Engineering a Scalable and Orthogonal Platform for Synthetic Communication in Mammalian Cells

Pistikou, Anna-Maria Makri; Cremers, Glenn A.O.; Nathalia, Bryan L; Bögels, Bas W.A.; Eijkens, Bruno V.; Dreu, Anne de; Bezembinder, Maarten; Stassen, Oscar M. J. A.; Bouten, Cvc Carlijn; Merkx, Maarten; Jerala, Roman; Greef, Tom F. A. de

doi:10.1101/2023.01.18.524631

Cited by 4 publications

(4 citation statements)

References 71 publications

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“…This application demonstrated the potential of CBPs in receptor engineering for sensing external cues, which is a first step towards sensing peptide or protein targets with bandpass behavior. Such systems could ultimately lead to the integration of bandpass filters into engineered cell communication networks for synthetic morphology or other autonomously controlled cell consortia 22,23 .…”

Section: Discussionmentioning

confidence: 99%

Rationally designed protein bandpass filters for controlling cellular signaling with chemical inputs

Shui

Scheller

Correia

2023

Preprint

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Biological mechanisms that rely on signal integration and processing are fundamental for cell function. These types of capabilities are analogous to those found in electronic circuits where individual components perform operations on input signals. In electronics, bandpass filters are crucial components to narrow frequencies within a specified range and reject frequencies outside of that range. However, no generalizable protein-based components are currently available to mimic such processes in engineered biological systems, representing an unmet need in controllable modules. Here, we propose a rational design approach to create protein-based chemically responsive bandpass filters (CBP) which pass chemical concentrations within a range and reject concentrations outside of that range, showing an OFF-ON-OFF regulatory pattern. The CBPs were designed using structure-based approaches where we created a heterodimeric construct which the assembly is triggered by low concentration of a small-molecule, and this interaction is inhibited at high concentrations of the drug, effectively creating a bandpass filter. The CBPs have a multidomain architecture where we used known drug-receptors, a computationally designed protein binder and small-molecule inhibitors. Owing to the modularity of the system, each domain of the CBPs can be rationally fine-tuned to optimize its performance, including bandwidth, maximum response, cutoff concentration and fold changes. These CBPs were used to regulate cell surface receptor signaling pathways showing the capability to control cellular activities in engineered cells.

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Section: Discussionmentioning

confidence: 99%

Rationally designed protein bandpass filters for controlling cellular signaling with chemical inputs

Shui

Scheller

Correia

2023

Preprint

View full text Add to dashboard Cite

show abstract

Section: Discussionmentioning

confidence: 99%

Protein-based bandpass filters for controlling cellular signaling with chemical inputs

Shui,

Scheller,

Correia

2023

Nat Chem Biol

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Biological signal processing is vital for cellular function. Similar to electronic circuits, cells process signals via integrated mechanisms. In electronics, bandpass filters transmit frequencies with defined ranges, but protein-based counterparts for controlled responses are lacking in engineered biological systems. Here, we rationally design protein-based, chemically responsive bandpass filters (CBPs) showing OFF-ON-OFF patterns that respond to chemical concentrations within a specific range and reject concentrations outside that range. Employing structure-based strategies, we designed a heterodimeric construct that dimerizes in response to low concentrations of a small molecule (ON), and dissociates at high concentrations of the same molecule (OFF). The CBPs have a multidomain architecture in which we used known drug receptors, a computationally designed protein binder and small-molecule inhibitors. This modular system allows fine-tuning for optimal performance in terms of bandwidth, response, cutoff and fold changes. The CBPs were used to regulate cell surface receptor signaling pathways to control cellular activities in engineered cells.

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“…Circuit generalizability should additionally extend amplifier compatibility beyond SJRs to other transcription factor based receptors as well. As the amplifiers are transcription factor based, they should be compatible with other transcription factor based receptors such as modular extracellular sensor architecture (MESA) and Tango/ChaCha [70][71][72][73][74][75][76][77][78] (Fig. 8C).…”

Section: Discussionmentioning

confidence: 99%

Design and Mathematical Analysis of Activating Amplifiers that Enable Modular Temporal Control in Synthetic Circuits

Lam

2023

Preprint

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The ability to control mammalian cells such that they self-organize or enact therapeutic effects as desired has incredible implications. Not only would it further our understanding of native processes such as development and the immune response, but it would also have powerful applications in medical fields such as regenerative medicine and immunotherapy. This control is typically obtained by synthetic circuits that use synthetic receptors, but control remains incomplete. For example, the synthetic juxtacrine receptors (SJRs) are widely used as they are fully modular and enable spatial control, but they have limited gene expression amplification and temporal control. I therefore designed transcription factor based amplifiers that amplify gene expression and enable unidirectional temporal control by prolonging duration of target gene expression. Using an in silico framework for SJR signaling, I combined these amplifiers with SJRs and show that these SJR amplifier circuits can improve the quality of self-organization and direct different spatiotemporal patterning. I then show that these circuits can improve chimeric antigen receptor (CAR) T cell tumor killing against two different types of tumors. These amplifiers are flexible tools that improve control over SJR based circuits and have both basic and therapeutic applications.

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Engineering a Scalable and Orthogonal Platform for Synthetic Communication in Mammalian Cells

Cited by 4 publications

References 71 publications

Rationally designed protein bandpass filters for controlling cellular signaling with chemical inputs

Rationally designed protein bandpass filters for controlling cellular signaling with chemical inputs

Protein-based bandpass filters for controlling cellular signaling with chemical inputs

Design and Mathematical Analysis of Activating Amplifiers that Enable Modular Temporal Control in Synthetic Circuits

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