Fragmentation of apolipoprotein E4 is required for differential expression of inflammation and activation related genes in microglia cells
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE173381 | GEO | 2021/04/27
REPOSITORIES: GEO
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Project description:The APOE gene is diversified by three alleles e2, e3, and e4 encoding corresponding apolipoprotein (apo) E isoforms. The e4 allele promotes age-related cognitive decline, risk of Alzheimer’s disease (AD), and the rate of AD dementia progression. ApoE is produced by astrocytes as high-density lipoprotein-like particles and these are internalized by neurons upon binding to neuron-expressed apoE receptors. ApoE isoforms differentially engage neuronal plasticity through poorly understood mechanisms. We examined here the effects of native apoE lipoproteins produced by immortalized astrocytes homozygous for e2, e3, and e4 alleles on the maturation and the transcriptomic profile of primary hippocampal neurons. Control neurons were grown in the presence of conditioned media from Apoe-/- astrocytes. ApoE2 and apoE3 significantly increase the dendritic arbor branching, the combined neurite length, and the total arbor surface of the hippocampal neurons, while apoE4 fails to produce similar effects and even significantly reduces the combined neurite length compared to the control. ApoE lipoproteins show no systemic effect on dendritic spine density, yet apoE2 and apoE3 increase the mature spines fraction, while apoE4 increases the immature spine fraction. This is associated with opposing effects of apoE2 or apoE3 and apoE4 on the expression of NR1 NMDA receptor subunit and PSD95. There are 1,062 genes differentially expressed across neurons cultured in the presence of apoE lipoproteins compared to the control. KEGG enrichment and gene ontology analyses show common for apoE2 and apoE3 activation of genes involved in neurite branching, and synaptic signaling. In contrast, apoE4 cultured neurons show upregulation of genes related to the glycolipid metabolism, which are involved in dendritic spine turnover and those which are usually silent in neurons and are related to cell cycle and DNA repair. In conclusion our work reveals that lipoprotein particles comprised of various apoE isoforms differentially regulate neuronal development through interaction with neuronal transcriptome. ApoE4 produces a functionally distinct transcriptomic profile, which is associated with attenuated neuronal development. Differential regulation of neuronal transcriptome by apoE isoforms is a newly identified biological mechanism, which has both implication in the development and aging of the CNS.
2022-05-10 | GSE193162 | GEO
Project description:Purpose: RNA-sequencing (RNA-seq) was used to identify the changes in gene expression profile in horse skin fibroblast cell line expressing one of the BPV genes encoding transforming proteins (BPV-E4 and BPV-E4^E1). The whole transcriptome sequencing allows us to establish the influence of BPV gene transfection on host cells and indicates which virus genes can be responsible for the neoplastic process. It is the first study concerning a cell model of horse skin transfected with BPV genes. Such a model could contribute to a more accurate understanding of changes inside cells during viral infection. Methods: The equine fibroblast cell lines were transfected using the nucleofection method with BPV-E4 and BPV-E4^E1 constructs. RNA was isolated from cell lines directly from culture dishes with PureLink™ RNA mini kit. The quality and quantity of obtained libraries (the TruSeq RNA Kit v2 kit (Illumina, San Diego, CA, USA) ) were assessed using Qubit 2.0 (Qubit™ dsDNA BR AssayKit, Invitrogen, Waltham, MA, USA ) and TapeStation 2200 (D100 screencaps, Agilent). Next, the cDNA libraries were sequenced on NextSeq 500 Illumina platform (Illumina, San Diego, CA, USA) and NextSeq 500/550 High Output KIT v 2.5 (75 cycles) according to protocol. The qPCR validation was used to confirm RNA-seq data. Then, the quality of raw reads was checked with FastQC software followed by removal of adapters and reads of low quality (under phred quality of 20) and reads under length of 36 (Flexbar software). Next, the filtered reads were mapped to EquCab3 genome with STAR software and reads were counted to specific gene thresholds provided in Ensembl gtf file version 100 by htseq-count software. Differential expresion extimation was followed with the use of Deseq2 software. Results: The transcriptome