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Knocking out CD70 rescues CD70-specific nanoCAR T cells from antigen induced exhaustion

View ORCID ProfileStijn De Munter, View ORCID ProfileJuliane Buhl, View ORCID ProfileLaurenz De Cock, View ORCID ProfileAlexander Van Parys, View ORCID ProfileWillem Daneels, View ORCID ProfileEva Pascal, Lucas Deseins, View ORCID ProfileJoline Ingels, Glenn Goetgeluk, View ORCID ProfileLore Billiet, View ORCID ProfileMelissa Pille, View ORCID ProfileNiels Vandamme, View ORCID ProfileJo Van Dorpe, View ORCID ProfileFritz Offner, Erik Depla, Jan Tavernier, View ORCID ProfileTessa Kerre, View ORCID ProfileJarno Drost, View ORCID ProfileBart Vandekerckhove
doi: https://doi.org/10.1101/2023.01.22.523482
Stijn De Munter
1Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
2Cancer Research Institute Ghent (CRIG), Ghent, Belgium
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Juliane Buhl
3Princess Máxima Center and Oncode Institute, Utrecht, The Netherlands
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Laurenz De Cock
2Cancer Research Institute Ghent (CRIG), Ghent, Belgium
4Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
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Alexander Van Parys
5Orionis Biosciences BV, Ghent, Belgium
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Willem Daneels
2Cancer Research Institute Ghent (CRIG), Ghent, Belgium
6Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
7Department of Hematology, Ghent University Hospital, Ghent, Belgium
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Eva Pascal
1Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
2Cancer Research Institute Ghent (CRIG), Ghent, Belgium
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Lucas Deseins
1Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
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Joline Ingels
1Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
2Cancer Research Institute Ghent (CRIG), Ghent, Belgium
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Glenn Goetgeluk
1Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
2Cancer Research Institute Ghent (CRIG), Ghent, Belgium
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Lore Billiet
1Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
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Melissa Pille
1Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
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Niels Vandamme
8VIB Single Cell Core, Ghent, Belgium
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Jo Van Dorpe
2Cancer Research Institute Ghent (CRIG), Ghent, Belgium
9Department of Pathology, Ghent University Hospital, Ghent, Belgium
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Fritz Offner
2Cancer Research Institute Ghent (CRIG), Ghent, Belgium
6Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
7Department of Hematology, Ghent University Hospital, Ghent, Belgium
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Erik Depla
5Orionis Biosciences BV, Ghent, Belgium
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Jan Tavernier
5Orionis Biosciences BV, Ghent, Belgium
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Tessa Kerre
1Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
2Cancer Research Institute Ghent (CRIG), Ghent, Belgium
6Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
7Department of Hematology, Ghent University Hospital, Ghent, Belgium
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Jarno Drost
3Princess Máxima Center and Oncode Institute, Utrecht, The Netherlands
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Bart Vandekerckhove
1Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
2Cancer Research Institute Ghent (CRIG), Ghent, Belgium
10GMP Unit Cell Therapy, Ghent University Hospital, Ghent, Belgium
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  • For correspondence: bart.vandekerckhove@ugent.be
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Abstract

CD70 is an attractive target for chimeric antigen receptor (CAR) T cell therapy as treatment for both solid and liquid malignancies. However, functionality of CD70-specific CARs is only modest. Here, 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 by using a diffuse large B cell lymphoma (DLBCL) patient-derived xenograft (PDX) model. Whereas the nanoCAR T cells were highly efficient in organoid co-cultures, they showed only modest efficacy in the PDX model. Knocking out CD70 expression by the nanoCAR T cells resulted in dramatically enhanced functionality in the PDX model, suggesting that endogenous CD70 interaction with the nanoCAR induces exhaustion. Through single-cell transcriptomics, we obtained evidence that CD70KO CD70-specific nanoCAR T cells are protected from antigen induced exhaustion. Our data shows that CARs targeted to 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, in this case CD70.

Competing Interest Statement

AVP, ED, JT are affiliated with Orionis Biosciences BV (as a scientific advisor and/or an employee) and holds equity interests in the Company. JT received financial research support from Orionis Biosciences BV. All the other authors declare no conflict of interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted January 22, 2023.
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Knocking out CD70 rescues CD70-specific nanoCAR T cells from antigen induced exhaustion
Stijn De Munter, Juliane Buhl, Laurenz De Cock, Alexander Van Parys, Willem Daneels, Eva Pascal, Lucas Deseins, Joline Ingels, Glenn Goetgeluk, Lore Billiet, Melissa Pille, Niels Vandamme, Jo Van Dorpe, Fritz Offner, Erik Depla, Jan Tavernier, Tessa Kerre, Jarno Drost, Bart Vandekerckhove
bioRxiv 2023.01.22.523482; doi: https://doi.org/10.1101/2023.01.22.523482
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Knocking out CD70 rescues CD70-specific nanoCAR T cells from antigen induced exhaustion
Stijn De Munter, Juliane Buhl, Laurenz De Cock, Alexander Van Parys, Willem Daneels, Eva Pascal, Lucas Deseins, Joline Ingels, Glenn Goetgeluk, Lore Billiet, Melissa Pille, Niels Vandamme, Jo Van Dorpe, Fritz Offner, Erik Depla, Jan Tavernier, Tessa Kerre, Jarno Drost, Bart Vandekerckhove
bioRxiv 2023.01.22.523482; doi: https://doi.org/10.1101/2023.01.22.523482

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