Spatial and temporal mapping of breast cancer lung metastases identify TREM2 macrophages at the metastatic boundary

Cancer mortality is primarily caused by metastatic recurrence, whereby tumor cells evade immune surveillance. Better understanding of the molecular and cellular events that occur in metastatic niches is essential to develop effective immunotherapies targeting metastasis. We employed a model of spontaneous breast cancer lung metastasis to create a single-cell RNA-sequencing temporal and spatial atlas that spans different metastatic stages and regions. We found that pre-metastatic lungs are infiltrated by inflammatory neutrophils and monocytes, followed by accumulation of suppressive macrophages with the emergence of metastases. Metastasis-associated immune cells are present in the metastasis core, with the exception of Trem2+ regulatory macrophages uniquely enriched in the metastatic invasive margin. These regulatory macrophages contribute to the formation of an immune-suppressive niche, cloaking the tumor cells from immune surveillance. Our study provides a comprehensive chart of immune cell dynamics across metastatic stages and niches, which could inform the development of immunotherapies that target metastasis. We utilized photoactivatable GFP (PA-GFP) mice as recipients of EO771 breast cancer (BC) tumors and emergent spontaneous metastasis, thus enabling spatial analysis by application of the NICHE-seq technology (Medaglia et al., 2017). We performed photoactivation on metastases-bearing lungs, labeling either the metastasis core or the metastasis invasive margin (ADJ). We isolated immune cells from lungs of control PA-GFP mice (Normal), and also included in our atlas immune cells from EO771-tdTomato primary tumors. Cells from all samples were isolated by FACS, gating on CD31-CD45+ immune cells or CD31-GFP+ (PA+) cells following photoactivation of metastatic tissues. In total scRNA-seq was performed on 63 samples from 27 mice