Unraveling changes in mitochondrial processes influenced by ancestry in APOEε4 carriers with Alzheimer disease

The APOEε4 allele is the strongest known genetic risk factor for late-onset Alzheimer disease (AD). However, the risk effect of APOEε4 varies substantially by ancestry, with individuals of African ancestry (AF) demonstrating markedly lower risk compared to those of European ancestry (EU). This difference in risk is associated with distinct levels of APOE gene expression. Here, we investigate whether mitochondrial processes in brain cells are also influenced by ancestry in AD APOEε4 carriers, potentially contributing to the observed risk differences.

Single nuclei RNA sequencing was performed on frontal cortex from 17 AD patients homozygous for APOEe4 with either African Local Ancestry (AF-LA; N = 7) or European Local Ancestry (EU-LA; N = 10). Differential gene expression was compared between AF and EU samples, with particular focus on mitochondrial pathways. Differential expression and functional enrichment analyses were performed using MAST and PathFindR, respectively. MitoXplorer was used to identify differential mitochondrial processes, while REACTOME facilitated the building of regulatory networks.

Multiple cell types and biological processes contribute to the differences in APOEe4 risk seen between individuals of AF and EU ancestry. AF astrocytes show a less reactive phenotype and L6 and L5/6 excitatory neurons appear to be less vulnerable in AF compared to EU samples. Mitochondrial alterations were more pronounced in EU-LA APOEe4 AD carriers relative to their AF counterparts. Cells highly expressing APOE (astrocytes, microglia, and vascular leptomeningeal cells) showed increased expression of mitochondrial genes, particularly in EU-LA samples. We observed increased expression of pro-apoptotic, oxidative phosphorylation, and mitophagy-related genes in EU samples. Regulatory network analysis identified the transcription factor PPARG as a potential mediator linking APOEε4 expression to mitochondrial gene programs in a cell-type- and ancestry-dependent manner.

Our snRNA-seq analysis demonstrates that ancestry-linked regulation of APOEε4 expression influences mitochondrial transcriptome and astrocyte activation in AD. The stronger APOE-PPARG-mitochondrial gene coupling in EU ancestry particularly in astrocytes may underlie increased AD risk, while AF ancestry confers partial decoupling of these pathways. These results underscore the importance of considering ancestry in AD research and suggest that precision therapeutic strategies targeting mitochondrial and glial pathways should account for APOE local ancestry.