Transcriptional profiling of astrocyte subtypes in naive mice and during experimental autoimmune encephalomyelitis

We isolated and gene expression profiled distinct astrocyte subtypes from three central nervous system regions: forebrain, hindbrain, and spinal cord, using a FACS-based protocol. Cell surface expression of Glast/Slc1a3 (G) and Acsa-2/Atp1b2 (A) was used to distinguish subpopulations of astrocytes. Furthermore, we assessed the transcriptome of cultured primary neonatal astrocytes. The local brain environment proved key in establishing different transcriptional programs in astrocyte subtypes. Functional differences between subtypes were also apparent in experimental autoimmune encephalomyelitics (EAE) mice, where these astrocyte subtypes showed distinct responses. While gene expression signatures associated with blood-brain-barrier maintenance were lost during EAE, signatures contributing to neuroinflammation were increased specifically in astrocytes in the spinal cord. Two main experiments: 1) Transcriptional profiles of astrocyte subpopulations (ACSA+Glast- and ACSA+Glast+) isolated from FVB/N mice from forebrain, hindbrain, and spinal cord, and primary neonatal astrocytes. 2) Transcriptional profiles of astrocyte subpopulations (ACSA+Glast- and ACSA+Glast+) from hindbrain and spinal cord from C57BL/6J mice during four stages of EAE (unimmunized control, stage 1, stage 4, chronic stage).