Circulating HLA Ligandomes Reflect Tumour Antigen Landscapes in Melanoma

ABSTRACT: Melanoma is a highly immunogenic malignancy in which T cell recognition of HLA-presented peptides plays a central role in tumour control. While immunopeptidomics has enabled detailed characterisation of melanoma antigen repertoires, its clinical application is limited by restricted access to tumour tissue. Soluble HLA (sHLA) complexes in circulation present a potential minimally invasive alternative; however, the extent to which circulating HLA repertoires reflect tumour-derived antigen presentation remains unclear. Here, we applied an optimised SAPrIm workflow coupled with Orbitrap Astral mass spectrometry to analyse the immunopeptidome of matched tumour tissue and plasma samples from five melanoma patients collected at the time of tumour resection. We identified 6,773–17,689 HLA-I peptides from tumour tissue (5-25 mg input) and 5,224–10,384 peptides from plasma-derived sHLA complexes (200-571 µL input). Plasma-derived sHLA ligandomes retained key features of membrane-bound tumour HLA-I presentation, including dominant 9-mer peptide length distributions and conserved HLA-binding characteristics. Peptide recovery was strongly concordant between compartments following normalisation (Pearson r = 0.92), indicating that ligandome depth and recovery were primarily driven by intrinsic biological variation rather than sample input. Tumour-associated antigens were consistently detected in circulating sHLA peptides. Cryptic peptides derived from “peptideins” were preserved from tumour to circulation and comprised approximately 1% of the total repertoire. To assess tumour specificity and biomarker potential, identified HLA peptides were mapped to their corresponding source proteins and compared against healthy sHLA and benign tissue reference datasets. This analysis identified 247 candidate melanoma-associated source proteins, including a refined list of 9 recurrent candidate circulating biomarkers detected in at least 4 of 5 patients. These findings demonstrate that circulating sHLA ligandomes closely reflect key features of tumour antigen presentation and support plasma immunopeptidomics as a minimally invasive approach for antigen discovery, biomarker development, and longitudinal monitoring of tumour antigenicity.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Blood Plasma, Skin

SUBMITTER: Gabriel Goncalves  

LAB HEAD: Pouya Faridi

PROVIDER: PXD078553 | Pride | 2026-10-29

REPOSITORIES: Pride