Major changes in AD brain gene expression caused by the T9861C mtDNA mutation

Abstract

AbstractBackgroundEvidence of mitochondrial dysfunction in Alzheimer’s Disease (AD) has accumulated over the years. We have previously identified a mutation in mitochondrial DNA (mtDNA) that is strongly associated with AD. This T9861C mutation changes a phenylalanine into a leucine at amino acid position 219 of cytochrome c oxidase subunit 3, resulting in a significant reduction of cytochrome oxidase activity. We report the effect of this mutation on the expression of genes involved in mitochondrial function in AD brains.MethodTotal RNA sequencing with ribosome depletion was performed on frozen archival tissue from parietal cortex of three control and eight sporadic AD (four AD, and four AD+ (AD patients possessing the T9861C mtDNA mutation)) brains. Reads were aligned to a transcriptome reference (Ensemble, GCRh38) containing all annotated mRNA and noncoding RNA using kallisto bus (v0.48). Read counts were calculated for genes using bustools (v0.41). Count data were analyzed using RNAfuzzyApp. Read count normalization was performed using TMM and differential gene expression was determined using edgeR. Pathway enrichment was performed using Gene Ontology (GO).ResultThe heatmap shown identifies a total of 472 deferentially expressed genes (DEGs, p value <0.05, FDR <0.05) in the comparison of control vs AD vs AD+ samples. Principal component analysis shows that gene expression in AD samples is significantly different from that in controls and that a more striking difference exists between the AD+ samples and both control and AD samples. The 472 DEGs can be grouped into five clusters. These clusters impact a variety of mitochondrial functions related to synaptic signaling, cell junctions, neuron projections, the HIF‐1 signaling pathway, voltage‐gated channel activity and carbohydrate metabolism.ConclusionThe presence of the T9861C mutation in the brains of AD patients has a significant effect on expression of the brain transcriptome in the parietal cortex. There is a general and robust decrease in expression of the majority of DEGs relative to control and non‐mutation containing AD brains. There is also a smaller number of DEGs that are upregluated compared to control and non‐mutation containing AD brains. These gene expression changes impact mitochondrial function resulting in neuronal failure and neurodegeneration.