RNA sequencing of hippocampus from Hoatz knockout mice exhibiting ventriculomegaly

Hydrocephalus and ventriculomegaly are frequently associated with dysfunction of motile cilia lining the ventricular system. Hoatz is a vertebrate-specific gene expressed in cells bearing motile cilia and flagella, and its deficiency causes ventriculomegaly in mice. However, the molecular responses occurring in the brain parenchyma in this condition remain poorly understood. In this study, we performed bulk RNA sequencing of hippocampal tissue from wild-type and Hoatz-deficient mice to investigate transcriptomic alterations associated with ventriculomegaly. Hippocampi were collected from male littermate mice at 15, 21, and 25 weeks of age. Total RNA was extracted and subjected to poly(A)-selected, strand-specific RNA sequencing using paired-end reads. Comparative transcriptomic analysis identified differential expression of genes associated with neuroimmune activation, synaptic remodeling, and lipid mediator biosynthesis in Hoatz-deficient mice. Notably, several microglia-associated genes, including Trem2, Tyrobp, and C1qa, were upregulated in mutant hippocampus. Gene ontology enrichment analysis further indicated activation of immune-related pathways. These data provide insight into neuroimmune responses associated with ventriculomegaly and complement structural analyses of the Hoatz-deficient mouse brain. The dataset may serve as a resource for investigating molecular mechanisms linking altered cerebrospinal fluid dynamics and neuroimmune activation.