Tracking changes in functionality and morphology of repopulated microglia in young and old mice

Microglia (MG) are resident myeloid cells in the central nervous system (CNS) that perform homeostatic or pathological functions. Microglia self-renewal is controlled by the macrophage colony-stimulating factor-1 (CSF-1). Inhibitors of CSF-1 receptor (i.a. BLZ-945) by blocking the CSF1R signaling deplete 99% of microglia in 21 days and after cessation of treatment microglia rapidly repopulate and restore normal density within 1 week in adult mice. The functions of these repopulated microglia are poorly known and they can vary according to age. To investigate the microglia repopulation process, we compared samples of repopulated microglia from young (3 months) and old (12 months) mice using single cell RNA sequencing (scRNA-seq). Overall design: We compared BLZ-945 depleted microglia from young (3 months) and old (12 months) GFP-M::Cx3cr1-CreERT2fl/fl::Rosa26-tdTomatotg/tg mice against undepleted controls. Four scRNA-seq libraries (Rep1 to Rep4) were constructed, each combining four animals representing all experimental conditions (control young, control old, repopulated young, repopulated old).