APOE4 Drives Uniquely Dysfunctional Human Microglial States in Alzheimer's Disease

Ee, R.; Amouzgar, M.; Afaghani, J.; Vijayaragavan, K.; Cannon, B. J.; Mrdjen, D.; Tebaykin, D.; Spence, A.; Sant, C.; Aley, D.; Guo, Z.; Sedov, K.; Zafar, F.; Montine, K. S.; Perna, A.; Serrano, G. E.; Beach, T. G.; Angelo, M.; Schüle, B.; Corces, M. R.; Montine, T. J.; Bendall, S. C.

doi:10.64898/2026.06.18.733295

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bioRxiv · 10.64898/2026.06.18.733295

APOE4 Drives Uniquely Dysfunctional Human Microglial States in Alzheimer's Disease

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Abstract

Variation in APOE, notably the {varepsilon}4 allele, profoundly shapes risk and severity of late-onset Alzheimers disease (AD), yet how it remodels human microglial states remains unresolved. We combine spatially resolved proteomic profiling with single-nuclear multiomic analyses to define microglial organization across APOE3/3 and APOE4/4 genotypes in AD. Quantifying condition-associated variation across the cellular manifold reveals a continuous landscape of microglial states. APOE4/4 shifts cells toward terminal states marked by loss of homeostatic identity, metabolic disruption, and incomplete acquisition of disease-associated programs. We identify an APOE4/4-enriched population in AD that exhibits inflammatory signaling without effective metabolic or phagocytic engagement, localizing to niches of gliosis and senescence, and coupled to chronic stress adaptation programs. Together with evidence that APOE4/4 potentiates the activation threshold of nascent microglia, these findings establish a unified framework for human microglial state change, linking genetic risk to spatial and molecular organization of immune responses in the AD brain. Graphical Abstract.APOE4/4 in Alzheimers disease reshapes microglial fate along continuous trajectories characterized by proteomic, transcriptional, and epigenetic programs consistent with chronic stress adaptation, alongside distinct composite spatial niches comprised of astrocytic gliosis and cellular senescence. O_FIG O_LINKSMALLFIG WIDTH=168 HEIGHT=200 SRC="FIGDIR/small/733295v1_ufig1.gif" ALT="Figure 1"> View larger version (75K): org.highwire.dtl.DTLVardef@b2afa4org.highwire.dtl.DTLVardef@12978f8org.highwire.dtl.DTLVardef@1c4e46dorg.highwire.dtl.DTLVardef@170e44d_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Ee, R., Amouzgar, M., Afaghani, J., Vijayaragavan, K., Cannon, B. J., Mrdjen, D., Tebaykin, D., Spence, A., Sant, C., Aley, D., Guo, Z., Sedov, K., Zafar, F., Montine, K. S., Perna, A., Serrano, G. E., Beach, T. G., Angelo, M., Schüle, B., Corces, M. R., Montine, T. J., Bendall, S. C.. 2026-06-19. APOE4 Drives Uniquely Dysfunctional Human Microglial States in Alzheimer's Disease. https://doi.org/10.64898/2026.06.18.733295

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