Neuro-Transcriptomic Responses to Polypharmacological Agents in Danio rerio: Implications for Translational Drug Repurposing in Neurodevelopmental Disorders

TL;DR

The study shows that different drugs affecting GABA receptors can have similar effects on gene activity in zebrafish neurons, which could help find new uses for existing drugs in treating brain development disorders.

Contribution

A novel high-throughput method for capturing transcriptional changes in neurons after drug exposure in vivo, enabling drug repurposing for neurodevelopmental disorders.

Findings

Distinct GABA-acting drugs produce shared transcriptional signatures in zebrafish neurons.

Two shared downregulated genes, SRC and GAD2, reflect a core module for modulating GABAergic tone.

The method enables rapid-omics profiling to accelerate repurposing of neuroactive compounds.

Abstract

What are the main findings?
This method rapidly extracts transcriptional signatures directly from intact primary neurons.Distinct GABA-acting drugs produce shared transcriptional signatures in zebrafish neurons influencing both GABAergic and glutamatergic synapses.

This method rapidly extracts transcriptional signatures directly from intact primary neurons.

Distinct GABA-acting drugs produce shared transcriptional signatures in zebrafish neurons influencing both GABAergic and glutamatergic synapses.

What are the implications of the main findings?
A focus on rapid-omics in neurons can accelerate repurposing efforts for neuroactive compounds with differential affinities for multiple targets.Identifying common mechanisms of action from neuroactive compounds that shift the excitatory/inhibitory balance in synapses could guide repurposing efforts for a broad range of neurodevelopmental disorders.

A focus on rapid-omics in neurons can accelerate repurposing efforts for neuroactive compounds with differential affinities for multiple targets.

Identifying common mechanisms of action from neuroactive compounds that shift the excitatory/inhibitory balance in synapses could guide repurposing efforts for a broad range of neurodevelopmental disorders.

Background: Neurodevelopmental disorders span a wide spectrum of deficits, often with a known or suspected genetic basis. While some genetic determinants may indicate treatment with selective compounds, more often both the molecular cause of the disorder and the mechanism of action for the therapeutic compound are more ambiguously matched. Due to the polypharmacological nature of most neuroactive compounds, measuring gene expression changes following drug perturbation could be an effective strategy to gain insight into shared therapeutic action downstream of diversity in receptor interaction. High-throughput drug discovery platforms have effectively measured changes in gene expression following drug perturbation in cell cultures, but unfortunately, these platforms often lack specificity for neuroactive compounds, fail to capture the developmental influence of cell–cell interactions, and do not accurately model drug metabolism in an intact system. Methods: In this study, we present a high-throughput, low-cost and cell-type-specific approach for capturing transcriptional changes in neural cell populations following neuroactive compound exposure through the combined use of transgenic zebrafish, cell sorting, and bulk RNA-seq. Results: Our system captures unique transcriptional profiles between neuronal and non-neuronal cell populations and demonstrates specific drug responsiveness within our neuronal cell population. We assessed two known positive allosteric modulators (PAMs) of γ-Aminobutyric acid sub-type A receptors (GABAAR), ivermectin and propofol, as a case study to explore shared pathway and gene expression changes following drug exposure; these chemically distinct agents share a mechanistic signature that dampens the neuronal hyperexcitability characteristic of a broad spectrum of neurodevelopmental disorders. Two shared downregulated genes reflect a core expression module for modulating GABAergic tone: SRC proto-oncogene, non-receptor tyrosine kinase (SRC), and Glutamate decarboxylase 2 (GAD2). Conclusions: We provide this methodology and analysis as a framework for exploring shared changes in gene expression following neuroactive compound exposure in vivo, leading to a more complete and nuanced understanding of therapeutic effects on neurons that can aid in drug repurposing efforts for neurodevelopmental disorders.

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