PXD066255

PXD066255 is an original dataset announced via ProteomeXchange.

Title	Tumor-associated peptides can be detected from the plasma-derived soluble immunopeptidome in human hepatocellular carcinoma patients – A pre-clinical study on the correlation of the soluble and hepatocellular carcinoma-derived membranous immunopeptidomes.
Description	Abstract Background and aims. Hepatocellular carcinoma (HCC) shows limited response to checkpoint inhibitors, leaving opportunity for antigen-based immunotherapy and improved disease monitoring. This study evaluates plasma-derived soluble HLA-I (sHLA-I) peptidome as a minimally invasive source of tumor antigens by comparing them to tumor and adjacent tissue HLA ligands to assess its value for personalized treatment and diagnostics in HCC. Methods. Plasma-derived soluble HLA-I complexes and membranous HLA-I ligands from paired tumor and adjacent liver tissues of HCC and non-HCC control patients were isolated using pan-HLA-I immunoprecipitation and analyzed by LC-MS/MS. Peptide identification and patient-specific HLA binding predictions were complemented by annotation of tumor-associated antigens (TAAs) to compare ligand repertoires across HLA sources. Results The plasma soluble HLA-I (sHLA-I) peptidome from HCC and non-HCC patients was successfully characterized, with 1,553 to 9,421 unique peptides identified per sample after contaminant filtering. Peptides were enriched for canonical 8–11-mer lengths, with most predicted to bind patient-specific HLA-I alleles. Among 3,907 source proteins delivering peptides to the HCC sHLA-I peptidome, 815 were unique to HCC patients, and protein interaction analysis revealed significantly increased network connectivity centered around tumor-associated proteins. Comparison with membranous HLA-I (mHLA-I) peptidomes from tumor and adjacent tissues yielded 20 peptides from 17 tumor-associated antigens (TAAs) that were shared between sHLA-I and mHLA-I. Nine of these were only identified from HCC plasma and not from non-HCC controls, five overlapped with tumor mHLA-I. Conclusions. This pilot study demonstrates that the plasma-derived soluble HLA-I immunopeptidome in HCC patients contains peptides derived from TAAs, at least partially reflective of those presented on tumor tissue. These findings support the potential of sHLA-I profiling as a minimally invasive strategy for identifying actionable targets and tumor-specific signatures in HCC. Future improvements in analytical sensitivity and throughput, and validation in larger cohorts are now needed to establish its clinical utility.
HostingRepository	PRIDE
AnnounceDate	2025-10-15
AnnouncementXML	Submission_2025-10-15_14:28:43.714.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jeroen Demmers
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2025-07-17 02:52:17	ID requested
⏵ 1	2025-10-15 14:28:44	announced

Dataset with its publication pending

submitter keyword: hepatocellular carcinoma, immunopeptidomics, soluble HLA,sHLA

Jeroen Demmers
contact affiliation	Proteomics Center, Erasmus MC
contact email	j.demmers@erasmusmc.nl
lab head
Jeroen Demmers
contact affiliation	Proteomics Center, Erasmus University Medical Center, Rotterdam, The Netherlands
contact email	j.demmers@erasmusmc.nl
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD066255
     1. Label: PRIDE project
     2. Name: Tumor-associated peptides can be detected from the plasma-derived soluble immunopeptidome in human hepatocellular carcinoma patients – A pre-clinical study on the correlation of the soluble and hepatocellular carcinoma-derived membranous immunopeptidomes.