Amyloid precursor protein gene expression in neural cell lines: influence of DNA cytosine methylation

Association of APP gene polymorphisms and promoter methylation with essential hypertension in Guizhou: a case-control study

BACKGROUND

Single-nucleotide polymorphisms (SNPs) and DNA methylation are crucial regulators of essential hypertension (EH). Amyloid precursor protein (APP) mutations are implicated in hypertension development. Nonetheless, studies on the association of APP gene polymorphism and promoter methylation with hypertension are limited. Therefore, this case-control aims to evaluate the genetic association of APP gene polymorphism and promoter methylation with EH in Guizhou populations.

OBJECTIVE AND METHODS

We conducted a case-control study on 343 EH patients and 335 healthy controls (including Miao, Buyi, and Han populations) in the Guizhou province of China to analyze 11 single-nucleotide polymorphisms (rs2040273, rs63750921, rs2211772, rs2830077, rs467021, rs368196, rs466433, rs364048, rs364051, rs438031, rs463946) in the APP gene via MassARRAY SNP. The MassARRAY EpiTYPER was employed to detect the methylation levels of the promoters.

RESULTS

In the Han population, the rs2211772 genotype distribution was significantly different between disease and control groups (χ² = 6.343, P = 0.039). The CC genotype reduced the risk of hypertension compared to the TT or TC genotype (OR 0.105, 95%CI 0.012-0.914, P = 0.041). For rs2040273 in the Miao population, AG or GG genotype reduced the hypertension risk compared with the AA genotype (OR 0.533, 95%CI 0.294-0.965, P = 0.038). Haplotype TCC (rs364051-rs438031-rs463946) increased the risk of EH in Guizhou (OR 1.427, 95%CI 1.020-1.996, P = 0.037). Each 1% increase in CpG_19 (- 613 bp) methylation level was associated with a 4.1% increase in hypertension risk (OR 1.041, 95%CI 1.002-1.081, P = 0.039). Each 1% increase in CpG_1 (- 296 bp) methylation level was associated with an 8% decrease in hypertension risk in women (OR 0.920, 95%CI 0.860-0.984, P = 0.015). CpG_19 significantly correlated with systolic blood pressure (r = 0.2, P = 0.03). The methylation levels of CpG_19 in hypertensive patients with rs466433, rs364048, and rs364051 minor alleles were lower than that with wild-type alleles (P < 0.05). Moreover, rs467021 and rs364051 showed strong synergistic interaction with EH (χ² = 7.633, P = 0.006). CpG_11, CpG_19, and rs364051 showed weak synergistic interaction with EH (χ² = 19.874, P < 0.001).

CONCLUSION

In summary, rs2211772 polymorphism and promoter methylation level of APP gene may be linked to EH in Guizhou populations. Our findings will provide novel insights for genetic research of hypertension and Alzheimer's disease.

AuNPs@MoSe2 heterostructure as a highly efficient coreaction accelerator of electrocheluminescence for amplified immunosensing of DNA methylation

Electrocheluminescence analysis amplified by coreaction accelerators has experienced breakthrough in ultrasensitive detection of biomarkers. Herein, a highly efficient coreaction accelerator, two-dimensional layered MoSe₂ nanosheets loaded with gold nanoparticles (AuNPs@MoSe₂ heterostructure), is proposed to enhance the ECL efficiency of Ru(bpy)₃²⁺/tripropylamine (TPrA) system. The presence of AuNPs avoids the aggregation of MoSe₂ nanosheets, and improves the electrical conductivity of modified surface. The AuNPs@MoSe₂ modified electrode also provides a large area for loading of abundant capture probe. MoSe₂ as an electroactive substrate can remarkably accelerate the generation of TPrA^•+ radicals to react with electrooxidized Ru(bpy)₃²⁺, which achieves about 3.4-fold stronger ECL intensity. Thus, an enhanced ECL immunoassay method can be achieved after Ru(bpy)₃²⁺-doped silica nanoparticle labeled antibody (Ab₂-Ru@SiO₂) is captured to the modified electrode via immunological recognition. Using methylated DNA as a target, the immunosensor was prepared by binding capture DNA on AuNPs@MoSe₂ modified electrode to successively capture the target, anti-5-methylcytosine antibody (anti-5mC) and Ab₂-Ru@SiO₂. The proposed strategy could detect 0.26 fM 5 mC (3σ) with a detectable concentration range of 1.0 fM - 10 nM at methylated DNA. This immunosensor showed excellent selectivity, good stability and reproducibility, and acceptable recovery, indicating the broad prospects of the novel coreaction accelerator in clinical diagnosis.

