Multifactorial Basis of T Cell Dysfunction in CLL: Disrupted Mitochondrial Metabolism Induces T Cell Senescence

Abstract

Despite being a B-cell malignancy, dysfunction of the T-cell compartment is a key feature of chronic lymphocytic leukemia (CLL). This leads to complications in acquired immunity and low success rates in autologous T cell-based therapies in these patients, particularly chimeric antigen receptor T cells (CAR-T). Despite exhibiting features of exhaustion, T cells from CLL patients are not reinvigorated by immune checkpoint inhibitors. Although T-cell dysfunction in CLL is heterogeneous, a consistent feature among all CLL patients is T-cell subset skewing towards effector T cells at the expenses of the central memory compartment (Martens et al., Leukemia 2023) and intact ability to produce inflammatory cytokines. A common feature of senescent T cells includes this maintained ability to produce pro-inflammatory cytokines alongside dysfunctions such as cell-cycle arrest, a decline in proliferation, and reduced activation. Notably, senescence often coincides with impaired mitochondrial function which is known to play a crucial role in the development of memory phenotypes and the efficacy of CAR-T cells (Van der Windt et al., Immunity 2012; Van Bruggen et al., Blood 2019). Given these associations, our aim is to comprehensively investigate the interplay between T-cell dysfunction, senescence, and mitochondrial impairment in CLL patients through a multifaceted approach encompassing analysis of T-cell metabolism, (epi)genetics, and functional phenotyping. Metabolic profiling of T cells from CLL patients and age-matched healthy donors (HD) was performed by extracellular flux analysis, flow cytometry, metabolomics and 13C tracing. A decreased mitochondrial respiration upon T-cell receptor stimulation was observed in all CLL patients. On the other hand, glycolytic activity correlated with T-cell activation status, which varied among patients. We identified alterations in the utilization of the three main mitochondrial fuels in T cells from CLL patients: i) induction of pseudohypoxia by CLL cells, leading to a re-routing of glucose-derived pyruvate into lactate rather than into the mitochondria; ii) a reduced rate of conversion of glutamine into glutamate resulting in decreased utilization of this fuel within the mitochondria; and iii) impaired lipid uptake, along with diminished fatty acid oxidation. Accordingly, mitochondria from CLL T cells showed intrinsic features of dysfunction including depolarization and increased production of reactive oxygen species (ROS). So far, these findings strongly demonstrate a misbalance in metabolic fueling resulting in mitochondrial dysfunction, aligning more closely with senescence rather than classical T-cell exhaustion. To further reinforce this observation, we assessed the expression of cell-surface proteins that characterize senescent T cells (e.g., absence of CD27/CD28 and presence of PD1/CD57/KLRG1). Indeed, we found an increased proportion of senescent cells in the T-cell compartment of CLL patients, as compared to HD. In response to stimulation, CLL T cells showed a strikingly distinct cell-cycle pattern whereby a larger proportion of cells resided in S and G2/M phases, indicating cell-cycle arrest. Cell cycle arrest is often induced by DNA damage. Transcriptomic and epigenomic profiling of T cells of CLL patients indeed revealed a molecular profile consistent with inflammation and an increased p53/DNA damage response upon stimulation. These features are known to be induced by dysfunctional mitochondria and ROS in senescent cells, underscoring a direct link between mitochondrial metabolism and senescence. Altogether, our results strongly point towards senescence as the dominant dysfunctional T-cell state in CLL patients, with impaired mitochondrial metabolism at its basis. The distinctive mechanisms leading to T-cell senescence, as opposed to classical exhaustion, underscore the necessity for different strategies to reinvigorate T cells in the context of immunotherapy. Therefore, interventions aimed at ameliorating T-cell dysfunction in CLL should prioritize enhancement of mitochondrial metabolism to attenuate DNA damage and the induction of senescence. This would be especially beneficial to improve the fitness of autologous CAR-T cells for these patients.