Cortical bulk RNA sequencing of APOE-TR mice under calorie restriction and normal diet

The efficacy of calorie restriction (CR) in enhancing cognition, promoting healthy aging, and extending lifespan is well-established. However, the influence of the apolipoprotein E (APOE) genotype, a key modifier of aging and age-related disorder, on the beneficial effects of CR remains unclear. In this study, we utilized humanized APOE mouse models expressing APOE2, APOE3, or APOE4 (referred to as E2, E3, and E4 mice, respectively). These mice were subjected to either standard ad libitum (AL) feeding or 30% CR feeding, starting at 12 months and continuing until 20 months of age (N = 11–20/genotype/group, mixed sex). To investigate how APOE genotype modifies brain transcriptional responses to CR, we performed bulk RNA sequencing on brain cortical tissues including 69 samples from all the groups. The RNA-seq data were adjusted for flow cell, exonic coverage, and extraction batch effects. Using preprocessed gene expression profiles, we conducted weighted gene co-expression network analyses (WGCNA) and differential gene expression analyses. Consistently across both approaches, our results revealed an upregulation of the cholesterol synthesis pathway in E3- and E4-CR mice, but not in E2-CR mice. CR related DEGs also predicted the enhanced myelination, which were further validated through immunofluorescent staining for PDGFRA (an OPC marker), ASPA (an OL marker), and MBP (a myelin sheath protein), as well as electron microscopy of corpus callosum tissues in E3- and E4-CR mice, but not in E2-CR mice. Overall, our study highlights the critical role of APOE genotype in modulating the brain’s response to CR, emphasizing the importance of considering APOE genotype in developing prevention strategies for aging and age-related disorders.