Histone acetylation in an Alzheimer's disease cell model promotes homeostatic amyloid-reducing pathways

Alzheimer's Disease (AD) is a disorder characterized by cognitive decline, neurodegeneration, and accumulation of amyloid plaques and tau neurofibrillary tangles in the brain. Dysregulation of epigenetic histone modifications may lead to expression of transcriptional programs that play a role either in protecting against disease genesis or in worsening of disease pathology. One such histone modification, acetylation of histone H3 lysine residue 27 (H3K27ac), is primarily localized to genomic enhancer regions and promotes active gene transcription. We previously discovered H3K27ac to be more abundant in AD patient brain tissue compared to the brains of age-matched non-demented controls. In this study, we use iPSC-neurons derived from familial AD patients with an amyloid precursor protein (APP) duplication (APPDup neurons) as a model to study the functional effect of lowering CBP/P300 enzymes that catalyze H3K27ac. We found that homeostatic amyloid-reducing genes were upregulated in the APPDup neurons compared to non-demented controls. We lowered CBP/P300 to reduce H3K27ac, which led to decreased expression of numerous of these homeostatic amyloid-reducing genes, along with increased extracellular secretion of a toxic amyloid-ß species, Aß(1-42). Our findings suggest that epigenomic histone acetylation, including H3K27ac, drives expression of compensatory genetic programs in response to AD-associated insults, specifically those resulting from APP duplication, and thus may play a role in mitigating AD pathology in neurons. Overall design: The purpose of this experiment is to compare the gene expression changes of human iPSC-neurons treated with EP300 or CBP KD with human iPSC-neurons treated with CTRL RNAi KD, and to compare the responses to knockdown between neurons with an APP duplication familial AD background vs control, non-demented control background. iPSCs from APP duplication donors (APPDup1 and APPDup2) w as well as from NDC donors (NDC 1 and NDC2) were obtained as a generous gift from the laboratory of Lawrence Goldstein. Undifferentiated iPSCs were cultured and harvested and mRNA was extracted to yield the samples labled "iPSC". iPSCs were differentiated and treated with either EP300, CBP, or CTRL RNAi and cultured for 21 days to yield the samples labeled "neuron". mRNA was isolated from 500 ng of RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490L) to prepare libraries with NEBNext Ultra II Directional RNA Library Prep Kit (NEB E7760L) following manufacture's instruction. RNA libraries were pooled and sequenced with NextSeq 500/550 High Output Kit (75 cycles) v2.5 kit (illumina 20024906) on NextSeq 550 platform (illumina) using paired-end sequencing (42:6:0:42).