RNA-seq Re-analysis Reveals Ciliary Pathway Disruption in Foxj1 Knockout Choroid Plexus

Publication Date

2026

Presentation Length

Poster/Gallery presentation

College

College of Sciences & Mathematics

Department

Psychological Sciences and Neurosciences, Department of

Student Level

Undergraduate

Faculty Mentor

Dr. Jinhee Park

Presentation Type

Poster

Summary

Hydrocephalus is a significant medical problem that affects 1–2 per 1,000 babies in the US. Hydrocephalus is an abnormal buildup of CSF in the ventricles of the brain, which increases brain pressure on other tissues. This can result in seizures, vomiting, blurry vision, balance issues, and in infants, rapid head growth.

Despite its clinical importance, the molecular mechanisms underlying hydrocephalus—particularly those related to choroid plexus (CP) dysfunction and CSF regulation—remain poorly understood.

Therefore, Understanding the molecular mechanisms underlying this condition is essential for identifying potential therapeutic targets and improving treatment strategies. Furthermore, general Choroid Plexus and CSF malfunction is very under-researched, thus learning more about different malfunction pathways will help uncover different diseases and potential treatment strategies.

In this study, we re-analyzed publicly available RNA sequencing (RNA-seq) data to investigate gene expression changes associated with Foxj1 knockout (KO) in the choroid plexus. Differential expression analysis was performed using edgeR to compare wild-type (WT) and Foxj1 KO conditions.

Using a false discovery rate (FDR) cutoff of 0.05, we identified a total of 162 differentially expressed genes (DEGs), including 12 upregulated and 150 downregulated genes. Notably, many of these genes are involved in ciliogenesis and ciliary function, consistent with the known role of Foxj1 as a key regulator of motile cilia.

These findings suggest that disruption of cilia-related pathways may contribute to impaired CSF dynamics and CP dysfunction, providing new insights into the molecular basis of hydrocephalus and highlighting potential therapeutic targets.

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