Search Results (2,917)

Background: The growing awareness of breast cancer’s molecular diversity has not changed the technical foundations of surgery itself, but it has profoundly reshaped how surgeons think about surgery. Rather than molecular biology prescribing specific surgery, it is the surgeon’s interpretation of biological behavior—tumor subtype, genomic risk, treatment responsiveness—that influences surgical timing, extent, and feasibility. This is particularly important in the developing world, where mastectomy continues to be the default surgery, not always because it is required, but because biological nuance is underutilized in surgical planning. This review integrates existing evidence, guidelines, and real-world clinical experience to show how a surgeon who understands tumor biology can meaningfully expand safe breast conservation, de-escalate axillary surgery, and align operative choices with systemic therapy. In essence, molecular biology becomes a lens through which surgeons can practice more personalized, precise, and less invasive surgery, without compromising oncologic safety. Recent findings: We present evidence-based algorithms focusing on Luminal A, Luminal B, HER2-positive, and triple-negative subtypes, while discussing the nuances of multifocal and multicentric disease, metaplastic histologies, and discordant lesion management. The review addresses axillary management in the molecular era, specifying the appropriateness of sentinel lymph node biopsy, targeted axillary dissection, or completion axillary dissection, and how subtype-specific nodal responses to neoadjuvant therapy can guide de-escalation strategies. Through clinical vignettes, we exemplify how molecular integration into surgical planning can modify clinical courses, enabling oncoplastic conservation in downstaged tumors and justifying definitive resection in chemo-resistant cases. We examine the implications of germline and somatic genetic testing on surgical decision-making, particularly in relation to BRCA1/2 and PALB2 mutation carriers, alongside ethical and practical counseling considerations. Additionally, we review emerging biomarkers—such as circulating tumor DNA and immune and radiomic signatures—and propose research priorities for their incorporation into surgical trials. Conclusions: Effective implementation necessitates enhanced surgeon education, standardized assays, and multidisciplinary coordination to promote equitable access, consistent utilization of biology-driven algorithms, and rigorous quality oversight. This review furnishes breast surgeons with a pragmatic framework for translating molecular knowledge into multidisciplinary, patient-centered care pathways that optimize oncological safety, aesthetic outcomes, and overall quality of life. Full article

Triple-negative breast cancer (TNBC) is characterized by marked immune microenvironment heterogeneity and variable chemotherapy response, yet the epithelial transcriptional programs governing cytotoxic immune activation remain poorly understood. We performed an exploratory, integrative analysis using single-cell RNA sequencing of 31,962 cells from eight TNBC patients operationally stratified into Good and Bad Prognosis groups based on pathological lymphoid infiltration, a discovery grouping subsequently validated against pathological complete response (pCR) in three independent bulk RNA-seq cohorts. This analysis identified four epithelial transcriptional states. The G5 DNA damage subpopulation—predominantly restricted to Good Prognosis tumors (29.2% vs. 0%)—and the G4 Metabolism subpopulation—2.4-fold enriched in Bad Prognosis—were the primary prognostic signatures. Machine learning validation using nested leave-one-cohort-out (LOCO) cross-validation across 614 samples demonstrated that G4 + G5 raw genes with random forest yielded the largest observed mean AUC of 0.653, though these results are exploratory and do not establish a validated clinical classifier. CellChat ligand–receptor interaction analysis revealed that G5 DNA-damage epithelial cells are the dominant immune activators in Good Prognosis TNBC, predominantly engaging CD8 cytotoxic T cells through MHC-I antigen presentation via HLA-A/B/C/E/F → CD8A/CD8B interactions, the highest-probability signaling pathway identified. Spatial transcriptomics independently validated significantly higher DNA damage and CD8 T-cell scores in Good Prognosis tissue. Together, these exploratory findings suggest a framework in which tumor-intrinsic DNA damage signaling is associated with MHC-I antigen presentation upregulation and CD8 cytotoxic T-cell engagement, supporting further investigation of this axis and its potential implications for combining DNA-damaging chemotherapy with immune checkpoint blockade in TNBC. Full article

