Determination of Copy Number Variations and Affected Gene Networks in Breast Cancer from Mexican Patients

Larios-Serrato, V.; Valdez-Salazar, H.-A.; Torres, J.; Camorlinga-Ponce, M.; Pina-Sanchez, P.; Mayani-Viveros, H.; Ruiz-Tachiquin, M.-E.

doi:10.1101/2025.08.28.672450

bioRxiv · 10.1101/2025.08.28.672450

Determination of Copy Number Variations and Affected Gene Networks in Breast Cancer from Mexican Patients

Larios-Serrato, V.·Valdez-Salazar, H.-A.·Torres, J.·Camorlinga-Ponce, M.·Pina-Sanchez, P.·Mayani-Viveros, H.·Ruiz-Tachiquin, M.-E.

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Abstract

Triple-negative breast cancer (TNBC) is an aggressive subtype with limited treatment options and high molecular heterogeneity. In this study, we performed a genome-wide analysis of copy number variations (CNVs) using high-density microarrays in tumor tissue (TUM), tumor adjacent tissue (ADJ), and leukocytes (LEU) from five Mexican TNBC patients. We identified both unique and shared CNVs across tissues, including alterations in key chromosomal regions such as 1q23.3, 1q32.1, and 8q24.3, which harbor oncogenes like MYC, MCL1, and BCL9. Losses in 6q25.2 affecting ESR1 were also detected. CNVs were enriched in genes related to the Hallmarks of Cancer, with TUM samples showing profiles associated with proliferation, metastasis, and immune evasion; ADJ samples with growth suppression; and LEU samples with genomic instability. Pathway enrichment analyses revealed disrupted functions in DNA repair, extracellular matrix organization, and TP53 signaling in TUM. Notably, EGFR, ERCC4, and HSP90AB1 emerged as central nodes in interaction networks and may serve as markers or therapeutic targets. This is the first CNV profiling study of its kind in TNBC from Mexican patients, highlighting the importance of including underrepresented populations in genomic research to uncover distinct molecular signatures and potential diagnostic or therapeutic avenues. ImplicationsMolecular signatures of breast cancer (BC), predicted bioinformatically, involve common and distinct CNV-Hallmarks of Cancer genes, which are suitable candidates for screening as potential BC markers.

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Larios-Serrato, V., Valdez-Salazar, H.-A., Torres, J., Camorlinga-Ponce, M., Pina-Sanchez, P., Mayani-Viveros, H., Ruiz-Tachiquin, M.-E.. 2025-08-31. Determination of Copy Number Variations and Affected Gene Networks in Breast Cancer from Mexican Patients. https://doi.org/10.1101/2025.08.28.672450

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