Zebrafish in the era of single-cell and spatial transcriptomics: a new paradigm for central nervous system drug discovery from natural products.

Abstract

Natural products (NPs) represent a an important chemical source for CNS therapeutics for central nervous system (CNS) therapeutics, yet elucidating their complex, multitarget mechanisms remains a major challenge. Zebrafish have emerged as a powerful vertebrate model bridging the translational gap between in vitro assays and rodent systems in CNS drug discovery. Their genetic tractability, optical transparency and rapid development make them ideal for high-throughput pharmacological screening. Recent advances in single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST), particularly Stereo-seq, are revolutionizing zebrafish-based drug discovery by enabling unprecedented resolution of cellular heterogeneity, tissue architecture and drug-induced transcriptomic changes. scRNA-seq allows for the dissection of individual cellular responses, uncovering dynamic and context-specific drug effects, while Stereo-seq maps gene expression within intact tissue landscapes, offering spatial precision. When integrated, these technologies empower researchers to conduct high-resolution compound screening, elucidate mechanisms of NPs, detect off-target effects and accelerate translational pipelines from zebrafish to human models. Coupled with CRISPR-based gene editing and phenotypic assays, this integrative approach positions zebrafish as a cornerstone of modern pharmacology and a transformative platform for CNS therapeutics.