Characterization of the metastatic TIME via spatial transcriptomics reveals unique cellular phenotypes post anti-CSF-1R and immuno-chemotherapy

Metastatic breast cancer is the main cause of breast cancer related deaths amongst diagnosed women. Current standard-of-care therapies with chemotherapy (CTX) and T cell activating immune checkpoint inhibitors (ICIs) are limited against metastatic disease. Clinical trials have revealed that the tumor immune microenvironments (TIME) with high levels of tumor associated macrophages (TAMs) are associated with ICI treatment failure. We have developed and extensively characterized several genetically engineered mouse models that lack the p53 gene that is most frequently altered in TNBC. These “claudin low” models closely phenocopy the high EMT/TAM subtype observed in patients. We previously showed that TAM ablation by anti-CSF1R mAb therapy coupled with CTX alters the TIME of multiple p53 null GEMMs. This new immunologically “hot” environment displayed elevated levels of IL-17, IL-5 and type II interferon response with residual inflamed- MHCII+ macrophages. A long-term anti-tumor adaptive immune response was accompanied by the infiltration of CD4+/CD8+ T and B cells. However, in lung metastases adjacent micro-metastases persisted and continued to display a “cold” TIME now with elevated PD-L1 indicative of intra-tumoral heterogeneity (ITH). The addition of ICB to SNDX-ms6352 and CTX resulted in sustained loss of TAMs, tumor cells, decreased PD-L1/PD-1 expression and was accompanied by B- and T cell infiltrations in both lung and liver tissues. To understand the differences within the metastatic TIME between single agent and combination treatments, we applied Vizgen's MERSCOPE platform that encompasses Multiplex Error-Robust Fluorescence in situ Hybridization (MERFISH) technology. Using a unique 500 gene mouse specific immuno-oncology panel we conducted spatial transcriptomics (SP) on lung and liver tissues from mice treated with IgG, SNDX-ms6352, CTX, CTX+SNDX-ms6352+/-aPD1. To study the TIME in depth we have pre-selected up to 8 regions of interest (ROIs) from each tissue, spanning both tumor macro- and micro-metastases, stromal and normal tissue. Collectively across 5 tissues we have been able to capture approximately 2 million single cells that have been identified as cancer, immune and stromal. With uniform manifold approximation and projection (UMAP) uncovering up to 60 cellular phenotypes. Strikingly the combination groups illustrate loss of Trem2, Arg1, Mcr1- TAMs with dense accumulation of Cd19- B, and activated Gzma, Nkg7 -NK and Gzmb , Cd3g -T cells compared to single agent treatment. Lymphoid, stromal and CAFs where spatially closer to tumor cells within combination treated neighborhoods. Thus, this novel combination treatment turns immunologically “cold” lung and liver metastases “hot”. We will compare our mouse SP to spatially resolved datasets from the NewSTART Clinical trial (NCT06959537).