PXD046711

PXD046711 is an original dataset announced via ProteomeXchange.

Title	Differential expression analysis of cutaneous squamous cell carcinoma and basal cell carcinoma proteomic profiles sampled with e-biopsy
Description	Clinical misdiagnosis between cutaneous squamous cell carcinoma (cSCC) and basal cell carcinoma (BCC) affects treatment plans and carries risks of potential for recurrence, metastases, morbidity and mortality. We report the development of a novel tissue sampling approach with molecular biopsy using electroporation. This method, coined e-biopsy, enables non-destructive non-thermal permeabilization of cells in the skin for efficient vacuum-assisted extraction of informative biomolecules for rapid diagnosis. We used e-biopsy for ex vivo proteome extraction from 3 locations per patient in 21 cSCC and 20 BCC pathologically validated human tissue samples. The total 123 extracted proteomes were profiled using LC/MS/MS. The obtained mass spectra presented significantly different proteome profiles for cSCC and BCC with several hundreds of proteins significantly differentially expressed in each tumor in comparison to the other. Notably, our study showed that proteomes sampled with e-biopsy from cSCC and BCC lesions are different, and that 7 proteins were significantly overexpressed in BCC in comparison to cSCC even after the Bonferroni correction (FDR=7.1e-03). Our results provide evidence that the e-biopsy approach could potentially be used as a tool to support cutaneous tumors classification with rapid molecular profiling.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:58:17.815.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Alexander Golberg
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF-X

Revision	Datetime	Status	ChangeLog Entry
0	2023-11-06 16:54:51	ID requested
1	2024-09-13 14:43:51	announced
⏵ 2	2024-10-22 06:58:18	announced	2024-10-22: Updated project metadata.

10.1016/J.XJIDI.2024.100304;

submitter keyword: diagnostics, molecular pathology, skin cancer, basal cell carcinoma, finite elements modeling, squamous cell carcinoma, electroporation

Alexander Golberg
contact affiliation	Porter School of Environment and Earth Sciences. Tel Aviv University, Tel Aviv, Israel
contact email	agolberg@tauex.tau.ac.il
lab head
Alexander Golberg
contact affiliation	Tel Aviv University
contact email	agolberg@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/2024/08/PXD046711

PRIDE project URI

• PRIDE
  1. PXD046711
     1. Label: PRIDE project
     2. Name: Differential expression analysis of cutaneous squamous cell carcinoma and basal cell carcinoma proteomic profiles sampled with e-biopsy