Stanford Center for Cancer Systems Biology

– Seminar Series – 2025

Kyle Daniels, PhD

Assistant Professor of Genetics and, by courtesy, of Neurosurgery, Stanford University

Mapping the structure-signaling-phenotype landscape in CAR T cells using synthetic signaling protein arrays and machine learning

Chimeric antigen receptor (CAR) T cells are powerful therapeutics for cancers. These CAR T cell therapies can be improved by providing JAK/STAT signaling to increase CAR T cell survival, proliferation, and anti-tumor activity. To design proteins that enhance CAR T cell efficacy, we sought to map the structure of JAK/STAT signaling domains to cell signaling and resulting CAR T cell phenotype. We recombined 14 signaling motifs to construct library of ~30,000 constitutively active synthetic cytokine receptors (SCRs) with intracellular domains composed of novel signaling motif combinations that activate different signaling cascades. We experimentally tested ~530 SCRs which generated a range of CAR T cell memory, cytotoxicity, and proliferation. To map the structure-signaling-phenotype landscape we trained models to predict CAR T cell signaling and phenotype that result from various motif combinations. Modeling also revealed a trade-off between memory and cytotoxicity, with a Pareto front defined by cell signaling. We identified signaling features associated with memory, cytotoxicity, or a balance between the two. SCRs with balanced pSTAT1/3/5 signaling encoded balanced memory and cytotoxicity to enhance CAR T cell tumor control in a mouse model of osteosarcoma. We also identified signaling features that promote unsafe autonomous CAR T cell proliferation. These findings demonstrate that combinatorial screening and machine learning can be combined to map the structure-signaling-function landscape of synthetic proteins in therapeutic immune cells. This approach and the resulting models may enable rational design of CAR T cells with improved cytotoxicity, memory, and safety profiles.

Friday, March 21, 2025

Clark Center, S360, 3rd floor

11:00AM -12:00PM

Refreshments will be provided