profiling allowed us to perform a comparison of the whole expression profile between the control and both BPV-E4 and BPV-E4^E1 groups. According to the comparison of control and BPV-E4 groups, the 1640 DEGs were identified, of which 624 were up-regulated and 1016 down-regulated in the BPV-E4 group. The highest number of DEGs – 3328 were detected from the control and BPV-E4^E1 comparison. Among them, 1626 genes were up-regulated and 1602 down-regulated in the BPV-E4^E1 group compared to control samples. The most overrepresented Gene Ontology Term between control and BPV-E4 groups were negative regulation of cell proliferation – 34 DEGs (FDR<0.002); positive regulation of cell migration – 24 DEGs (FDR<0.0001); cell adhesion and cell migration; 21 DEGs in both GO terms (FDR<0.003 and 0.0005; respectively). The enrichment analysis performed for differentially expressed genes between control and BPV-E4^E1 samples showed the focal adhesion GO terms were overrepresented by 99 DEGs of which 65 were up-regulated and 34 down-regulated (FDR<0.0001). For cells transfected BPV-E4 and BPV-E4^E1 constructs, the most significant were pathways: of the cell cycle, cytoskeleton, and ECM-matrix remodelling; regulation of actin cytoskeleton; focal adhesion and ECM-receptor interaction. The Pathways in cancer were identified uniquely for cells transfected by BPV-E4 construct, while only for BPV-E4^E1 cells the FoxO, Rap1, and TNF-signaling path-ways and Proteoglycans in cancer. Conclusions: The results obtained showed that both transfection types significantly affected cells transcriptome towards cancer transformation. Nevertheless, cells transfected with BPV-E4^E1 genes seem to be closer to the molecular modification that occurred in vivo in equine sarcoids. The present study showed how equine fibroblast cells could be modified, at the molecular level, in the presence of BPV E4 gene. These findings broaden the knowledge about the possible interaction of BPV viruses on host cells.
2022-01-21 | GSE193906 | GEO
Project description:Despite its clear impact on Alzheimer’s Disease (AD) risk, apolipoprotein (apo) E4’s contributions to AD etiology remain poorly understood. Progress in answering this and other questions in AD research has been limited by an inability to model human-specific phenotypes in an in vivo environment. Here we transplanted human induced pluripotent stem cell (hiPSC)-derived neurons carrying normal apoE3 or pathogenic apoE4 into human apoE3 or apoE4 knock-in mouse hippocampi, enabling us to disentangle the effects of apoE4 produced in human neurons and in the brain environment. Using single nucleus RNA-sequencing (snRNA-seq), we identified key transcriptional changes specific to human neuron subtypes in response to endogenous or exogenous apoE4. We also found that Aβ from transplanted human neurons formed plaque-like aggregates, with differences in localization and interaction with microglia depending on the transplant and host apoE genotype. These findings highlight the power of in vivo chimeric disease modeling for studying AD.
2020-06-20 | GSE152867 | GEO
Project description:Alcanivorax sp. E4 strain:E4 Genome sequencing
| PRJNA489579 | ENA
Project description:Bartonella birtlesii E4 strain:E4 Genome sequencing and assembly
| PRJNA169101 | ENA
Project description:The full impact of apolipoprotein E4 (APOE4), the strongest genetic risk factor for Alzheimer's disease (AD), on neuronal and network function remains unclear. We found hippocampal region-specific network hyperexcitability in young APOE4 knock-in (E4-KI) mice which predicted cognitive deficits at old age. Network hyperexcitability in young E4-KI mice was mediated by hippocampal region-specific subpopulations of smaller and hyperexcitable neurons that were eliminated by selective removal of neuronal APOE4. Aged E4-KI mice exhibited hyperexcitable granule cells, a progressive inhibitory deficit, and E/I imbalance in the dentate gyrus, exacerbating hippocampal hyperexcitability. Single-nucleus RNA-sequencing revealed neuronal cell type-specific and age-dependent transcriptomic changes, including Nell2 overexpression in E4-KI mice. Reducing Nell2 expression in specific neuronal types of E4-KI mice with CRISPRi rescued their abnormal excitability phenotypes, implicating Nell2 overexpression as a cause of APOE4-induced hyperexcitability. These findings highlight the early transcriptomic and electrophysiological alterations underlying APOE4-induced hippocampal network dysfunction and its contribution to AD pathogenesis with aging.
