Cancer systems immunology reveals myeloid—T cell interactions and B cell activation mediate response to checkpoint inhibition in metastatic breast cancer

Sensitization of the immune-suppressed tumor microenvironment (TME) of breast cancer by histone deacetylase inhibition shows promise, but the mechanisms of sensitization are unknown. We investigated the TME of breast-to-lung metastases by combining experimental and clinical data with theory. Knowledge-guided subclustering of single-cell RNA-sequencing data and cell circuits analysis identified 39 cell states and salient interactions, of which myeloid, T cell and B cell subpopulations were most affected by treatment. Using functional immunologic assays, we verified that inhibition of the ICAM pathway partially recapitulated treatment effects. Mathematical modeling of tumor-immune dynamics confirmed that tumor reduction required simultaneous modulation of multiple TME interactions. We found evidence that treatment affected anti-tumor antibody production. Analysis of patient biopsies via spatial proteomics corroborated preclinical findings: in responders we observed increased B cell activation, mature tertiary lymphoid structures, and increased CD8+ T cell—macrophage distances with treatment. Overall, this study provides a framework for the discovery of cell-cell interactions that govern responses in complex TMEs. Overall design: Lung metastases from NeuN mice (NT2.5-LM) under six different treatment conditions (V, E, EP, EC, EPC, PC) were dissected. Tumor microenvironment samples were analyzed using scRNA-seq. V: vehicle condition E: HDAC inhibitor (entinostat) only EP: entinostat and anti-PD-1 (nivolumab) EC: entinostat and anti-CTLA-4 (ipilimumab) EPC: entinostat and anti-PD-1 and anti-CTLA-4 PC: anti-PD-1 and anti-CTLA-4