UC Berkeley

Cell-cell interactions play diverse and essential roles in biology, from immune surveillance and cancer recognition to cell differentiation, neural synaptic interactions, and tissue homeostasis. Microfluidics enables the study of individual cell pairs, but current approaches are limited in throughput due to suboptimal cell health in microcompartments and the sparse loading required to achieve single-cell resolution. This dissertation outlines two separate droplet microfluidic workflows that advance our ability to study functional cell interactions at scale: Pair Isolation by Coalescence and Sorting (PICS), and Functional Cytotoxicity Screening and Transcriptomic Profiling of Immune and Cancer Cells in Semi-permeable Capsules (FUSIC). PICS is a microfluidic platform that can generate specific cell pairs through droplet merging and sorting (‘merge-sorting’). PICS detects target combinations using fluorescence and triggers simultaneous electrocoalescence and dielectrophoretic sorting. PICS allows for the off-chip pre-incubation of droplets before pairing, the merger of reagents for multi-step assays, and the rapid isolation of desired droplet pairs: capabilities not jointly accessible with existing approaches. FUSIC is a system that isolates cytotoxic immune cells and cancer cells in sortable, semi-permeable capsules (SPCs) to study immune cytotoxicity and tumor evasion. FUSIC leverages ultra-high-throughput encapsulation and a novel SPC polymerization workflow to enable functional interactions of tens of thousands of high-viability cell pairs. These SPCs are (a) semi-permeable, allowing media/reagent exchange; (b) amenable to sorting on a commercial FACS instrument; and (c) enzymatically digestible, allowing the release of sorted cell pairs for downstream analysis. We demonstrate how FUSIC can be used to study NK-92 natural killer cell cytotoxicity against K-562 leukemia cells through live imaging, time-course assays, and functional sorting followed by RNAseq.