2025-12-18 | GSE279550 | GEO
Project description:Cerebrovascular dysfunction is a hallmark feature of Alzheimer's disease (AD). One of the greatest risk factor for AD is the apolipoprotein E4 (E4) allele. APOE4 genotype has been shown to negatively impact on perivascular amyloid clearance, however, its direct influence along with the other APOE variants (APOE2 and APOE3) on the molecular integrity of the cerebrovasculature has not been largely explored. To address this, we employed a 10-plex tandem isobaric mass tag approach in combination with an ultra-high pressure liquid chromatography MS/MS (Q-Exactive) method, to interrogate unbiased proteomic changes in cerebrovessels from AD and healthy control brains on different APOE genotype backgrounds. We first interrogated changes between healthy control homozygote E2/E2, E3/E3 and E4/E4 cases to identify underlying genotype specific effects on cerebrovessels. EIF2 signaling, regulation of eIF4 and 70S6K signaling and mTOR signaling were the top significantly altered pathways in E4/E4 compared to E3/E3 cases. EIF2, nitric oxide and sirtuin signaling pathways were the top significantly altered pathways in E4/E4 compared to E2/E2 cases. We used a Two-way ANOVA analysis to identify AD-dependent changes and their interactions with APOE genotype. The highest number of significantly regulated proteins from this interaction was observed in E3/E4 (192) and E4/E4 (189) cases. As above, EIF2, mTOR signaling and eIF4 and 70S6K signaling were the top three significantly altered pathways in E4 allele carriers (i.e. E3/E4 and E4/E4 genotypes). Of all the cerebrovascular cell specific markers identified in our proteomic analyses, endothelial cell, astrocyte, and smooth muscle cell specific protein markers were significantly altered in E4/E4 cases, while endothelial cells and astrocyte specific protein markers were altered in E3/E4 cases. These proteomic changes provide novel insights to explain the longstanding link between APOE4 and cerebrovascular dysfunction. The early and converging APOE4 dependent changes we identified could provide novel targets in the cerebrovasculature for developing disease modifying strategies to mitigate the effects of APOE4 genotype on increasing the risk for, and the path towards AD pathogenesis.
2021-03-23 | PXD023340 | Pride
Project description:This study assessed the effects of amino terminal ApoE4 fragments (residues 1-151) on modulating the transcriptome of BV2 microglial cells. Treatment with amino terminal ApoE4 fragments caused the upregulation of nearly four-thousand genes, and further analysis revealed a significant upregulation of genes related to the inflammatory immune response. As a control, an amino terminal ApoE3 fragment was tested and produced a similar but reduced level of upregulation of an identical set of genes. This set of genes affected pathways including Toll receptor signaling, chemokine/cytokine signaling and apoptosis signaling. Additionally, each treatment regulated a unique set of genes. Amino terminal ApoE3 fragments uniquely regulated 14 times as many genes (1,674), many of which are involved in physiological functions within microglia. Amino terminal ApoE4 fragments uniquely upregulated 119 genes, with many of the top upregulated genes having unknown functions. Our results suggest that while amino terminal ApoE3 fragments may serve a more physiological role in microglia amino terminal ApoE4 fragments may activate genes with a more pathological purpose. These data support the hypothesis that the link between harboring the APOE4 allele and dementia risk could be enhanced inflammation through activation of microglia.
2020-07-31 | GSE153454 | GEO
Project description:Apolipoprotein E (APOE) is a lipid and cholesterol transport molecule known to influence Alzheimer's disease (AD) risk in an isoform-specific manner. In particular, the APOE E4 allele is the largest genetic risk factor for late-onset sporadic AD. Our recent findings uncovered activated, clonally expanded T cells in AD cerebrospinal fluid (CSF). This T cell phenotype occurred concomitantly with altered expression of APOE in CSF monocytes. Yet, whether APOE variants differentially affect peripheral immunity systems remains unknown. In this study, we performed targeted immune profiling using single-cell epigenetic and transcriptomic analysis of peripheral blood mononuclear cells (PBMC). We analyzed 55 age-matched healthy control (HC) and AD patients with equal distribution of APOE E3/E3, E3/E4, and E4/E4 genotypes. We reveal dysregulation in monocytes and clonally expanded T cells that are distinct to AD patients carrying the APOE E4/E4 genotype. Additionally, we find APOE isoform-dependent chromatin accessibility differences that correspond to RNA expression changes. Cumulatively, these results uncover APOE isoform-dependent changes to peripheral immunity in AD.
2024-03-22 | GSE227991 | GEO