RNA Sequencing (RNA-Seq) analysis of sex-matched neural stem cells derived from early-onset Alzheimer’s disease (EOAD), late-onset Alzheimer’s disease (LOAD), and wild-type controls

Neural stem cells derived from early-onset Alzheimer’s disease (EOAD) patients with PSEN1 mutations, late-onset Alzheimer’s disease (LOAD) patients with APOE4 genotypes, and sex-matched wild-type (WT) controls were cultured and differentiated to neurons. Undifferentiated cells (UD, cultured for 1 day) and differentiated cells (DIF, cultured for 35 days) were compared to study gene expression changes. Oligomeric amyloid beta (Aβ, 0.5 µM) was applied to differentiated WT neurons for 24 hours prior to RNA sequencing. Differential gene expression analysis revealed that genetic background differences between healthy controls, as well as between EOAD and LOAD, contribute as many expression changes as AD-specific mutations. Comparing differentiation-induced gene expression changes between AD neurons and corresponding healthy controls circumvents background variability and highlights disease-specific alterations.Analysis of over 100 AD-associated genes showed altered expression in differentiated EOAD and LOAD neurons, consistent with roles in neuronal functions and AD etiopathogenesis. Notably, LOAD neurons, but not EOAD neurons, exhibited significant deficiencies in heme and redox homeostasis, with reduced expression of genes associated with heme metabolism, oxidative phosphorylation, and NAD/NADH homeostasis. These deficiencies may underlie neuronal dysfunction and contribute to LOAD pathogenesis. Gene Ontology enrichment analysis identified pathways uniquely dysregulated in EOAD and LOAD, offering insights into the molecular mechanisms distinguishing these forms of Alzheimer’s disease. This study emphasizes the critical role of redox and heme homeostasis in LOAD and identifies gene expression patterns altered specifically by AD mutations.