Abstract
CAR-T cell therapy is a promising new immunotherapy for a number of difficult-to-treat cancers, however, it has yet to yield broad success in glioblastoma (GBM). In particular, tumor heterogeneity presents a major therapeutic challenge, and a detailed understanding of the complex interplay between different neoplastic, non-neoplastic, and CAR-T cells is critical for developing better treatments. Using a patient-derived GBM organoid model of CAR-T cell therapy, we performed single-cell multi-omics to examine the longitudinal dynamics of the adaptive tumor response, changes in cell states, and evolution of cell-to-cell interaction networks. We find that all tumor cell types - neoplastic and non-neoplastic - respond to CAR-T cell activity, and they generate to an initially anti-tumor, but subsequently pro-tumor and immune-inhibitory microenvironment, which is accompanied by eventual CAR-T cell dysfunction and exhaustion. Unexpectedly, CAR-T cell activity also leads to attenuation of glioma stem-like states in both antigen-positive and antigen-negative neoplastic cells and reduces their proliferation via diffusible factors, of which IFNɣ is required but not sufficient. These findings are supported by analyses in patient samples from CAR-T cell therapy clinical trials, and they are consistent across both de novo and recurrent tumors with different somatic mutational landscapes. Our study unravels how the complex heterogeneity of GBM interacts with CAR-T cell therapy, and we identify previously unappreciated possibilities to affect antigen-negative neoplastic cells in ways that may be further augmented for enhanced therapeutic efficacy.