PXD008445

PXD008445 is an original dataset announced via ProteomeXchange.

Title	Patients with early stage oropharyngeal squamous cell carcinoma can be identified with label-free serum proteomics
Description	Increased incidence of oropharyngeal squamous cell carcinoma (OPSCC) is mainly related to Human Papilloma Virus (HPV) infection. As OPSCCs are often diagnosed at an advanced stage, mortality and morbidity remain high. There are no diagnostic biomarkers for early stage detection of OPSCC. Serum from 25 patients with stage I-II OPSCC and 12 disease- individuals were studied with quantitative label-free proteomics using ultra-definition MSE. Statistical analyses were performed to identify proteins most reliably distinguishing early stage OPSCCs from controls. P16 was used as a surrogate marker for HPV. P16-positive and -negative tumours were also analysed separately. With two or more unique proteins per identification, 176 proteins were quantified. A clear separation between patients with early-stage tumours and controls was seen in principal component analysis. Latent structures discriminant analysis identified 96 proteins most reliably differentiating OPSCC patients from controls, with 13 upregulated and 83 downregulated in study cases. The set of proteins was studied further with network, pathway and protein-protein interaction analyses, and found to participate in e.g. lipid metabolism. We identified patients with early stage OPSCC from controls based on their serum proteome, and suggest a protein set for further evaluation as a diagnostic biomarker panel for OPSCC.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:42:45.031.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sakari Joenväärä
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Synapt MS

Revision	Datetime	Status	ChangeLog Entry
0	2017-12-14 01:19:43	ID requested
1	2018-07-11 05:44:21	announced
2	2020-06-21 22:30:25	announced	2020-06-22: Updated publication reference for PubMed record(s): 32542012, 29961760.
⏵ 3	2024-10-22 04:42:51	announced	2024-10-22: Updated project metadata.

10.1038/s41416-018-0162-2;

10.1371/journal.pone.0233974;

Tuhkuri A, Saraswat M, M, ä, kitie A, Mattila P, Sil, é, n R, Dickinson A, Carp, é, n T, Tohmola T, Joenv, ä, ä, r, ä S, Renkonen S, Patients with early-stage oropharyngeal cancer can be identified with label-free serum proteomics. Br J Cancer, 119(2):200-212(2018) [pubmed]

Dickinson A, Saraswat M, Syrj, ä, nen S, Tohmola T, Sil, é, n R, Rand, é, n-Brady R, Carp, é, n T, Hagstr, ö, m J, Haglund C, Mattila P, M, ä, kitie A, Joenv, ä, ä, r, ä S, Sil, é, n S, Comparing serum protein levels can aid in differentiating HPV-negative and -positive oropharyngeal squamous cell carcinoma patients. PLoS One, 15(6):e0233974(2020) [pubmed]

curator keyword: Biomedical

submitter keyword: Oropharyngeal squamous cell carcinoma

serum proteomics

multivariate data analysis

Complement factor H-related protein 2

Myosin regulatory light chain 12A

Suvi Renkonen
contact affiliation	Department of Otorhinolaryngology – Head and Neck Surgery, University of Helsinki and Helsinki University Hospital, Helsinki 00130, Finland and Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm 11382, Sweden
contact email	suvi.renkonen@helsinki.fi
lab head
Sakari Joenväärä
contact affiliation	Helsinki University
contact email	sakari.joenvaara@helsinki.fi
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/2018/07/PXD008445

PRIDE project URI

• PRIDE
  1. PXD008445
     1. Label: PRIDE project
     2. Name: Patients with early stage oropharyngeal squamous cell carcinoma can be identified with label-free serum proteomics