# Transcriptomic Profiling of Zebrafish Mutant for cdkl5 Reveals Dysregulated Gene Expression Associated with Neuronal, Muscle, Visual and Skeletal Development

## TL;DR

This study uses zebrafish to explore how the loss of the cdkl5 gene affects gene expression related to muscle, neuronal, visual, and skeletal development, offering insights into CDKL5 deficiency disorder.

## Contribution

The study reveals novel gene expression patterns in cdkl5 mutant zebrafish linked to multiple developmental systems affected in CDKL5 deficiency disorder.

## Key findings

- Cdkl5 loss leads to dysregulated genes in muscle, neuronal, and visual systems, mirroring symptoms of CDKL5 deficiency disorder.
- Downregulated genes are enriched in muscle development and ECM functions, while upregulated genes relate to eye development at 35 dpf.
- Key downregulated genes in cartilage and bone development may explain skeletal defects in zebrafish and CDD patients.

## Abstract

Zebrafish is a well-recognized model for studying human genetic disorders. Recently, we proposed the homozygous cdkl5sa21938 mutant zebrafish as a model of CDKL5 deficiency disorder (CDD), a developmental epileptic encephalopathy with diverse symptoms. This study aimed to explore Cdkl5-associated molecular mechanisms in zebrafish and assess their similarity to those in mammals. We conducted RNA sequencing on whole cdkl5−/− zebrafish and wild-type siblings at 5 and 35 days post-fertilization (dpf) to compare their gene expression profiles. Most significant differentially expressed genes (DEGs) were related to muscle, neuronal, and visual systems which are affected in CDD. Gene Ontology analysis revealed downregulated DEGs enriched in muscle development, extracellular matrix, and actin cytoskeleton functions at both stages, while upregulated DEGs were enriched in eye development functions at 35 dpf. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed enrichment of downregulated DEGs in focal adhesion and extracellular matrix (ECM)-receptor interaction pathways at both stages. Neuronal development DEGs were mainly downregulated at both stages, while synaptic signaling DEGs were upregulated at 35 dpf. Crossing cdkl5−/− mutants with the Hb9:GFP transgenic line showed fewer motor neuron cells with shorter axons compared to the wild type, which may explain the impaired motor phenotype observed in zebrafish and CDD patients. Moreover, we identified key downregulated DEGs related to cartilage development at both stages and bone development at 35 dpf, potentially explaining the skeletal defects seen in zebrafish and CDD individuals. In conclusion, Cdkl5 loss in zebrafish leads to dysregulation of genes involved in CDKL5-associated functions in mammals, providing new insights into its less studied functions and phenotypes.