PXD037651

PXD037651 is an original dataset announced via ProteomeXchange.

Title	Characterisation of colorectal cancer cell lines through proteomic profiling of their extracellular vesicles
Description	Colorectal cancer (CRC) is one of the most prevalent cancers, driven by several factors including deregulations in intracellular signalling pathways. Small extracellular vesicles (sEVs) are nanosized protein-packaged particles released from cells, which are present in liquid biopsies. Here, we characterised the proteome landscape of sEVs and their cells of origin in three CRC cell lines HCT116, HT29 and SW620 in order to explore molecular traits that could be exploited as cancer biomarker candidates and how intracellular signalling can be assessed by sEV analysis instead of directly obtaining the cell of origin itself. Our findings revealed that sEV cargo clearly reflects its cell of origin with proteins of the PI3K-AKT pathway highly represented in sEVs. Proteins known to be involved in CRC were detected in both cells and sEVs including KRAS, ARAF, mTOR, PDPK1 and MAPK1, while TGFB1 and TGFBR2, known to be key players in epithelial cancer carcinogenesis, were found to be enriched in sEVs. Furthermore, phosphopeptide-enriched profiling of cell lysates demonstrated a distinct pattern between cell lines and highlighted potential phosphoproteomic targets to be investigated in sEVs. The total proteomic and phosphoproteomics profiles described in the current work can serve as source to identify candidates for cancer biomarkers that can potentially be assessed from liquid biopsies.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:43:56.904.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Animesh Sharma
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2022-10-24 00:56:18	ID requested
1	2023-03-11 11:36:26	announced
⏵ 2	2023-11-14 08:44:06	announced	2023-11-14: Updated project metadata.

Heck KA, Lindholm HT, Niederdorfer B, Tsirvouli E, Kuiper M, Flobak Å, L, æ, greid A, Thommesen L, Characterisation of Colorectal Cancer Cell Lines through Proteomic Profiling of Their Extracellular Vesicles. Proteomes, 11(1):(2023) [pubmed]

submitter keyword: proteomics, sEVs,Extracellular vesicles, phosphoproteomics, intracellular signalling, colorectal cancer

Åsmund Flobak
contact affiliation	MD, MSc, PhD Department of Clinical and Molecular Medicine asmund.flobak@ntnu.no +47 72573717 Gastrosenteret, Øya, Olav Kyrres gate 13
contact email	asmund.flobak@ntnu.no
lab head
Animesh Sharma
contact affiliation	Engineer at NTNU, Norway
contact email	sharma.animesh@gmail.com
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/2023/03/PXD037651

PRIDE project URI

• PRIDE
  1. PXD037651
     1. Label: PRIDE project
     2. Name: Characterisation of colorectal cancer cell lines through proteomic profiling of their extracellular vesicles