Spatial and single-nucleus transcriptomic analysis of genetic and sporadic forms of Alzheimer's Disease.

The pathogenesis of Alzheimer's disease (AD) depends on environmental and heritable factors, with remarkable differences evident between individuals at the molecular level. Here we present a transcriptomic survey of AD using spatial transcriptomics (ST) and single-nucleus RNA-seq in cortical samples from early-stage AD, late-stage AD, and AD in Down Syndrome (AD in DS) donors. Studying AD in DS provides an opportunity to enhance our understanding of the AD transcriptome, potentially bridging the gap between genetic mouse models and sporadic AD. Our analysis revealed spatial and cell-type specific changes in disease, with broad similarities in these changes between sAD and AD in DS. We performed additional ST experiments in a disease timecourse of 5xFAD and wildtype mice to facilitate cross-species comparisons. Finally, amyloid plaque and fibril imaging in the same tissue samples used for ST enabled us to directly link changes in gene expression with accumulation and spread of pathology.

Alzheimer's disease ferroptotic associations with oxidative damage and neuronal loss.

The role of reactive iron in Alzheimer's Disease (AD) remains unresolved. Little is known of how AD may alter iron transport, glutathione-mediated oxidative repair, and their associations with ApoE alleles. Postmortem brain intravascular blood was minimized by washing minced brain (n=24/group). HNE from iron-associated lipid peroxidation increased in AD prefrontal cortex by 50% for whole tissue and in subcellular lipid rafts, where Aß-peptides are produced. HNE correlated with iron storage ferritin light chain (FTL; r=0.35); both were higher in ApoE4. Iron chelation by DFO in EFAD mice decreased HNE consistent with ferroptosis. Neuronal and synaptic loss in AD was inversely correlated to FTL (r=-0.55). AD decreased levels of ferroptosis suppressor protein 1, glutamate cysteine ligase modulator subunit (GCLM), and lipid raft glutathione peroxidase 4 (GPx4), mitigators of ferroptosis. These findings provide a mechanistic framework for iron-associated neurodegeneration during AD by impaired lipid peroxidation repair mechanisms involving glutathione.

Amyloid futures in the expanding pathology of brain aging and dementia.

Positron emission tomography (PET) imaging studies of Alzheimer's disease (AD) patients show progressive increases of fibrillar Aß-amyloid. Because current PET ligands underestimate nonfibrillar forms, we assayed soluble Aß in AD and controls. To identify the mechanisms responsible for soluble Aß 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 Aß40 and Aß42 were similar for intermediate- and later-stage AD (Braak 2-3 and 4-6). Clinical-grade AD showed a greater increase in soluble Aß40 than Aß42 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 Aß levels in controls with AD contrasts with the PET findings on fibrillar Aß. These findings further support fibrillar Aß as a biomarker for AD treatments and show the need for more detailed postmortem analysis of diverse soluble and insoluble Aß aggregates in relation to PET.

Single-nucleus chromatin accessibility and transcriptomic characterization of Alzheimer's disease.

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.