PXD059597-1

PXD059597 is an original dataset announced via ProteomeXchange.

Title	Integrating Proteomics and Bioinformatics Methods for the Identification of Breast Cancer Biomarkers Interacting with Telomeric G-Quadruplex
Description	The identification of reliable biomarkers is imperative for enhancing early detection, prognosis, and treatment of breast cancer. This study investigates a human telomeric dimeric G-quadruplex (G4) model, Tel46, which has been functionalized on Controlled Pore Glass (CPG) support, as a novel tool for biomarker discovery. Tel46 closely mimics multimeric G4 structures found in telomeric overhangs. Utilizing the affinity purification-mass spectrometry (AP-MS) approach, we identified 93 nuclear proteins that interacted with Tel46 in MCF7 breast cancer cells. Functional enrichment analyses revealed that these proteins were linked to DNA replication, repair, and genome stability pathways, which are frequently altered in cancer. To further refine these findings, we integrated AP-MS data with quantitative proteomics, comparing MCF7 and non-tumorigenic MCF10a cells. This approach led to the identification of 27 Tel46 interactors that were overexpressed. The subsequent functional analyses of these proteins revealed their enrichment in DNA replication, damage repair, and genome maintenance pathways, emphasising their potential as cancer biomarkers. Conversely, the downregulated proteins were associated with basic cellular functions such as protein synthesis and cytoskeletal organisation. Subsequent bioinformatics analyses incorporating public cancer genomics and transcriptomics data identified 19 potential biomarkers, including MSH6, MSH2, ESRP1, and WDHD1, which were further linked to poor clinical outcomes in breast cancer subtypes. This study validates the use of Tel46-functionalized CPG as a novel tool for isolating cancer-related proteins and highlights the potential of telomeric G4-interacting proteins as biomarkers for breast cancer diagnosis and therapy. These findings provide a foundation for future research into G4-mediated molecular mechanisms in cancer.
HostingRepository	PRIDE
AnnounceDate	2025-09-15
AnnouncementXML	Submission_2025-09-14_16:43:50.272.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Flora Cozzolino
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2025-01-09 08:03:25	ID requested
⏵ 1	2025-09-14 16:43:51	announced

10.1186/s12935-025-03955-z;

Iacobucci I, Cipollone I, Cozzolino F, Gaglione R, Mentino MR, Platella C, Musumeci D, Arciello A, Montesarchio D, Monti M, Integrating proteomics and bioinformatics for the identification of breast cancer biomarkers interacting with telomeric G-quadruplex. Cancer Cell Int, 25(1):319(2025) [pubmed]

submitter keyword: Bioinformatics, Telomeric G-Quadruplex,Proteomics, DNA-protein interactions., Breast Cancer Biomarkers

maria monti
contact affiliation	Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia, 21 – 80126 – Naples and CEINGE Advanced Biotechnologies s.c.a r.l. “Franco Salvatore”, Via Gaetano Salvatore, 486 – 80145 - Naples
contact email	montimar@unina.it
lab head
Flora Cozzolino
contact affiliation	University of Naples "Federico II"
contact email	flora.cozzolino@unina.it
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/2025/09/PXD059597

PRIDE project URI

• PRIDE
  1. PXD059597
     1. Label: PRIDE project
     2. Name: Integrating Proteomics and Bioinformatics Methods for the Identification of Breast Cancer Biomarkers Interacting with Telomeric G-Quadruplex