Reprogramming CLL T-Cell Mitochondrial Fitness Using PI3K Inhibition for Enhancing CAR T-Cell Therapy
Authors: Gamal Wael , Goedhart Nienke B. , Simon-Molas Helga , Mediavilla Varela Melanie , Uriepero Palma Angimar , Peters Fleur S. , Sahakian Eva , Kater Arnon P. , Pinilla-Ibarz Javier 
Published: December 2024

Chronic lymphocytic leukemia (CLL) presents a significant clinical shortfall, as the number of patients developing resistance to both BTK inhibitors and Bcl2-targeted therapies is rapidly increasing. To date, chimeric antigen receptor (CAR) T cells have shown restricted success in CLL, attributed to CLL-induced T-cell dysfunction and a shift toward terminally differentiated cell subsets. The mechanisms behind these T-cell changes are still not well-understood. T-cell activation and differentiation are metabolically demanding processes. Previously, we identified abnormal T-cell metabolic properties in CLL (van Bruggen et al, Blood 2019). The link between metabolic activity and T-cell differentiation indicates that modulating metabolic pathways could improve the effectiveness of T-cell therapies. However, this approach has not yet been explored in CAR T-cell production for CLL. We aim to uncover the relationship between differentiation and metabolism in CLL T cells and identify the factors driving T-cell dysfunction to revitalize CAR T cells.
Flow cytometry, mitochondrial stress tests and metabolomics were used to analyze healthy and CLL patients' T cells at baseline and post-T-cell receptor (TCR) activation. For murine experiments, splenocytes obtained from transgenic Eμ-TCL1 mice were adoptively transferred (AT) into wild-type C57BL/6 mice, and splenic T cells were studied at various disease stages. Regarding ex vivo reprogramming experiments, human or mouse T-cell cultures were treated with the PI3Kδ inhibitor idelalisib. Generation of CAR T cells was done using T cells from AT Eμ-TCL1 mice, stimulated ex vivo with or without idelalisib, and virally transduced with a GFP-tagged m1928z CAR construct. Leukemic mice infused with these CAR T cells were monitored over time.
Mitochondrial depolarization, indicated by a reduced mitochondrial membrane potential relative to mass, was observed in human and murine CLL T cells. T cells from AT Eμ-TCL1 mice demonstrated disturbed mitochondrial function alongside a shift toward terminally differentiated exhausted-like cells during CLL progression. Furthermore, extracellular flux analysis following TCR stimulation indicated diminished mitochondrial spare respiratory capacity in CLL T cells, consistent in both human and mouse models. Metabolomics and 13C fractional labeling demonstrated decreased mitochondrial fueling and lower levels of mitochondrial metabolites in CLL T cells. These observations of metabolic disturbance aligned with an exhausted-like T-cell differentiation phenotype controlled at the epigenetic level. An increase in PI3K/Akt signaling was identified in T cells from AT Eμ-TCL1 mice. Ex vivo reprogramming of human and murine CLL T cells with the PI3Kδ inhibitor idelalisib resulted in metabolically reprogrammed T cells with improved memory formation and mitochondrial activity. Adding idelalisib during the generation of murine CD19 CAR T cells significantly enhanced the in vivo persistence of infused cells in the immunocompetent Eμ-TCL1 mice and led to long-term leukemia-free remissions, underscoring the clinical relevance of these findings.
Overall, we found that the buildup of dysfunctional, depolarized mitochondria is a marker of T-cell metabolic abnormalities associated with terminal differentiation in CLL progression. PI3K inhibition is a potential strategy to improve CLL T-cell metabolic plasticity and enhance the efficacy and persistence of autologous CAR T-cell infusion products.
WG, NG, and HSM share the first co-authorship.
JPI and APK share senior authorship.