Engineering combinatorial and dynamic decoders using synthetic immediate-early genes

Ravindran, Pavithran; Wilson, Maxwell Z.; Jena, Siddhartha G.; Toettcher, Jared E.

doi:10.1038/s42003-020-01171-1

Cited by 8 publications

(8 citation statements)

References 56 publications

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“…However, screens for altered dynamics are limited in scale due to the large number of time points needed to track short time scale signaling events and longer time scale phenotypic outputs [21]. Circuits can be used to discriminate between sustained and pulsatile signaling [23,24]. One such circuit, called a dynamic decoder, discriminates a continuous signal from a transient signal pulse.…”

Section: Microphysiological Systems (Mps)mentioning

confidence: 99%

“…One such circuit, called a dynamic decoder, discriminates a continuous signal from a transient signal pulse. By incorporating native posttranscriptional regulatory elements into a reporter gene, the dynamic decoder recapitulates native circuit feedback on the reporter gene to identify cells with sustained signaling (Figure 2H) [24].…”

Section: Microphysiological Systems (Mps)mentioning

confidence: 99%

“…However, the time scale of neurodegeneration makes connecting GCaMP measurements to cell-fate outcomes within the same assay challenging. Alternatively, circuits that sense neuronal activation frequency and duration may improve long-term tracking and mapping of neuronal signaling events, druginduced changes, and phenotypic outcomes [24]. Potentially, hyperexcitability could be monitored using engineered receptors in combination with synthetic circuits.…”

Section: A Vision For Circuit-based Screening In Neurodegenerative Diseasesmentioning

confidence: 99%

“…For example, we envision that synthetic circuits utilizing engineered receptors for glutamate could be developed to activate a frequency-decoding circuit. By designing the circuit to regulate transcription, mRNA stability, and protein stability over different time scales, reporter expression can be selectively activated in response to higher frequency receptor activation (Figure 5B) [24]. By enabling the simultaneous monitoring of proteostasis and hyperexcitability over the time scale of neurodegeneration, synthetic circuits can be used to identify compounds that selectively affect these processes in the diseaseaffected neuronal subtype.…”

Section: A Vision For Circuit-based Screening In Neurodegenerative Diseasesmentioning

confidence: 99%

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Synthetic gene circuits as tools for drug discovery

Beitz

Oakes

Galloway

2022

Trends in Biotechnology

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Within mammalian systems, there exists enormous opportunity to use synthetic gene circuits to enhance phenotype-based drug discovery, to map the molecular origins of disease, and to validate therapeutics in complex cellular systems. While drug discovery has relied on marker staining and high-content imaging in cell-based assays, synthetic gene circuits expand the potential for precision and speed. Here we present a vision of how circuits can improve the speed and accuracy of drug discovery by enhancing the efficiency of hit triage, capturing disease-relevant dynamics in cell-based assays, and simplifying validation and readouts from organoids and microphysiological systems (MPS). By tracking events and cellular states across multiple length and time scales, circuits will transform how we decipher the causal link between molecular events and phenotypes to improve the selectivity and sensitivity of cell-based assays. Enhancing phenotypic drug discovery with synthetic biologyDevelopment of new drugs requires identification and optimization of functional molecules that often proceeds sequentially through high-throughput discovery screening, hit validation, hit expansion and optimization, and preclinical disease modeling (see Glossary) (Figure 1, Key figure)[1]. Target-based drug discovery (TDD) programs aim to identify drug candidates that modulate a defined biological target that is hypothesized to play a causal role in initiating or sustaining a disease. TDD programs offer precision by directly screening for drug candidate efficacy using purified molecular targets [2]. By contrast, phenotypic drug discovery (PDD) programs aim to identify drug candidates that modulate a physiologically-relevant biological system or cellular signaling pathway and screen for drug efficacy using cell-based assays [2]. Cell-based assays are target-agnostic and provide the opportunity to identify therapeutics that resolve diseaseassociated phenotypic deficits even when the disease etiology remains obscure and targets are undefined. Thus, PDD has recently received renewed interest for its potential to identify first-in-class drugs that act via a novel mechanism of action (MoA) as well as identify drugs for disease with complex or unknown etiology [1][2][3][4]. In order to identify drug candidates that translate to effective therapeutics in the clinic, PDD programs require cell-based assays that faithfully recapitulate and report on disease-relevant processes. To efficiently and effectively screen in phenotypic models, assay development for initial discovery screens must balance throughput with the ability to capture these disease processes [1]. As PDD probes a larger biological space than TDD to identify potential therapeutics, the number of hits from an initial discovery screen in a PDD program may be very large [2]. Following initial discovery screens, hit validation and triage are required to produce a small number of high-confidence candidates to proceed to the resource-intensive stages of hit expansion, compound optimization, and hig...

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Section: Microphysiological Systems (Mps)mentioning

confidence: 99%

Section: Microphysiological Systems (Mps)mentioning

confidence: 99%

Section: A Vision For Circuit-based Screening In Neurodegenerative Diseasesmentioning

confidence: 99%

Section: A Vision For Circuit-based Screening In Neurodegenerative Diseasesmentioning

confidence: 99%

See 2 more Smart Citations

Synthetic gene circuits as tools for drug discovery

Beitz

Oakes

Galloway

2022

Trends in Biotechnology

View full text Add to dashboard Cite

show abstract

“…These circuits were then combined with gene networks that act on slower time-scales, similar to natural cellular decision making circuits [14]. Furthermore, synthetic immediate early genes were constructed that can process dynamic ERK activity [13,15].…”

Section: Main Text Introductionmentioning

confidence: 99%