Cerebrospinal fluid-linked periventricular gradient pathology in multiple sclerosis associates with ependymal cell reactivity and cell adhesion disruption

Cerebrospinal fluid (CSF)-adjacent brain surfaces – namely the subpial cortical and ependyma-adjacent periventricular regions – are uniquely vulnerable to diffuse pathology in multiple sclerosis (MS). So-called surface-in gradients, which predict disease relapses independent of white matter lesions, are thought to arise from CSF-borne cytotoxic factors and represent a distinct therapeutic target. Yet, how such factors access the brain, particularly at the ventricular border, remains unclear. While ependymal injury in MS has been suggested, a comprehensive assessment of cell health in the disease is lacking. Using ultra-high-field MRI-guided histology, electron microscopy, and single-nucleus multiomics, we deeply profiled human ependymal cells in MS. We found that ependymal pathology correlates with periventricular gradients and involves an immune-reactive state marked by transporter and junctional protein dysregulation. We then further defined the gene regulatory networks underpinning the MS ependymal state, predicted ligands known to be enriched in MS CSF that could drive the emergence of this state, and tested one candidate in vivo. IFNγ increased murine ependymal permeability and conditional knockout of its receptor (Ifngr1) reversed this effect. These findings implicate ependymal dysfunction in periventricular pathology and highlight how CSF ligands modulate ependymal function and regional inflammation.