A method for polyclonal antigen-specific T cell-targeted genome editing (TarGET) for adoptive cell transfer applications

Adoptive cell therapy of donor-derived, antigen-specific T cells expressing native T cell receptors (TCRs) is a powerful strategy to fight viral infections in immunocompromised patients. Determining the fate of T cells following patient infusion hinges on the ability to track them in vivo. While this is possible by genetic labeling of parent cells, the applicability of this approach has been limited by the non-specificity of the edited T cells. Here, we devised a method for CRISPR-targeted genome integration of a barcoded gene into Epstein-Barr virus-antigen-stimulated T cells and demonstrated its use for exclusively identifying expanded virus-specific cell lineages. Our method facilitated the enrichment of antigen-specific T cells, which then mediated improved cytotoxicity against EBV-transformed target cells. Single-cell and deep sequencing for lineage tracing revealed the expansion profile of specific T cell clones and their corresponding gene expression signature. This approach has the potential to enhance the traceability and the monitoring capabilities during immunotherapeutic T cell regimens. Overall design: PBMCs from two EBV reactive healthy donors were pulsed with Peptivator EBV Consensus peptide pool in presence of IL4 and IL7. After three days of culture, T cells were engineered using CRISPR/Cas9 genome editing to integrate a GFP barcoded reporter gene with a library diversity of 3x10e4 into the CCR5 locus. After 7 additional days of expansion, single cell RNA sequencing data of GFP+ and GFP- sorted samples was generated.