Single cell and genomic profiling of PBMC-expanded NK cells in first-in-dog clinical trial of allogeneic adoptive NK cell therapy for dogs with cancer

Abstract Natural killer (NK) cells are innate cytotoxic cells with a crucial role in anti-tumor responses, making them a promising candidate for adoptive immunotherapy (IT). CD5 depletion was previously used to isolate CD5 dim-expressing NK cells as a source of expanded NK cells for IT, but this technique can limit the yield of the final NK product. Here, we used bulk and single cell (SC) sequencing to compare ex vivo culture conditions using standard CD5 depletion versus unmanipulated PBMCs as the source of expanded NK cells comparing transcriptomic profiles from 5 matched healthy beagle donors using both techniques and subsequently from 5 dogs with naturally occurring malignant melanoma who received allogeneic PBMC-expanded NK cells in a first-in-dog clinical trial. Notably, beagle-derived PBMC-expanded cells had upregulation of NK pathways related to activation and function compared to CD5 depleted cells, suggesting bulk PBMCs may yield a superior product. Clinically, there were no serious adverse events using PBMC-expanded allogeneic NK cells, and one dog survived 445 days post-treatment, suggesting possible clinical benefit. SC analysis of PBMCs from this dog before, during, and after treatment showed a robust NK cell population across timepoints with high expression of cytotoxicity-related genes, such as GZMB and NCR3, lasting 14 days post-NK transfer. SC data also suggested a previously uncharacterized concordance of NK and CD8 T cell gene expression profiles in canine peripheral blood. Overall, allogeneic NK transfer using PBMC-expanded NK cells appears promising in dogs with cancer, and pre-clinical and clinical data support the use of SC analysis as a valuable technique for biomarker identification and optimizing NK IT in dogs. This study was funded by the National Institutes of Health/National Cancer Institute grant U01 CA224166-01, the 3U01CA224166-02S1 and 5R03CA252793-02 grants, and the V Foundation Victory over Cancer through the Canter Laboratory. Student support was provided by the AVMA/AVMF 2nd Opportunity Summer Research Scholarship.