ABSTRACT: Comprehensive molecular and phenotypic characterization of tumor models is still needed for robust understanding of breast cancer mechanisms and therapies. Here, we explore genome, transcriptome, and proteome of treated and untreated 4T1 triple-negative breast cancer cells. 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 (Trp53, Brca2, Bard1, Cdh1, Nf1, and Chek2) and deciphered the function consequences leveraging on the higher throughput Illumina NovaSeq X and NextSeq 1000 sequencers and highly accurate predicting power of AlphaFold. We found ~5700000 single nucleotide variations (SNVs) and 329448 indels achieving an important upgrade over previous literature data. 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 can modulate oncogenic transcription factors and induce caspase-dependent execution-phase ROS-mediated apoptosis through pPAK1Thr212 dephosphorylation, downregulation of pPI3Kp85αγ(Tyr467/199)/pAKT1Thr450/mTOR signaling, and modulation of pJAK3Tyr785/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.
