snRNA‐seq analysis of human brains suggests cell type‐specific synergistic effects of APOE4 and TREM2‐R47H and potential drug targets in Alzheimer’s Disease

Abstract Background Alzheimer’s Disease (AD) risk variants APOE4 and TREM2‐R47H have been shown to impact glial cell functions and transcriptional profiles. We hypothesize that TREM2‐APOE may have synergistic effects in driving pathogenesis and disease progression of AD in a cell type‐specific manner. Methods We investigated cell‐type specific transcriptional changes associated with APOE4 ‐ and TREM2‐R47H ‐carrier status. We conducted single‐nuclei RNA‐sequencing (snRNA‐seq) analysis, including cell type clustering and annotation, and identification of differentially expressed genes (DEGs). We used integrative genomic analysis for pathway enrichment and drug‐target network inference. Our investigation was between APOE‐TREM2 groups: APOE4‐carrier+TREM2‐R47H ( E4‐R47H ) (n = 18) vs non‐APOE4+R47H (nonE4‐R47H) (n = 6), APOE4‐carrier+TREM2‐common variant ( E4‐CV) (n = 16) vs nonE4‐CV (n = 6), E4‐R47H vs nonE4‐R47H , and E4‐CV vs nonE4‐CV . Results We found that APOE‐TREM2 status had synergistic effects on cell abundance in several cell types, especially in oligodendrocytes, excitatory neurons and pericytes. Pathway enrichment analysis suggests a possible APOE4 ‐ and TREM2‐R47H ‐dependent regulation of cell type‐specific pathway signaling. Of note, preliminary analysis suggests an APOE4 ‐dependent regulation of TREM2‐R47H ‐associated PI3K‐Akt signaling in microglia such that APOE4‐R47H carriers had significantly upregulated PI3K‐Akt signaling but nonAPOE4‐R47H carriers had comparatively downregulated PI3K‐Akt signaling. Oligodendrocyte clusters show R47H ‐dependent effects of APOE4 ‐carrier status on relevant signaling pathways as well. Oligodendrocytic signaling pathways for long‐term depression and serotonin/anxiety events, as well as sleep regulation and circadian entrainment have R47H ‐dependent regulation between APOE4 vs non‐ APOE4 carriers. We employed integrative network‐based analysis of single‐nuclei transcriptomic and drug‐gene signatures and identified an FDA‐approved drug clidinium bromide , a treatment for irritable bowel syndrome and enterocolitis, to be a possible antagonist of the synergistic R47H‐APOE4 effects in microglia. Conclusion In summary, this study suggests possible synergistic effects of APOE4 ‐carrier and TREM2‐R47H ‐carrier status on cell type abundance and cell type‐specific specific signaling pathways. Hence, further classification of differences between joint APOE‐TREM2 genotypes will improve our understanding of glial cell alterations in AD, and could lead to novel microglia‐targeted therapeutic interventions. Such findings enhance our knowledge of druggable therapeutic targets and support the need for precision and personalized medicine. Independent cohort validation and functional observations of candidate targets and treatments are warranted.