PXD048046

PXD048046 is an original dataset announced via ProteomeXchange.

Title	Mapping the interactome of OSCC prognostic-associated proteins NDRG1 and PGK1 through proximity labeling using TurboID
Description	Oral squamous cell carcinoma (OSCC) is a prevalent type of head and neck cancer, accounting for more than 90% of all oral malignancies worldwide. The identification of diagnostic and prognostic markers for OSCC is crucial for improving patient outcomes, as early detection and treatment are critical for successful management of this disease. In this regard, our group recently demonstrated that N-myc downstream-regulated gene 1 (NDRG1) and phosphoglycerate kinase 1 (PGK1) are prognostic markers in OSCC, however, little is known about the role of these proteins in OSCC development. To better understand their signaling pathways, we used TurboID-based proximity labeling to identify the interactomes of NDRG1 and PGK1 in HEK293 cells. Here, protein abundance patterns associated with three distinct time-points were utilized for protein clustering, allowing the identification of protein clusters with a “fast” or “slow” response to biotin. Functional enrichment of GO terms revealed processes mostly associated with mRNA processing for both PGK1 and NDRG1 “fast” clusters, while GO processes related to protein localization and catalytic activity were identified in PGK1 and NDRG1 “slow” clusters, respectively. A total of 65 out of 361 proteins from different clusters were also identified in neoplastic islands of OSCC tissues from our previous study. Additionally, 28 of these proteins have their gene expression associated with prognostic features such as death, metastasis and/or relapse in OSCC patients. Ultimately, our data enabled the identification of 17 previously known physical interactions and functional associations among these proteins, as well as 30 new putative interactions, characterizing a prognostic-associated interactome composed of 28 proteins. This interactome enables the prioritization of candidates that can be further explored in OSCC progression.
HostingRepository	PRIDE
AnnounceDate	2025-05-06
AnnouncementXML	Submission_2025-05-06_12:26:26.577.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Adriana Franco Paes Leme
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2023-12-21 08:21:00	ID requested
⏵ 1	2025-05-06 12:26:27	announced

C, â, mara GA, Yokoo S, Granato DC, Simabuco FM, Ribeiro-Filho HV, Melo RM, Pauletti BA, Nascimento Filho EG, Domingues RR, Paes Leme AF, Mapping the Interactome of OSCC Prognostic-Associated Proteins NDRG1 and PGK1 Through Proximity Labeling Using TurboID. J Proteome Res, 24(6):2741-2756(2025) [pubmed]

10.1021/acs.jproteome.4c01039;

submitter keyword: NDRG1,Oral cancer, PGK1, TurboID, Interactome, Proximity Labeling, Prognostic

Adriana Franco Paes Leme
contact affiliation	Head of Mass Spectrometry Laboratory, Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil
contact email	adriana.paesleme@lnbio.cnpem.br
lab head
Adriana Franco Paes Leme
contact affiliation	CNPEM
contact email	adriana.paesleme@lnbio.cnpem.br
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/2025/05/PXD048046

PRIDE project URI

• PRIDE
  1. PXD048046
     1. Label: PRIDE project
     2. Name: Mapping the interactome of OSCC prognostic-associated proteins NDRG1 and PGK1 through proximity labeling using TurboID