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Bacteria

ABSTRACT: 16S rRNA sequencing of pleural effusions

PROVIDER: PRJNA865295 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR20828900_1.fastq.gz	Fastqsanger.gz
	SRR20828900_2.fastq.gz	Fastqsanger.gz
	SRR20829000_1.fastq.gz	Fastqsanger.gz
	SRR20829000_2.fastq.gz	Fastqsanger.gz
	SRR20828901_1.fastq.gz	Fastqsanger.gz

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

Project description: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.

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