Normalization of gene expression using SYBR green qPCR: A case for paraoxonase 1 and 2 in Alzheimer's disease brains

Leduc, Valérie; Legault, Véronique; Dea, Doris; Poirier, Judes

doi:10.1016/j.jneumeth.2011.05.026

Cited by 35 publications

(32 citation statements)

References 27 publications

(36 reference statements)

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“…We also examined a subset of AD (n = 34) and age-matched control brains (n = 24) for the mRNA prevalence of hFPPS using QrtPCR as previously reported. 28 Human FPPS mRNA levels were markedly elevated in the cortical cortices of the AD versus the control subjects (Figure 7b), consistent with a hyperactivation of the isoprenoid pathway in Alzheimer's disease. Although these finding do not imply that hFPPS is causally related to Alzheimer's disease, they support a genetic association between specific genetic variants in hFPPS (rs4971072) and the P-Tau concentrations in the human AD brain.…”

Section: Journal Of Medicinal Chemistrymentioning

confidence: 56%

Multistage Screening Reveals Chameleon Ligands of the Human Farnesyl Pyrophosphate Synthase: Implications to Drug Discovery for Neurodegenerative Diseases

et al. 2014

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Human farnesyl pyrophosphate synthase (hFPPS) is the gate-keeper of mammalian isoprenoids and the key target of bisphosphonate drugs. Bisphosphonates suffer from poor "drug-like" properties and are mainly effective in treating skeletal diseases. Recent investigations have implicated hFPPS in various nonskeletal diseases, including Alzheimer's disease (AD). Analysis of single nucleotide polymorphisms in the hFPPS gene and mRNA levels in autopsy-confirmed AD subjects was undertaken, and a genetic link between hFPPS and phosphorylated tau (P-Tau) levels in the human brain was identified. Elevated P-Tau levels are strongly implicated in AD progression. The development of nonbisphosphonate inhibitors can provide molecular tools for validating hFPPS as a therapeutic target for tauopathy-associated neurodegeneration. A multistage screening protocol led to the identification of a new monophosphonate chemotype that bind in an allosteric pocket of hFPPS. Optimization of these compounds could lead to human therapeutics that block tau metabolism and arrest the progression of neurodegeneration.

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Section: Journal Of Medicinal Chemistrymentioning

confidence: 56%

Multistage Screening Reveals Chameleon Ligands of the Human Farnesyl Pyrophosphate Synthase: Implications to Drug Discovery for Neurodegenerative Diseases

et al. 2014

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“…We selected RG candidates based on their extensive use in RT-qPCR studies from the literature as well as their presence in ready to use commercial kits for RG selection. Several of the RG candidates have previously been investigated under different conditions101223242526, and a few have been tested in AD and/or PD112728. MSA and PSP are atypical parkinsonian disorders and have a clinical manifestation highly similar to PD29.…”

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confidence: 99%

Assessment of brain reference genes for RT-qPCR studies in neurodegenerative diseases

Rydbirk

Folke

Winge

et al. 2016

Sci Rep

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Evaluation of gene expression levels by reverse transcription quantitative real-time PCR (RT-qPCR) has for many years been the favourite approach for discovering disease-associated alterations. Normalization of results to stably expressed reference genes (RGs) is pivotal to obtain reliable results. This is especially important in relation to neurodegenerative diseases where disease-related structural changes may affect the most commonly used RGs. We analysed 15 candidate RGs in 98 brain samples from two brain regions from Alzheimer’s disease (AD), Parkinson’s disease (PD), Multiple System Atrophy, and Progressive Supranuclear Palsy patients. Using RefFinder, a web-based tool for evaluating RG stability, we identified the most stable RGs to be UBE2D2, CYC1, and RPL13 which we recommend for future RT-qPCR studies on human brain tissue from these patients. None of the investigated genes were affected by experimental variables such as RIN, PMI, or age. Findings were further validated by expression analyses of a target gene GSK3B, known to be affected by AD and PD. We obtained high variations in GSK3B levels when contrasting the results using different sets of common RG underlining the importance of a priori validation of RGs for RT-qPCR studies.

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“…ACTB was found to be upregulated by 10.2 folds in AD cerebral cortex compared with age-matched control brain [104]. Further, immunoprecipitation of proteins from AD and control brain showed oxidative modification of β-actin in the AD brain [105]. In addition, β-Secretase-cleaved APP is shown to accumulate at actin inclusions in neurons induced by stress or Aβ [106].…”

Section: Discussionmentioning

confidence: 99%

Genomic convergence and network analysis approach to identify candidate genes in Alzheimer's disease

et al. 2014

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BackgroundAlzheimer’s disease (AD) is one of the leading genetically complex and heterogeneous disorder that is influenced by both genetic and environmental factors. The underlying risk factors remain largely unclear for this heterogeneous disorder. In recent years, high throughput methodologies, such as genome-wide linkage analysis (GWL), genome-wide association (GWA) studies, and genome-wide expression profiling (GWE), have led to the identification of several candidate genes associated with AD. However, due to lack of consistency within their findings, an integrative approach is warranted. Here, we have designed a rank based gene prioritization approach involving convergent analysis of multi-dimensional data and protein-protein interaction (PPI) network modelling.ResultsOur approach employs integration of three different AD datasets- GWL,GWA and GWE to identify overlapping candidate genes ranked using a novel cumulative rank score (SR) based method followed by prioritization using clusters derived from PPI network. SR for each gene is calculated by addition of rank assigned to individual gene based on either p value or score in three datasets. This analysis yielded 108 plausible AD genes. Network modelling by creating PPI using proteins encoded by these genes and their direct interactors resulted in a layered network of 640 proteins. Clustering of these proteins further helped us in identifying 6 significant clusters with 7 proteins (EGFR, ACTB, CDC2, IRAK1, APOE, ABCA1 and AMPH) forming the central hub nodes. Functional annotation of 108 genes revealed their role in several biological activities such as neurogenesis, regulation of MAP kinase activity, response to calcium ion, endocytosis paralleling the AD specific attributes. Finally, 3 potential biochemical biomarkers were found from the overlap of 108 AD proteins with proteins from CSF and plasma proteome. EGFR and ACTB were found to be the two most significant AD risk genes.ConclusionsWith the assumption that common genetic signals obtained from different methodological platforms might serve as robust AD risk markers than candidates identified using single dimension approach, here we demonstrated an integrated genomic convergence approach for disease candidate gene prioritization from heterogeneous data sources linked to AD.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-199) contains supplementary material, which is available to authorized users.

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Normalization of gene expression using SYBR green qPCR: A case for paraoxonase 1 and 2 in Alzheimer's disease brains

Cited by 35 publications

References 27 publications

Multistage Screening Reveals Chameleon Ligands of the Human Farnesyl Pyrophosphate Synthase: Implications to Drug Discovery for Neurodegenerative Diseases

Multistage Screening Reveals Chameleon Ligands of the Human Farnesyl Pyrophosphate Synthase: Implications to Drug Discovery for Neurodegenerative Diseases

Assessment of brain reference genes for RT-qPCR studies in neurodegenerative diseases

Genomic convergence and network analysis approach to identify candidate genes in Alzheimer's disease

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