Lead-induced neurodevelopmental lesion and epigenetic landscape: Implication in neurological disorders

Lead (Pb) was implicated in multiple genotoxic, neuroepigenotoxic, and chromosomal-toxic mechanisms and interacted with varying synaptic plasticity pathways, likely underpinning previous reports of links between Pb and cognitive impairment. Epigenetic changes have emerged as a promising biomarker for neurological disorders, including cognitive disorders, Alzheimer's disease (AD), and Parkinson's disease (PD). In the present review, special attention is paid to neural epigenetic features and mechanisms that can alter gene expression patterns upon environmental Pb exposure in rodents, primates, and zebrafish. Epigenetic modifications have also been discussed in population studies and cell experiment. Further, we explore growing evidence of potential linkage between Pb-induced disruption of regulatory pathway and neurodevelopmental and neurological disorders both in vivo and in vitro. These findings uncover how epigenome in neurons facilitates the development and function of the brain in response to Pb insult.

Optical bio-sensing of DNA methylation analysis: an overview of recent progress and future prospects

DNA methylation as one of the most important epigenetic modifications has a critical role in regulating gene expression and drug resistance in treating diseases such as cancer. Therefore, the detection of DNA methylation in the early stages of cancer plays an essential role in disease diagnosis. The majority of routine methods to detect DNA methylation are very tedious and costly. Therefore, designing easy and sensitive methods to detect DNA methylation directly and without the need for molecular methods is a hot topic issue in bioscience. Here we provide an overview on the optical biosensors (including fluorescence, FRET, SERs, colorimetric) that have been applied to detect the DNA methylation. In addition, various types of labeled and label-free reactions along with the application of molecular methods and optical biosensors have been surveyed. Also, the effect of nanomaterials on the sensitivity of detection methods is discussed. Furthermore, a comprehensive overview of the advantages and disadvantages of each method are provided. Finally, the use of microfluidic devices in the evaluation of DNA methylation and DNA damage analysis based on smartphone detection has been discussed.

Here, we provide an overview on the optical biosensors (including fluorescence, FRET, SERs, colorimetric) that have been applied to detect the DNA methylation.

Application of lateral flow and microfluidic bio-assay and biosensing towards identification of DNA-methylation and cancer detection: Recent progress and challenges in biomedicine

DNA methylation is an important epigenetic alteration that results from the covalent transfer of a methyl group to the fifth carbon of a cytosine residue in CpG dinucleotides by DNA methyltransferase. This modification mostly happens in the promoter region and the first exon of most genes and suppresses gene expression. Therefore, aberrant DNA methylation cause tumor progression, metastasis, and resistance to current anti-cancer therapies. So, the detection of DNA methylation is an important issue in diagnosis and therapy of most diseases. Conventional methods for the assay of DNA methylation and activity of DNA methyltransferases are time consuming. So, we need to multiplex operations and expensive instrumentation. To overcome the limitations of conventional methods, new methods such as microfluidic platforms and lateral flow tests have been developed to evaluate DNA methylation. The microfluidic tests are based on optical and electrical biosensing. These tests able us to can analyze DNA methylation with high efficiency and sensitivity without the need for expensive equipment and skilled people. Lateral flow strip tests are another type of rapid, simple, and sensitive test with advanced technology used to assess DNA methylation. Lateral flow strip tests are based on optical biosensors. This review attempts to evaluate new methods for assessing DNA extraction, DNA methylation and DNA methyltransferase activity as well as recent developments in microfluidic technology application for bisulfite treatment and restriction enzyme (bisulfite free), and lateral flow relying on their application in the field of recognition of DNA methylation in blood and body fluids. Also, the advantages and disadvantages of each test are reviewed. Finally, future prospects for the development of the microfluidics biodevices for the detection of DNA methylation is briefly discussed.

