Anti-CAR Immunity Drives Acquired Therapeutic Resistance to GD2-CAR T Cell Therapy in Diffuse Midline Glioma

GD2-CAR T cell therapy has demonstrated clinical benefit in patients with H3K27M+ diffuse midline glioma (DMG), but the durability of response has been limited in many patients1,2. To identify mechanisms of therapeutic resistance, we conducted longitudinal single-cell RNA and TCR sequencing of cerebrospinal fluid (CSF) lymphocytes from DMG patients receiving intravenous followed by sequential intracerebral GD2-CAR therapy, with lymphodepleting chemotherapy administered once prior to the start of CAR T cell therapy (NCT04196413). CSF GD2-CAR T cells manifested limited persistence and clonal expansion, while non-engineered CSF lymphocytes underwent significant clonal expansion and repertoire stabilization, ultimately dominating the CSF immune compartment. Concurrently, peripheral blood CD4+ and CD8+ T cells manifested anti-CAR immune reactivity targeting epitopes enriched within murine-derived and engineered junctional regions of the CAR construct. This was associated with appearance of circulating Human Anti-CAR Antibodies (HACAs) that bound cells expressing the GD2-CAR, as well as clonal expansion of CSF B cells which produced HACA which impeded the cytotoxic activity of GD2-CAR T cells. In several cases, appearance of circulating HACA temporally correlated with disease progression and across the patient population, and levels of circulating HACA inversely correlated with circulating CAR T cell persistence. These findings reveal robust induction of systemic and CNS adaptive T cell and B cell responses to GD2-CAR T cells following intravenous then sequential intracerebroventricular GD2-CAR therapy and provide strong evidence that anti-CAR immunity is a significant contributor to therapeutic resistance in this setting.