Background/Objectives: Triple negative breast cancer remains the most difficult breast cancer to treat as there are no specific targeted therapies. The tumor stroma is recognized as essential for the development of solid tumors. Cancer associated myofibroblasts are known to play a major role in the construction of a tumor microenvironment conducive to tumor progression. Therefore, we established a co-culture system to identify potential molecular targets controlling myofibroblast conversion. Methods: Co-cultures of MDA-MB-468 triple negative breast cancer cells and skin fibroblasts were either mixed prior to seeding or seeded individually on opposite sides of a culture dish and incubated in complete medium. Inhibitors were preincubated with cells for 1 h. Inflammatory cytokines were measured by ELISA. Proteins were analyzed using the Wes-Protein Simple System. Immunostaining was visualized using a Hamamatsu Photonics Nanozoomer. Statistical analysis was done by student’s t-test and one-way ANOVA. Results: The data indicate that co-culturing the cells promotes myofibroblast differentiation and cytokine release and this requires direct contact between the two cell types. Both myofibroblast conversion and cytokine release were prevented by inhibitors of TLR5, TGF-β and EDA-fibronectin. Conclusions: Data suggest that the TLR5 receptor on the MDA-MB-468 cells binds to EDA-fibronectin expressed by fibroblasts thus inducing inflammatory cytokine expression. Expression of EDA fibronectin is regulated through TGF-β whose synthesis is induced by TLR5 signaling in the tumor cells. The data are consistent with a model in which TLR5-mediated crosstalk between the cancer cells and the stromal fibroblasts creates a tissue microenvironment conducive to tumor growth and metastasis. Full article

Triple-negative breast cancer (TNBC) lacks effective targeted therapeutic strategies, and cisplatin resistance remains a major challenge in clinical treatment. This study aimed to investigate whether inorganic phosphate (Pi) influences cellular responses to cisplatin and to explore the potential molecular mechanisms involving RB1–E2F signaling, DNA repair regulation, and oxidative stress. Clinical associations between serum biochemical parameters and tumor histologic grade were evaluated in 246 patients with invasive ductal carcinoma. Triple-negative breast cancer cell line (MDA-MB-231), estrogen receptor-positive breast cancer cell line (MCF-7), and non-tumorigenic breast epithelial cell line (MCF-10A) were treated with control, Pi, cisplatin, or Pi combined with cisplatin.. Cellular proliferation, cell-cycle distribution, DNA damage, intracellular reactive oxygen species (ROS), inflammatory responses, and transcriptomic alterations were assessed using functional assays and RNA sequencing-based analyses. Pi levels showed an inverse association with tumor grade. In MDA-MB-231 cells, Pi combined with cisplatin resulted in enhanced growth inhibition, increased DNA damage accumulation, elevated cellular ROS production, and activation of inflammatory responses compared with cisplatin alone. Transcriptomic analyses revealed alterations in RB1–E2F-related transcriptional programs and reduced expression of DNA repair-associated gene sets. TCGA-BRCA analysis further indicated that elevated DNA repair pathway activity was associated with unfavorable survival outcomes. These findings suggest that Pi may modulate cisplatin responses through coordinated regulation of RB1–E2F signaling, DNA repair capacity, and oxidative stress responses, providing a potential mechanistic basis for further investigation of phosphate-associated therapeutic strategies in TNBC. Full article

