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

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 starting from nuclear extract of MCF7 cells, linking them to pathways in DNA replication, repair, and genome stability, which are frequently altered in cancer. Integrating AP-MS data with quantitative proteomics comparing MCF7 to non-tumorigenic MCF10A cells, 27 tel₄₆ interactors were identified among upregulated proteins. Functional analyses revealed enrichment in genome maintenance and repair pathways, while downregulated proteins were associated with fundamental cellular functions. Further bioinformatics analysis using public cancer proteomics database 19 were validated. Bioinformatic analysis based on transcriptomics and clinical data revealed MSH6, MSH2, ESRP1, and WDHD1 as the most promising potential biomarkers for breast cancer. Indeed, these proteins are highly expressed in BC and generally correlated to poor prognosis: in addition to their role as potential biomarkers for early diagnosis, these proteins might be used as targets for specific treatment, enhancing radiation sensitivity or decreasing tumour cell proliferation. As a proof-of-concept, this study proposes tel₄₆-functionalized CPG as a potential tool for isolating cancer-related proteins and underscores the potential of G4-interacting proteins as biomarkers for BC diagnosis and therapy. Moreover, these findings establish a basis for further research into G4-mediated cancer mechanisms.