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Proteomic profiling of single cells from human prefrontal cortex in Alzheimer's Disease using multiplexed data independent acquisition (plexDIA) mass spectrometry

ABSTRACT: Here we provide a dataset of over 2000 isolated single cells from human prefrontal cortex (Brodmann area 9) from eight female individuals - six Alzheimer's disease patients at distinct stages of disease progression (Braak II, V, VI) and two non-AD control subjects (Braak 0).

INSTRUMENT(S): timsTOF Ultra 2, timsTOF SCP

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Nikolai Slavov

PROVIDER: MSV000098015 | MassIVE | Wed May 28 07:16:00 BST 2025

SECONDARY ACCESSION(S): PXD064377

REPOSITORIES: MassIVE

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Project description:Alzheimer's disease (AD) is a chronic neurodegenerative disorder characterized by progressive deterioration of cognitive function. Evidence suggests a role for epigenetic regulation, in particular the cytosine modifications 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC,) in AD. 5hmC is highly enriched in the nervous system and displays neurodevelopment and age-related changes. To determine the role of 5hmC in AD, we performed genome-wide analyses of 5hmC in DNA from prefrontal cortex of post-mortem AD as well as RNA-Seq to correlate changes in methylation status with transcriptional changes. We also utilized the existing AD fly model to further test the functional significance of these epigenetically altered loci. We identified 325 genes containing differentially hydroxymethylated loci (DhMLs) in both the discovery and replication datasets, and these are enriched for pathways involved in neuron projection development and neurogenesis. Of the 325 genes identified, 140 also showed changes in gene expression by RNA-Seq. Proteins encoded by genes identified in the current analysis form direct protein-protein interactions with AD-associated genes, expanding the network of genes implicated in AD. Furthermore, we identified AD-associated single nucleotide polymorphisms (SNPs) located within or near DhMLs, suggesting that these SNPs may identify regions of epigenetic gene regulation that play a role in AD pathogenesis. Finally using the existing AD fly model we showed that some of these genes could modulate the toxicity associated with AD. Our data implicate neuron projection development and neurogenesis pathways as potential targets in AD. These results indicate that incorporating epigenomic and transcriptomic data with GWAS data can expand the known network of genes involved in disease pathogenesis. Combination of epigenome profiling and Drosophila model enables us to identify the epigenetic modifiers of Alzheimer's disease. University of Kentucky Alzheimer's Disease Research Center (3 control, 3 Alzheimer's) and Emory University Alzheimer's Disease Research Center (2 control, 2 Alzheimer's)

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Proteomic profiling of single cells from human prefrontal cortex in Alzheimer's Disease using multiplexed data independent acquisition (plexDIA) mass spectrometry

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