Dataset Information

Combining proteomics and machine learning to identify triple negative breast cancer biomarkers binding telomeric G-Quadruplex

ABSTRACT: Triple-negative breast cancer (TNBC) lacks ER, PR and HER2 expression, represents ~10–20% of invasive breast cancers, and is clinically aggressive with limited targeted treatment options. Its pronounced molecular heterogeneity challenges single-marker diagnostics, motivating the development of robust biomarker panels for early detection and disease monitoring. Aptamers, and particularly guanine-rich DNA sequences forming G-quadruplexes (G4s), provide stable and versatile molecular recognition tools. Telomeric G4 structures are biologically relevant in genome maintenance and can enrich disease-related protein interactors, making them attractive baits for translational biomarker discovery. Here, we employed an overhang human telomere model capable of forming two consecutive G4s (tel46) immobilized on Controlled Pore Glass (CPG) to profile the nuclear G4 interactome in two TNBC cell lines, MDA-MB-231 and BT-549. Using affinity purification–mass spectrometry (AP-MS) with CPG-tel46 combined with quantitative proteomics and stringent background subtraction, we identified tel46-associated proteins consistently upregulated in both tumour models and prioritized 11 candidates supported by downstream bioinformatic validation. To move beyond single-marker evaluation, we implemented a machine-learning framework to assess candidate proteins as a coordinated molecular signature. Regularized models with embedded feature selection and cross-validation were used to identify stable, discriminative combinations while controlling overfitting. This integrative strategy supports G4-based capture as a practical approach to enrich clinically relevant interactors and prioritize diagnostic panels. We propose a five-protein signature (KIF4A, ACIN1, RBM12, FOXK1 and NCAPD2) as a candidate classifier for TNBC early diagnosis, providing a foundation for independent validation in clinical cohorts.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Breast

DISEASE(S): Breast Cancer

SUBMITTER: ilaria iacobucci

LAB HEAD: Maria Monti

PROVIDER: PXD072964 | Pride | 2026-05-29

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	BT1_REP1_20250714044634.raw	Raw
	BT1_REP2_20250714061946.raw	Raw
	BT1_REP3_20250714075300.raw	Raw
	BT2_REP1_20250714095944.raw	Raw
	BT2_REP2_20250714113258.raw	Raw

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Publications

Integrating proteomics and bioinformatics for the identification of breast cancer biomarkers interacting with telomeric G-quadruplex.

Iacobucci Ilaria I Cipollone Irene I Cozzolino Flora F Gaglione Rosa R Mentino Maria Rosaria MR Platella Chiara C Musumeci Domenica D Arciello Angela A Montesarchio Daniela D Monti Maria M

Cancer cell international 20250902 1

The identification of reliable biomarkers is essential for improving breast cancer (BC) detection, prognosis, and treatment. This study explores a human telomeric G-quadruplex (G4) model, tel46, functionalized on Controlled Pore Glass (CPG) support, as a novel biomarker discovery tool. The oligonucleotide tel46 mimics multimeric G4 structures in telomeric overhangs. Using affinity purification-mass spectrometry, 93 proteins interacting with tel46 were identified ...[more]

PMID: 40898188

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Project description:DNA secondary structures are important for fundamental genome functions such as transcription and replication1. The G-quadruplex (G4) structural motif has been linked to gene regulation2,3 and genome instability4,5 and may be important to cancer development and other diseases6-8. Recently, ~700,000 discrete G4s have been observed in naked human single-stranded genomic DNA using G4-seq, a high-throughput sequencing technique that detects structural features in vitro.9 It is of vital importance to investigate G4 structures within an endogenous chromatin context, which until now remained elusive10,11. Herein, we address this via the development of G4 ChIP-seq, an antibody-based G4 chromatin immunoprecipitation and high-throughput sequencing approach. We identified ~10,000 endogenous G4 structures and show that G4s are predominantly seen in regulatory, nucleosome-depleted, chromatin regions. G4s were enriched in the promoters and 5âUTR regions of highly transcribed genes, particularly in genes related to cancer and in somatic copy number amplifications, such as MYC. Reorganization of the chromatin landscape using a histone deacetylase inhibitor, resulted in de novo G4 formation in new and more prominent regulatory, nucleosome-depleted regions associated with increased transcriptional output. Our findings suggest a striking relationship between promoter nucleosome-depleted regions, G4 formation and elevated transcriptional activity. Comparison between normal human epidermal keratinocytes and their immortalized counterparts revealed a ï¾7-fold greater G4 abundance in immortalized cells, of which 80 % were found in regulatory, nucleosome-depleted regions common to both cell types. Consequently, cells exhibiting more G4s displayed significantly increased transcriptional output and were more sensitive to growth inhibition by a small molecule G4 ligand. Overall, our results provide new mechanistic insights into where and when DNA adopts G4 structure in vivo. Our findings show for the first time that regulatory, nucleosome-depleted chromatin and transcriptional states predominantly shape the endogenous G4 DNA landscape. Two cell lines, treated with entinostat or untreated, analyzed to detect gene expression differences, presence of G-Qudruplexes and chromatin state. Each combination of conditions replicated in duplicates or triplicates.