Cellular Architecture of Human Brain Metastases

Here we present an integrative analysis of 15 human parenchymal BrMs as a resource, generated by single-cell transcriptomics, and complemented with two mouse models- and in silico- approaches. We interrogated the composition of BrM niches, molecularly defined the blood-tumor interface, and reveal stromal immunosuppressive states, enriched with infiltrated T cells and macrophages. Specific single-cell interrogation of metastatic tumor cells provides a novel framework of 8 functional cell programs that coexist or anticorrelate. Collectively, these programs delineate two functional BrM archetypes, one proliferative and the other inflammatory, that are evidently shaped through tumor-immune interactions. Our resource provides a foundation to understand the molecular basis of BrM in patients with tumor cell-intrinsic and host environmental- traits. We obtained fresh surgically resected BrM specimens from fifteen patients with diagnosis of melanoma (n=3), breast cancer (n=3), lung cancer (n=3), ovarian cancer (n=2), CRC (n=1), renal cell carcinoma (n=1), unknown primary carcinoma (n=1) and a case of adult rhabdomyosarcoma that was a non-carcinoma, non-melanoma sample used for comparison. All cases were diagnosed as parenchymal BrM, located predominantly in brain cortex. Each tumor was dissociated into single cell suspensions, dead cells were removed, and live cells were profiled by single cell RNA sequencing (scRNAseq) with the 10x drop-seq platform (10x Genomics). For the experimental brain metastasis models, 0,25x106/100ml MDAMB231Br (nude mice) and 0,2X10^6 4T1Br (Balb/c mice) cells were injected into the left ventricle of the heart under anesthesia. After reaching ethical end-point, Viable (Ghost Dye negative), hCD298+ (Just MDAMB231Br), mCherry+, mCD45-, mTer119-, mCD31- single cells were sorted by FACS and processed using 10x drop-seq platform (10X Genomics). For more details, refer to the original study DOI:10.1016/j.cell.2021.12.043, PMID:35063085 Note from submitter: we did not upload the human raw data files because of confidentiality and patient privacy issues with clinical samples.