Hydrocephalus (HC) is a heterogeneous neurodevelopmental disorder resulting from aberrant brain-cerebrospinal fluid (CSF) homeostasis which leads to elevated intracranial pressure (Kahle et al., 2016; Tomycz et al., 2017; Hale et al., 2025a). HC is one of the most common indications for neurological surgery in the world, especially in children (Simon et al., 2008; Dewan et al., 2018), but surgical treatment options are prone to failure. The current treatments for HC include insertion of a ventricular CSF shunt and endoscopic third ventriculostomy (ETV) with or without choroid plexus cauterization (Kahle et al., 2016; Kulkarni et al., 2017). While clinical trials have attempted pharmacological strategies to treat HC (Whitelaw et al., 2001), these approaches have been unsuccessful, largely due to an incomplete understanding of underlying molecular mechanisms (Tomycz et al., 2017; Hale et al., 2025a; Hale et al., 2024; Pan et al., 2023). Moreover, many studies have evaluated the efficacy and cost of HC surgical interventions (Lim et al., 2018), but long-term morbidity remains unacceptably high. Key obstacles to non-surgical treatments is our incomplete mechanistic and genetic understanding of the disease (Kousi and Katsanis, 2016). We believe that agnostic human genetic approaches to identify HC genes and mutations coupled with detailed mechanistic understanding can lead to precision surgical and pharmacological treatments.

There are a number of challenges to identifying the genetic etiology for many cases of HC including phenotypic variability, comorbid neurodevelopmental disorders, polygenicity, and pleiotropy. Varying approaches have been used to understand the genetic basis of HC including trio-based whole-exome sequencing (WES) to identify inherited and de novo mutations (Furey et al., 2018; Jin et al., 2020) and genome-wide & transcriptome-wide association studies (GWAS/TWAS) (Hale et al., 2021; Hale et al., 2025b; Hale et al., 2025c), where TWAS identifies gene-level associations with the disease of interest. Prior work from our group using multi-omics analysis, including human TWAS, of HC patients of European ancestry identified maelstrom (MAEL) in the brain cortex reaching experiment-wide significance as the leading gene-tissue pair associated with HC (Hale et al., 2021). However, that report did not define developmental timing, cell-type expression, evolutionary constraint, or direct evidence of MAEL expression in human HC cortical tissue.

Here, we address these gaps by integrating evolutionary genomics, large-scale single-cell RNA sequencing (snRNA-seq) of prenatal brain development, inference of somatic CNV burden consistent with MAEL's knock biological role, and direct measurement of MAEL expression in human HC cortical tissue. We use functional genomics approaches to identify the evolutionary, temporal, and spatial cellular origin of MAEL expression in the developing human brain. We perform taxonomic analysis of MAEL to identify the evolutionary origin of the gene across species to prioritize model systems for downstream mechanistic studies. Based on the hypothesized role of MAEL in non-brain cell types regulating DNA structure, we estimate the global and single cell copy number variant (CNV) burden across prenatal time in the human brain. Using large-scale snRNA-seq atlases of the neonatal human brain, we identify the cellular and temporospatial origins of MAEL which correlate with cell types enriched for CNV, consistent with the reported role of MAEL in non-brain tissues. Finally, we analyze snRNA-seq data from primary human HC brain tissue, recapitulating reduced MAEL expression and functionally validating a human HC TWAS analysis (Hale et al., 2021). Intriguingly, these data also identify MAEL expression enriched in excitatory neurons (ENs), which may also explain frequently diagnosed comorbid disorders associated with HC, including autism spectrum disorder (ASD), epilepsy, etc. Taken together, these analyses extend beyond gene-tissue statistical association to framing the role of MAEL in the cellular and developmental context relevant to human HC biology. Moreover, these analyses highlight the need for a human in vitro model system to elucidate human HC disease mechanisms, including the role of MAEL.