Lysosomal routing geometry drives immunosuppressive secretion in triple negative breast cancer

Triple-negative breast cancer (TNBC) shows markedly elevated secretory activity, which contributes to a highly immunosuppressive tumor microenvironment. Lysosomes are central to both degradation and regulated secretion, but how their routing choices influence cytokine release has not been well explored. To investigate this, we developed a Subcellular Causal Geometry Model (SCGM) that maps nanoscale lysosomal routing behavior and identifies patterns in TNBC cells associated with the production of immunosuppressive cytokines. SCGM brings together lysosomal proteomics, LAMP1/LAMP2 vesicle distributions, RAB-GTPase interaction profiles, and intracellular pH gradients derived from patient samples. The mapping of the vesicle-routing paths using a geometry-aware transformer revealed several patterns. Acidic microdomains appeared more fragmented, V-ATPase activity shifted, and the interaction between RAB27A and LAMP1 shifted in a consistent way. To determine the biological impact of these changes, we compared them with cytokine levels, trends in macrophage polarization, exosome characteristics, and interferon-response markers. We also ran perturbation simulations for LAMP1, CTSB, ATP6V1C1, RAB27A, and RAB7A, and evaluated their influence through a geometry-informed Shapley ranking. These findings revealed three distinct routing programs, including a secretory-dominant state, a degradative state, and a recycling-oriented state. The secretory pattern showed fragmented acidic microdomains, stronger interactions between RAB27A and LAMP1, and faster vesicle fusion. Tumors associated with this state released higher levels of TGF-beta1, IL-10, galectin-3, and CXCL12 (macro-AUC 0.95) and exhibited nearly fourfold higher M2-like macrophage polarization along with reduced antigen-presenting capacity. Perturbation modeling suggested that reducing RAB27A function could lower immunosuppressive cytokine release by almost two-thirds. Disrupting LAMP1 destabilized the secretory routing framework, and ATP6V1C1 inhibition shifted tumors toward a more immune-activating phenotype. CTSB, RAB7A, ATP6V0A1, and the LAMP1→RAB27A transition repeatedly emerged as major regulators. Taken together, these results outline an unrecognized lysosomal-routing architecture that shapes immunosuppressive cytokine release in TNBC and point to lysosomal geometry as a potential biomarker and intervention point for reshaping the TNBC immune environment.