PXD041751

PXD041751 is an original dataset announced via ProteomeXchange.

Title	Mass spectrometry analysis of extracellular vesicles from malignant ascites in ovarian cancer patients
Description	Ovarian cancer (OC) ranks among the deadliest cancers in women. Lack of symptoms, rapid spread of metastases and common chemoresistance contribute to unfortunate fate of majority of OC patients, especially those having high-grade serous carcinoma of the ovary, fallopian tube and peritoneum (HGSC), the most common type of OC. Many HGSC patients have excess fluid in the peritoneum at the stage of diagnosis called ascites. Ascites is basically a tumor microenvironment (TME) in the liquid form containing various cells, proteins and also extracellular vesicles (EVs). EVs are small membrane-bound particles that convey proteins, lipids and nucleic acids between cells and their cargo reflects the cell of origin. EVs play important role in cancerogenesis and hold great promise as disease biomarkers as well as potential therapeutic targets. Small size and polydispersity of EVs bring various challenges to their isolation and characterization, including method-dependent enrichment of different EV subtypes as well as contaminants. We isolated EVs from ascites of 11 patients by two different methods (ultracentrifugation coupled to sucrose cushion and size-exclusion chromatography, qEV column) and analyzed them by mass spectrometry. We identified core ascitic EV proteins present in all patients that contain typical EV markers and are devoid of method-dependent contaminants. To cover interpatient heterogeneity, we expanded this “core proteome” with proteins found in majority of patients. Next, we compared them with proteins of EVs from related control fluids and uncovered proteins present only on EVs from HGSC patients. We believe this list of proteins contain both important players of HGSC progression as well as potential biomarkers. Using single cell RNA sequencing data, we mapped the origin of EVs to different types of cells present in malignant ascites. Our results suggest that EVs in ascites do not come predominantly from tumor cells, but rather from variety of non-malignant cell types including cancer-associated fibroblasts and tumor-associated macrophages, which presence in ascites was confirmed by flow cytometry. This emphasizes the recently appreciated role of TME in the progression of HGSC. To conclude, this is the first study attempting to link EV composition to the cell types producing it. As such it opens numerous avenues both for better understanding of EV role in tumor promotion/prevention and for the improved HGSC diagnostics.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:42:54.120.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	David Potesil
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2023-04-23 15:30:05	ID requested
1	2024-05-24 04:12:39	announced
⏵ 2	2024-10-22 06:42:55	announced	2024-10-22: Updated project metadata.

Vyhl, í, dalov, á, Kotrbov, á A, G, ö, m, ö, ryov, á K, Mikulov, á A, Ple, š, ingerov, á H, Slade, č, ek S, Kravec M, Hrachovinov, á Š, Pot, ě, š, il D, Dunsmore G, Bl, é, riot C, Bied M, Kotou, č, ek J, Bedna, ř, í, kov, á M, Hausnerov, á J, Min, á, ř L, Crha I, Felsinger M, Zdr, á, hal Z, Ginhoux F, Weinberger V, Bryja V, Posp, í, chalov, á V, Proteomic analysis of ascitic extracellular vesicles describes tumour microenvironment and predicts patient survival in ovarian cancer. J Extracell Vesicles, 13(3):e12420(2024) [pubmed]

10.1002/jev2.12420;

submitter keyword: tandem mass spectrometry (MS/MS), macrophage,ovarian cancer (OC), ascites, high-grade serous carcinoma of the ovary, extracellular vesicles (EV), fallopian tube and peritoneum (HGSC), tumor microenvironment

Zbynek Zdrahal
contact affiliation	Proteomics Core Facility and Research Group Proteomics, CEITEC-MU, Masaryk University, Brno, Czech Republic
contact email	zdrahal@sci.muni.cz
lab head
David Potesil
contact affiliation	Proteomics Core Facility and Research Group Proteomics CEITEC-MU Masaryk University Brno, Czech Republic
contact email	david.potesil@ceitec.muni.cz
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD041751
     1. Label: PRIDE project
     2. Name: Mass spectrometry analysis of extracellular vesicles from malignant ascites in ovarian cancer patients