Abstract 5672: Facile generation of single-cell transcriptome and immune repertoire freshly isolated from clinical tumor specimens

Immunotherapies including cell-based therapies generate deep and durable responses in patients with chemotherapy-refractory cancers. However, in solid tumors, particularly those with stereotypic driver mutations and resultant neoantigens, the clonality and cell states of tumor-infiltrating lymphocytes (TILs) remain poorly understood. Here, we use a droplet-based 59 single-cell RNA-sequencing (scRNA-seq) to simultaneously profile transcriptome and immune repertoire of the same cells, enabling the phenotypic characterization (including cytotoxic and helper T, B, T regulatory and exhausted T cells) of each clonotype. We performed scRNA-seq on unsorted and CD45+-FACS sorted cells from fresh clinical samples of multiple tissue types, including lung, liver and kidney, and obtained on average tens of thousands of cells per sample. We demonstrated that high-quality single-cell suspension can be rapidly and reliably generated from clinical samples. We devised different diversity metrics to appropriately classify the immune repertoire within samples, and cross samples of different tissues. We observed distinct cell type compositions and, more importantly, context-specific T-cell clonal expansion patterns, suggesting the activation of different molecular programs in these tumors. In addition, comparison of non-small cell lung cancer (NSCLC) tumors varying by histology type and patient smoking status showed differences among these phenotypes, suggesting a potential link between immune microenvironments and cancer etiology. In summary, we provide a proof of concept for rapid generation of large number of single-cell transcriptomes of TILs paired with their corresponding TCR cDNA sequence in fresh tumor samples across different tissue types. Further analysis with this methodology on larger clinical cohorts will provide robust correlative prognostic markers of clinical phenotypes of immunotherapy responses. Our analysis strategy of TCR sequences among large clinical cohorts across multiple tumor types will facilitate cell-based therapeutic efforts, including CAR T cell or autologous T cell therapies. Citation Format: Junjie Zhu, Ameen A. Salahudeen, Valeria Giangarra, Luz Montesclaros, Jerald Sapida, Osman Sharifi, Josephine Lee, Grace X. Zheng, Dhananjay Wagh, John Coller, Chiara Sabatti, Calvin J. Kuo. Facile generation of single-cell transcriptome and immune repertoire freshly isolated from clinical tumor specimens [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5672.