Triple-negative breast cancer (TNBC) is associated with recurrence, metastasis, and limited durable responses to immunotherapy, in part due to persistence of breast cancer stem cells (BCSCs). We investigated whether CD6-directed immunotherapy with the monoclonal antibody UMCD6 enhances immune-mediated killing and alters function of BCSC in stem cell-enriched TNBC models. The SUM-149 and SUM-159 cell lines were analyzed for CD6 ligand expression, cocultured with human peripheral blood mononuclear cells (PBMCs) treated with UMCD6, pembrolizumab, or isotype control, and assessed by live-cell cytotoxicity imaging, flow cytometry, soft agar colony formation, and extreme limiting dilution sphere assays. Both TNBC lines co-expressed the CD6 ligands CD44, CD166/ALCAM, and CD318/CDCP1. UMCD6 significantly increased PBMC-mediated apoptosis and reduced tumor cell survival in both models, with greater activity than pembrolizumab under these in vitro conditions. In surviving SUM-159 cells, UMCD6 reduced the ALDH⁺ population wit×hout significantly altering CD44⁺CD24⁻ frequency, indicating preferential effects on a distinct stem-like compartment. Functionally, UMCD6 decreased anchorage-independent colony formation and reduced sphere-forming frequency from 1/33.6 to 1/68.3 cells (p = 0.0186). These findings identify the CD6 ligand axis as a therapeutic vulnerability in BCSC-enriched TNBC and support further preclinical evaluation of CD6-directed immunotherapy as a strategy to enhance antitumor immunity while limiting tumor-initiating capacity. Full article

Background: Immune checkpoint inhibitors (ICIs) have moved from the metastatic setting into neoadjuvant, adjuvant, and fully perioperative strategies across several solid tumors. This shift has created a new clinical interface between medical oncology, surgery, anesthesia, pathology and postoperative care because immune activation may improve pathological response and survival while also generating immune-related adverse events (irAEs) that mimic or aggravate perioperative complications. Methods: We conducted a scoping review according to PRISMA-ScR. PubMed/MEDLINE and Web of Science were searched for studies published between 2016 and 2026 that evaluated adult patients with solid tumors receiving ICIs in relation to surgery. Thirty-three studies were included and synthesized descriptively across surgical feasibility, perioperative safety, irAEs, anesthetic considerations, and oncological outcomes. Results: The strongest evidence was found in resectable non-small-cell lung cancer, where neoadjuvant or perioperative ICI-based regimens improved pathological response and, in several trials, event-free or overall survival. Evidence in triple-negative breast, bladder, gastric/gastroesophageal junction, and ovarian cancers supported broader applicability but remained heterogeneous, with variable efficacy across tumor types and treatment regimens. Surgery following ICI exposure was generally feasible, without a consistent increase in postoperative mortality. However, pneumonitis, myocarditis, endocrinopathies, hepatitis, colitis, and cytokine release syndrome may mimic conventional postoperative complications. Direct evidence comparing anesthetic or perioperative management strategies was scarce. Conclusions: Perioperative ICI-based therapy is no longer an experimental concept, but its safe implementation requires structured preoperative screening, individualized surgical timing, organ-specific toxicity surveillance, careful corticosteroid decision-making, and close multidisciplinary communication. Future prospective studies should integrate standardized perioperative endpoints, anesthesia-related variables, biomarker-driven risk stratification, and long-term oncological outcomes. Full article

