Soluble HLA peptidome of pleural effusions is a valuable source for tumor antigens

Sofia Khazan-Kost, Gal Cafri, Dganit Melamed Kadosh, Navit Mooshayef, Sumit Chatterji, Dan Dominissini, Sigal Manor, Bracha Zisser, Limor Broday, Efrosiniia Talalai, Anat Shemer, Oranit Zadok, Efrat Ofek, Amir Onn, Arie Admon*, Michael Peled*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

3 Scopus citations


Background Soluble human leucocyte antigen (sHLA) molecules, released into the plasma, carry their original peptide cargo and provide insight into the protein synthesis and degradation schemes of their source cells and tissues. Other body fluids, such as pleural effusions, may also contain sHLA-peptide complexes, and can potentially serve as a source of tumor antigens since these fluids are drained from the tumor microenvironment. We explored this possibility by developing a methodology for purifying and analyzing large pleural effusion sHLA class I peptidomes of patients with malignancies or benign diseases. Methods Cleared pleural fluids, cell pellets present in the pleural effusions, and the primary tumor cells cultured from cancer patients' effusions, were used for immunoaffinity purification of the HLA molecules. The recovered HLA peptides were analyzed by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) and the resulting LC-MS/MS data were analyzed with the MaxQuant software tool. Selected tumor antigen peptides were tested for their immunogenicity potential with donor peripheral blood mononuclear cells (PBMCs) in an in vitro assay. Results Mass spectrometry analysis of the pleural effusions revealed 39,669 peptides attributable to 11,305 source proteins. The majority of peptides identified from the pleural effusions were defined as HLA ligands that fit the patients' HLA consensus sequence motifs. The membranal and soluble HLA peptidomes of each individual patient correlated to each other. Additionally, soluble HLA peptidomes from the same patient, obtained at different visits to the clinic, were highly similar. Compared with benign effusions, the soluble HLA peptidomes of malignant pleural effusions were larger and included HLA peptides derived from known tumor-associated antigens, including cancer/testis antigens, lung-related proteins, and vascular endothelial growth factor pathway proteins. Selected tumor-associated antigens that were identified by the immunopeptidomics were able to successfully prime CD8 + T cells. Conclusions Pleural effusions contain sHLA-peptide complexes, and the pleural effusion HLA peptidome of patients with malignant tumors can serve as a rich source of biomarkers for tumor diagnosis and potential candidates for personalized immunotherapy.

Original languageEnglish
Article numbere003733
JournalJournal for ImmunoTherapy of Cancer
Issue number5
StatePublished - 17 May 2022


FundersFunder number
G. Baum Fund
Greta Koppel SCLC
Smoler Proteomics Center
TB Tel-Aviv Clinic
National Cancer Institute
Israel Cancer Research Fund18-204-AG
Flight Attendant Medical Research Institute
Israel Science FoundationISF-I-CORE 1775/12, ISF 1435/16
Technion-Israel Institute of Technology


    • antigen presentation
    • antigens
    • immunotherapy
    • lung neoplasms
    • tumor biomarkers


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