Transcriptomic profiling of oligodendrocytes, astrocytes, and microglia in an experimental autoimmune encephalomyelitis (EAE) model of demyelination

The experimental autoimmune encephalomyelitis (EAE) mouse model is widely used to study the pathophysiology of multiple sclerosis (MS), including brain inflammation and demyelination. This study investigates cell-type-specific transcriptional changes in oligodendrocytes, astrocytes, and microglia at day 30 post-induction of EAE using MOG peptide (amino acids 35–55) emulsified in complete Freund’s adjuvant (CFA) containing Mycobacterium tuberculosis, followed by pertussis toxin injections. CFA control mice received only CFA and pertussis toxin, without MOG peptide. Oligodendrocytes, astrocytes, and microglia were isolated using magnetic-activated cell sorting (MACS) from brain and spinal cord of CFA-treated and EAE-induced mice. Bulk RNA sequencing was conducted to uncover transcriptional changes associated with EAE-induced demyelination. These findings will enhance our understanding of glial cell contributions to MS pathogenesis and help identify potential therapeutic targets. Three-month-old C57BL/6 mice were received CFA and pertussis toxin (CFA control mice), or MOG peptide (35–55) emulsified in CFA and pertussis toxin to induce EAE. At day 30 post-induction,brain cell suspensions were prepared, and oligodendrocytes, astrocytes, and microglia were isolated using magnetic-activated cell sorting (MACS) with cell type-specific markers. Experimental groups for RNA sequencing: (1) Oligodendrocytes from CFA control mice (CFA_Ctrl_OL); (2) Oligodendrocytes from EAE mice (MOG_Ctrl_OL); (3) Astrocytes from CFA control mice (CFA_Ctrl_Astro); (4) Astrocytes from EAE mice (MOG_Ctrl_Astro); (5) Microglia from CFA control mice (CFA_Ctrl_MG); (6) Microglia from EAE mice (MOG_Ctrl_MG). Bulk RNA sequencing was performed for all cell types and conditions. Each group has 3 or 4 repeats.