A multi-kinase inhibitor screen identifies inhibitors preserving stem-cell-like chimeric antigen receptor T cells

Feifei Song; Ourania Tsahouridis; Simone Stucchi; Tara Walhart; Sophie Mendell; P Brian Hardy; Matthew Axtman; Shiva K R Guduru; Thomas S K Gilbert; Lee M Graves; Laura E Herring; Barbara Savoldo; Xingcong Ma; Mark Woodcock; Justin J Milner; Anastasia Ivanova; Kenneth H Pearce; Yang Xu; Gianpietro Dotti

doi:10.1038/s41590-024-02042-1

A multi-kinase inhibitor screen identifies inhibitors preserving stem-cell-like chimeric antigen receptor T cells

Nat Immunol. 2025 Jan 8. doi: 10.1038/s41590-024-02042-1. Online ahead of print.

Authors

Feifei Song¹, Ourania Tsahouridis¹, Simone Stucchi¹, Tara Walhart¹, Sophie Mendell¹, P Brian Hardy², Matthew Axtman², Shiva K R Guduru², Thomas S K Gilbert³, Lee M Graves⁴, Laura E Herring⁵, Barbara Savoldo^{1

6}, Xingcong Ma^{1

7}, Mark Woodcock^{1

8}, Justin J Milner^{1

9}, Anastasia Ivanova¹⁰, Kenneth H Pearce², Yang Xu^{11

12}, Gianpietro Dotti^{13

14}

Affiliations

¹ Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
² Center for Integrative Chemical Biology and Drug Discovery, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
³ Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
⁴ Center for Nanotechnology in Drug Delivery, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
⁵ Michael Hooker Proteomics Center, Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
⁶ Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
⁷ Department of Oncology, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.
⁸ Oncology division, department of medicine, University of North Carolina, Chapel Hill, NC, USA.
⁹ Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
¹⁰ Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
¹¹ Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. [email protected].
¹² School of Medicine, Southern University of Science and Technology, Shenzhen, China. [email protected].
¹³ Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. [email protected].
¹⁴ Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. [email protected].

PMID: 39779871
DOI: 10.1038/s41590-024-02042-1

Abstract

Chimeric antigen receptor T cells (CAR T cells) with T stem (T_SCM) cell-like phenotypic characteristics promote sustained antitumor effects. We performed an unbiased and automated high-throughput screen of a kinase-focused compound set to identify kinase inhibitors (KIs) that preserve human T_SCM cell-like CAR T cells. We identified three KIs, UNC10225387B, UNC10225263A and UNC10112761A, that combined in vitro increased the frequency of CD45RA⁺CCR7⁺TCF1^hi T_SCM cell-like CAR T cells from both healthy donors and patients with cancer. KI-treated CAR T cells showed enhanced antitumor effects both in vitro and in vivo in mouse tumor models. The KI cocktail maintains T_SCM cell-like phenotype preferentially in CAR T cells originating from naive T cells and causes transcriptomic changes without arresting T cell activation or modulating the chromatin organization. Specific kinases, ITK, ADCK3, MAP3K4 and CDK13, targeted by the KI cocktail in a dose-dependent manner are directly associated with the preservation of T_SCM cell-like CAR T cells. Knockdown of these kinases individually or in combination enriches for T_SCM cell-like CAR T cells, but only CAR T cells generated in the presence of the KI cocktail show robust expansion and differentiation on stimulation with tumor cells. Overall, transient pharmacological inhibition of strategically targeted kinases maintains stem-like features in CAR T cells and improves their antitumor activity.

Abstract

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