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Integrated Metabolic Complex Genetic Interaction 1 Network of Chromosome 4p Loss in Basal Breast Cancer

Karam, L.; Pacis, A.; Dandage, R.; Schwartz, M.; Alzial, G.; Gherghi, A.; Djambazian, H. H. V.; Zapata, G.; Schapfl, M.; Asadi, P.; Castrillon, M.; Orr, A.; Hernandez, B.; Kargar, P.; Vandeloo, M.; Santosa, S.; Villunger, A.; Hart, T.; Ragoussis, J.; Deblois, G.; Bergdahl, A.; Park, M.; Bourque, G.; Kuzmin, E.

2025-10-15 genomics
10.1101/2025.10.15.682593 bioRxiv
Show abstract

Basal breast cancer subtype is enriched for triple-negative breast cancer (TNBC) and exhibits a recurrent large chromosomal deletion in chromosome 4p (chr4p). Chr4p loss is associated with poor survival, evolves early in tumorigenesis and confers on cells a proliferative state. Here, we map the integrated metabolic complex genetic interaction network of chr4p in basal breast cancer to identify targetable vulnerabilities. Differential gene expression analysis of patient derived xenografts and cancer cell models revealed that chr4p loss is associated with changes in cellular energetics and reduction/oxidation balance. Analysis of DepMap pooled genome-wide CRISPR-Cas9 screens identified complex genetic interactions specific to chr4p deletion in basal breast cancer cell models. Functional assays revealed that chr4p loss is associated with disrupted mitochondrial respiratory function and reduced glycolytic capacity, suggesting metabolic rewiring. Increased reactive oxygen species and lipid peroxidation compromised antioxidant defense mechanisms. Ultimately, this study sheds light on targeted therapies for basal breast cancer harboring large chromosomal deletions.

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