Skull and vertebral bone marrow are myeloid reservoirs for meninges and CNS parenchyma

EAE is a chronic demyelinating condition characterized by central nervous system immune infiltration. Spinal cord injury results in damage to the spinal cord, partially due to leukocyte infiltration and inflammatory contributions. Here we performed single-cell RNA-sequencing of spinal cord tissue to examine how CNS-infiltrating cells from different niches may play distinct roles in different disease pathogenesis. Overall design: Three pairs of female WT and UBC-GFP C57BL/6J mice were parabiotically joined at two months of age. Mice were allowed to recover for 60 days, where after experimental autoimmune encephalomyelitis (EAE) was induced in both pairs by MOG35-55 immunization. After 15 days, mice were sacrificed and spinal cord tissue was collected from the WT parabionts. In a separate experiment, four pairs of female WT and UBC-GFP C57BL/6J mice were parabiotically joined at two months of age. Mice were allowed to recover for 60 days, where after spinal cord injury was performed in both pairs by a T9 crush with fone forceps. After three days, mice were sacrificed and spinal cord tissue was collected from the WT parabionts. Tissues from both experiments were dissociated with collagenase 8 to obtain a single cell suspension and sorted by FACS based on the following phenotypes: DAPI- CD45hi IVCD45- GFP- or DAPI- CD45hi IVCD45- GFP+.