Background: The efficacy of chemotherapy in triple-negative breast cancer (TNBC) is limited by intrinsic resistance and the tumor microenvironment (TME). Accumulating evidence reveals a mechanistic connection between programmed death-ligand 1 (PD-L1) and c-x-c motif chemokine receptor 4 (CXCR4), which dominate stroma barriers, immune escape, and cancer metastasis. Earlier studies have shown that dual suppression of c-x-c motif ligand 12 (CXCL12)/CXCR4 and programmed cell death-1 (PD-1)/PD-L1 pathways regulates extracellular matrix (ECM) deposition, activation of cancer-associated fibroblasts (CAFs), and epithelial–mesenchymal transition (EMT) of pancreatic cancer cells. Methods: We combined BsNb PX4, a bispecific nanobody targeting PD-L1 and CXCR4, with paclitaxel or gemcitabine in multiple tumor cell lines and human peripheral blood mononuclear cell (hPBMC)-reconstituted xenograft mouse models. Antitumor activity was assessed by CCK-8, flow cytometry, and ELISA, and immune cell infiltration and TME remodeling were examined by immunofluorescence, immunohistochemistry, cytokine assays, and RNA-seq. Results: In MDA-MB-231 cells, BsNb PX4 synergistically enhanced paclitaxel-induced growth inhibition and apoptosis via G₂/M cycle arrest. This combinatorial strategy profoundly remodeled tumor immunity by expanding CD8⁺ T cells and depleting Foxp3⁺ CD4⁺ regulatory T cells (Tregs), while concurrently restoring T-cell cytotoxicity and skewing the cytokine balance toward an antitumor state, with elevated IFN-γ and reduced TGF-β1. Notably, compared with paclitaxel monotherapy, the combination significantly elevated intratumoral CD8⁺ T-cell infiltration, decreased Treg abundance, and exerted robust inhibitory effects on tumor growth and metastasis in humanized TNBC xenografts. Conclusions: These findings reveal that dual blockade of PD-L1 and CXCR4 acts synergistically with chemotherapy by triggering tumor cell apoptotic effects and reversing the immunosuppressive microenvironment, thereby emerging as a promising therapeutic strategy for TNBC. Full article

Background: Near-perfect machine-learning performance on public clinical datasets can arise from data leakage or predictors unavailable at the intended prediction time. We audited a breast cancer vital-status workflow and established a censoring-aware benchmark. Methods: The public SEER-derived dataset contained 4024 women diagnosed in 2006–2010. After removing one duplicate, 616 of 4023 records had status “Dead”. We reproduced a support-vector machine workflow that oversampled the complete dataset before an 80:20 split, quantified exact train-test row overlap, and repeated the analysis with training-only oversampling. A baseline-only support-vector machine and a penalized Weibull accelerated failure-time model were then evaluated using training-only tuning and an untouched test set. Results: Pre-split oversampling placed duplicate feature rows from 50.5% of test observations in training and yielded an area under the receiver operating characteristic curve (AUROC) of 0.998. Splitting first eliminated overlap and reduced AUROC to 0.715 under the retained legacy model. The tuned baseline-only model achieved AUROC 0.745 (95% confidence interval 0.696–0.793). The survival model achieved a test concordance index of 0.753 (0.708–0.797). Conclusions: Resampling order and post-baseline information materially inflated apparent performance. The corrected results support moderate internal prognostic discrimination, not breast cancer diagnosis, triple-negative subtype classification, or clinical deployment. Full article

Background/Objectives: Breast cancer is the most frequent malignant neoplasm in women and presents marked biological heterogeneity. The androgen receptor (AR) has emerged as a biomarker with important prognostic and therapeutic implications, its effect varying according to the molecular subtype. The objective of this study was to analyze AR expression in breast carcinoma samples and its relationship with the different molecular subtypes and clinicopathological variables. Methods: An observational, descriptive, cross-sectional, and prospective study was conducted based on the immunohistochemical analysis of 215 formalin-fixed, paraffin-embedded breast carcinoma samples. AR expression was digitally evaluated as the percentage of positive tumor cells after incubation with an anti-AR monoclonal antibody. Results: A high frequency of AR expression was demonstrated in the cohort, with a median of 53.3%. There were statistically significant differences between molecular subtypes (p < 0.001), detecting greater expression in luminal tumors and markedly low levels in triple-negative breast cancer (TNBC) (median 0.41%). A significant negative correlation was evidenced between AR expression and the Ki-67 proliferation index (ρ = −0.272; p < 0.001), both in the overall sample and in the TNBC subgroup. Conclusions: The androgen receptor is associated with specific molecular subtypes and lower tumor proliferation, suggesting a less aggressive phenotype and supporting its role as a biological biomarker and potential therapeutic target in the management of breast cancer. Full article