Quantitative analysis of global 5-methyl- and 5-hydroxymethylcytosine in TET1 expressed HEK293T cells

DNA methylation at the 5-position of cytosine bases (5-methylcytosine, 5mC) in genomic DNA is representative epigenetic modification and is involved in many cellular processes, including gene expression and embryonic development. The hydroxylation of 5mC provide 5-hydroxymethylcytosine (5hmC), the so-called sixth base rediscovered recently in mammalian cells, is also considered to act as an epigenetic regulator. We report herein the immunochemical assessment of 5hmC achieved by an enzyme-linked immunosorbent assay (ELISA) using our linker technology. The keys to this assay are 1) the immobilization of genomic DNA with the bifunctional linker molecule, and 2) quantitative analysis by using guaranteed standard samples containing defined amounts of 5hmC. We succeeded in the sensitive and quantitative detection of 5hmC as well as 5mC in HEK293T cells transfected with TET1, and also monitored the effect of ascorbate on the TET1 catalyzed conversion of 5mC to 5hmC. Our linker technology enables the rapid and stable immobilization of genomic samples and thus contributes to the realization of a reproducible 5hmC evaluation method.

Epigenetics: Recent Advances and Its Role in the Treatment of Alzheimer's Disease

Objective: This review summarizes recent findings on the epigenetics of Alzheimer's disease (AD) and provides therapeutic strategies for AD.

Methods: We searched the following keywords: “genetics,” “epigenetics,” “Alzheimer's disease,” “DNA methylation,” “DNA hydroxymethylation,” “histone modifications,” “non-coding RNAs,” and “therapeutic strategies” in PubMed.

Results: In this review, we summarizes recent studies of epigenetics in AD, including DNA methylation/hydroxymethylation, histone modifications, and non-coding RNAs. There are no consistent results of global DNA methylation/hydroxymethylation in AD. Epigenetic genome-wide association studies show that many differentially methylated sites exist in AD. Several studies investigate the role of histone modifications in AD; for example, histone acetylation decreases, whereas H3 phosphorylation increases significantly in AD. In addition, non-coding RNAs, such as microRNA-16 and BACE1-antisense transcript (BACE1-AS), are associated with the pathology of AD. These epigenetic changes provide us with novel insights into the pathogenesis of AD and may be potential therapeutic strategies for AD.

Conclusion: Epigenetics is associated with the pathogenesis of AD, including DNA methylation/hydroxymethylation, histone modifications, and non-coding RNAs, which provide potential therapeutic strategies for AD.

FMRP Regulates the Nuclear Export of Adam9 and Psen1 mRNAs: Secondary Analysis of an N6-Methyladenosine Dataset

Fragile X mental retardation protein (FMRP) binds to and regulates the translation of amyloid-β protein precursor (App) mRNA, but the detailed mechanism remains to be determined. Differential methylation of App mRNA could underlie FMRP binding, message localization and translation efficiency. We sought to determine the role of FMRP and N⁶-methyladeonsine (m⁶A) on nuclear export of App mRNA. We utilized the m⁶A dataset by Hsu and colleagues to identify m⁶A sites in App mRNA and to determine if the abundance of message in the cytoplasm relative to the nucleus is altered in Fmr1 knockout mouse brain cortex. Given that processing of APP to Aβ and soluble APP alpha (sAPPα) contributes to disease phenotypes, we also investigated whether Fmr1^KO associates with nuclear export of the mRNAs for APP protein processing enzymes, including β-site amyloid cleaving enzyme (Bace1), A disintegrin and metalloproteinases (Adams), and presenilins (Psen). Fmr1^KO did not alter the nuclear/cytoplasmic abundance of App mRNA. Of 36 validated FMRP targets, 35 messages contained m⁶A peaks but only Agap2 mRNA was selectively enriched in Fmr1^KO nucleus. The abundance of the APP processing enzymes Adam9 and Psen1 mRNA, which code for a minor alpha-secretase and gamma-secretase, respectively, were selectively enriched in wild type cytoplasm.

