Proteomics

Dataset Information

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Mapping the soluble human leukocyte antigen peptidome of pleural effusions reveals lung and tumor-associated antigens


ABSTRACT: Soluble HLA (sHLA) molecules released to 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. Thus, we developed a methodology for purifying and analysing large pleural effusion sHLA class I peptidomes of patients inflicted with malignancies or benign diseases. The cleared pleural fluids, the 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 capillary chromatography coupled to tandem mass spectrometry and the resulting LC-MS/MS data was analyzed with the MaxQuant software tool. Large HLA peptidomes were obtained by the analysis of the pleural effusions. 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 were somewhat similar to each other. Many of the HLA peptides were derived from known tumor-associated antigens, lung-related proteins, and VEGF pathway proteins. Thus, the pleural effusion HLA peptidome of patients with malignant tumors can serve as a rich source of biomarkers for tumor diagnosis and personalized immunotherapy.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Pleural Fluid, Cell Line Cell

DISEASE(S): Non-small Cell Lung Carcinoma

SUBMITTER: Dganit Melamed Kadosh  

LAB HEAD: Arie Admon

PROVIDER: PXD027766 | Pride | 2022-05-25

REPOSITORIES: Pride

Dataset's files

Source:
Action DRS
Human_proteome_June_2019_74416_entries.fasta Fasta
MaxQuant_1.6.10.43.zip Other
Mutations_P12.fasta Fasta
Mutations_P13.fasta Fasta
Mutations_P14.fasta Fasta
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Publications


<h4>Background</h4>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  ...[more]

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