Background/Objectives: This study engineered and evaluated a targeted, folate-functionalized chitosan nanoparticle (CS-FA NP) delivery system to enhance the therapeutic efficacy of standard quercetin and Coriandrum sativum seed extract against breast cancer. Methods: Phytochemical profiling confirmed a 14% crude yield for the methanolic extract, with gas chromatography–mass spectrometry (GC-MS) and high-performance liquid chromatography (HPLC) identifying quercetin as the principal bioactive agent. The synthesized CS-FA NPs exhibited a core size of 7–20 nm, an average hydrodynamic diameter of 150–160 nm, a stable zeta potential of −55 mV, and high encapsulation efficiencies (87.2% for quercetin and 80.5% for coriander). Kinetic assessments confirmed a biphasic, diffusion-controlled release matching Higuchi matrix kinetics. Anticancer activity was evaluated in vitro using MTT cytotoxicity, Annexin V-FITC/PI apoptosis analysis, RT-qPCR, and ex vivo rat aortic ring assays, followed by validation in a syngeneic 4T1 mammary tumor mouse model. Results: In vitro, folate-receptor-targeted quercetin nanoparticles (T4) demonstrated superior, selective cytotoxicity, particularly against triple-negative MDA-MB-231 cells, while sparing normal fibroblasts. Annexin V-FITC/PI apoptosis profiling and ex vivo aortic ring assays revealed profound, cell-line-dependent programmed cell death and up to 90% inhibition of microvessel sprout outgrowth. Mechanistically, RT-qPCR verified that nano-formulations induced complete transcriptional silencing of NANOG, MMP-1, VEGFA, TSPAN8, TWIST, EMMPRIN, and CDK1, alongside marked upregulation of P27^KIP1 and P21^CIP1. In vivo, these nano-formulations successfully improved tumor-associated pathological features, reduced aggressive tumor spindle-cell proliferation, and suppressed elevated serum CA15-3 and arginase biomarkers. Conclusions: Folate-functionalized chitosan nano-formulations significantly enhanced the anticancer efficacy of quercetin and Coriandrum sativum seed extract through improved targeted delivery, potent antiproliferative, anti-angiogenic, and pro-apoptotic activities, together with favorable modulation of multiple molecular pathways associated with breast cancer progression. These findings support their potential as promising targeted nanotherapeutic strategies for breast cancer treatment. Full article

Breast cancer (BC) is the most frequently diagnosed malignancy and generally the leading cause of cancer-related mortality among women worldwide. Molecular targeted therapies, including endocrine treatment for hormone-responsive tumors, anti-HER2 agents for HER2-positive tumors and PARP inhibitors (PARPis) for homologous recombination-deficient (HRD) tumors, have significantly improved patient outcomes, but several clinical challenges are still open. The development of acquired resistance strongly limits the long-term efficacy of current treatment strategies, underscoring the necessity to identify novel therapeutic approaches for breast cancer therapy. In this review, we summarize and discuss recently investigated natural compounds with anti-breast cancer activity, ranging from polyphenols, terpenoids, alkaloids, sulfur-containing compounds and the emerging plant-derived extracellular vesicles. We focus on their ability to induce DNA damage or oxidative stress, modulating the DNA damage response (DDR) and interfering with key oncogenic signaling pathways. We also discuss the potential of these compounds to enhance the efficacy of conventional therapies, thereby offering a promising role in overcoming clinical resistance. Despite clinical relevance remains under development and further studies are required; many of the natural compounds examined here appear to effectively target DDR signaling and oncogenic pathways, supporting their potential use in breast cancer therapy. Full article

