CDKL5 deficiency alters cell subtype-specific molecular programmes and intercellular signalling in the mouse hippocampus

Abstract CDKL5 deficiency disorder (CDD) is a severe neurodevelopmental condition characterised by epilepsy, intellectual disability, and motor dysfunction. Loss of CDKL5 leads to altered synapse development, excitatory-inhibitory imbalances and glial changes, but the underlying molecular mechanisms remain incompletely understood, particularly at the level of individual brain cell subtypes. Here, we performed single-nucleus RNA sequencing (snRNA-seq) on the hippocampus of 12 weeks old heterozygous female Cdkl5 exon 6 deletion ( Cdkl5 tm1.1Joez/J ) and wild-type mice to characterise cell-subtype-specific transcriptional alterations associated with CDKL5 deficiency. Analysis of 11,791 high-quality nuclei revealed cell-subtype-specific transcriptional changes across neuronal and non-neuronal populations. Differential expression was most prominent in intratelencephalic and extratelencephalic (IT–ET) glutamatergic neurons, which showed altered expression of genes involved in neuronal signalling and activity-dependent transcription, and in dentate gyrus (DG) neurons, which exhibited coordinated upregulation of multiple ribosomal protein genes. Gene set enrichment analysis revealed broader molecular alterations, with neuronal populations showing recurrent changes in pathways associated with synaptic organisation, neuronal development, axonal and dendritic processes, and neurotransmission. Altered gene expression was also evident among non-neuronal populations, although these displayed fewer changes. CellChat analysis inferred changes in predicted intercellular communication across excitatory and inhibitory neuronal populations, particularly Sema3c signalling, suggesting reorganization of hippocampal neuronal subtypes. These findings provide a single-nucleus transcriptional atlas of the hippocampus in a CDD mouse model. In our dataset, CDKL5 deficiency was associated with cell-subtype-specific alterations in gene expression, including enrichment of gene pathways related to cellular metabolism, neuronal development and synaptic organisation, alongside alteration in predicted intercellular signalling. This dataset provides a resource for investigating the cellular and molecular mechanisms underlying CDD and for prioritising candidate pathways for future therapeutic investigation.