Cell-interaction based CRISPR screening using intercellular barcode transfer

Abstract

Abstract Cell to cell interaction is one of the fundamental paradigms in cell biology and it is central to immune processes. While recent advances have allowed us to monitor cell interactions both in vitro and in vivo, doing so at large scales with complex interactions remain challenging. We have developed Relay, a scalable technology by which cellular interactions can be tracked via molecular barcoding and intercellular transfer of barcodes. We employed our system to perform a novel cell interaction-based CRISPR screen that was not possible with conventional CRISPR screening strategies. In our screen, we investigated factors that are involved in antigen processing, presentation, and transfer in myeloid cells using a myeloid-T cell co-culture system. By utilizing CRISPR/Cas9 together with Relay, we were able to perform genome-wide perturbations in myeloid cells and concurrently track myeloid-T cell interactions, allowing us to directly associate antigen sampling by T cells to genetic perturbations affecting antigen processing in the myeloid cells. Supported by grant from NIH (U01 CA217882).