Molecular and spatial profiling of multiple sclerosis lesions identifies dysfunctional lipid efflux as a driver of chronic active inflammation

Compartmentalized inflammation is considered a critical factor in driving the progression of multiple sclerosis (MS). Yet, the mechanisms sustaining its persistence remain poorly understood. A hallmark of this persistent and slowly evolving inflammatory process are chronic active MS lesions. In this study, we created a high-resolution, single-cell molecular and spatial atlas of chronic inflammation in MS. To accomplish this, we combined single-nucleus RNA sequencing (snRNA-seq) with single-cell spatial transcriptomics using multiplexed error-robust fluorescence in situ hybridization (MERFISH) to examine MS lesions, specifically focusing on those exhibiting chronic active immune pathology characterized by lymphocyte presence. Our integrative profiling uncovered the molecular landscape of glial and immune cells, their disease-associated states, and the surrounding microenvironments. Within the lesion rim, we identified CD8+ T cell niches with lipid-associated microglia. To demonstrate the utility of this spatially resolved atlas of chronic active MS lesions as a resource for future discovery, we investigated the role of lipid-associated microglia in experimental autoimmune encephalomyelitis (EAE). Our findings showed that inhibiting cholesterol efflux increased the formation of lipid-storing phagocytes, "foamy microglia," which actively drive inflammatory processes in EAE and represent tractable therapeutic targets for pharmacological modulators of sterol metabolism. These results provide a framework for system-level insights into cell-type diversity and represent a valuable resource for advancing the study of neuroinflammation in MS.