Human fetal derived microglia display profound age-related changes in epigenetic and transcriptomic features

Microglia (MG) are the principal immune cells of the central nervous system, constituting 10% of all cells in the brain. MG cells perform many critical functions involved in normal CNS homeostasis and in neuroinflammation and degenerative diseases. MG cells are derived from embryonic yolk sac progenitors and persist through self-renewal into adulthood. Their behavior and dynamics evolve significantly with aging.
As individuals age, microglia undergo profound phenotypic changes. The lack of markers to differentiate between monocyte-derived and resident microglia makes it difficult to assess age-related ontogenetic shifts. Research shows that microglia can be differentiated by unique DNA methylation patterns, forming a "memory trace" of their fetal state, quantified through a fetal cell origin (FCO) score.
The FCO score helps determine the epigenetic age of microglia. While generally high in younger individuals, indicating fetal origin, FCO scores decrease significantly in those over 60, suggesting epigenetic remodeling with aging.
We hypothesize that aging leads to a large-scale ontogenetic shift in microglial populations, alongside changes in DNA methylation and transcriptomic features. To investigate, microglia samples have been sequenced using RNA-seq, focusing on:
1. DeWitte microglia show strong FCO variation with age; 2. DeWitte also did RNA-Seq data on N=50 of the same samples; 3. Obtain RNA-Seq information from paired samples, then compare expression in samples stratified by high/low FCO or by age (<60 vs >60); 4. Obtain DEGs for FCO high cells, rank all DEGs by logFC high to low expression; 5. Determine the genes in the FCO that discriminate fetal and adult stem cells; 6. Use the fetal gene list and the ranked DEGs from the high/low FCO analysis to perform a gene enrichment analysis. Ask if fetal genes are enriched in the leading edge of overexpressed genes in the FCO high/low ranked list; 7. Determine if fetal genes are enriched in differentially expressed microglial genes; 8. Explore specific gene transcription methylation correlations.

Microglia (MG) are the principal immune cells of the central nervous system, constituting 10% of all cells in the brain. Aging leads to profound changes in microglial phenotypes and the lack of distinguishing markers for monocyte-derived versus resident MG has made it impossible to discern if normal aging leads to age-related ontogenetic shifts in MG populations. The ontogeny of fetal versus adult stem cell-derived populations can be traced to DNA methylation marks using the fetal cell origin (FCO) score. Using published data, we computed the FCO scores of isolated human MG from different brain regions and subjects of varying ages. The results showed the FCO scores in MGs were highly age-dependent. Microglia from older donors demonstrated significantly lower FCO scores, indicating an epigenetic shift or remodeling in the aging CNS population. Here, we hypothesize that aging is associated with a large-scale ontogenetic shift in the MG populations and that this shift will be accompanied by characteristic changes in DNA methylation signatures and associated transcriptomic features.