Transcriptional effects of co-culture on the spatiotemporal dynamics of T cell motility and cancer-T cell interactions [bulk_seq_IFN]

Insufficient infiltration of cytotoxic T cells into solid tumors poses a major challenge in cancer immunotherapy, largely due to the intricate tumor microenvironment. To address this, we co-cultured mouse cancer cell lines (B16-WT or B16-OVA) with cancer-specific cytotoxic T cells (activated OT-1) in vitro to uncover the impact of cancer-T cell interactions on T cell motility, pivotal for effective tumor infiltration. To investigate the potential molecular mechanisms underlying T cell motility patterns in the two coculture contexts, we performed both bulk and single-cell RNA sequencing of cancer and T cells sorted from the co-culture systems at specific time points. The goal is to test whether the two tumor cell lines, B16-F10-OVA and B16-F10-WT, respond differently to IFN-gamma treatment. We measured their bulk gene expressions before and after 24 hours of continuous treatment with IFN-gamma at a concentration of 50 ng/ml.