PXD040956-2

PXD040956 is an original dataset announced via ProteomeXchange.

Title	Urinary proteomics for discovery of gastric cancer biomarkers
Description	Although blood-based protein biomarkers have been described for diagnosis of some cancers, detection of tumor-derived peptides/proteins in urine provides an attractive and non-invasive alternative for diagnostic or screening purposes. For instance, bladder tumor antigen (BTA) assay is FDA approved urine-based biomarker assay to detect the bladder cancer. In this study, we decided to investigate the possibility of discovering proteins as biomarkers in urine from individuals diagnosed with gastric cancer. We carried out comprehensive quantitative profiling of urine samples using tandem mass tags (TMT)-based multiplexed mass spectrometry approach. Of the 1,504 total number of proteins identified, 246 proteins were differentially expressed in a gastric cancer cohort. Ephrin A1 (EFNA1), pepsinogen A3 (PGA3) and vitronectin (VTN) were among the upregulated proteins which are known to play crucial role in the progression of gastric cancer. Notably, our analysis also revealed other overexpressed proteins including shisa family member 5 (SHISA5), mucin like 1 (MUCL1) and leukocyte cell derived chemotaxin 2 (LECT2), which had not previously been linked to gastric cancer. We decided to deploy a recently developed targeted method, SureQuant, for validating a subset of potential proteins discovered in this study. We confirmed the overexpression of EFNA1, VTN and SORT1 in an independent set of urine samples. Our study demonstrates the potential of urinary proteomics to identify promising diagnostic biomarkers of cancers in a non-invasive fashion.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:54:20.311.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Akhilesh Pandey
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; acetylated residue; monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Eclipse; Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2023-03-17 15:50:51	ID requested
1	2024-08-10 12:30:59	announced
⏵ 2	2024-10-22 06:54:21	announced	2024-10-22: Updated project metadata.

Joshi N, Bhat F, Bellad A, Sathe G, Jain A, Chavan S, Sirdeshmukh R, Pandey A, Urinary Proteomics for Discovery of Gastric Cancer Biomarkers to Enable Precision Clinical Oncology. OMICS, 27(8):361-371(2023) [pubmed]

10.1089/omi.2023.0077;

submitter keyword: urine, proteomics, mass spectrometry, biomarkers,Gastric cancer, SureQuant

Akhilesh Pandey
contact affiliation	Mayo Clinic, Rochester, MN, USA
contact email	pandey.akhilesh@mayo.edu
lab head
Akhilesh Pandey
contact affiliation	Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905
contact email	pandey.akhilesh@mayo.edu
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/PXD040956

PRIDE project URI

• PRIDE
  1. PXD040956
     1. Label: PRIDE project
     2. Name: Urinary proteomics for discovery of gastric cancer biomarkers