PXD007686

PXD007686 is an original dataset announced via ProteomeXchange.

Title	Comparative proteomics of dying and surviving cancer cells improves the identification of drug targets and sheds light on cell life/death decisions
Description	Chemotherapeutics cause the detachment and death of adherent cancer cells. When studying the proteome changes to determine the protein target and mechanism of action of anticancer drugs, the still-attached cells are normally used, while the detached cells are usually ignored. Here we tested the hypothesis that proteomes of detached cells contain valuable information and therefore separately analyzed the proteomes of detached and attached HCT-116, A375 and RKO cells obtained 48 h after treatment with 5-fluorouracil, methotrexate and paclitaxel. Combined proteome data provided a more accurate identification of drug targets. Six proteins consistently up- or down-regulated in the detached vs attached cells regardless of the drug and cell type were targeted by siRNA. Knocking down USP11, CTTN, ACAA2 and EIF4H had anti-proliferative effects, targeting UHRF1 additionally sensitized the cells to the anticancer drugs, while knocking down RNF-40 increased cell survival against the treatments. Therefore, these proteins are likely to be involved in general cell death and survival decisions. Adding detached cells to the analysis could become a standard practice in expression proteomics of drug-treated cells.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:40:22.473.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Amir Ata Saei
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2017-09-07 02:27:29	ID requested
1	2018-03-28 07:18:37	announced
⏵ 2	2024-10-22 04:40:23	announced	2024-10-22: Updated project metadata.

Saei AA, Sabatier P, Tokat Ü G, Chernobrovkin A, Pirmoradian M, Zubarev RA, Comparative Proteomics of Dying and Surviving Cancer Cells Improves the Identification of Drug Targets and Sheds Light on Cell Life/Death Decisions. Mol Cell Proteomics, 17(6):1144-1155(2018) [pubmed]

10.1074/mcp.ra118.000610;

curator keyword: Biological, Biomedical

submitter keyword: cell death, mass spectrometry, survival, drug mechanism, chemotherapeutic

Roman Zubarev
contact affiliation	Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
contact email	roman.zubarev@ki.se
lab head
Amir Ata Saei
contact affiliation	Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
contact email	amirata.saei.dibavar@ki.se
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/2018/03/PXD007686

PRIDE project URI

• PRIDE
  1. PXD007686
     1. Label: PRIDE project
     2. Name: Comparative proteomics of dying and surviving cancer cells improves the identification of drug targets and sheds light on cell life/death decisions