Characterisation of young, old and old repopulating microglia in spinal cord and brain of C57BL/6 wild type male mice

To address whether, after depletion by Csf1r inhibition, microglia repopulating the CNS revert to a “younger” phenotype, we treated a group of 23 months old mice with the Csf1r inhibitor for 5 days and let microglia repopulate the central nervous system for 7 days. Young (3 months old) and old (23 months old) mice were included as controls. After the repopulation time, whole spinal cord samples and Fluorescence Activated Sorting (FACS)-sorted microglia cells from brain tissue were collected to perform bulk transcriptome (RNAseq) analysis. Analysis of whole spinal cord suggested that repopulating microglia tend to re-acquire its original aged phenotype. Gene expression in FACS-sorted microglia was then analyzed to better characterize its intrinsic phenotype after repopulation. In contrast to the whole spinal cord samples, old and old-treated replicates separated in Principal Component Analysis, suggesting that repopulating microglia displayed a different phenotype compared to old microglia. Overall design: NGS based mRNA profiling of whole spinal cord and FACS-sorted microglia of young (3 months), old and old repopulating (23 months) samples. 8 replicates per group were used.