Colorimetric and electrochemical quantification of global DNA methylation using a methyl cytosine-specific antibody

We report a simple colorimetric (naked-eye) and electrochemical method for the rapid, sensitive and specific quantification of global methylation levels using only 25 ng of input DNA. Our approach utilises a three-step strategy; (i) initial adsorption of the extracted, purified and denatured bisulfite-treated DNA on a screen-printed gold electrode (SPE-Au), (ii) immuno-recognition of methylated DNA using a horseradish peroxidase (HRP)-conjugated methylcytosine (HRP-5mC) antibody and (iii) subsequent colorimetric detection by the enzymatic oxidation of 3,3',5,5'-tetramethylbenzidin (TMB)/H₂O₂ which generated a blue-coloured product in the presence of methylated DNA and HRP-5mC immunocomplex. As TMB_(ox) is electroactive, it also produces detectable amperometric current at +150 mV versus a Ag pseudo-reference electrode (electrochemical detection). The assay could successfully differentiate 5-aza-2'-deoxycytidine drug-treated and untreated Jurkat DNA samples. It showed good reproducibility (relative standard deviation (% RSD) = <5%, for n = 3) with fairly good sensitivity (as low as 5% difference in methylation levels) and specificity while analysing various levels of global DNA methylation in synthetic samples and cell lines. The method has also been tested for analysing the methylation level in fresh tissue samples collected from eight patients with oesophageal squamous cell carcinoma. We believe that this assay could be potentially useful as a low-cost alternative for genome-wide DNA methylation analysis in point-of-care applications.

Immobilization of DNA with nitrogen mustard-biotin conjugate for global epigenetic analysis

We report the quantitative analysis of 5-methylcytosine, a representative epigenetic modification in genomic DNA, with an enzyme-linked immunosorbent assay (ELISA). We synthesized a novel hetero-bifunctional linker molecule consisting of nitrogen mustard and biotin to capture DNA on the surface of biosensing devices. The molecule can successfully immobilize genomic DNA on a streptavidin coated 96-well microplate, which was then employed for immunochemical epigenetic assessment. We achieved the sensitive and quantitative detection of 5-mC in genomic DNA samples. The CpG methylation ratios obtained from our system for mouse brain and mouse small intestine genomes were 79% and 82%, respectively. These numbers are in good agreement with the previously reported methylation ratio of 75-85%, which was identified by whole genome bisulfite sequencing. Accordingly, the present technology using our novel bifunctional linker molecule provides a fast, easy, and inexpensive method for epigenetic assessment, without the need for any conventional bisulfite treatment, polymerase chain reaction (PCR), or sequencing.

Microfluidic platforms for DNA methylation analysis

In the field of genetics, epigenetics is the study of changes in gene expression without any change in DNA sequences. Chemical base modification in DNA by DNA methyltransferase, and specifically methylation, has been well studied as the main mechanism of epigenetics. Therefore, the determination of DNA methylation of, for example, 5'-methylcytosine in the CpG sequence in mammals has attracted attention because it should prove valuable in a wide range of research fields including diagnosis, drug discovery, and therapy. Methylated DNA bases and DNA methyltransferase activity are analyzed using conventional methods; however, these methods are time-consuming and require complex multiple operations. Therefore, new methods and devices for DNA methylation analysis are now being actively developed. Furthermore, microfluidic technology has also been applied to DNA methylation analysis because the microfluidic platform offers the promising advantage of making it possible to perform thousands of DNA methylation reactions in small reaction volumes, resulting in a high-throughput analysis with high sensitivity. This review discusses epigenetics and the microfluidic platforms developed for DNA methylation analysis.

Changes in methylation patterns of multiple genes from peripheral blood leucocytes of Alzheimer's disease patients

BACKGROUND

Efforts aiming at identifying biomarkers and corresponding methods for early diagnosis of Alzheimer's disease (AD) might be the most appropriate strategy to initiate promising new treatments and/or prevention of AD OBJECTIVE: The aim of our study is to assess the association of DNA methylation pattern of various leucocyte genes with AD pathogenesis in order to find potential biomarkers and corresponding methods for molecular diagnosis of AD.

