Microglial ERK signaling is a critical regulator of pro-inflammatory immune responses in Alzheimer’s disease

ABSTRACTBackgroundThe mitogen-activated protein kinase (MAPK) pathway is a central regulator of gene expression, pro-survival signaling, and inflammation. However, the importance of MAPK pathway signaling in regulating microglia-mediated neuroinflammation in Alzheimer’s Disease (AD) remains unclear. Here we examined the role of MAPK signaling in microglia using pre-clinical in-vitro and in-vivo models of AD pathology integrated with quantitative proteomics studies of post-mortem human brains.MethodsWe performed multiplexed immunoassay analyses of MAPK phosphoproteins, particularly ERK1/2, in acutely-isolated microglia and brain tissue from wild-type and 5xFAD mice. Neuropathological studies of mouse and human brain tissues were performed to quantify total and phosphorylated ERK protein in AD. The importance of ERK signaling in unstimulated and interferon γ (IFNγ)-stimulated primary microglia cultures was investigated using NanoString transcriptomic profiling, coupled with functional assays of amyloid β (Aβ) and neuronal phagocytosis. Receptor tyrosine kinases (RTKs) likely responsible for ERK signaling in homeostatic microglia and disease-associated-microglia (DAM) states and ERK-regulated human AD risk genes were identified using gene expression data. Total and phosphorylated MAPKs in human post-mortem brain tissues were measured in quantitative proteomic datasets.ResultsPhosphorylated ERK was the most strongly up-regulated signaling protein within the MAPK pathway in microglia acutely isolated from 5xFAD brains. Neuroinflammatory transcriptomic and phagocytic profiling of mouse microglia confirmed that ERK is a critical regulator of IFNγ-mediated pro-inflammatory activation of microglia, although it was also important for constitutive microglial functions. Phospho-ERK was an upstream regulator of disease-associated microglia (DAM) gene expression (Trem2, Tyrobp), as well as of several human AD risk genes (Bin1, Cd33, Trem2, Cnn2). Among RTKs that signal via ERK, CSF1R and MERTK were primarily expressed by homeostatic microglia while AXL and FLT1 were likely regulators of ERK signaling in DAM. Within DAM, FLT4 and IGF1R were specifically expressed by pro- and anti-inflammatory DAM sub-profiles respectively. In quantitative proteomic analyses of post-mortem human brains from non-disease, asymptomatic and cognitively-impaired AD cases, ERK1 and ERK2 were the only MAPK pathway signaling proteins with increased protein expression and positive associations with neuropathological grade. Moreover, in a phospho-proteomic study of post-mortem human brains from controls, asymptomatic and symptomatic AD cases, we found evidence for a progressive increased flux through the ERK signaling pathway.ConclusionsOur integrated analyses using pre-clinical models and human proteomic data strongly suggest that ERK phosphorylation in microglia is a critical regulator of pro-inflammatory immune response in AD pathogenesis and that modulation of ERK via upstream RTKs may reveal novel avenues for immunomodulation.

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RNA Quality in Post-mortem Human Brain Tissue Is Affected by Alzheimer’s Disease

Frontiers in Molecular Neuroscience ◽

10.3389/fnmol.2021.780352 ◽

2021 ◽

Vol 14 ◽

Author(s):

Blake Highet ◽

Remai Parker ◽

Richard L. M. Faull ◽

Maurice A. Curtis ◽

Brigid Ryan

Keyword(s):

