Catechol-O-methyltransferase gene promoter methylation as a peripheral biomarker in male schizophrenia

AbstractAs an epigenetic modification, DNA methylation may reflect the interaction between genetic and environmental factors in the development of schizophrenia (SCZ). Catechol-O-methyltransferase (COMT) gene is a promising candidate gene of SCZ. In the present study, we investigate the association of COMT methylation with the risk of SCZ using bisulfite pyrosequencing technology. Significant association between DNA methylation of COMT and the risk of SCZ is identified (P = 1.618e−007). A breakdown analysis by gender shows that the significance is driven by males (P = 3.310e−009), but not by females. DNA methylation of COMT is not significantly associated with SCZ clinical phenotypes, including p300 and cysteine level. No interaction is found between COMT genotypes and the percent methylation of this gene. Receiver operating characteristic (ROC) curve shows that DNA methylation of COMT is able to predict the SCZ risk in males (area under curve [AUC] = 0.802, P = 1.91e−007). The current study indicates the clinical value of COMT methylation as a potential male-specific biomarker in SCZ diagnosis.

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Locus-Specific DNA Methylation Editing in Mammalian Cells using a CRISPR-Based System

10.1101/2021.10.12.463855 ◽

2021 ◽

Author(s):

Jim Smith ◽

Rakesh Banerjee ◽

Reema Waly ◽

Arthur Urbano ◽

Gregory Gimenez ◽

...

Keyword(s):

Dna Methylation ◽

Mammalian Cells ◽

Epigenetic Modification ◽

Gene Promoter ◽

Human Melanoma ◽

Melanoma Metastasis ◽

Targeted Screening ◽

Transcriptional Deregulation ◽

Transient System ◽

Target Activity

AbstractDNA methylation is a key epigenetic modification implicated in the pathogenesis of numerous human diseases, including cancer development and metastasis. Gene promoter methylation changes are widely associated with transcriptional deregulation and disease progression. The advent of CRISPR-based technologies has provided a powerful toolkit for locus-specific manipulation of the epigenome. Here, we describe a comprehensive global workflow for the design and application of a dCas9-SunTag-based tool for editing a DNA methylation locus in human melanoma cells, alongside protocols for downstream techniques used to evaluate subsequent methylation and gene expression changes in methylation-edited cells. Using transient system delivery, we demonstrate both highly efficacious methylation and demethylation of the EBF3 promoter, a putative epigenetic driver of melanoma metastasis, achieving up to 304.00% gain of methylation and 99.99% relative demethylation, respectively. Further, we employ a novel, targeted screening approach to confirm minimal off-target activity and high on-target specificity of our editing sys-tem within our target locus.

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Locus-Specific DNA Methylation Editing in Melanoma Cell Lines Using a CRISPR-Based System

Cancers ◽

10.3390/cancers13215433 ◽

2021 ◽

Vol 13 (21) ◽

pp. 5433

Author(s):

Jim Smith ◽

Rakesh Banerjee ◽

Reema Waly ◽

Arthur Urbano ◽

Gregory Gimenez ◽

...

Keyword(s):

Dna Methylation ◽

Epigenetic Modification ◽

Gene Promoter ◽

Human Melanoma ◽

Melanoma Metastasis ◽

Guide Rna ◽

Targeted Screening ◽

Transcriptional Deregulation ◽

Transient System ◽

Target Activity

DNA methylation is a key epigenetic modification implicated in the pathogenesis of numerous human diseases, including cancer development and metastasis. Gene promoter methylation changes are widely associated with transcriptional deregulation and disease progression. The advent of CRISPR-based technologies has provided a powerful toolkit for locus-specific manipulation of the epigenome. Here, we describe a comprehensive global workflow for the design and application of a dCas9-SunTag-based tool for editing the DNA methylation locus in human melanoma cells alongside protocols for downstream techniques used to evaluate subsequent methylation and gene expression changes in methylation-edited cells. Using transient system delivery, we demonstrate both highly efficacious methylation and demethylation of the EBF3 promoter, which is a putative epigenetic driver of melanoma metastasis, achieving up to a 304.00% gain of methylation and 99.99% relative demethylation, respectively. Furthermore, we employ a novel, targeted screening approach to confirm the minimal off-target activity and high on-target specificity of our designed guide RNA within our target locus.

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Association ofP2Y12Gene Promoter DNA Methylation with the Risk of Clopidogrel Resistance in Coronary Artery Disease Patients

BioMed Research International ◽

10.1155/2014/450814 ◽

2014 ◽

Vol 2014 ◽

pp. 1-8 ◽

Cited By ~ 9

Author(s):

Jia Su ◽

Xiaojing Li ◽

Qinglin Yu ◽

Yahui Liu ◽

Yaqing Wang ◽

...

