PXD016727

PXD016727 is an original dataset announced via ProteomeXchange.

Title	In-parallel proteomics and glycopeptidomics: Novel diagnostic glycopeptide biomarkers in serum identify patients with early-stage oropharyngeal squamous cell carcioma
Description	This is the proteomics part of the above project. Purpose: No blood-based biomarkers to detect OPSCC early before symptoms develop or before clinically visible. Diagnosis is solely based on histology of a visible tumour. Most OPSCC patients are diagnosed at an advanced stage, which leads to significant morbidity and poor survival. If high-risk patients were identified with blood-based biomarkers before clear clinical manifestations, tumours could be detected and treated at an earlier stage. Causes of OPSCC include smoking, alcohol misuse, and human papillomavirus (HPV). Tumours are separated according to WHO recommendations into HPV+ OPSCC and HPV- OPSCC using the proxy histological marker p16. We additionally separated our patients into these groups to determine whether the serum glycopeptides would differ between HPV+ and HPV- tumours, as these are distinct clinical entities. Patients and Methods: Pre-treatment sera from 74 patients with OPSCC (including 26 p16- tumours and 48 p16+ tumours) and 12 controls were used, collected between the years 2012 and 2015 at the Department of Otorhinolaryngology – Head and Neck Surgery, Helsinki University Hospital, Helsinki, Finland. Samples were grouped as follows: early stage p16+ OPSCC (stage I only), early stage p16- OPSCC (stage I-II), p16+ (any stage), p16- (any stage), controls. In-parallel quantitative bulk serum proteomics and serum glycopeptidomics were performed. Results: We identified 78 bulk proteins in the serum, of which 33 significantly differed between early-stage p16- OPSCC and controls, 22 between early-stage p16+ OPSCC and controls, 1 between early-stage p16+ and early-stage p16- OPSCCs, and 30 between all p16+ and p16- OPSCCs. We identified glycopeptides from proteins including but not limited to alpha-1-antitrypsin, haptoglobin, and Immunoglobulin heavy constant alpha 1, and compared these with the protein expression levels in each comparison. Conclusions: We have identified novel serum glycopeptide biomarkers detect early-stage OPSCCs, to be evaluated further as a diagnostic panel to detect preclinical OPSCC in at-risk patients.
HostingRepository	PRIDE
AnnounceDate	2024-01-27
AnnouncementXML	Submission_2024-01-26_17:34:38.678.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD016727
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Sakari Joenväärä
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	Ammonia-loss; Dehydrated; Oxidation; Carbamidomethyl
Instrument	Synapt MS

Revision	Datetime	Status	ChangeLog Entry
0	2019-12-12 07:24:46	ID requested
⏵ 1	2024-01-26 17:34:39	announced

10.1096/fba.2023-00066;

Dickinson A, Joenv, ä, ä, r, ä S, Tohmola T, Renkonen J, Mattila P, Carp, é, n T, M, ä, kitie A, Sil, é, n S, Altered microheterogeneity at several N-glycosylation sites in OPSCC in constant protein expression conditions. FASEB Bioadv, 6(1):26-39(2024) [pubmed]

10.6019/PXD016727;

submitter keyword: glycopeptidomics, proteomics, head and neck cancer, mass spectrometry, serum,OPSCC

Suvi Silén
contact affiliation	1 Department of Otorhinolaryngology - Head and Neck Surgery, University of Helsinki and HUS Helsinki University Hospital, P.O.Box 263, FI-00029 HUS, Helsinki, Finland 2 Department of Biosciences and Nutrition, Karolinska Institutet, SE-171 76, Stockholm, Sweden. 3 Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
contact email	suvi.silen@helsinki.fi
lab head
Sakari Joenväärä
contact affiliation	Helsinki University
contact email	sakari.joenvaara@helsinki.fi
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD016727
     1. Label: PRIDE project
     2. Name: In-parallel proteomics and glycopeptidomics: Novel diagnostic glycopeptide biomarkers in serum identify patients with early-stage oropharyngeal squamous cell carcioma