Comprehensive molecular and phenotypic characterization of tumor models is still needed for a robust understanding of breast cancer mechanisms and therapies. Here, we explore the genome, transcriptome, and proteome of treated and untreated 4T1 triple-negative breast cancer cells to integrate genomic vulnerabilities and mutational profiling with novel treatment-induced delivery, signaling, and apoptotic responses. Nanoencapsulation (AuNPs) of berry-derived polyphenolic compounds was influenced by limited clinical use due to poor stability and bioavailability. Several physicochemical characterizations employed include TEM, FTIR, and targeted UPLC/MS-QQQ assays. We identified significant mutations to breast cancer-related tumor suppressor genes (TP53, BRCA2, BARD1, CDH1, NF1, and CHEK2) and deciphered the functional consequences leveraging the higher throughput Illumina NovaSeq X and NextSeq sequencing and the highly accurate predictive power of AlphaFold. We found ~5,700,000 single-nucleotide variations (SNVs) and 329448 indels, achieving an important upgrade over existing literature data. Multiple sequence alignment with WT mouse and human protein sequences demonstrated that mutations present in 4T1 cells are within highly conserved motifs of key tumor suppressors, emphasizing their relevance to human breast cancer biology. Key findings from differentially expressed gene enrichment analyses (GSEA) revealed positive gene enrichments of DNA repair regulators and TGF-β signaling, while having negative enrichments of cell adhesion, cadherin and MAPK signaling via PI3K/AKT/MAPK/Wnt pathways, potentially influencing apoptosis and immune evasion intrinsic to cancer. Notably, decreased expression of PIK3CG, PALLD, PTPRZ1, and CDH8 and increased expression of SEMA6C, WWOX, NHEJ1, and MAML3 suggested suppression of epithelial-to-mesenchymal transition (EMT) and metastatic potential. Further assessment of immunohistochemical, immunofluorescent, and flow cytometric data revealed that berry-derived nanoparticles are associated with the modulation of oncogenic transcription factors and linked to induced caspase-dependent execution-phase ROS-mediated apoptosis through pPAK1 dephosphorylation, downregulation of pPI3K/pAKT1/mTOR signaling, and modulation of pJAK3/STAT3 pathway supporting transcriptomic and transcriptional reprogramming of 4T1 treated cells. Together, our findings uncover a new strategy to capture berry-derived polyphenols required to regulate apoptosis, autophagy, immune response, and metastasis-related gene networks in breast cancer, thereby underscoring the therapeutic potential of functionalized AuNPs as delivery platforms for dietary phytochemicals.