Single cell RNA-sequencing of human brain metastasis-infiltrating T cells

The goal of this study is to understand the biology of brain metastasis-infiltrating T cells. Overall design: Single cell suspensions were generated from surgically-resected metastatic brain tumors. For five patients (5, 14, 15, 16, and 17), tumor-infiltrating PD-1+ CD8 T cells were isolated by FACS from each patient, combined with patient-matched circulating naive CD8 T cells and subjected to scRNA-seq with VDJ sequencing. Hashing antibodies were used to distinguish naïve (Totalseq C0251) from tumor-infiltrating (Totalseq C0252) cells. Separate captures and sequencing libraries were generated for each patient. An additional scRNA-seq experiment was performed on pooled tumor-infiltrating total (CD4 + CD8) T cells from patient 16 (Totalseq C0251), patient 26 (Totalseq C0252), and patient 27 (Totalseq C0253). Circulating T cells were also sorted from a healthy donor and included with this experiment (Totalseq C0254). Cells were pooled, two captures were performed, and libraries were sequenced. In this latter experiment, cells were also stained with anti-CD8 Totalseq C0046, anti-CD4 Totalseq C0045, and anti-PD-1 biotin followed by streptavidin Totalseq C0961. Please note that each processed data was generated from GEX, CITE-seq, and VDJ libraries, and is linked to the corresponding GEX sample records.