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Pleiotropy is the phenomenon in which a single gene impacts multiple, seemingly unrelated phenotypic traits. For example, defects in the SOX10 gene cause Waardenburg Syndrome Type 4, or WS4, which can cause defects in pigmentation, hearing impairments, and an absence of intestinal contractions necessary for elimination. This diversity of phenotypes results from the expression pattern of SOX10 in early embryonic and fetal development. SOX10 is found in neural crest cells that form melanocytes,...
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Transcriptomic Profiling of Zebrafish Mutant for cdkl5 Reveals Dysregulated Gene Expression Associated with Neuronal,

Tatiana Varela1,2, Débora Varela1,2, Natércia Conceição1,2,3

  • 1Centre of Marine Sciences, University of Algarve, 8005-139 Faro, Portugal.

International Journal of Molecular Sciences
|July 12, 2025
PubMed
Summary

Loss of Cdkl5 in zebrafish models CDKL5 deficiency disorder (CDD). RNA sequencing revealed molecular mechanisms in muscle, neuronal, and visual systems, offering insights into CDD pathogenesis.

Keywords:
CDKL5 deficiency disorderCdkl5RNA-seqtranscriptomiczebrafish model

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Area of Science:

  • Genetics and Molecular Biology
  • Developmental Biology
  • Neuroscience

Background:

  • Zebrafish serve as a valuable model for human genetic disorders.
  • CDKL5 deficiency disorder (CDD) is a severe neurodevelopmental condition.
  • The homozygous cdkl5 mutant zebrafish (cdkl5-/-) was recently established as a model for CDD.

Purpose of the Study:

  • To investigate the molecular mechanisms underlying CDD in zebrafish.
  • To compare Cdkl5-associated molecular pathways in zebrafish with those in mammals.
  • To identify gene expression changes in cdkl5-/- zebrafish relevant to CDD phenotypes.

Main Methods:

  • RNA sequencing was performed on cdkl5-/- zebrafish and wild-type siblings at 5 and 35 days post-fertilization.
  • Differential gene expression analysis was conducted to identify significant gene changes.
  • Gene Ontology and KEGG pathway analyses were used to interpret the functional roles of differentially expressed genes.
  • Motor neuron analysis was performed using the Hb9:GFP transgenic line.

Main Results:

  • Most differentially expressed genes (DEGs) were associated with muscle, neuronal, and visual systems.
  • Downregulated DEGs were enriched in muscle development, extracellular matrix, and actin cytoskeleton functions.
  • Upregulated DEGs were enriched in eye development functions at 35 dpf.
  • KEGG analysis revealed enrichment in focal adhesion and ECM-receptor interaction pathways.
  • Neuronal development genes were downregulated, while synaptic signaling genes were upregulated at 35 dpf.
  • Fewer motor neurons with shorter axons were observed in cdkl5-/- mutants.
  • Downregulated DEGs related to cartilage and bone development were identified.

Conclusions:

  • Cdkl5 deficiency in zebrafish dysregulates genes involved in CDD-associated functions observed in mammals.
  • This study provides novel insights into the molecular underpinnings of CDD.
  • The zebrafish model effectively recapitulates key molecular and developmental aspects of CDD, aiding further research.