A Spatially-Defined Metastasis-Associated Microglia Subset Promotes Brain Metastasis Outgrowth through Cx3cr1-Mediated Interferon Response

We use single cell RNA-seqencing (Drop-seq based) to profile and compare (1) the transcriptomes of naïve brain myeloid cells from wild type C57Bl/6 mice to brain metastasis-associated myeloid cells (Br.MAM) from C57Bl/6 mice bearing E0771 brain metastases and (2) the transcriptomes of Br.MAM in Cx3cr1+/- (het) mouse hosts bearing E0771 brain metastases to Br.MAM in Cx3cr1-/- (KO) mouse hosts bearing E0771 brain metastases. Naïve brains were obtained from 2-3 month old female C57Bl/6 mice without brain metastases. Brains bearing metastases initiated by cardiac injection of E0771 cells were obtained from 2-3 month old female mice (C57Bl/6; Cx3cr1+/-; Cx3cr1-/-) with established brain metastases (2-3 weeks post cardiac injection). Cell suspensions were prepared by percoll gradient centrifugation followed by MACS-based Cd11b enrichment to obtain suspensions enriched for myeloid cells. Suspensions were run on Drop-seq platform and sequenced either on HiSeq or NextSeq sequencers.