DynaKiller-Scan: Multimodal characterization of single-cell killing dynamics via combinatorial encoding of target lysis

Cytotoxic lymphocytes are crucial for eradicating infected or cancerous cells. To comprehensively characterize their killing capacity at single-cell level is challenging. Here we introduce DynaKiller-Scan, a high-throughput platform utilizing DNA barcodes to simultaneously interrogate the killing dynamics and molecular underpinnings of individual effector cells. DynaKiller-Scan reveals variable kinetics in serial killing between CD4+ and CD8+ CAR-T killers. The highly heterogeneous killing behaviors are associated with distinct molecular signatures orchestrating cell activation, secretion, migration, and metabolic fitness. While rapid killing involves cells with stronger type-I cytokine secretion, persistent killing is accompanied with more of type-II cytokine response. Furthermore, gene expression patterns closely linked to serial-killing were identified. DynaKiller-Scan could be a valuable tool for improving the development of precision immunotherapy.