In-Silico identification and optimization of therapeutic peptides against breast cancer via transcriptomic profiling

This study integrates transcriptomic, proteomic, and immunoinformatic analyses to identify peptide-based and repurposed drug candidates for Breast cancer therapy. Differential gene expression profiling across four independent datasets (GSE134938, GSE213481, GSE214054, and GSE148657) identified 455 significantly upregulated and 439 downregulated genes out of 6,124, with ANKFY1 (GSE134938) and ATE1 (GSE148657) emerging as robust markers. Functional clustering highlighted consistent upregulation of genes involved in extracellular matrix (ECM) remodeling, tumor invasion, and metabolic reprogramming (COL1A1, FN1, SPP1, MMPs, SCD), alongside downregulation of adhesion and mitochondrial genes, suggesting epithelial-mesenchymal transition (EMT) and metabolic vulnerabilities. Protein-protein interaction network analysis revealed ANKFY1, STARD4/5, and CADM1 as central hubs enriched in lipid metabolism, ECM regulation, and cytoskeletal signaling. Functional enrichment underscored cholesterol transport, steroid biosynthesis, and PPAR/AMPK signaling as key pathways in BC pathogenesis. Proteomic profiling of 21 breast cancer-associated proteins generated 28,732 human-specific peptides, prioritized using a composite scoring system integrating immunogenicity, physicochemical traits, and safety. Top peptides, including SCAMP2, CADM1, and FNBP1, exhibited high MHC binding affinity (IC50 < 30 nM), non-allergenic and non-toxic profiles, and favorable solubility, with motif analysis identifying conserved functional patterns across SCAMP2, CADM1, and FNBP1. Structural modeling and virtual screening validated these proteins as tractable targets, with nilotinib and tucatinib emerging as promising multitarget repurposed drug candidates. At the same time, terfenadine displayed strong binding but cardiotoxic potential. Collectively, these results highlight lipid-driven oncogenesis and ECM remodeling as central to BC biology and provide a translational framework for peptide-based immunotherapy and drug repurposing.