Triple-negative breast cancer (TNBC) is the most clinically aggressive subtype of breast cancer, characterized by the absence of targetable hormone receptors and HER2 amplification, significantly constraining treatment choices. Estrogen Receptor Beta (ERβ) has emerged as a biologically relevant yet underutilized target in TNBC, with its re-expression linked to tumor suppression and improved prognosis, prompting the development of selective ERβ modulators as a precision therapeutic approach. We introduce ERβ-Score, an interpretable machine learning scoring system developed using a curated dataset of 1699 ERβ bioactive chemicals obtained from ChEMBL, characterized by 39 physicochemical and three-dimensional molecular descriptors. After implementing scaffold-disjoint train/test partitioning to avert structural data leakage, a Gradient Boosting Classifier, fine-tuned through Bayesian hyperparameter optimization, attained in five-fold cross-validation a Precision–Recall AUC (Area Under the Curve) of 0.891, a ROC-AUC (Receiver Operating Characteristic) of 0.888, a Matthews Correlation Coefficient of 0.664, an F1-score of 0.838, and a balanced accuracy of 0.831; on the scaffold-disjoint hold-out test set it attained a Precision–Recall AUC of 0.905, a ROC-AUC of 0.864, and a Matthews Correlation Coefficient of 0.578, indicating strong and balanced discrimination between active and inactive ERβ modulators. We note explicitly that this scaffold-disjoint hold-out constitutes internal validation, since it derives from the same curated ChEMBL workflow used for model development, and it is therefore reported throughout as scaffold-disjoint internal validation rather than as independent external validation. The applicability domain boundaries were established using a k-nearest-neighbor Tanimoto-similarity method with ECFP4 (Extended-Connectivity Fingerprint with a Diameter of 4) fingerprints, offering a quantitative confidence metric that identifies structurally new molecules beyond the model’s reliable prediction range. External validation against independent Tox21 ERβ bioassay data confirmed genuine, statistically significant predictive signal (ROC-AUC = 0.71) while revealing reduced sensitivity for structurally novel active compounds. The model was subsequently used for extensive virtual screening of natural product and drug-like compound libraries, with prioritized candidates undergoing structure-based molecular docking against the ERβ co-crystal structure (PDB: 7XWQ) using Smina, facilitating a comprehensive evaluation of hits based on both ligand and structural properties. To enhance accessibility, the complete pipeline was implemented as an open-access interactive web application utilizing Streamlit, enabling researchers to input any SMILES string and obtain, in real time, an activity prediction with a probability score, applicability domain classification, Lipinski drug-likeness assessment, interactive three-dimensional visualization of protein–ligand interactions, and on-demand docking within the ERβ active site. Full article

Background/Objectives: With the advent of genome sequencing and its widespread use in the clinic, there is a great need to identify mutational biomarkers that predict therapeutic responses. DNA polymerase beta (Polβ) and the base excision repair (BER) pathway have been previously implicated as modulators of response to platinum-based chemotherapies and are mutated in as many as 30% of cancers. Methods: Here, we show in a triple-negative breast cancer (TNBC) model that two classes of mutations in Polβ, reduced catalytic activity (E295K and D256A mutations) and reduced fidelity (I260M), are sufficient to drive cisplatin and carboplatin-specific sensitivity. Cellular response to oxaliplatin in these Polβ mutant models is minimal relative to cisplatin and carboplatin. Results: We show that sensitivity is associated with reduced repair of both platinum-induced DNA intrastrand adducts and interstrand crosslinks (ICLs). Downregulation of the upstream BER factor uracil DNA glycosylase (UNG) reverses drug sensitivity, which is consistent with these Polβ mutations negatively impacting ICL DNA repair to drive drug sensitivity. In addition, the intrastrand adduct repair readout indicates that these lesions also play a role in the sensitivity observed in Polβ mutant models. In vivo studies demonstrate a significant effect on tumor growth delay with cisplatin treatment in tumor xenografts harboring Polβ mutations. Conclusions: These results support the potential for using Polβ mutations as predictive biomarkers for cisplatin and carboplatin therapies in the clinical setting. Full article

