Engineered Feedback Employing Natural Hypoxia-Responsive Factors Enhances Synthetic Hypoxia Biosensors

Abstract

DNA-based hypoxia biosensors conditionally express a gene of interest when a cell is in a state of inadequate oxygen supply, which is a feature of several acute and chronic diseases. These biosensors can be deployed in engineered cells to study or treat disease. Although the central mediators of hypoxia responsiveness have been characterized, the dynamics of this response are generally less understood, and there is no general approach to modulate hypoxia biosensors to tune their performance to meet application-specific needs. To address the need for high-performing hypoxia biosensors, we investigated strategies to enhance biosensor performance by identifying minimal promoter choices and positive feedback circuits that both achieved low background and amplified hypoxia-induced gene expression. To generate insight into the mechanisms by which feedback drives differential performance, we developed an explanatory mathematical model. Our analysis suggests a previously unreported dual regulatory mechanism that was necessary to explain the full set of experimental observations and that provides new insights into regulatory dynamics in chronic hypoxia. This study exemplifies the potential of using synthetic gene circuits to perturb natural systems in a manner that uniquely enables the elucidation of novel facets of natural regulation.