Sequential single cell transcriptional and protein marker profiling reveals TIGIT as a marker of CD19 CAR-T cell dysfunction in patients with non-Hodgkin lymphoma

Abstract

Chimeric antigen receptor T cell (CAR-T cell) therapy is known to produce durable remissions in the treatment of CD19+ relapsed/refractory B cell malignancies. Nonetheless, a significant portion of patients receiving the therapy experience poor outcomes in the acute response for unknown reasons. Given the decreased expansion and persistence of CD8 CAR-T cells in poor outcome groups, this failure may be attributed to CAR-T cell dysfunction. However, a comparison of the post-infusion transcriptional profiles and phenotypes between CAR-T cells of poor and favorable response groups has not been performed. Here, we employed single cell RNA sequencing and protein surface marker profiling of serial CAR-T cell blood samples from patients with CD19+ relapsed/refractory non-Hodgkins lymphoma (NHL) to reveal CAR-T cell evolution, identify biomarkers of response, and test for evidence of exhaustion in CAR-T cells of poor responders. At the transcriptional and protein levels, we note the evolution of a majority of CAR-T cells toward a non-proliferative and highly-differentiated state. In poor outcome patients, we observed a more marked enrichment of an exhaustion profile as compared to favorable outcome patients. Lastly, we identified the checkpoint receptor TIGIT (T cell immunoreceptor with Ig and ITIM domains) as a novel prognostic biomarker and potential driver of CAR-T cell exhaustion. Altogether, we provide evidence of CAR-T cell dysfunction marked by TIGIT expression driving poor response in NHL patients.