Microfluidic system-based time-course tracking of physical proximity between cells and its effect on gene expression for elucidating live single cancer-immune cell interactions

Cell-cell communication and physical interactions play a vital role in cancer initiation, homeostasis, progression, and immune response. Here, we report a system that combines live capture of different cell types, co-incubation, time-lapse imaging, and gene expression profiling of doublets using a microfluidic integrated fluidic circuit (IFC) that enables measurement of physical distances between cells and the associated transcriptional profiles due to cell-cell interactions. The temporal variations in natural killer (NK) - triple-negative breast cancer (TNBC) cell distances were tracked and compared with terminally profiled cellular transcriptomes. The results showed the time-bound activities of regulatory modules and alluded to the existence of transcriptional memory. Our experimental and bioinformatic approaches serve as a proof of concept for interrogating live cell interactions at doublet resolution, which can be applied across different cancers and cell types. ### Competing Interest Statement K.H and N.R. are employees and stockholders of Fluidigm Corporation. M.L is a former employee and stockholder of Fluidigm Corporation. D.S. is a partner and equity holder at CareOnco Biotech Pvt. Ltd. S.S.J. serves as a scientific advisor for Quantumcyte and Ravel Biotechnology.