Programmable and dynamically-responsive bacterial therapeutics for cancer immunotherapy

Living bacteria therapies have been proposed as an alternative approach to treat tumors. Microbes can be engineered to respond to different environments and deliver therapeutic payloads to tumors. Unlike human live-cell therapeutics, which are almost prohibitively expensive, microbial therapeutics can be manufactured at low costs and therefore hold promise as broadly applicable therapeutics. To address two major outstanding challenges for bacterial immunotherapy, our interdisciplinary aims will integrate engineering for new bacterial sensing platforms and basic life sciences research to understand bacterial tumor targeting.

The first major challenge is that therapeutic bacteria need to have high specificity for disease tissue. Ideally, bacteria would target protein antigens displayed on cancer cells, but engineered extracellular protein sensing is currently not possible. To address this biosensing challenge, in Aim 1 we propose a unique E. coli sensing system to recognize extracellular cancer antigens and transduce a signal across the E. coli double membrane. In Aim 2, we will construct E. coli that produce a toxic, immunostimulatory payload in response to tumor antigen signals (Aim 1) and/or chemical features of the tumor microenvironment. We will evaluate tumor growth as well as T-cell infiltration and activation in a mouse tumor model.

A second, independent challenge is to deliver bacteria systemically without causing widespread inflammation, which is important because most tumors are not accessible to direct intratumoral injection. To address this safe delivery challenge, in Aim 3 we will engineer E. coli that display extracellular factors that evade the host complement system. In parallel, we will employ pooled, genome-wide CRISPR-Cas screens in bacteria to identify genes that improve the trafficking of bacteria to tumors, which will allow for systemic intravenous delivery at low doses to reduce the risk of widespread inflammation.

This project is a collaboration between the labs of Roger Geiger (Institute for Research in Biomedicine, CH) who has expertise in immunology and immunotherapy [1–3], and Jesse Zalatan (University of Washington, USA) who has expertise in bacterial engineering [4–7]. To initiate the project, Jesse Zalatan is spending the 2023-24 academic year on sabbatical in the Geiger lab.

If our approach is successful, we will deliver improved bacterial live-cell therapeutics with synthetic signaling systems that allow autonomous responses in vivo. In parallel, we will develop safer methods for systemic bacterial delivery. In addition to cancer therapeutics, our approach will have utility for a broad range of disease or pathogen sensing applications. These capabilities will transform our ability to engineer bacterial cells as the next generation of living therapeutics.