Triple negative breast cancer (TNBC) continues to have a poor prognosis relative to other forms of this disease. Previous studies have shown that the HOX family of transcription factors generally show increased expression in breast cancer and may have a primarily pro-oncogenic role. In this study, we assessed the sensitivity of a range of TNBC-derived cell lines to an inhibitor of HOX protein function, HTL-001, which blocks the interaction between HOX proteins and the Pre-B-cell Leukaemia Homeobox (PBX) cofactor. The sensitivity of cell lines was measured by MTS viability assays, and gene expression by RT-qPCR. Combination studies were performed with epigenetic modifiers (5-azacytidine (5-aza), Trichostatin A (TSA)) and standard-of-care chemotherapeutic drugs including Paclitaxel. A mouse tumour flank model of MDA-MB-231 cells was used to assess response to HTL-001, paclitaxel, or combination therapy. All the cell lines exhibited high levels of HOX dysregulation compared to an immortalised line derived from normal breast cells, and greater sensitivity to HTL-001-induced apoptosis. Epigenetic changes have previously been shown to be key modulators of HOX expression and, correspondingly, we show that reversing epigenetic changes in these cell lines significantly alters HOX expression and generally reduces sensitivity to HTL-001. In addition, HTL-001 shows synergistic interactions with several established chemotherapeutic agents in vitro. We further demonstrate that HTL-001 can significantly reduce tumour growth in a mouse model of TNBC. Our findings indicate that HOX/PBX dimers are a potential therapeutic target in this cancer. Full article

Phosphatidylinositol 5-phosphate 4-kinase type 2 alpha (PIP4K2A) is a key oncogenic driver that regulates the PI5P/PIP2 axis to promote metastatic migration in breast cancer. This study aimed to investigate the therapeutic potential of a crude extract from Tamarix aphylla against breast cancer progression and identify its primary active constituents. The crude extract was initially evaluated against MDA-MB-231 and MCF7 breast cancer cell lines using wound healing assays. Bioassay-guided isolation and screening were deployed to isolate individual components, and the most potent lead compound was structurally characterized using preparative HPLC and FTIR. To analyze its interaction with PIP4K2A, in silico molecular docking, MM/GBSA calculations, and 200 ns molecular dynamics simulations were conducted. In vitro validation was subsequently performed via dose-dependent cytotoxicity assays, scratch assays, single-cell tracking, and RT-qPCR expression analysis. Quercetin was identified as the most potent lead inhibitor against PIP4K2A. Computational modeling revealed that quercetin binds tightly within the PIP4K2A ATP-binding pocket, yielding a superior binding affinity of −10.77 kcal/mol and enhanced thermodynamic stability (ΔGMM/GBSA = −42.6 ± 2.1 kcal/mol) compared to the native ligand (ΔG MM/GBSA = −23.3 ± 1.8 kcal/mol). Molecular dynamics simulations confirmed an induced-fit structural transition that locked the complex into an ultra-stable conformation within a deep global energy minimum basin (−10.8 kcal/mol). In vitro assays demonstrated dose-dependent cytotoxicity, with aggressive triple-negative MDA-MB-231 cells exhibiting higher sensitivity (IC₅₀ = 82.23 µg/mL) than luminal MCF7 cells (IC₅₀ = 97.14 µg/mL). Furthermore, scratch and single-cell tracking assays showed a profound suppression of migration speed and wound closure (reduced to ~40%), while RT-qPCR revealed a near-complete transcriptional knockdown of PIP4K2A mRNA expression (down to 0.025-fold). Collectively, these findings elucidate a unique dual-action mechanism for Tamarix aphylla-derived quercetin—characterized by both direct competitive enzymatic inhibition and downstream transcriptional silencing—positioning it as a promising therapeutic scaffold for targeted anti-metastatic breast cancer interventions. Full article