Digital spatial profiling of α-PD-1 treated breast cancer bone metastases reveals region-specific signaling and enrichment of immune-suppressive markers

Bone is the most common and preferential site for breast cancer metastasis. Upon dissemination to the bone, breast cancer cells engraft into multiple niches, but it is unclear whether there are region-specific differences that may drive breast cancer progression in bone. We used a proteomic digital spatial profiling (DSP) approach to investigate which proliferation, cell death, and immune-related markers and pathways are enriched in immune and cancer cells residing 1) in the bone marrow or 2) along the endosteal surface, in an E0771, α-PD-1 treated pre-clinical model of breast cancer bone metastasis. We selected morphological markers to identify breast cancer cells and immune cells and applied a multiplexed set of probes targeting >70 proteins to characterize breast cancer and immune cell signaling in the marrow and endosteal regions using a DSP platform. We found multiple immune suppressive markers were enriched in the endosteum, including Foxp3, CD163, CD27, Pd-1, and Pd-l1, while proliferation markers were enriched in tumor cells in the marrow, including p38 Mapk, pan-Ras, Mek1, and phospho-Erk1/2. These findings shed light on the niche-specific proteins and pathways that are activated in breast cancer bone metastases and establish a user-friendly highly multiplexed approach for spatial proteomics in pre-clinical models of bone metastasis.