Spatial transcriptomics of the aging mouse brain reveals origins of inflammation in the white matter

To systematically understand age-induced molecular changes, we performed spatial transcriptomics of young, middle-aged, and old mouse brains and identified seven transcriptionally distinct regions. All regions exhibited age-associated upregulation of inflammatory mRNAs and downregulation of mRNAs related to synaptic function. Notably, aging white matter fiber tracts showed the most prominent changes with pronounced effects in females. The inflammatory signatures indicated major ongoing events: microglia activation, astrogliosis, complement activation, and myeloid cell infiltration. Immunofluorescence and quantitative MRI analyses confirmed physical interaction of activated microglia with fiber tracts and concomitant reduction of myelin in old mice. In silico analyses identified potential transcription factors influencing these changes. Our study provides a resourceful dataset of spatially resolved transcriptomic features in the naturally aging murine brain encompassing three age groups and both sexes. The results link previous disjointed findings and provide a comprehensive overview of brain aging identifying fiber tracts as a focal point of inflammation. We performed spatial transcriptomics on a total of 36 coronal brain sections across 3 age groups (young (Y, ~11 weeks), middle-aged (M, ~57.5 weeks), and old (O, ~126 weeks) and two sexes (male and female) of C57BL/6JN mice. In round 1, each age group contained 4 biological replicates (males (M) n=2 and females (F) n=2) and 2 technical replicates (A or B), i.e., independent, succeeding coronal sections from the same OCT block. In round 2, one technical replicate from each young and old mouse with the added 6 biological replicates (males (M) n=3 and females (F) n=3) for young and old groups were sequenced and analyzed together.