PXD016061-1

PXD016061 is an original dataset announced via ProteomeXchange.

Title	Quantitative proteomic analysis identifies TUBB2A as a novel protein biomarker for prediction of distant metastatic breast cancer
Description	Metastasis of breast cancer to other distant organs is fatal to patients. However, few studies have revealed biomarkers associated with distant metastatic breast cancer. Furthermore, the inability of current biomarkers such as HER2, ER and PR, in accurately differentiating between distant metastatic breast cancers from non-distant metastatic ones necessitates the development of novel biomarkers. An integrated proteomics approach that combines filter-aided sample preparation, tandem mass tag labeling (TMT), high pH fractionation, and high resolution MS was applied to acquire in-depth proteome data of distant metastatic breast cancer FFPE tissue. Bioinformatics analyses for gene ontology and signaling pathways using differentially expressed proteins (DEPs) were performed to investigate molecular characteristics of distant metastatic breast cancer. In addition, real-time polymerase chain reaction (RT-PCR) and invasion/migration assays were performed to validate the differential regulation and functional capability of biomarker candidates. A total of 9,459 and 8,760 proteins were identified from the pooled sample set and the individual sample set, respectively. Through our stringent criteria, TUBB2A was selected as a novel biomarker. The metastatic functions of the candidate were subsequently validated. Bioinformatics analysis using DEPs were able to characterize the overall molecular features of distant metastasis as well as investigate the differences across breast cancer subtypes. Our study is the first to explore the distant metastatic breast cancer proteome using FFPE tissue. The depth of our dataset enabled the discovery of novel biomarker and the investigation of proteomic characteristics of distant metastatic breast cancer. The distinct molecular features of breast cancer subtypes were also observed. Our proteomic data has important utility as a valuable resource for the research on distant metastatic breast cancer.
HostingRepository	PRIDE
AnnounceDate	2020-06-05
AnnouncementXML	Submission_2020-06-05_03:51:14.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Dongyoon Shin
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	2019-10-29 02:40:14	ID requested
⏵ 1	2020-06-05 03:51:15	announced

Shin D, Park J, Han D, Moon JH, Ryu HS, Kim Y, Identification of TUBB2A by quantitative proteomic analysis as a novel biomarker for the prediction of distant metastatic breast cancer. Clin Proteomics, 17():16(2020) [pubmed]

submitter keyword: Distant metastatic breast cancer, Formalin-fixed paraffin-embedded (FFPE) tissue, Biomarkers, tandem mass tag (TMT), quantitative proteomics

Youngsoo Kim
contact affiliation	Department of Biomedical Sciences, Seoul National University College of Medicine 103 Daehakro Seoul 30380, Korea.
contact email	biolab@snu.ac.kr
lab head
Dongyoon Shin
contact affiliation	Seoul National University
contact email	sdymath777@naver.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/2020/06/PXD016061

PRIDE project URI

• PRIDE
  1. PXD016061
     1. Label: PRIDE project
     2. Name: Quantitative proteomic analysis identifies TUBB2A as a novel protein biomarker for prediction of distant metastatic breast cancer