Engineering Chemotactic Biosensors for a Diverse Spectrum of Metastatic Markers

Project Information

Biosensor Design

Grant agreement ID: 842200

DOI

10.3030/842200

Project closed

EC signature date 19 March 2019

Start date 1 February 2020

End date 31 January 2022

Funded under

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Total cost

€ 191 149,44

EU contribution

€ 191 149,44

Coordinated by

ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE
Switzerland

Periodic Reporting for period 1 - Biosensor Design (Engineering Chemotactic Biosensors for a Diverse Spectrum of Metastatic Markers)

Reporting period: 2020-02-01 to 2022-01-31

Summary of the context and overall objectives of the project

The directional movement of cells in response to environmental signals (chemotaxis) is essential in biology. Immune cells use chemotaxis to traffic towards disease sites, however, metastatic cells often remain undetected. The design of chemotactic biosensors for metastatic markers can manipulate the immune system's spectrum of actions. Studies have identified soluble secreted factors that promote the initial escape of tumour cells, their intravasation into circulation, and extravasation into metastatic niches. The EU-funded Biosensor Design project aims to build and validate a general computation-based platform for rational biosensor design. The immediate objective is to create biosensors that will elicit migration of engineered cytotoxic immune cells towards vulnerable metastatic cells.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

We developed a computational strategy for designing highly sensitive receptor biosensors of chemokines. We used the structurally well-characterized chemokine receptor, CXCR4 as a template, which we have investigated by engineering variants that alter the quaternary structure of the dimeric and can be tuned for downstream biased signaling functions. We then developed a computational strategy that allowed us to carve ligand binding sites and engineer potent and efficacious signaling into peptide-sensing GPCRs, such as chemokine receptors, from homology models without the need for solved active state structures, which are still in short supply. From our method, we generated several Conformationally Adaptive Peptide Biosensors (CaPSens) that have enhanced chemotactic responses, which we demonstrated in primary T cells. Our designs extend membrane protein engineering and synthetic biology, providing insight into mechanisms of signal transduction, and act as useful tools in engineered cells for redirecting and promoting lymphocyte trafficking. Further methodological developments were established to engineer receptor loops for selective ligand-binding and coupling extracellular ligand-sensing domains to intracellular G-protein coupling within a single-domain GPCR.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

The project has produced several novel chemotactic biosensor designs based on limited homologous structural information and confronting the design challenge of the inherent flexibility of receptor:peptide signaling systems. Typical peptide-sensing biosensors rely on rigid bidning domains and fluorescent or transcriptional reporters that offer little route to direct cellular function. Our CaPSens go beyond the state-of-the-art by accounting for the high conformational flexibility inherent to both the peptide ligand and the receptor binding pocket. These biosensors are a major first step towards engineering biosensors that can elicit migration and other cellular processes in response to flexible peptide ligands. Our flexible receptor:peptide design pipeline, along with our design strategies to engineer receptor loops with ligand-specific selectivity, and allosteric rewiring of hybridized GPCRs fold into our development of a holistic biosensor design platform. Our engineered CaPSens have direct applications in immune cell homing and synthetic biology, while our design methods set the stage for generation of immunotherapy tools that can circumvent existing barriers to cancer treatment.

Design strategy for (A) ultrasensitive flexible peptide:receptor, (B) selective hybrid biosensors.