METHODS

DNA methylation level of various genes in AD patients and normal population were compared by bisulphite sequencing PCR and methylation-specific PCR (MSP). Furthermore, real-time PCR was used to explore the effects of DNA methylation on the expression of target genes.

RESULTS

Results showed significant hypermethylation of mammalian orthologue of Sir2 (SIRT1) gene in AD patients compared with normal population. Meanwhile, changes in methylation level of SIRT1 gene between different severities of AD were also found. Specific primers were designed from the SIRT1 CpG islands to differentiate AD and control group by MSP method. Besides, significant demethylation of β-amyloid precursor protein (APP) gene was observed in AD patients, whereas no difference was observed in other AD-related genes. Moreover, significant decrease in expression of SIRT1 gene and increase in expression of APP gene were also found in AD patients. In addition, the expression level of SIRT1/APP genes was associated with the severity, but not with the age or gender, of AD patients.

CONCLUSION

SIRT1 and APP might be the interesting candidate biomarkers and valuable for clinical diagnosis or treatment of AD.

DNA methylation analysis triggered by bulge specific immuno-recognition

We report the sequence-selective discrimination of the cytosine methylation status in DNA with anti methylcytosine antibody for the first time. This was realized by employing an affinity measurement involving the target methylcytosine in a bulge region and anti methylcytosine antibody, following hybridization with a bulge-inducing DNA to ensure that only the target methylcytosine is located in the bulge. The affinity of the antibody for methylcytosine in the bulge was 79% of that in a single strand of DNA; however, the affinity for nontarget methylcytosine in a double strand of DNA decreased greatly. This is because the antibody cannot bind with an inwardly turned methylcytosine in the duplex region owing to the large antibody size. In contrast, the methylcytosine in the bulge is recognized by the antibody because it is available to rotate freely owing to the single bond between deoxyribose and phosphate in a DNA chain. By employing the difference between the affinity in the bulge and that in the duplex, we could determine selectively whether or not the target cytosine was methylated in an O(6)-methylguanine DNA methyltransferase (MGMT) promoter sequence with a single base level. The proposed bulge-specific assay technique can be combined with a widely used absorbance measurement method that employs the color change in tetramethyl benzidine induced by horseradish peroxidase-labeled secondary antibody. The sequence-selective discrimination of the methylation status could also be obtained with various types of interfering genomic DNA contamination without any conventional bisulfite treatment, polymerase chain reaction, (PCR) or electrophoresis.

Determination of DNA methylation using electrochemiluminescence with surface accumulable coreactant

Cytosine methylation in DNA was determined by an enzyme linked immunosorbent assay (ELISA) with electrochemiluminescence (ECL) detection and employed for the DNA methylation assay of a long and real genomic sample for the first time. The developed method employed an antimethyl cytosine antibody labeled with acetylcholinesterase, which was added to recognize single methylated cytosine in a DNA oligomer. The acetylcholinesterase converted acetylthiocholine (substrate) to thiocholine (product), which was accumulated on a gold electrode surface via gold-thiol binding. This surface accumulated preconcentration made it possible to observe bright and distinctive ECL by applying a potential to the gold electrode in the presence of a tris(2,2-bipyridyl)ruthenium complex luminophore when the analyte DNA contained a methylation region. Methyl-cytosine was measured quantitatively in the 1-100 pmol range, which exhibits sufficiently high sensitivity to achieve real DNA measurements without amplification by a polymerase chain reaction (PCR). The proposed ECL method also exhibited high selectivity for methyl-cytosine against nonmethylated cytosine, guanine, thymine, and adenine nucleotides. Finally, original and methylated DNA samples were clearly distinguished with our method using a real DNA bacteriophage sample (48,502 base pairs).

