Rapid screening of engineered microbial therapies in a 3-D multicellular model

Abstract

Synthetic biology is transforming therapeutic paradigms by engineering living cells and microbes to intelligently sense and respond to diseases including inflammation1,2, infections3-5, metabolic disorders6,7, and cancer8,9. However, the ability to rapidly engineer new therapies far outpaces the throughput of animal-based testing regimes, creating a major bottleneck for clinical translation10,11. In vitro approaches to address this challenge have been limited in scalability and broad-applicability. Here, we present a bacteria-in-spheroid co-culture (BSCC) platform that simultaneously tests host species, therapeutic payloads and synthetic gene circuits of engineered bacteria within multicellular spheroids over a timescale of weeks. Long-term monitoring of bacterial dynamics and disease progression enables quantitative comparison of critical therapeutic parameters such as efficacy and biocontainment. Specifically, we screen S. typhimurium strains expressing and delivering a library of antitumor therapeutic molecules via several synthetic gene circuits. We identify novel candidates exhibiting significant tumor reduction and demonstrate high similarity in their efficacies using a syngeneic mouse model. Lastly, we show that our platform can be expanded to dynamically profile diverse microbial species including L. monocytogenes, P. mirabilis, and E. coli in various host cell types. This high-throughput framework may serve to accelerate synthetic biology for clinical applications and understanding the host-microbe interactions in disease sites.