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

  Kyle Daniels, PhD
   Assistant Professor of Genetics at Stanford University.  Daniel's Lab is interested in harnessing the principles of modularity to engineer receptors and gene circuits to control cell functions.

Friday, March 21, 2025
11:00am - 12:00pm  
James H. Clark Center, Room S360, 3rd floor next to the Coffee Shop
Zoom link

Abstract
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.

Biography
Dr. Kyle Daniels is an Assistant Professor of Genetics and, by courtesy, of Neurosurgery. Kyle obtained his BS in Biochemistry from the University of Maryland College Park in 2010, conducting undergraduate research with Dr. Dorothy Beckett, PhD. He obtained his PhD in Biochemistry with a certificate in Structural Biology and Biophysics. His dissertation is titled "Kinetics of Coupled Binding and Conformational Change in Proteins and RNA" and was completed in the laboratory of Dr. Terrence G. Oas, PhD. Kyle performed postdoctoral training with Dr. Wendell A. Lim, PhD at UCSF studying how CAR T cell phenotype is encoded by modular signaling motifs within chimeric antigen receptors. Kyle's lab opened in May 2023 and is interested in harnessing the principles of modularity to engineer receptors and gene circuits to control cell functions.