PXD018258

PXD018258 is an original dataset announced via ProteomeXchange.

Title	Proteomic analysis of necroptotic extracellular vesicles
Description	Necroptosis is a regulated but inflammatory form of cell death. We and others have previously reported that necroptotic cells release extracellular vesicles (EVs). We found that necroptotic EVs are loaded with proteins, including the key necroptosis executor factor, phosphorylated mixed lineage kinase domain-like (pMLKL). However, the exact necroptotic EVs proteins composition and impact have not been delineated yet. To characterize their content, EVs from necroptotic and untreated U937 cells were isolated by ultracentrifugation and analyzed by mass spectrometry. A total of 3337 proteins were identified, sharing high similarity with exosome proteome databases. Unsupervised hierarchical clustering of identified proteins distinguished between necroptotic and control EVs. A total of 353 proteins was significantly upregulated in the necroptotic EVs. Among these are MLKL and caspase-8, as validated by immunoblot. Components of ESCRTIII machinery and inflammatory signaling were found to be enriched in the necroptotic EVs, as well as yet unreported components of vesicles formation and transport and necroptosis signaling pathways. Moreover, we show that necroptotic EVs can be phagocytosed by macrophages to modulate cytokine and chemokine secretion. Finally, we reveal that necroptotic EVs contain tumor neoantigen and are enriched with proteins annotated as “antigen processing and presentation” biological process. In summary, our study reveals a new layer of regulation during the early stage of necroptosis by the secretion of specific EVs that influence their microenvironment and may instigate innate and adaptive immune responses. Future investigation will shed light on new players in the necroptosis signaling and its related EVs, and will uncover the functional tasks accomplished by the cargo of these necroptotic EVs.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:30:16.653.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Tamar Geiger
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Exactive Plus

Revision	Datetime	Status	ChangeLog Entry
0	2020-03-30 00:30:06	ID requested
1	2021-11-11 08:29:43	announced
⏵ 2	2024-10-22 05:30:17	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

submitter keyword: Necroptosis, neoantigens, extracellular vesicles, MLKL, proteome, cell death

Tamar Geiger
contact affiliation	Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv university, Tel Aviv, Israel
contact email	geiger@tauex.tau.ac.il
lab head
Tamar Geiger
contact affiliation	Weizmann Institute of Science
contact email	geiger@tauex.tau.ac.il
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/11/PXD018258

PRIDE project URI

• PRIDE
  1. PXD018258
     1. Label: PRIDE project
     2. Name: Proteomic analysis of necroptotic extracellular vesicles