Abstract

Alzheimer’s disease (AD) is the most common form of dementia and is characterized by the accumulation of amyloid plaques and tau-based neurofibrillary tangles, ultimately leading to progressive neurodegeneration and brain atrophy. Apolipoprotein E (APOE) plays a central role in lipid transport and distribution throughout the body, including within the central
nervous system (CNS), where it is predominantly synthesized and secreted by astrocytes. The human APOE gene encodes three major isoforms--APOE2, APOE3, and APOE4. APOE4 is recognized as the most significant genetic risk factor for sporadic AD and APOE2 is associated with reduced AD risk and appears to confer neuroprotection, while APOE3 is the most prevalent and generally considered risk-neutral. Despite these associations, the molecular mechanisms underlying the isoform-specific effects of APOE on brain function and disease risk remain incompletely defined.
In this study, we leveraged transcriptomic data from two publicly available RNA-seq datasets (GSE18867 and GSE234711) derived from brain tissue of human APOE-targeted replacement (TR) mice expressing APOE2, APOE3, or APOE4 isoforms. Brain samples were collected from 12- and 18-month-old mice to evaluate aging-associated gene expression
changes across APOE genotypes. Differentially expressed genes (DEGs) were identified using a false discovery rate (FDR) threshold of <0.05 and | log2 fold change | > 0.25.
Compared to APOE3, APOE2 TR mice exhibited 250 upregulated and 464 downregulated genes, while APOE4 TR mice displayed 1,021 upregulated and 993 downregulated genes.
Among the DEGs, Pla2g4e, a member of the group IV phospholipase A2 family, was significantly upregulated in APOE2 TR brains at both 12- and 18-month time points compared to APOE3 and APOE4 mice. Notably, other group IV PLA2 family members did not exhibit similar changes. PLA2G4E exhibits unique enzymatic activity with a preference for N-acyltransferase reactions over phospholipid hydrolysis, generating N-acyl
phosphatidylethanolamines (NAPEs). NAPEs serve as precursors to N-acyl ethanolamines (NAEs), a group of lipid signaling molecules that includes the endocannabinoid anandamide. The upregulation of Pla2g4e in APOE2 mice may enhance NAPE production. At the same time, expression levels of NAPE-degrading enzymes Faah and Naaa remained unchanged
across APOE genotypes, suggesting a potential accumulation of NAPEs in APOE2 brains.
 
NAPEs are lipid neurotransmitters known to rise following brain injury or exposure to
neurotoxic stress and are thought to exert protective effects. They also serve as substrates for N-acylphosphatidylethanolamine phospholipase D (Napepld), which produces NAEs, another group of lipid neurotransmitters. Although Napepld expression was only slightly elevated in APOE2 brains (P > 0.05), the combined upregulation of Pla2g4e and stable expression of NAPE-degrading enzymes supports the hypothesis that both NAPEs and NAEs are increased in APOE2 mice, contributing to a more neuroprotective lipid neurotransmitters’ environment.
Another gene of interest is Cyp2j13, a cytochrome P450 enzyme involved in lipid metabolism, which converts arachidonic acid into epoxyeicosatrienoic acids (EETs), also
bioactive lipid neurotransmitters with vasoprotective and neuroprotective functions. Cyp2j13 showed a similar expression pattern to Pla2g4e, with significantly increased expression in the brains of APOE2 mice compared to APOE3 and APOE4. Given the protective role of EETs against ischemic and neurodegenerative damage, the upregulation of Cyp2j13 may contribute to the enhanced resilience observed in APOE2 brains.
Conclusion
This study reveals novel isoform-specific regulation of lipid messenger genes in aging APOE-targeted mouse brains. The selective upregulation of Pla2g4e and Cyp2j13 in APOE2 mice suggests a mechanistic link between APOE genotype and the modulation of
neuroprotective lipid neurotransmitters, including NAPEs, NAEs, and EETs. These findings support a model in which APOE2 confers protection against neurodegeneration through enhanced lipid signaling and reduced inflammation. Furthermore, PLA2G4E and CYP2J13 (human ortholog of Cyp2j13) emerge as promising targets for future therapeutic strategies aimed at promoting neuroprotection and mitigating Alzheimer’s disease progression.