To dissect cellular heterogeneity and understand molecular changes in inflammatory cells, neurons and glial cell types by single-cell genomics of MS and control brain samples.

Multiple sclerosis (MS) is a chronic inflammatorydemyelinating disease with early relapsing-remitting and late progressive phases. Neurodegeneration and astrogliosis accompany lesion formation with damage and loss of oligodendrocytes.

We utilized single-nucleus RNA sequencing (snRNAseq) and multiplex in situ hybridization to dissect transcriptional profiles of inflammatory cells, neurons and glial cell types during MS lesion progression.

Phase-associated signatures were primarily driven by upregulation of long-noncoding RNAs and cell stress pathway genes in projection neurons and oligodendrocytes. We identified selective loss of excitatory cortical projection neurons in areas underlying meningeal inflammation associated with plasma cell infiltration. Oligodendrocytes in MS showed activation of stress signatures and dysregulation of genes involved in myelin production and function. Lymphocyte infiltrates were associated with MS-specific stromal and endothelial cell populations suggesting niche interactions. We found distinct markers of reactive astrocytes in gray versus white matter MS lesions.

Our findings provide a comprehensive view of cellular, spatial and stage-associated transcriptomic changes that characterize the progressive MS brain and identify cell type-specific pathways that contribute to leukocortical degeneration.