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Identification of Conserved Proteomic Networks in Neurodegenerative Dementia.

ABSTRACT: Data-driven analyses are increasingly valued in modern medicine. We integrate quantitative proteomics and transcriptomics from over 1,000 post-mortem brains from six cohorts representing Alzheimer's disease (AD), asymptomatic AD, progressive supranuclear palsy (PSP), and control patients from the Accelerating Medicines Partnership - Alzheimer's Disease consortium. We define robust co-expression trajectories related to disease progression, including early neuronal, microglial, astrocyte, and immune response modules, and later mRNA splicing and mitochondrial modules. The majority of, but not all, modules are conserved at the transcriptomic level, including module C3, which is only observed in proteome networks and enriched in mitogen-activated protein kinase (MAPK) signaling. Genetic risk enriches in modules changing early in disease and indicates that AD and PSP have distinct causal biological drivers at the pathway level, despite aspects of similar pathology, including synaptic loss and glial inflammatory changes. The conserved, high-confidence proteomic changes enriched in genetic risk represent targets for drug discovery.

SUBMITTER: Swarup V

PROVIDER: S-EPMC8221021 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Frontotemporal dementia (FTD) is a frequent form of early-onset dementia and can be caused by mutations in MAPT encoding the microtubule-associated protein tau. Due to limited availability of neural cells from patients` brains, however, the underlying mechanisms of neurodegeneration in FTD are still only poorly understood. Here, we derived induced pluripotent stem (iPS) cells from individuals with FTD-associated MAPT mutations and differentiated them into neurons for mechanistic studies. Patient-derived neurons demonstrated pronounced tau pathology with increased fragmentation and AT8-immunoreactivity, disturbed neurite extension and increased but reversible oxidative stress response to inhibition of mitochondrial respiration. Furthermore, FTD-neurons showed activation of the unfolded protein response and presented with distinct, disease-associated gene expression profiles in a whole-genome transcriptome analysis. These findings indicate distinct, early neurodegenerative changes in FTD caused by mutant tau and highlight the unique opportunity to use patient-specific iPS cells to identify potential targets for drug screening purposes and therapeutic intervention. RNA samples for microarray analysis were prepared using RNeasy columns (Qiagen, Germany) with on-column DNA digestion. 300 ng of total RNA per sample were used as the input in the linear amplification protocol (Ambion), which involved the synthesis of T7-linked double-stranded cDNAs and 12hrs of in vitro transcription incorporating biotin-labeled nucleotides. Purified and labeled cRNA was then hybridized for 18 hrs onto HumanHT-12 v4 expression BeadChips (Illumina, USA) following the manufacturer’s instructions. After the recommended washing, the chips were stained with streptavidin-Cy3 (GE Healthcare) and scanned using the iScan reader (Illumina) and the accompanying software. The samples were exclusively hybridized as biological replicates. The bead intensities were mapped to the corresponding gene information using BeadStudio 3.2 (Illumina) and background correction was performed using the Affymetrix Robust Multi-array Analysis (RMA) background correction model (Irizarry et al., 2003). Variance stabilization was performed using the log2 scaling, and gene expression normalization was calculated with the quantile method implemented in the lumi package of R-Bioconductor. Data post-processing and graphics were performed with in-house developed functions in MATLAB. Hierarchical clusters of genes and samples were performed with the one minus the sample correlation metric and the Unweighted Pair-Group Method using Average (UPGMA) linkage method.

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Identification of Conserved Proteomic Networks in Neurodegenerative Dementia.

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