ValveCCI-seq: An Advanced Microfluidic Approach for Deciphering Cell–Cell Interactions

Immunotherapy eliminates diseased cells by precisely activating or enhancing the patient’s immune responses, with its efficacy critically dependent on the accurate modulation of immune cell interaction networks with disease-relevant targets. However, existing methodologies for analyzing cell–cell interactions face inherent trade-offs among throughput, efficiency, and cellular compatibility, and transcriptome-based methods for probing interaction states often result in the loss of cell-pair identities. To address these limitations, we have developed ValveCCI-seq, a microfluidic platform that integrates a deterministic cell-pairing module with an in situ sequencing module for high-resolution profiling of cell–cell interactions. The pairing module achieves a throughput of up to 32,000 cell pairs per hour with an efficiency exceeding 86% and is broadly compatible with diverse cell types. The sequencing module enables direct transcriptome profiling of coencapsulated cell pairs within droplets, eliminating the need for postinteraction demulsification and thereby preserving the identities of both interacting cells. Utilizing Jurkat and T2 cells as a model system, ValveCCI-seq revealed gene expression signatures associated with T-cell activation and demonstrated its capability for the precise identification of tumor antigens and their cognate T-cell receptor (TCR) sequences. In conclusion, ValveCCI-seq preserves interacting cell identities and enables high-throughput analysis, potentially facilitating systematic studies of cellular interactions in clinical samples, supporting parallel TCR screening across multiple antigens, and providing a robust framework to advance cell therapy development.