PXD011496

PXD011496 is an original dataset announced via ProteomeXchange.

Title	ADAPT identifies an ESCRT complex composition that discriminates VCaP from LNCaP prostate cancer cell exosomes
Description	Libraries of single-stranded oligodeoxynucleotides (ssODNs) can be enriched for sequences that specifically bind molecules on naïve complex biological samples like cells or tissues. Depending on the enrichment strategy, the ssODNs can identify molecules specifically associated with a defined biological condition, for example a pathological phenotype, and thus are potentially useful for biomarker discovery. We performed ADAPT, a variant of SELEX, on exosomes secreted by VCaP prostate cancer cells. A library of ~1011 ssODNs was enriched for those that bind to VCaP exosomes and discriminate them from exosomes derived from LNCaP prostate cancer cells. Next-generation sequencing (NGS) identified the best discriminating ssODNs, nine of which were resynthesized and their discriminatory ability confirmed by qPCR. Affinity purification with one of the sequences (Sequence 7) combined with LC-MS/MS identified its molecular target complex, whereof most proteins are part of or associated with the multiprotein ESCRT complex participating in exosome biogenesis. Within this complex, YBX1 was identified as the directly bound target protein. ADAPT thus is able to differentiate exosomes from cancer cell subtypes from the same lineage. The composition of ESCRT complexes in exosomes from VCaP versus LNCaP cells might constitute a discriminatory element between these prostate cancer subtypes.
HostingRepository	PRIDE
AnnounceDate	2020-01-13
AnnouncementXML	Submission_2020-02-17_03:17:51.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Matthew Rosenow
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2018-10-29 03:37:49	ID requested
1	2020-01-13 08:22:02	announced
⏵ 2	2020-02-17 03:17:53	announced	2020-02-17: Updated publication reference for PubMed record(s): 31989173.

Hornung T, O'Neill HA, Logie SC, Fowler KM, Duncan JE, Rosenow M, Bondre AS, Tinder T, Maher V, Zarkovic J, Zhong Z, Richards MN, Wei X, Miglarese MR, Mayer G, Famulok M, Spetzler D, ADAPT identifies an ESCRT complex composition that discriminates VCaP from LNCaP prostate cancer cell exosomes. Nucleic Acids Res, 48(8):4013-4027(2020) [pubmed]

curator keyword: Biomedical

submitter keyword: Aptamers, ESCRT complex, Exosomes, Prostate Cancer Cells, ADAPT

David Spetzler
contact affiliation	Caris Science Inc
contact email	dspetzler@carisls.com
lab head
Matthew Rosenow
contact affiliation	Caris Life Science
contact email	mrosenow@carisls.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/2020/01/PXD011496

PRIDE project URI

• PRIDE
  1. PXD011496
     1. Label: PRIDE project
     2. Name: ADAPT identifies an ESCRT complex composition that discriminates VCaP from LNCaP prostate cancer cell exosomes