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Differential expression analyses in microglial cells from APP-Psen1/+ Cx3cr1-Cre::ERT2/+ Vhl Flox/– mice treated with tamoxifen vs APP-Psen1/+ Cx3cr1-Cre::ERT2/+ Vhl Flox/– mice non treated

ABSTRACT: Differential expression analyses in microglial cells from APP-Psen1/+ Cx3cr1-Cre::ERT2/+ Vhl Flox/– mice treated with tamoxifen vs APP-Psen1/+ Cx3cr1-Cre::ERT2/+ Vhl Flox/– mice non treated

PROVIDER: PRJNA705986 | ENA |

REPOSITORIES: ENA

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Differential expression analyses in microglial cells from APP-Psen1/+;Cx3cr1-Cre::ERT2/+; Vhl Flox/– mice treated with tamoxifen vs APP-Psen1/+;Cx3cr1-Cre::ERT2/+; Vhl Flox/– mice non treated

Project description:Microglial cells were isolated by flow citometry using specific markers (CD45+/ CD11b+) and their global gene expression profile was analyzed. This data were used to study the role of HIF1A in microglia associated to Aβ plaques. In this dataset, we include the expression data obtained in microglial cells from a model of gain of function of HIF1A in APP-PSEN1/+ mice. (18 moth-old-age) mice model using a specific marker for this cell type (CD31+). Functional enrichment analyses were carried out through GSEA, where we have included specific categories potentially involved with blood vessel formation.

2021-03-08 | GSE168059 | GEO

DNA methylation profiles across different brain regions in APP/PSEN1 mice

Project description:Genome wide DNA methylation profiling of normal and APP/PSEN1 mice. A custom Illumina Golden Gate DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 800 CpGs. Bisulphite converted DNA from the 96 samples were hybridised to the Illumina custom golden gate DNA methylation array.

2015-12-05 | E-GEOD-42745 | biostudies-arrayexpress

Differential expression analyses in endothelial cells from APP/Psen1 mouse model

Project description:Endothelial cells were isolated by flow cytometry using a specific marker (CD31) and their global gene expression profile was analyzed. CD11b marker was contraselected. This data were used to study molecular mechanisms implicated in endothelial cells from App/Psen1 mouse model. In this dataset, we include the expression data obtained in endothelial cells from APP/Psen1 (18 month-old) mouse model using a specific marker for this cell type (CD31+). Functional enrichment analyses were carried out through GSEA, where we have included specific categories potentially involved with blood vessel formation.

2021-03-22 | GSE121729 | GEO

DNA methylation profiles across different brain regions in APP/PSEN1 mice

2015-12-05 | GSE42745 | GEO

VHL loss reprograms the immune landscape to promote an inflammatory myeloid microenvironment in renal tumorigenesis

Project description:Clear cell renal cell carcinoma (ccRCC) is an aggressive disease characterized by dysregulated hypoxia signaling, metabolic defects, and a complex tumor microenvironment (TME) highly enriched in lymphoid and myeloid immune cells. Loss of the oxygen sensing gene, von Hippel Lindau (VHL), is a critical early event in ccRCC pathogenesis and promotes stabilization of hypoxia inducible factors (HIF) that upregulate pro-growth signaling pathways, including angiogenesis and aerobic glycolysis. However, whether VHL loss in cancer cells impacts the composition, metabolism, or function of immune cells in the TME remains unclear. Using Vhl wildtype (WT) and knockout (KO) in vivo murine kidney cancer models, we found that Vhl KO tumors were less proliferative and more infiltrated by immune cells. Tumor-associated macrophages (TAM) demonstrated enhanced proinflammatory transcriptional signatures from Vhl deficient tumors, and intratumoral myeloid cells residing in the Vhl KO TME showed increased in vivo glucose consumption. Vhl loss did not confer increased in vivo glucose uptake in cancer cells or lymphocytes, or detectable changes in metabolites in the interstitial fluid. Mechanistically, enhanced secretion of the chemokine, CX3CL1, was observed in Vhl KO cancer cells and its cognate receptor, CX3CR1, was significantly elevated on myeloid cells residing in the TME of Vhl deficient tumors. Human ccRCC tumors exhibit high expression of CX3CL1 and CX3CR1 as well as enhanced myeloid metabolism and proinflammatory properties. Here, we identify the importance of cancer cell-specific genetic features to drive environmental reprograming and shape the tumor immune landscape and identify a potential therapeutic target in the treatment of ccRCC.

