Genetic therapy and CAR T treatment restores function to exhausted T cells

A multi-institutional study has mapped the genetic circuitry that determines whether CD8 killer T cells become durable immune defenders or lapse into exhaustion, and has shown that disabling two specific genes can restore tumour-killing capacity without loss of immune memory

A multi-institutional study led by researchers at the Salk Institute for Biological Studies and the University of California San Diego, California, USA alongside the University of North Carolina (UNC) Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina, USA, has identified genetic rules that govern how CD8 ‘killer’ T cells choose between long-lasting immune protection and functional exhaustion. The investigators reported that deactivation of just two genes enabled exhausted T cells to regain tumour-killing capacity while they retained features of durable immune memory.

The findings have established a predictive framework to guide researchers who seek to programme T cells with precision. The work has implications for cancer immunotherapy and for efforts to control chronic viral infection where immune cells often lose potency after prolonged stimulation.

CD8 killer T cells occupy a central position in adaptive immunity by detecting and eliminating virus-infected cells and malignant cells through targeted cytotoxic attack. In acute infection, many of these cells persist after pathogen clearance and form a pool of memory cells that can mount a rapid and effective response upon re-exposure. In chronic infection and within the tumour microenvironment, however, sustained antigen exposure can drive T cells into a state known as exhaustion. In this condition, they exhibit diminished proliferation, reduced cytokine production and impaired cytotoxicity.

Because protective memory cells and exhausted cells can appear superficially similar, the research team sought to determine whether these states could be distinguished at the level of gene regulation. A major component of the study was the construction of a detailed genetic atlas that captured CD8 T cell states across a functional spectrum that ranged from highly protective to profoundly dysfunctional.

“Our long-term goal is to make immune therapies work better by creating clear ‘recipes’ for designing T cells,” said Dr. Susan Kaech, who was a professor at the Salk Institute for Biological Studies at the time of the study and served as co-corresponding author.

“To do that, we first needed to identify which molecular ingredients are uniquely active in one T cell state but not others. By building a comprehensive atlas of CD8 T cell states, we were able to pinpoint the key factors that define protective versus dysfunctional programmes. That information is essential to engineer effective immune responses with precision,” she added.

The investigators combined advanced laboratory assays, genetic perturbation tools, mouse models and computational analysis to characterise nine distinct CD8 T cell states. They focused in particular on transcription factors, proteins that regulate gene expression and that act as molecular switches to steer cell fate.

Among the transcription factors that emerged from the analysis were ZSCAN20 and JDP2, neither of which had previously been associated with T cell exhaustion. When the team suppressed these factors experimentally, exhausted T cells recovered their capacity to destroy tumour cells. Notably, this restoration of effector function did not compromise traits linked to long-term immune memory.

“We flipped specific genetic switches in the T cells to see if we could restore their tumour-killing function without damage to their ability to provide long-term immune protection,” said Dr. H. Kay Chung, assistant professor at the UNC Lineberger Comprehensive Cancer Center and co-corresponding author. Chung initiated the research at the Salk Institute before joining UNC.

“We found that it was indeed possible to separate these two outcomes,” she said.

The study has challenged a long-standing assumption that immune exhaustion represents an unavoidable cost of sustained immune activation. Instead, the data suggest that exhaustion and durable function can diverge through distinct circuits of regulation that researchers can manipulate independently.

The atlas now provides a structured map to inform the design of enhanced cellular therapies, including adoptive cell transfer and chimeric antigen receptor T cell (CAR T) therapy. Such approaches involve extraction, genetic modification and reinfusion of patient T cells to target cancer. A persistent limitation has been the tendency of transferred cells to lose efficacy within solid tumours where hostile microenvironments promote exhaustion.

“Once we had this map, we could start to give T cells much clearer instructions.

“We can help them retain the traits that allow them to fight cancer or infection over the long term, while we avoid the pathways that cause them to burn out.

“By separating these two programmes, we can begin to design immune cells that are both durable and effective in cancer and chronic infection,” said Kaech.

The findings may prove especially significant for treatment of solid tumours, which account for the majority of cancer deaths and where immune suppression within the tumour microenvironment poses a formidable barrier to therapy.

The team has indicated that it will integrate laboratory experimentation with artificial intelligence-guided computational modelling to refine genetic ‘recipes’ for T cell programming. Because gene networks operate through complex and interconnected pathway regulation, computational tools are necessary to disentangle causal drivers from downstream effects.

“Because gene [regulation networks are] complex [and] difficult to decipher, powerful computational tools are essential to pinpoint which regulators drive specific cell states,” said Dr. Wei Wang, professor at the University of California San Diego and co-corresponding author.

“This study shows that we can begin to manipulate immune cell fates with precision and unlock further possibilities to enhance immune therapies,” he added.

By delineating how killer T cells select between resilience and exhaustion, the research has moved the field closer to intentional control of immune function. Instead of acceptance of cellular burnout as an inevitable outcome of chronic stimulation, investigators can now seek to redirect immune trajectories with defined genetic interventions, a prospect that could reshape the design of future cancer and infection therapies.

For further reading please visit: 10.1038/s41586-025-09989-7