Gene expression profiling of choline-deprived neural precursor cells isolated from mouse brain

Choline is an essential nutrient and an important methyl donor. Choline deficiency alters fetal development of the hippocampus in rodents and these changes are associated with decreased memory function lasting throughout life. Also, choline deficiency alters global and gene-specific DNA methylation in several models. This gene expression profiling study describes changes in cortical neural precursor cells from embryonic day 14 mice, after 48 h of exposure to a choline-deficient medium. Using Significance Analysis of Microarrays, we found the expression of 1003 genes to be significantly changed (from a total of 16,000 total genes spotted on the array), with a false discovery rate below 5%. A total of 846 genes were overexpressed while 157 were underexpressed. Classification by gene ontology revealed that 331 of these genes modulate cell proliferation, apoptosis, neuronal and glial differentiation, methyl metabolism, and calcium-binding protein classes. Twenty-seven genes that had changed expression have previously been reported to be regulated by promoter or intron methylation. These findings support our previous work suggesting that choline deficiency decreases the proliferation of neural precursors and possibly increases premature neuronal differentiation and apoptosis.

The functions of the amyloid precursor protein gene

The amyloid precursor protein (APP) gene and its protein products have multiple functions in the central nervous system and fulfil criteria as neuractive peptides: presence, release and identity of action. There is increased understanding of the role of secretases (proteases) in the metabolism of APP and the production of its peptide fragments. The APP gene and its products have physiological roles in synaptic action, development of the brain, and in the response to stress and injury. These functions reveal the strategic importance of APP in the workings of the brain and point to its evolutionary significance.

Alzheimer's beta-amyloid precursor protein is expressed on the surface of immediately ex vivo brain cells: a flow cytometric study

Beta-amyloid precursor protein (beta APP) is ubiquitously expressed, but deposition of the beta APP proteolytic fragment A beta is virtually restricted to the brain, suggesting cell-specific processing of this molecule. Our laboratory has investigated expression of beta APP in mechanically dissociated, unfixed, immediately ex vivo cells from various mouse and rat organs by flow cytometry. Epitopes of predicted extracellular domains of beta APP recognized by the N-terminal 22C11 monoclonal antibody (mAb) and the juxtamembrane 4G8 mAb were not detectable on the surface of lymphoid cells, hepatocytes, or kidney cells. In contrast, surface 22C11 and 4G8 beta APP immunoreactivity was abundant on intact (propidium iodide-excluding) dissociated brain cells. The predicted C-terminal intracellular beta APP determinant recognized by the mAb Jonas was not detectable on the surface of intact brain cells, but was present in ethanol-permeabilized cells, consistent with a transmembrane configuration of beta APP in brain cells. Trypsinization of intact brain cells abolished cell surface immunoreactivity for 22C11, which was then reestablished by short-term culture. Augmentation of 22C11 and 4G8 surface immunoreactivity occurred when brain cells were cultured short-term in phenylarsine oxide, a general endocytosis inhibitor. By double staining protocols of brain cells with mAbs directed against beta APP ectodomain epitopes and the neuronal surface proteins Thy-1 or neural cell adhesion molecule (NCAM), we observed that all Thy-1+ and NCAM+ cells (approximately 50%) were immunoreactive for surface beta APP, but that some beta APP+ cells (approximately 20%) were negative for these neuronal markers. Our data suggest that neurons and a subpopulation of other brain cells, unlike peripheral cells, can support beta APP as a type 1 intrinsic membrane molecule with an intact ectodomain, and that beta APP surface abundance is regulated by an equilibrium between membranes vesicle insertion and endocytotic internalization. Transmembrane beta APP holoprotein may be a critical determinant of brain-predominant processing of beta APP to A beta, and may participate in a receptor/transducer function unique to brain cells.

Hypomethylation of the amyloid precursor protein gene in the brain of an Alzheimer's disease patient

Aberrant expression of the amyloid precursor protein (APP) gene may contribute to the beta-amyloid deposition seen in Alzheimer's disease and Down syndrome patients. Genomic DNA was isolated from human brain tissue and digested with HpaII, an enzyme sensitive to CpG methylation. Southern-blot analysis revealed the absence of methylation at a site in the APP gene of an Alzheimer's disease subject. This site was methylated in a nondemented subject and a subject with a non-Alzheimer's type of dementia (Pick's disease). This is the first report of an epigenetic defect in an Alzheimer's disease patient and the observation suggests that hypomethylation of the APP gene may be one of several factors contributing to aberrant gene expression in Alzheimer's disease.