PXD008654

PXD008654 is an original dataset announced via ProteomeXchange.

Title	Proteomic profiling of paired interstitial fluids revealed dysregulated pathways and salivary NID1 as a biomarker of oral cavity squamous cell carcinoma
Description	Patients with oral cavity squamous cell carcinoma (OSCC) are frequently first diagnosed at an advanced stage, leading to poor prognosis and high mortality rate. Early detection of OSCC using body fluid-accessible biomarkers may help improve the prognosis and survival rate of OSCC patients. As tumor interstitial fluid (TIF) is a proximal fluid enriched with cancer-related proteins, it is therefore a valuable reservoir suitable for the discovery of cancer biomarkers as well as dysregulated biological pathways in tumor microenvironment. Thus, we harvested and analyzed the paired tumor (TIF) and adjacent noncancerous (NIF) interstitial fluids from ten OSCC patients using one-dimensional gel electrophoresis coupled with the nano-liquid chromatography-tandem mass spectrometry (GeLC-MS/MS) approach and label-free spectral counting method. The results showed that 113 proteins were up-regulated in at least six OSCC TIFs compared to their respective NIFs, and that the aminoacyl tRNA biosynthesis was statistically enriched in TIFs by Gene Set Enrichment Analysis (GSEA). The enrichment of aminoacyl tRNA biosynthesis in OSCC was verified that four members (IARS, KARS, WARS, and YARS) were revealed to be elevated in OSCC by IHC (n = 12). Among the 113 up-regulated proteins, two candidates (NID1 and SERPINH1) were selected based on an integrated bioinformatics analysis and verified that the salivary NID1 levels were significantly higher in OSCC patients (n = 48) compared to health (n = 51) and OPMD individuals (n = 53). Moreover, the IHC results (n = 222) showed that the expression of NID1 was higher in OSCC compared to adjacent noncancerous epithelium and correlated with pathological T, N, and overall stage as well as survivals of OSCC patients. These results collectively indicate that the analysis of TIF is help to understand the tumor microenvironment, and that salivary NID1 is a potentially useful biomarker for the OSCC.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:08:02.516.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD008654
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Chih-Ching Wu
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	Oxidation; Carbamidomethyl
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2018-01-11 02:34:22	ID requested
1	2019-08-15 01:40:21	announced
⏵ 2	2024-10-22 04:08:03	announced	2024-10-22: Updated project metadata.

Hsu CW, Chang KP, Huang Y, Liu HP, Hsueh PC, Gu PW, Yen WC, Wu CC, Proteomic Profiling of Paired Interstitial Fluids Reveals Dysregulated Pathways and Salivary NID1 as a Biomarker of Oral Cavity Squamous Cell Carcinoma. Mol Cell Proteomics, 18(10):1939-1949(2019) [pubmed]

10.1074/mcp.ra119.001654;

10.6019/PXD008654;

curator keyword: Biomedical

submitter keyword: tumor interstitial fluid, saliva, oral cavity squamous cell carcinoma, aminoacyl tRNA biosynthesis, nidogen-1, biomarker

Chih-Ching Wu
contact affiliation	Department of Medical Biotechnology and Laboratory Sciences, College of Medicine, Chang Gung University, Taiwan
contact email	luckywu@mail.cgu.edu.tw
lab head
Chih-Ching Wu
contact affiliation	Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University
contact email	luckywu@mail.cgu.edu.tw
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/2019/08/PXD008654

PRIDE project URI

• PRIDE
  1. PXD008654
     1. Label: PRIDE project
     2. Name: Proteomic profiling of paired interstitial fluids revealed dysregulated pathways and salivary NID1 as a biomarker of oral cavity squamous cell carcinoma