, we show that sORF-derived peptides are efficiently incorporated into MHC-I. sORFs thus encode a novel class of stress-responsive antigens in human cells. Our findings have broad implications on the functional, regulatory and immunogenic role of sORFs in fundamental cellular processes like infection and cancer.

2018-04-05 | PXD007203 | Pride

HLA-peptidome of human primary islets

Project description:Interferon (IFN)-α is the earliest cytokine signature observed in individuals at risk for type 1 diabetes (T1D), but its effect on the repertoire of HLA Class I (HLA-I)-bound peptides presented by pancreatic β-cells is unknown. Using immunopeptidomics, we characterized the peptide/HLA-I presentation in in-vitro resting and IFN-α-exposed β-cells. IFN-α increased HLA-I expression and peptide presentation, including neo-sequences derived from alternative mRNA splicing, post-translational modifications - notably glutathionylation - and protein cis-splicing. This antigenic landscape relied on processing by both the constitutive and immune proteasome. The resting β-cell immunopeptidome was dominated by HLA-A-restricted ligands. However, IFN-α only marginally upregulated HLA-A and largely favored HLA-B, translating into a major increase in HLA-B-restricted peptides and into an increased activation of HLA-B-restricted vs. HLA-A-restricted CD8+ T-cells. A preferential HLA-B hyper-expression was also observed in the islets of T1D vs. non-diabetic donors, and islet-infiltrating CD8+ T-cells from T1D donors were reactive to some HLA-B-restricted granule peptides. Thus, the inflammatory milieu of insulitis may skew the autoimmune response toward epitopes presented by HLA-B, hence recruiting a distinct T-cell repertoire that may be relevant to T1D pathogenesis.

2025-01-08 | PXD045211 | Pride

HLA-peptidome of human beta cells exposed to interferon-alpha

2025-01-08 | PXD045265 | Pride

HLA class I peptidome analysis of synthetic long peptide-fed human dendritic cells for therapeutic vaccine design

Project description:Synthetic long peptides (SLPs) are a promising vaccine modality that exploit dendritic cells (DC) to treat chronic infections or cancer. Currently, the design of SLPs relies on in silico prediction and multifactorial T cells assays to determine which SLPs are best cross-presented on DC human leukocyte antigen class I (HLA-I). Furthermore, it is unknown how TLR ligand-based adjuvants affect DC cross-presentation. Here, we generated a unique, high-quality immunopeptidome dataset of human DCs pulsed with 12 hepatitis B virus (HBV)-based SLPs combined with either a TLR1/2 (Amplivant®) or TLR3 (PolyI:C) ligand. The obtained immunopeptidome reflected adjuvant-induced differences, but no differences in cross-presentation of SLPs. We uncovered dominant (cross-)presentation on B-alleles, and identified 33 unique SLP-derived HLA-I peptides, several of which were not in silico predicted and some were consistently found across donors. Our work puts forward DC immunopeptidomics as a valuable tool for therapeutic vaccine design.

2025-01-19 | PXD051490 | Pride

Unveiling conserved HIV-1 open reading frames encoding T cell antigens using ribosome profiling

Project description:The development of ribosomal profiling (Riboseq) revealed the immense coding capacity of human and viral genomes. Here, we used Riboseq to delineate the translatome of HIV-1 in infected CD4+ T cells. In addition to canonical viral protein coding sequences (CDSs), we identify 98 alternative open reading frames (ARFs), corresponding to small Open Reading Frames (sORFs) that are distributed across the HIV genome including the UTR regions. Using a database of HIV genomes, we observe that most ARF amino-acid sequences are likely conserved among clade B and C of HIV-1, with 8 ARF-encoded amino-acid sequences being more conserved than the overlapping CDSs. Using T cell-based assays and mass spectrometry-based immunopeptidomics, we demonstrate that ARFs encode viral polypeptides. In the blood of HIV-infected individuals, ARF-derived peptides elicit potent poly-functional T cell responses mediated by both CD4+ and CD8+ T cells. Our discovery expands the list of conserved viral polypeptides that are targets for vaccination strategies and might reveal the existence of viral microproteins or pseudogenes.