2024-04-17 | GSE239889 | GEO

Gene expression profile of sporadic and PSEN1 early-onset Alzheimer’s Disease

Project description:Alzheimer’s disease (AD) is the most common neurodegenerative dementia. Around 10% of cases present an age of onset before 65 years-old, which in turn can be divided in monogenic or familial AD (FAD) and sporadic early-onset AD (EOAD). Mutations in PSEN1, PSEN2 and APP genes have been linked with FAD. The aim of our study was to describe the brain whole-genome RNA expression profile of the posterior cingulate area in EOAD and FAD caused by PSEN1 mutations (FAD-PSEN1). 14 patients (7 EOAD and 7 FAD-PSEN1) and 7 neurologically healthy controls were selected and samples were hybridized in a Human Gene 1.1 microarray from Affymetrix. When comparing controls with EOAD and controls with FAD-PSEN1, we found 3183 and 3351 differentially expressed genes (DEG) respectively (FDR corrected p<0.05). However, any DEG was found in the comparison of the two groups of patients. Microarrays were validated through quantitative-PCR of 17 DEG. In silico analysis of the DEG revealed an alteration in biological pathways related to calcium-signaling, axon guidance and long-term potentiation (LTP), among others, in both groups of patients. These pathways are mainly related with cell signalling cascades, synaptic plasticity and learning and memory processes. In conclusion, the altered biological final pathways in EOAD and FAD-PSEN1 are highly coincident. Also, the findings are in line with those previously reported for late-onset AD (LOAD, onset >65 years-old), which implies that the consequences of the disease at the molecular level are similar in the final stages of the disease. 21 Samples were analyzed: 7 controls, 7 Early-onset Alzheimer's disease (AD) patients and 7 early-onset AD genetically determined by a mutation in PSEN1 gene.

2015-01-20 | E-GEOD-39420 | biostudies-arrayexpress

ChIP NS5 Ascl1-ERT2

Project description:ChIP NS5 Ascl1-ERT2

| PRJEB5781 | ENA

RAD21-TEV ERt2-TEV RNAseq

Project description:RNA-seq of and Ethonal and Tamoxifen-treated Rad21-TEV primary neuron transduced with ERT2-TEV

2021-02-28 | GSE150129 | GEO

Human PSEN1 Mutant Glia Improve Spatial Learning and Memory in Aged Mice

Project description:PSEN1 ΔE9 mutation causes a familial form of Alzheimer's disease. We have previously shown that human induced pluripotent stem cell (iPSC)-derived astrocytes carrying PSEN1 ΔE9 mutation exhibit transcriptional and functional abnormalities (Stem Cell Reports. 2017;9:1885-1897). Here we injected glial progenitors derived from 2 pairs of PSEN1 ΔE9 mutant- isogenic CTRL iPSCs intracerebroventricularly into newborn mice. At the age of 18 months, mouse hippocampi containing human cells (5 x PSEN1 ΔE9 + 6 x CTRL, all from male mice) were quickly dissected out and bulk RNA sequencing analysis was performed. Our results shed more light on the efffect of PSEN1 ΔE9 mutation on human glia in vivo as well as on the effect of the presence of mutant human glia on the surrounding healthy mouse cells.

2022-12-15 | GSE221027 | GEO

Staging Alzheimer’s disease in brains and retinas of APP/PSEN1 mice by transcriptional profiling

Project description:Alzheimer’s disease (AD) is a common form of dementia characterized by amyloid plaque deposition, TAU pathology, neuroinflammation and neurodegeneration. Mouse models recapitulate some key features of AD. For instance, the B6.APP/PS1 model (carrying human transgenes for mutant forms of APP and PSEN1) shows plaque deposition and associated neuroinflammatory responses involving both astrocytes and microglia beginning around 6 months of age. However, in our colony, TAU pathology, significant neurodegeneration and cognitive decline are not apparent in this model even at older ages. Therefore, this model is ideal for studying neuroinflammatory responses to amyloid deposition. Here, RNA sequencing of brain and retinal tissue, generalized linear modeling (GLM), functional annotation followed by validation by immunofluorescence (IF) was performed in B6.APP/PS1 mice to determine the earliest molecular changes prior to and around the onset of plaque deposition (2-6 months of age).

2019-11-25 | GSE136861 | GEO

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