Transcriptomic Profiling of Zebrafish Mutant for cdkl5 Reveals Dysregulated Gene Expression Associated with Neuronal and Skeletal Development
Zebrafish has been recognized as a robust model organism in biomedical research for the investigation of human genetic disorders. Recently, we proposed the homozygous cdkl5sa21938 mutant zebrafish as a model of CDKL5 deficiency disorder (CDD), a rare developmental epileptic encephalopathy associated with broad range of symptoms.  Since neurological phenotypes are the primary focus of investigations, the understanding of CDKL5 function beyond the brain remains limited. Therefore, the aim of this study was to expand the knowledge about Cdkl5-associated molecular mechanisms using the proposed cdkl5 zebrafish model and to evaluate their similarity to findings in mammalian systems. For this purpose, we conducted RNA-sequencing of whole cdkl5-/- mutant zebrafish and compare it to their wild-type siblings at two different stages of development (5 and 35 dpf). Most significant DEGs were related to muscle, neuronal and visual systems which are affected in CDD. Gene Ontology (GO) analysis revealed that at both stages the downregulated DEGs were mainly enriched in muscle development, extracellular matrix and actin cytoskeleton functions while at 35 dpf the upregulated DEGs were mainly enriched in eye development functions. KEGG pathway analysis showed the enrichment of downregulated DEGs in focal adhesion and ECM-receptor interaction pathways at both stages. Additionally, we found that DEGs related to neuronal development were mainly downregulated at both stages while several upregulated DEGs were enriched in synaptic signaling at 35dpf. Moreover, we identified many downregulated key DEGs of cartilage development at both stages and bone development at 35 dpf, potential explaining the impaired cdkl5-/- mutant craniofacial cartilage and bone mineralization defects and the CDD skeletal phenotypes. In conclusion, this study shows that Cdkl5 loss in the cdkl5-/- mutant zebrafish lead to the dysregulation of several genes involved in functions known to be associated with CDKL5 in mammalian systems and provide novel insights into the less studied CDKL5 functions and phenotypes. Overall design: RNAseq of homozigous cdkl5sa21938 zebrafish and their WT siblings at 5 and 35 days post-fertilization. Five biological replicates were performed for each condition.