I will begin by discussing strategies to engineer the manufacturing process of these living therapeutics. Unlike traditional small molecule drugs or biomolecules, the production of cell-based therapies involves “guiding” heterogeneous populations of living cells through intricate differentiation and expansion processes in an artificial ex vivo environment. The choice of initial cell populations and the timing of providing key signals profoundly influence the resulting therapeutic product—a heterogeneous cell population, a significant fraction of which may already be predisposed to dysfunction before infusion into patients. By applying a systems approach (Lee* & Su* et al Nat. Biotechnol. 2022), I modeled the metabolic states within an atlas of T cell dysfunction and identified mannose metabolism as a crucial gatekeeper of T cell dysfunction. Engineering T cells to modulate mannose metabolism or the engineer manufacturing process with mannose supplementation—successfully redirected their differentiation trajectories, and preventing premature dysfunction before infusion (Qiu* & Su* et al Cancer Cell 2024).
Next, I will transition to engineering T cells to overcome the hostile tumor microenvironment (TME). Even with optimal manufacturing, the resulting better-qualitied T cells entering the TME will still face severe barriers, including T cell exhaustion and mitochondrial dysfunction. Through a systems-level analysis of T cell exhaustion and mitochondrial health, I identified a multifunctional E3 ligase that simultaneously regulates both pathways. Rational engineering of this E3 ligase in T cells led to significantly improved antitumor activity across multiple preclinical models, highlighting a powerful strategy to sustain T cell function in the TME (Cheng* & Su* et al under revision).
Finally, I will present an integrated approach that bridges preclinical models with real human clinical trials to refine engineering solutions for living therapeutics. For the first time, we analyzed TCR-engineered T cells that successfully infiltrated the TME of pancreatic cancer patients and discovered a novel dysfunctional state shaped by TME-specific cues. This phenotype was recapitulated in a genetically engineered mouse model, providing an invaluable platform for dissecting the interplay between engineered T cells and the TME through targeted perturbations on both sides. By combining high-dimensional single-cell and spatial multi-omics with high-throughput in vivo CRISPR perturbations, we identified a combinatorial engineering strategy: knocking out a master transcription factor while introducing a protein-engineered immuno-fusion construct that converts apoptotic signals into survival cues. This approach successfully restored T cell function and overcame a clinically relevant barrier in solid tumors (Su et al In prep).
These systems-driven approaches exemplify my interdisciplinary vision at the nexus of engineering, systems biology, and immunology. Moving forward, my research will continue to harness high-dimensional and high-throughput technologies to develop next-generation living therapeutics capable of surmounting the formidable challenges of the solid tumor TME. I look forward to sharing this vision and contributing to the future of engineered immunity through systems-based innovations.