The strongest genetic risk factor influencing susceptibility to lateonset Alzheimer's disease (AD) is apolipoprotein E (APOE) genotype. APOE has three common isoforms in humans, E2, E3, and E4. The presence of two copies of the E4 allele increases risk by ∼12-fold whereas E2 allele is associated with an ∼twofold decreased risk for AD. These data put APOE central to AD pathophysiology, but it is not yet clear how APOE alleles modify AD risk. Recently we found that astrocytes, a major central nervous system cell type that produces APOE, are highly phagocytic and participate in normal synapse pruning and turnover. Here, we report a novel role for APOE in controlling the phagocytic capacity of astrocytes that is highly dependent on APOE isoform. APOE2 enhances the rate of phagocytosis of synapses by astrocytes, whereas APO4 decreases it. We also found that the amount of C1q protein accumulation in hippocampus, which may represent the accumulation of senescent synapses with enhanced vulnerability to complement-mediated degeneration, is highly dependent on APOE alleles: C1q accumulation was significantly reduced in APOE2 knock-in (KI) animals and was significantly increased in APOE4 KI animals compared with APOE3 KI animals. These studies reveal a novel allele-dependent role for APOE in regulating the rate of synapse pruning by astrocytes. They also suggest the hypothesis that AD susceptibility of APOE4 may originate in part from defective phagocytic capacity of astrocytes which accelerates the rate of accumulation of C1q-coated senescent synapses, enhancing synaptic vulnerability to classical-complement-cascade mediated neurodegeneration.A lzheimer's disease (AD), the most common cause of dementia, is characterized clinically by a progressive and irreversible loss of cognitive functions. The neuropathological hallmarks of AD include profound synaptic loss and selective neuronal cell death, as well as the formation of extracellular amyloid beta plaques (Aβ) (1) and intracellular neurofibrillary tangles (2). Most cases of AD are the late-onset form, which develops after age 60. The causes of lateonset AD are not yet completely understood; however, genetic studies have shown that apolipoprotein E (APOE) alleles profoundly affect AD susceptibility, with APOE4 being the major genetic risk factor. APOE, a 299-amino acid lipid transport protein, has three common isoforms in humans-APOE2 (Cys-112 and -158), APOE3 (Cys-112 and Arg-158), and APOE4 (Arg-112 and -158)-that are products of alleles at a single gene locus (3, 4). The APOE3 is the most common and mediates intermediate risk for AD. The APOE4 allele is significantly overrepresented in lateonset AD patients and has a dosage effect on the risk and age of onset of AD (5), whereas APOE2 is protective against AD (6). Moreover, recent whole-genome sequencing of humans that age without developing diseases showed that there is a significant depletion of APOE4 alleles in the healthy aging population (7). How do different APOE isoforms influence the age of onset and course of d...