PXD007532

PXD007532 is an original dataset announced via ProteomeXchange.

Title	LC-MS/MS analysis of human thyroid cystic fluid and thyroid cancer cell secreted proteins
Description	Thyroid ultrasound and ultrasound-guided fine-needle aspiration (USG/FNA) biopsy are currently used for diagnosing papillary thyroid carcinoma (PTC), but their detection limit could be improved by combining other biomarkers. To discover novel PTC biomarkers, we herein applied a GeLC-MS/MS strategy to analyze the proteome profiles of serum-abundant-protein-depleted FNA cystic fluid from benign and PTC patients, as well as two PTC cell line secretomes. From them, we identified 346, 488, and 2105 proteins, respectively. Comparative analysis revealed that 191 proteins were detected in the PTC but not the benign cystic fluid samples, and thus may represent potential PTC biomarkers. Among these proteins, 101 were detected in the PTC cell line secretomes, and seven of them (NPC2, CTSC, AGRN, GPNMB, DPP4, ERAP2, and SH3BGRL3) were reported in public PTC transcriptome datasets as having 4681 elevated mRNA expression in PTC. Immunoblot analysis confirmed the elevated expression levels of five proteins (NPC2, CTSC, GPNMB, DPP4, and ERAP2) in PTC versus benign cystic fluids. Immunohistochemical studies from near 100 pairs of PTC tissue and their adjacent non-tumor counterparts further showed that AGRN (n = 98), CTSC (n = 99), ERAP2 (n = 98) and GPNMB (n = 100) were significantly (p<0.05) overexpressed in PTC and higher expression levels of AGRN and CTSC were also significantly associated with metastasis and poor prognosis of PTC patients. Collectively, our results indicate that an integrated analysis of FNA cystic fluid proteome, cancer cell secretome and tissue transcriptome datasets represents a useful strategy for efficiently discovering novel PTC biomarker candidates.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_03:59:38.849.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Chia-Chun Wu
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2017-08-22 03:58:27	ID requested
1	2018-03-21 02:00:50	announced
⏵ 2	2024-10-22 03:59:47	announced	2024-10-22: Updated project metadata.

10.18632/oncotarget.23951;

Wu CC, Lin JD, Chen JT, Chang CM, Weng HF, Hsueh C, Chien HP, Yu JS, Integrated analysis of fine-needle-aspiration cystic fluid proteome, cancer cell secretome, and public transcriptome datasets for papillary thyroid cancer biomarker discovery. Oncotarget, 9(15):12079-12100(2018) [pubmed]

curator keyword: Biological, Biomedical

submitter keyword: Human, Thyroid cystic fluid, Thyroid cancer cell, LC-MS/MS

Jau Song Yu
contact affiliation	Graduate Institute of Biomedical Sciences, department of Cell and Molecular Biology, College of Medicine, and Molecular Medicine Research Center, Chang Gung University, Taoyuan 33302, Taiwan. Liver Research Center, Chang Gung Memorial Hospital and Chang Gung University, Taoyuan 33302, Taiwan.
contact email	yusong@mail.cgu.edu.tw
lab head
Chia-Chun Wu
contact affiliation	Molecular Medicine Research Center, Chang Gung University
contact email	wuchiachun9@gmail.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/2018/03/PXD007532

PRIDE project URI

• PRIDE
  1. PXD007532
     1. Label: PRIDE project
     2. Name: LC-MS/MS analysis of human thyroid cystic fluid and thyroid cancer cell secreted proteins