Repression of lysosomal transcription factors Tfeb and Tfe3 is essential for the migration and function of microglia

As the primary phagocytic cells of the central nervous system, microglia exquisitely regulate their lysosomal activity to facilitate brain development and homeostasis. However, mechanisms that coordinate lysosomal activity with microglia development, migration, and function remain unclear. Here we show that embryonic macrophages require the lysosomal GTPase RagA and the GTPase-activating protein Folliculin to colonize the brain in zebrafish. We demonstrate that embryonic macrophages in rraga mutants show increased expression of lysosomal genes but display significant downregulation of immune and migration-related genes. Furthermore, we find that RagA and Folliculin repress the key lysosomal transcription factor Tfeb, and its homologs Tfe3a and Tfe3b, in the macrophage lineage. Using RNA-Sequencing, we establish that Tfeb and Tfe3 are required for activation of lysosomal target genes under conditions of stress but not for basal expression of lysosomal pathways. Collectively, our data define a lysosomal regulatory circuit essential for macrophage development and function in vivo. Teaser The degradation machinery of the cell must be carefully controlled for the normal formation and function of key immune cells called microglia.