Programmable protein expression with RNA sensors

Abstract

RNA sequencing continues to reveal new cell type markers and gene expression profiles1. Biological tools that directly couple gene expression information to transgene expression are desirable for cell-type and state specific transgene expression. We developed Reprogrammable ADAR Sensors (RADARS), a technology that uses base-pairing and RNA editing by adenosine deaminases acting on RNA (ADAR) to translate a transgene cargo only in cells with target RNA expression. RADARS is reprogrammable based on RNA target sequence, which positions RADARS to deliver therapeutic cargoes to diseased cell-types or tissues that exhibit unique RNA expression, such as cancer. Many cancer types have unique fusion RNAs as consequence of gene fusions, which arise through somatic structural variation and often drive cancer progression. Given their cancer-specificity, targeting fusions has precedent in oncology–yet many cancers driven by fusions do not have targeted therapies. We hypothesize that RADARS can leverage cancer specific RNA fusions as therapeutic vulnerabilities. We tested the selective activation of cell killing payloads using RADARS against three clinically relevant fusion RNA classes: (1) a driver fusion in fibrolamellar hepatocellular carcinoma; (2) gene fusions found in therapy-resistant metastatic breast cancer; (3) endogenous fusion RNAs in breast cancer lines. Preliminary data suggest that fusion RNAs may serve as conditional biomolecules for delivering cancer-killing protein payloads.