Differential accumulation of storage bodies with aging defines discrete subsets of microglia in the healthy brain

To date, microglia subsets in the healthy CNS have not been identified. Utilizing autofluorescence (AF) as a discriminating parameter, we identified two novel microglia subsets in both mice and non-human primates, termed autofluorescence-positive (AF(+)) and negative (AF(−)). While their proportion remained constant throughout most adult life, the AF signal linearly and specifically increased in AF(+) microglia with age and correlated with a commensurate increase in size and complexity of lysosomal storage bodies, as detected by transmission electron microscopy and LAMP1 levels. Post-depletion repopulation kinetics revealed AF(−) cells as likely precursors of AF(+) microglia. At the molecular level, the proteome of AF(+) microglia showed overrepresentation of endolysosomal, autophagic, catabolic, and mTOR-related proteins. Mimicking the effect of advanced aging, genetic disruption of lysosomal function accelerated the accumulation of storage bodies in AF(+) cells and led to impaired microglia physiology and cell death, suggestive of a mechanistic convergence between aging and lysosomal storage disorders.