Metabolomic Signatures of Alzheimer's Disease Indicate Brain Region-Specific Neurodegenerative Progression

Abstract

Pathological mechanisms contributing to Alzheimer's disease (AD) are still elusive. Here, we identified the metabolic signatures of AD in human post-mortem brains. Using ¹H NMR spectroscopy and an untargeted metabolomics approach, we identified (1) metabolomic profiles of AD and age-matched healthy subjects in post-mortem brain tissue, and (2) region-common and region-unique metabolome alterations and biochemical pathways across eight brain regions revealed that BA9 was the most affected. Phenylalanine and phosphorylcholine were mainly downregulated, suggesting altered neurotransmitter synthesis. N-acetylaspartate and GABA were upregulated in most regions, suggesting higher inhibitory activity in neural circuits. Other region-common metabolic pathways indicated impaired mitochondrial function and energy metabolism, while region-unique pathways indicated oxidative stress and altered immune responses. Importantly, AD caused metabolic changes in brain regions with less well-documented pathological alterations that suggest degenerative progression. The findings provide a new understanding of the biochemical mechanisms of AD and guide biomarker discovery for personalized risk prediction and diagnosis.

Keywords: GABA; aging; cognitive function; energy metabolism; glucose metabolism; mitochondrial dysfunction; neurodegenerative disease; neuropathology; neurotransmission; oxidative stress; phenylalanine; proton nuclear magnetic resonance (1H NMR) spectroscopy.

Figure 1

Post-mortem brain tissues (Brodmann areas BA9, BA17, BA22, BA24, BA40, DN, HPC, and PB) were retrieved from the Calgary Brain Bank from categorized control (non-AD) and AD patients. Tissues were processed (metabolic extraction and NMR sample preparation) and analyzed using ¹H NMR spectroscopy. Both univariate analysis and a multivariate machine learning approach involving permutation testing were used to determine metabolite signatures across the eight brain regions. The results focus on the differences observed in AD tissues compared to non-AD controls. The complete list of metabolites altered in AD tissues compared to controls was used for the pathway topology analysis.

Figure 2

Brain heat maps illustrating the total number of metabolites and regulation changes across brain regions in AD tissues compared to non-AD controls. (A) The darkest blue indicates the brain region (BA9) with the most metabolic changes in AD (BA9), while the lighter blue indicates the least number of changes (PB). (B) Bar graph showing the actual number of metabolites altered in each region. (C) The heat map shows the predominant metabolic regulation changes for each brain region, with red indicating downregulation and green showing upregulation. (D) Bar graph indicating % of metabolites upregulated and downregulated in each brain region.

Figure 3

Venn diagrams showing common and unique metabolites across brain regions and specific metabolites identified via VIAVC analysis as biomarkers of AD. (A–E) Illustrate common metabolites found across various regions that may serve as potential biomarkers of AD. For example, four common metabolites were identified in BA9, BA40, and DN that play roles in signaling between cortex and cerebellum. (F–O) Illustrate potential biomarkers of AD, as determined via VIAVC best subset analysis. NAA (K) and GABA (H) were predominately upregulated in all brain regions of AD tissues, while phenylalanine and phosphorylcholine were downregulated.

Figure 4

Sub- and super-biochemical pathways involved in neurotransmission and energy regulation throughout brain regions in AD compared to non-AD controls. (A) Specific biochemical pathways affected multiple brain regions, with alanine, aspirate, and glutamate metabolism being altered in 6/8 regions. (B) Illustration of sub-pathways within super-pathways, showing that most altered metabolites belonged to the amino acid category. (C,D) Pie diagrams indicating AD-altered pathways involved in neurotransmission and energy regulation.