The Ig Superfamily Ligand B7H6 Subjects Activated T Cells to NK Cell Surveillance and Limits CAR T Cell Persistence

Understanding the mechanisms that regulate T cell immunity is critical for the development of effective therapies for diseases associated with T cell dysfunction. Co-inhibitory ‘checkpoint molecules’ are tightly connected to T cell activation and balance excessive or prolonged immune activation by suppressing clonal expansion. Previous studies have suggested that NK cells might also suppress lymphocyte expansion, but the specific ligands enabling T cell recognition by natural cytotoxicity receptors (NCRs) remain unknown. In this study, we describe the physiological expression of the immunoglobulin superfamily ligand B7H6 on activated T cells and elucidated the functional and clinical implication of its recognition by autologous NK cells. In a targeted proteomics screen for mediators of NK cell recognition on T cells, we identified the Ig superfamily ligand B7H6 ( NCR3LG1) to be highly expressed by T cells upon activation. We show that, unlike other checkpoint molecules, B7H6 mediates NKp30-dependent recognition and subsequent cytolysis of activated T cells by autologous NK cells. Time-resolved deep RNA-sequencing of anti-CD3/CD28-stimulated peripheral blood-derived T cells from n=24 human donors revealed that NCR3LG1 transcript expression changes dynamically upon stimulation and that B7H6 surface protein recognition by NK cells initiates Granzyme B-mediated ‘fratricide’ as early as 8 hours post T cell stimulation. Genomic knockout of NCR3LG1 rendered activated T cells resistant to NK cell-mediated killing without affecting their viability or proliferative capacity. By analyzing transcriptomic profiles of 313,303 CD8+ and 283.930 CD4+ T cells in datasets of multiple sclerosis (MS, n = 62 patients), inflammatory bowel disease (IBD, n = 4 patients), hepatitis B virus infection (HBV, n = 23 patients) and 9 different cancer entities (n = 47 patients), we found a conserved B7H6+ T cell population that is prevalent in the tissue and blood of most individuals at 1-5% frequency. In line with our experimental data, B7H6 positivity was coupled to a highly activated cell state of T cells. Considering CAR T cell manufacturing involves robust activation and clonal expansion, we hypothesized the B7H6-NKp30 axis is a yet unknown, but relevant factor in limiting CAR T cell persistence. Clinical-grade CD19.CD28.4-1BBzeta-CAR T cell products as well as circulating CAR T cells in lymphoma patients indeed uniformly expressed NCR3LG1 transcripts and B7H6 surface protein and were lysed by autologous NK cells in vitro. We then co-injected CD19.CAR T cells and patient-autologous NK cells in leukemia-engrafted mice and observed reduced CAR T cell persistence in the peripheral blood of mice with NK cell co-injection. Co-injection of NK cells further increased tumor burden and resulted in significantly decreased survival in leukemia-bearing mice treated with CD19-recognizing CAR-T cells, while these effects could be minimized by NKp30 antibody blockade or prior genetic editing of NCR3LG1 on CAR T cells. Given the physiological coupling T cell activation and B7H6 expression, any T cell-directed immunotherapy regimen might trigger the B7H6-NKp30-cytolysis mechanism. We therefore analyzed tissue of patients that were treated with nivolumab and ipilimumab (NCT03416244). In contrast to the previous notion of largely tumor-targeting NK cell function, we observed an increased NK cell abundance in patients that failed to respond to treatment. Notably, we found both B7H6+ CD8+ and CD4+ T cells in situ and that their abundance and a high NK/T ratio was associated with reduced progression-free survival (PFS), even in initial clinical responders, and experimentally deducted a NKp30 dependent cytolysis of these T cells. Together, our data demonstrates a mechanism that couples T cell expansion to eventual clearance by NK cells. This concept differs from the previously known immune checkpoints, as those molecules act through intracellular downstream signaling in T cells. We show that NK cell surveillance via B7H6 counteracts anti-tumor activity of CAR-T cells in vivo and that the genetic or antibody-mediated inhibition of B7H6 enhances T cell persistence. We therefore suggest an alternative immune checkpoint that limits T cell expansion and persistence in physiological and cellular engineering contexts. Targeting the B7H6-NKp30 axis may offer a means to modulate T cell immunity across multiple disease entities.