Engineered Protein Circuits for Cancer Therapy

Author: Lu, Andrew C.

Year: 2025

Degree: Dissertation (Ph.D.)

Advisor: Elowitz, Michael B.

Committee Members: Shapiro, Mikhail G.; Gradinaru, Viviana; Voorhees, Rebecca M.; Dawson, David; Elowitz, Michael B.

Option: Systems Biology; Biological Engineering

DOI: 10.7907/kxvr-r291

Abstract

Engineered protein circuits seek to treat cancer by directly rewiring oncogenic signaling to cell death. However, it has remained unclear what circuit designs could operate effectively, and what advantages protein circuits could provide compared to existing small molecule inhibitors. Here, we introduce Ras-targeting circuits that accurately discriminate and kill Ras-mutant cells, circumventing drug resistance mechanisms and suppressing cancer in vivo. These circuits combine three modules: a protease-based sensor that responds to a broad spectrum of clinically relevant Ras mutations, an optional protease amplifier, and protease-triggered cell death effectors of the apoptosis and pyroptosis cell death pathways. When delivered as mRNA in lipid nanoparticles (LNPs), the circuits were effective against Ras-mutant human cancer cell lines with minimal off-target killing of wild-type Ras cells. In immunocompetent mice bearing aggressive, multifocal Ras-driven liver tumors, systemically delivered mRNA-LNP circuits strongly reduced tumor burden. Further, therapeutic circuits provided more complete killing of Ras-mutant cancer cells than the Ras inhibitors Sotorasib and RMC-7977 and did not require oncogene addiction. They also exhibited increased potency against Sotorasib-resistant cells. These results establish a programmable mechanism for treating cancer and other human diseases.

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