DNA Methylation Alteration in Early‐Stage of PSEN1/PSEN2 Gene Double Knockout Mouse Models: Integrated Bioinformatics Analysis of Hippocampal Changes Underlying Age‐Related Neurodegeneration

ABSTRACT Age‐related neuronal loss is a critical feature of neurodegenerative disorders, including Alzheimer's disease (AD), but its underlying molecular mechanisms, particularly those involving epigenetic regulation, remain incompletely understood. To analyze DNA methylation patterns in early‐stage AD pathogenesis, we employed female presenilin‐1/presenilin‐2 double knockout (PSEN1/PSEN2 dKO, hereafter referred to as dKO) mice as a model system, This animal model have the age‐dependent progressive neurodegenerative changes characteristic of neurodegenerative disorders. Using reduced representation bisulfite sequencing (RRBS), we comprehensively profiled hippocampal DNA methylation patterns in 9‐month‐old dKO mice compared with age‐matched wild‐type controls. Based on RRBS detection results, subsequent bioinformatics analysis through Bismark (v0.7.4) and DAVID v6.8 revealed 1216 differentially methylated sites across multiple chromosomes, corresponding to 796 genes. Through stringent filtering criteria, we identified 50 candidate genes exhibiting significant methylation changes in dKO hippocampal tissue as shown in hierarchical clustering. These genes were functionally enriched in DNA‐dependent transcriptional regulation ( p < 0.01) and protein binding activities ( p < 0.05), with pathway analysis highlighting their involvement in ErbB signaling (FDR = 0.03), melanogenesis (FDR = 0.04), and oncogenic pathways (FDR = 0.05). Our study identifies significant hippocampal DNA methylation changes during the early stages of neurodegeneration in dKO mice. These epigenetic alterations highlight pathways potentially contributing to presenilin‐dependent neuronal loss and suggests potential targets for modulating neurodegeneration linked to presenilin dysfunction.