PXD005830

PXD005830 is an original dataset announced via ProteomeXchange.

Title	Proteome Analysis of Non-Small Cell Lung Cancer Cell Line Secretomes and Patient Sputum Reveals Biofluid Biomarker Candidates for Cisplatin Response Prediction
Description	We profiled the secretomes of six NSCLC cell lines with varying IC50-values for cisplatin, using label-free GeLC-MS/MS-based proteomics. Out of a total dataset of 2618 proteins, 304 proteins showed significant differences in expression levels between cisplatin sensitive and insensitive cell lines. Functional data mining revealed that the secretion of typically extracellular factors was associated with a higher sensitivity towards cisplatin, while cisplatin insensitivity correlated with increased secretion of theoretically intra-cellular proteins, in line with enhanced levels of non-conventional secretion in cisplatin insensitive cell lines. Stringent statistical analysis and quantitative filtering yielded 41 top biomarker candidates, many of which could also be detected in NSCLC patient sputum using label-free GeLC-MS/MS-based proteomics. A published gene expression dataset was used to determine which of our top secretome cisplatin response prediction candidates might have predictive value in terms of overall survival in patients that received platinum-based treatment. This analysis yielded two cisplatin sensitivity (UGGT1 and MATN2) and one cisplatin resistance (MAP4) candidates that may serve as potential biomarkers for cisplatin response prediction in NSCLC patients in the future.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:34:16.876.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sander Piersma
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	LTQ FT; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2017-02-01 06:59:29	ID requested
1	2022-02-28 04:10:27	announced
⏵ 2	2024-10-22 05:34:17	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

curator keyword: Biomedical

submitter keyword: Human, sputum, cisplatin resistance, non-small cell lung cancer (NSCLC), NSCLC cancer, secretome

Connie Ramona Jimenez
contact affiliation	OncoProteomics Laboratory, Dept of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
contact email	c.jimenez@vumc.nl
lab head
Sander Piersma
contact affiliation	OncoProteomics Laboratory, dept of Medical Oncology, VUmc Medical Center, Amsterdam, The Netherlands
contact email	s.piersma@vumc.nl
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/2022/02/PXD005830

PRIDE project URI

• PRIDE
  1. PXD005830
     1. Label: PRIDE project
     2. Name: Proteome Analysis of Non-Small Cell Lung Cancer Cell Line Secretomes and Patient Sputum Reveals Biofluid Biomarker Candidates for Cisplatin Response Prediction