Gene Expression ◽

Alzheimer’S Disease ◽

Parkinson’S Disease ◽

Alzheimer's Disease ◽

Neurodegenerative Disease ◽

Huntington's Disease ◽

Brain Tissue ◽

Post Mortem ◽

Rna Quality ◽

Neurologically Normal

Gene expression studies of human post-mortem brain tissue are useful for understanding the pathogenesis of neurodegenerative disease. These studies rely on the assumption that RNA quality is consistent between disease and neurologically normal cases; however, previous studies have suggested that RNA quality may be affected by neurodegenerative disease. Here, we compared RNA quality in human post-mortem brain tissue between neurologically normal cases (n = 14) and neurodegenerative disease cases (Alzheimer’s disease n = 10; Parkinson’s disease n = 11; and Huntington’s disease n = 9) in regions affected by pathology and regions that are relatively devoid of pathology. We identified a statistically significant decrease in RNA integrity number (RIN) in Alzheimer’s disease tissue relative to neurologically normal tissue (mixed effects model, p = 0.04). There were no statistically significant differences between neurologically normal cases and Parkinson’s disease or Huntington’s disease cases. Next, we investigated whether total RNA quality affected mRNA quantification, by correlating RIN with qPCR threshold cycle (CT). CT values for all six genes investigated were strongly correlated with RIN (p < 0.05, Pearson correlation); this effect was only partially mitigated by normalization to RPL30. Our results indicate that RNA quality is decreased in Alzheimer’s disease tissue. We recommend that RIN should be considered when this tissue is used in gene expression analyses.

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Increased excitatory to inhibitory synaptic ratio in parietal cortex samples from individuals with Alzheimer’s disease

Nature Communications ◽

10.1038/s41467-021-22742-8 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Julie C. Lauterborn ◽

Pietro Scaduto ◽

Conor D. Cox ◽

Anton Schulmann ◽

Gary Lynch ◽

...

Keyword(s):

Gene Expression ◽

Alzheimer’S Disease ◽

Alzheimer's Disease ◽

Down Syndrome ◽

Parietal Cortex ◽

Direct Evidence ◽

Synaptic Membranes ◽

Post Mortem ◽

Expression Studies ◽

Gene Expression Studies

AbstractSynaptic disturbances in excitatory to inhibitory (E/I) balance in forebrain circuits are thought to contribute to the progression of Alzheimer’s disease (AD) and dementia, although direct evidence for such imbalance in humans is lacking. We assessed anatomical and electrophysiological synaptic E/I ratios in post-mortem parietal cortex samples from middle-aged individuals with AD (early-onset) or Down syndrome (DS) by fluorescence deconvolution tomography and microtransplantation of synaptic membranes. Both approaches revealed significantly elevated E/I ratios for AD, but not DS, versus controls. Gene expression studies in an independent AD cohort also demonstrated elevated E/I ratios in individuals with AD as compared to controls. These findings provide evidence of a marked pro-excitatory perturbation of synaptic E/I balance in AD parietal cortex, a region within the default mode network that is overly active in the disorder, and support the hypothesis that E/I imbalances disrupt cognition-related shifts in cortical activity which contribute to the intellectual decline in AD.

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Genome-Wide Integrative Analysis Reveals Common Molecular Signatures in Blood and Brain of Alzheimer’s Disease

Biointerface Research in Applied Chemistry ◽

10.33263/briac112.86868701 ◽

2020 ◽

Vol 11 (2) ◽

pp. 8686-8701

Keyword(s):

Gene Expression ◽

Alzheimer’S Disease ◽

Alzheimer's Disease ◽

Enrichment Analysis ◽

Integrative Analysis ◽

Gene Set Enrichment Analysis ◽

Brain Gene Expression ◽

Sensitivity Specificity ◽

Eqtl Data ◽

Brain Tissues

The currently utilized neuroimaging and cerebrospinal fluid-based detection of Alzheimer’s disease (AD) suffer several limitations, including sensitivity, specificity, and cost. Therefore, the identification of AD by analyzing blood gene expression may ameliorate the early diagnosis of the AD. We aimed to identify common genes commonly deregulated in blood and brain in AD. Comprehensive analysis of blood and brain gene expression datasets of AD, eQTL, and epigenetics data was analyzed by the integrative bioinformatics approach. The integrative analysis showed nine differentially expressed genes common to blood cells and brain (CNBD1, SUCLG2-AS1, CCDC65, PDE4D, MTMR1, C3, SLC6A15, LINC01806, and FRG1JP). Analysis of SNP and cis-eQTL data showed 18 genes; namely, HSD17B1, GAS5, RPS5, VKORC1, GLE1, WDR1, RPL12, MORN1, RAD52, SDR39U1, NPHP4, MT1E, SORD, LINC00638, MCM3AP-AS1, GSDMD, RPS9, and GNL2 were observed deregulated AD blood and brain tissues. Functional gene set enrichment analysis demonstrated a significant association of these genes in neurodegeneration-associated molecular pathways. Integrative biomolecular networks revealed dysregulation of several hub transcription factors and microRNAs in AD. Moreover, hub genes were observed associated with significant histone modification. This study detected common molecular biomarkers and pathways in blood and brain tissues in AD that may be potential biomarkers and therapeutic targets in AD.