2025-01-15 | PXD043984 | Pride

Proteogenomics-based identification of the repertoire of human MHC class I-associated peptides

Project description:We have develop a proteogenomics-based approach for identification of human MHC class I-associated peptides, including those deriving from polymorphisms, mutations and non-canonical reading frames

2016-12-22 | GSE67174 | GEO

Early Kinetics of the HLA Class I-Associated Peptidome of MVA.HIVconsv-Infected Cells.

Project description:UnlabelledCytotoxic T cells substantially contribute to the control of intracellular pathogens such as human immunodeficiency virus type 1 (HIV-1). Here, we evaluated the immunopeptidome of Jurkat cells infected with the vaccine candidate MVA.HIVconsv, which delivers HIV-1 conserved antigenic regions by using modified vaccinia virus Ankara (MVA). We employed liquid chromatography-tandem mass spectrometry (LC-MS/MS) to identify 6,358 unique peptides associated with the class I human leukocyte antigen (HLA), of which 98 peptides were derived from the MVA vector and 7 were derived from the HIVconsv immunogen. Human vaccine recipients responded to the peptide sequences identified by LC-MS/MS. Peptides derived from the conserved HIV-1 regions were readily detected as early as 1.5 h after MVA.HIVconsv infection. Four of the seven conserved peptides were monitored between 0 and 3.5 h of infection by using quantitative mass spectrometry (Q-MS), and their abundance in HLA class I associations reflected levels of the whole HIVconsv protein in the cell. While immunopeptides delivered by the incoming MVA vector proteins could be detected, all early HIVconsv-derived immunopeptides were likely synthesized de novo. MVA.HIVconsv infection generally altered the composition of HLA class I-associated human (self) peptides, but these changes corresponded only partially to changes in the whole cell host protein abundance.ImportanceThe vast changes in cellular antigen presentation after infection of cells with a vectored vaccine, as shown here for MVA.HIVconsv, highlight the complexity of factors that need to be considered for efficient antigen delivery and presentation. Identification and quantitation of HLA class I-associated peptides by Q-MS will not only find broad application in T-cell epitope discovery but also inform vaccine design and allow evaluation of efficient epitope presentation using different delivery strategies.

| S-EPMC4442425 | biostudies-literature

Public T cell epitopes shared among SARS-CoV-2 Public T cell epitopes shared among SARS-CoV-2 variants are presented on prevalent HLA class I alleles variants are presented on prevalent HLA class I alleles

Project description:In this project, we used MS-based immunopeptidomics and T-cell screening assays to identify SARS-CoV-2 epitopes. The MS identified epitopes were further valdiated for CD8 T cell immunogenecity. PBMC from a large number of patients infected with SARS-CoV-2 were used for valdiation of MS identifed and predected CD 8 T cell epotipes.

2023-03-11 | PXD028862 | Pride

A large peptidome dataset improves HLA class I epitope prediction across most of the human population

Project description:Prediction of HLA epitopes is important for the development of cancer immunotherapies and vaccines. However, current prediction algorithms have limited predictive power, in part because they were not trained on high-quality epitope datasets covering a broad range of HLA alleles. To enable prediction of endogenous HLA class I-associated peptides across a large fraction of the human population, we used mass spectrometry to profile >185,000 peptides eluted from 95 HLA-A, -B, -C and -G mono-allelic cell lines. We identified canonical peptide motifs per HLA allele, unique and shared binding submotifs across alleles and distinct motifs associated with different peptide lengths. By integrating these data with transcript abundance and peptide processing, we developed HLAthena, providing allele-and-length-specific and pan-allele-pan-length prediction models for endogenous peptide presentation. These models predicted endogenous HLA class I-associated ligands with 1.5-fold improvement in positive predictive value compared with existing tools and correctly identified >75% of HLA-bound peptides that were observed experimentally in 11 patient-derived tumor cell lines.

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Upstream open reading frames regulate proto-oncogene translation and encode HLA-presented immunogenic tumor antigens

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