Multi-omics profiling of the choroid plexus reveals developmental cellular remodeling, early immune gene activation, and epithelial cell heterogeneity

Brain development and function are influenced by the choroid plexus, whose dynamic cellular and transcriptional changes shape immune cell trafficking and cerebrospinal fluid composition. Here, we performed a comprehensive multi-omics analysis—including bulk and single-cell transcriptomics and epigenomics—of the lateral ventricle choroid plexus across postnatal and adult stages in mice and rats. We identified changes in the choroid plexus cellular composition and gene expression profiles, including early and progressive activation of several immune related genes in main cell types from early postnatal to young adult stage. Epithelial cells exhibited developmental remodeling over time, characterized by distinct gene expression programs, locus-specific changes in chromatin accessibility, and cellular diversity. In addition, we uncovered an epithelial cell population characterized by a distinct transcriptional signature. Our study offers a comprehensive atlas of transcriptional activity and chromatin accessibility in choroid plexus cells, providing a valuable resource to guide future research.