2025 AIChE Annual Meeting

(106c) Rewiring T Cell Fate: A Systems and Computational Approach to Engineering a Master Regulator of Exhaustion and Metabolic Dysfunction in T Cell Therapy for Cancer

Authors

Yapeng Su - Presenter, California Institute of Technology
Hongcheng Cheng, Suzhou Institute of Systems Medicine
Xiaoli Pan, Suzhou Institute of Systems Medicine
Yue Xu, Suzhou Institute of Systems Medicine
Jing Du, Suzhou Institute of Systems Medicine
Daniel Chen, Fred Hutch Cancer Research Center
Xiaomeng Dai, Suzhou Institute of Systems Medicine
Ermei Xie, Suzhou Institute of Systems Medicine
Raphael Gottardo, Fred Hutch Cancer Research Center
Philip Greenberg, Fred Hutch Cancer Research Center
Guideng Li, Suzhou Institute of Systems Medicine
Adoptive T cell immunotherapy as a “living drug” has brought cures to many previous untreatable cancers. A major challenge in adoptive T cell therapy is overcoming the multifaceted dysfunction that limits its efficacy—chiefly, T cell exhaustion and mitochondrial failure. While previous strategies have attempted to address these barriers individually, a more powerful approach lies in engineering master regulators that simultaneously reprogram multiple dysfunctions. Through a Systems-Immunology guided CRISPR-Cas9 screen targeting protein homeostasis pathways, we identified a key E3 ubiquitin ligase as an orchestrator of T cell fate. Chronic antigen stimulation suppresses its expression, driving two interlinked failures: accumulation of exhaustion-inducing transcription factors and severe mitochondrial impairment. Our study reveals that reinstating this E3 ligase in engineered T cells rewires metabolic fitness, restores mitochondrial integrity, and recalibrates exhaustion dynamics, leading to significantly enhanced persistence and anti-tumor efficacy across multiple solid tumor models. Single-cell transcriptomics of tumor-infiltrating lymphocytes from over 300 patients further underscore its role as a central node linking proteostasis, metabolism, and T cell immunity. By leveraging this multi-functional regulator, we introduce a next-generation T cell engineering strategy—one that goes beyond checkpoint blockade and single-gene modifications to holistically reprogram T cell fate. This approach represents a potential paradigm shift in immunotherapy, offering a transformative blueprint for engineering resilient, long-lived T cells that can sustain potent anti-tumor responses in the face of persistent immune suppression in cancer.