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Monocyte-specific changes in gene expression implicate LACTB2 and PLIN2 in Alzheimer’s disease

10.1101/2020.06.05.136275 ◽

2020 ◽

Author(s):

Janet C. Harwood ◽

Ganna Leonenko ◽

Rebecca Sims ◽

Valentina Escott-Price ◽

Julie Williams ◽

...

Keyword(s):

Gene Expression ◽

Alzheimer’S Disease ◽

Alzheimer's Disease ◽

Association Studies ◽

Genetic Data ◽

Genome Wide Association ◽

Genome Wide Association Studies ◽

Risk Genes ◽

Genome Wide ◽

Immune Pathways

AbstractMore than 50 genetic loci have been identified as being associated with Alzheimer’s disease (AD) from genome-wide association studies (GWAS) and many of these are involved in immune pathways and lipid metabolism. Therefore, we performed a transcriptome-wide association study (TWAS) of immune-relevant cells, to study the mis-regulation of genes implicated in AD. We used expression and genetic data from naive and induced CD14+ monocytes and two GWAS of AD to study genetically controlled gene expression in monocytes at different stages of differentiation and compared the results with those from TWAS of brain and blood. We identified nine genes with statistically independent TWAS signals, seven are known AD risk genes from GWAS: BIN1, PTK2B, SPI1, MS4A4A, MS4A6E, APOE and PVR and two, LACTB2 and PLIN2/ADRP, are novel candidate genes for AD. Three genes, SPI1, PLIN2 and LACTB2, are TWAS significant specifically in monocytes. LACTB2 is a mitochondrial endoribonuclease and PLIN2/ADRP associates with intracellular neutral lipid storage droplets (LSDs) which have been shown to play a role in the regulation of the immune response. Notably, LACTB2 and PLIN2 were not detected from GWAS alone.

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Human Tau Isoform Aggregation and Selective Detection of Misfolded Tau from Post-Mortem Alzheimer’s Disease Brains

10.1101/2019.12.31.876946 ◽

2020 ◽

Cited By ~ 1

Author(s):

Ling Wu ◽

Zerui Wang ◽

Shradha Ladd ◽

Darren T. Dougharty ◽

Sidharth S. Madhavan ◽

...

Keyword(s):

Alzheimer’S Disease ◽

Alzheimer's Disease ◽

High Specificity ◽

Full Length ◽

Spectrometric Analysis ◽

Kinetic Properties ◽

Post Mortem ◽

C Terminus ◽

Tau Isoforms ◽

Brain Tissues

AbstractTau aggregates are present in a large number of neurodegenerative diseases known as “tauopathies”, including Alzheimer’s disease (AD). As there are six human tau isoforms in brain tissues and both 3R and 4R isoforms have been observed in the neuronal inclusions, we tested whether tau isoforms behave differently in aggregation. We discovered that all six tau isoforms are capable of forming PHF-tau like filaments and the 3R tau isoforms aggregate significantly faster than their 4R counterparts. We further mapped key segments of tau isoforms that contribute to their aggregation kinetics, where it was determined that microtubule binding domains R2 and R3 were the major contributors to tau aggregation. To evaluate the feasibility of using the six recombinant tau isoforms as substrates to amplify misfolded tau, we demonstrated that full-length human tau isoforms can seed and detect misfolded tau from the post-mortem AD brain tissues with high specificity by an ultrasensitive technology termed real-time quaking-induced conversion (RT-QuIC). Mass spectrometric analysis of PHF-tau samples extracted from AD brains identified peptides corresponding to all major forms of human brain tau isoforms along with a consensus hyperphosphorylated peptide near the C-terminus. Together, our findings not only reveal new aggregation kinetic properties of human tau isoforms, support the development of methods to quantitatively measure misfolded human tau isoforms in AD brains, but also uncover the capability of full-length human tau isoforms as substrates for “prion-like” tau seeding by RT-QuIC assays that may be used for new biomarker development for AD and other tauopathy diagnosis.

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