Mapping Stromal And Immune Cell Dynamics During Breast Cancer Metastasis By scRNA-seq

Mortality from most cancers is almost exclusively a result of tumor metastasis. Since advanced metastatic cancers are incurable, understanding the biology of tumor metastasis is a significant challenge in cancer research today. The microenvironment of tumors has been proven as crucial in supporting tumor growth, however the role of the metastatic microenvironment, and how the immune system is suppressed in it, in supporting the multistage process of tumor metastasis is still unresolved. A major challenge is therefore uncovering the dynamic plasticity of the microenvironment during the early stages of metastasis, which orchestrates the formation of a hospitable metastatic niche.

We used a mouse model of spontaneous lung metastasis following surgical resection of breast cancer primary tumor. We applied our NICHE-seq technology by using photoactivatable-GFP mice, which allowed us to label cells in lung tissues residing in either metastatic sites (MET), areas adjacent to metastatic sites (ADJ), or non-metastatic areas (non-MET). Single-cell RNA-seq profiling of immune and stromal cells in each spatial compartment was performed. Moreover, we examined as a reference whole lung tissues from mice prior to primary tumors resection (pre-MET), and healthy mice (NT).

Analysis of the expression profiles of immune and stromal cells revealed shifts in cell states throughout the metastatic process. First, compared to NT controls, pre-MET lung tissues (from mice still harboring the primary breast tumor) showed a large infiltration of monocyte and neutrophil populations, and reduction of macrophages, NK, T and B lymphocytes, implying that alterations in the lung microenvironment occur very early in the metastatic process. Second, lung from mice that went through primary tumor resection but did not developed lung metastases were by and large comparable to those of NT mice, showing a decrease in macrophages and B lymphocytes, and an increase of neutrophils. Finally, MET and ADJ tissues were highly infiltrated by large amounts of macrophages, including two metastases-specific subsets with unique expression profiles.

Our findings illustrate the diverse transcriptional landscape of immune and stromal subpopulations in spatial compartments of metastatic tissues, shedding a light on the early events that occur during metastases formation, and in the future may assist in the development of effective therapeutic strategies to prevent metastatic relapse.