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Table S2 from Knocking Out CD70 Rescues CD70-Specific NanoCAR T Cells from Antigen-Induced Exhaustion

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posted on 2024-09-03, 07:21 authored by Stijn De Munter, Juliane L. Buhl, Laurenz De Cock, Alexander Van Parys, Willem Daneels, Eva Pascal, Lucas Deseins, Joline Ingels, Glenn Goetgeluk, Hanne Jansen, Lore Billiet, Melissa Pille, Julie Van Duyse, Sarah Bonte, Niels Vandamme, Jo Van Dorpe, Fritz Offner, Georges Leclercq, Tom Taghon, Erik Depla, Jan Tavernier, Tessa Kerre, Jarno Drost, Bart Vandekerckhove

Differentially expressed genes in nanoCAR T-cells from cluster CD8KO vs CD8WT

Funding

Universitair Ziekenhuis Gent (UZ Gent)

Fonds Wetenschappelijk Onderzoek (FWO)

Ghent University IOF

History

ARTICLE ABSTRACT

CD70 is an attractive target for chimeric antigen receptor (CAR) T-cell therapy for the treatment of both solid and liquid malignancies. However, the functionality of CD70-specific CAR T cells is modest. We optimized a CD70-specific VHH-based CAR (nanoCAR). We evaluated the nanoCARs in clinically relevant models in vitro, using co-cultures of CD70-specific nanoCAR T cells with malignant rhabdoid tumor organoids, and in vivo, using a diffuse large B-cell lymphoma patient-derived xenograft (PDX) model. Although the nanoCAR T cells were highly efficient in organoid co-cultures, they showed only modest efficacy in the PDX model. We determined that fratricide was not causing this loss in efficacy but rather CD70 interaction in cis with the nanoCAR-induced exhaustion. Knocking out CD70 in nanoCAR T cells using CRISPR/Cas9 resulted in dramatically enhanced functionality in the diffuse large B-cell lymphoma PDX model. Through single-cell transcriptomics, we obtained evidence that CD70 knockout CD70-specific nanoCAR T cells were protected from antigen-induced exhaustion. In addition, we demonstrated that wild-type CD70-specific nanoCAR T cells already exhibited signs of exhaustion shortly after production. Their gene signature strongly overlapped with gene signatures of exhausted CAR T cells. Conversely, the gene signature of knockout CD70-specific nanoCAR T cells overlapped with the gene signature of CAR T-cell infusion products leading to complete responses in chronic lymphatic leukemia patients. Our data show that CARs targeting endogenous T-cell antigens negatively affect CAR T-cell functionality by inducing an exhausted state, which can be overcome by knocking out the specific target.