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The role of reactive iron in Alzheimer’s Disease (AD) has major gaps. Little is known of AD changes in iron transport, glutathione-mediated oxidative repair, and associations with ApoE alleles. Intravascular blood was minimized by washing minced postmortem brains. HNE from iron-associated lipid peroxidation was increased in AD prefrontal cortex by 50% for whole tissue and subcellular lipid rafts, where Aβ-peptides are produced. Proteins mediating iron deposition and oxidative repair were extensively altered by AD. Protein oxidation was proportionate to the iron storage protein ferritin light chain (FTL); both higher in ApoE4. Loss of neurons and synapses in AD was proportionate to FTL. Iron transport was impaired with lower transferrin, transferrin receptor, and ferroportin. AD decreased Ferroptosis suppressor protein 1 and glutamate cysteine ligase modulator subunit (GCLM), which regulates glutathione synthesis. These findings provide a mechanistic framework for iron-associated neurodegeneration during AD through impairment of lipid peroxidation repair mechanisms involving glutathione.Graphical AbstractHypothesis: lipid peroxidation is driven by increased iron stores and decreased antioxidant defenses during AD. Schema shows proteins that mediate iron metabolism in relation to lipid peroxidation (HNE) and antioxidant defenses in prefrontal cortex. AD-associated increase (red), decrease (blue), or no change (grey) relative to cognitively normal elderly controls. Aβ; amyloid beta, ALDH2; alcohol dehydrogenase, APP; amyloid precursor protein, DMT1; divalent metal transporter 1; FPN, ferroportin; FSP1, ferroptosis suppressor protein 1; FTH1, ferritin heavy chain; FTL; ferritin light chain; GCLC, glutathione cysteine ligase catalytic subunit; GCLM, glutathione cysteine ligase modulator; GPx4, glutathione peroxidase 4; GSH, glutathione; GSSG, glutathione disulfide; GSTA4, glutathione S-transferase A4; HMOX; heme oxygenase; IRP, iron regulatory protein; LAT1, large neutral amino acid transporter 1; LOOH, Lipid hydroperoxides; Nrf2, Nuclear factor erythroid 2-related factor 2; Prdx6, peroxiredoxin 6; TF, transferrin, TfR; Transferrin receptor; xCT, cysteine-glutamate antiporter.

Positron emission tomography (PET) imaging studies of Alzheimer's disease (AD) patients show progressive increases of fibrillar Aβ-amyloid. Because current PET ligands underestimate nonfibrillar forms, we assayed soluble Aβ in AD and controls. To identify the mechanisms responsible for soluble Aβ in AD brains, we examined lipid rafts (LRs), where amyloid precursor protein (APP) is enzymatically processed. Frontal cortex was compared with cerebellum, which has minimal AD pathology. Compared with cognitively normal controls (CTL; Braak 0-1), elevations of soluble Aβ40 and Aβ42 were similar for intermediate- and later-stage AD (Braak 2-3 and 4-6). Clinical-grade AD showed a greater increase in soluble Aβ40 than Aβ42 relative to CTL. LR raft yield per gram AD frontal cortex was 20% below that of controls, whereas cerebellar LR did not differ by Braak score. The extensive overlap of soluble Aβ levels in controls with AD contrasts with the PET findings on fibrillar Aβ. These findings further support fibrillar Aβ as a biomarker for AD treatments and show the need for more detailed postmortem analysis of diverse soluble and insoluble Aβ aggregates in relation to PET.

The gene-regulatory landscape of the brain is highly dynamic in health and disease, coordinating a menagerie of biological processes across distinct cell types. Here, we present a multi-omic single-nucleus study of 191,890 nuclei in late-stage Alzheimer’s disease (AD), accessible through our web portal, profiling chromatin accessibility and gene expression in the same biological samples and uncovering vast cellular heterogeneity. We identified cell-type-specific, disease-associated candidate cis-regulatory elements and their candidate target genes, including an oligodendrocyte-associated regulatory module containing links to APOE and CLU. We describe cis-regulatory relationships in specific cell types at a subset of AD risk loci defined by genome-wide association studies, demonstrating the utility of this multi-omic single-nucleus approach. Trajectory analysis of glial populations identified disease-relevant transcription factors, such as SREBF1, and their regulatory targets. Finally, we introduce single-nucleus consensus weighted gene coexpression analysis, a coexpression network analysis strategy robust to sparse single-cell data, and perform a systems-level analysis of the AD transcriptome. An integrative analysis of single-nucleus assay for transposase-accessible chromatin with sequencing and RNA sequencing in normal and Alzheimer’s disease brain tissue identifies cell-type-specific cis-regulatory elements and candidate target genes at disease-associated loci.