Keyword(s):

Dna Methylation ◽

Fasting Blood Glucose ◽

Clinical Markers ◽

Bisulfite Pyrosequencing ◽

Clopidogrel Resistance ◽

Cpg Dinucleotides ◽

Promoter Dna Methylation ◽

Artery Disease ◽

Promoter Dna ◽

Pyrosequencing Technology

Background. Clopidogrel inhibits the ADP receptorP2Y12to keep down the platelet aggregation. The goal of our study is to investigate the contribution ofP2Y12promoter DNA methylation to the risk of clopidogrel resistance (CR).Methods. The platelet functions were measured by the VerifyNowP2Y12assay. Applying the bisulfite pyrosequencing technology, DNA methylation levels of two CpG dinucleotides onP2Y12promoter were tested among 49 CR cases and 57 non-CR controls. We also investigated the association amongP2Y12DNA methylation, various biochemical characteristics, and CR.Result. Lower methylation of two CpGs indicated the poorer clopidogrel response (CpG1,P=0.009; CpG2,P=0.022) in alcohol abusing status. Meanwhile CpG1 methylation was inversely correlated with CR in smoking patients (P=0.026) and in subgroup of Albumin < 35 (P=0.002). We observed that the level of DNA methylation might be affected by some clinical markers, such as TBIL, LEVF, Albumin, AST. The results also showed that the quantity of stent, fasting blood-glucose, and lower HbAC1 were the predictors of CR.Conclusions. The evidence from our study indicates thatP2Y12methylation may bring new hints to elaborate the pathogenesis of CR.

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DNA modifications in schizophrenia

Psychotic Disorders ◽

10.1093/med/9780190653279.003.0021 ◽

2020 ◽

pp. 177-183

Author(s):

Ehsan Pishva ◽

Bart P. F. Rutten

Keyword(s):

Gene Expression ◽

Risk Factors ◽

Dna Methylation ◽

Alternative Splicing ◽

Epigenetic Modification ◽

Control Gene ◽

Dna Modifications ◽

Genetic And Environmental Factors ◽

The Brain ◽

Epigenetic Processes

Interplay between genetic and environmental factors plays a major role in shaping the neurodevelopmental origins of schizophrenia. Epigenetic processes act to dynamically control gene expression and are known to regulate key neurobiological and cognitive processes in the brain. Along with mediating the effects of environmental risk factors on the development of disease, epigenetic processes play a central role in the differentiation and development of the human brain. Therefore, investigating epigenetic variations associated with schizophrenia may shed new light on our understanding about the developmental and environmental origins of schizophrenia. DNA methylation is the best-characterized epigenetic modification, playing a role in regulating gene expression, alternative splicing and other transcriptional processes such as X-chromosome inactivation and genomic imprinting. This chapter discusses the evidence to support a role for DNA modifications in schizophrenia, and highlights the opportunities and challenges of ongoing studies.

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Aberrant DNA Methylation Patterns in Chronic Idiopathic Myelofibrosis.

Blood ◽

10.1182/blood.v104.11.2443.2443 ◽

2004 ◽

Vol 104 (11) ◽

pp. 2443-2443

Author(s):

Edgar Jost ◽

Gerald Gehbauer ◽

Christoph E. Maintz ◽

Peter Jousten ◽

Leo Habets ◽

...

Keyword(s):

Dna Methylation ◽

Tumor Suppressor ◽

Tumor Suppressor Genes ◽

Epigenetic Modification ◽

Cpg Islands ◽

Gene Promoter ◽

Aberrant Methylation ◽

Idiopathic Myelofibrosis ◽

Suppressor Genes ◽

Chronic Idiopathic Myelofibrosis

Abstract Chronic idiopathic myelofibrosis (CIMF) is a clonal myeloproliferative disorder characterized by bone marrow fibrosis, angiogenesis and extramedullary hematopoiesis. No specific genetic defect underlying the disease has been identified so far. The spectrum of cytogenetic abnormalities in CIMF includes del (13q), del (20q) and partial trisomy 1q as well as abnormalities of chromosomes 1, 7 and 9. Hypermethylation of CpG islands within gene promoter regions is associated with transcriptional inactivation and represents an important mechanism of gene silencing in the pathogenesis of hematopoietic malignancies. This epigenetic phenomenon acts as an alternative to mutations and deletions to disrupt tumor suppressor gene function in cancerogenesis. In order to investigate the role of DNA methylation changes in the pathogenesis of CIMF, we have analyzed the methylation status of the promoter-associated CpG islands of 13 well-characterized tumor suppressor genes by methylation-specific polymerase chain reaction in peripheral blood cells from 20 adult patients with CIMF. The frequency of aberrant methylation among the patient samples was 25.0 % (5/20) for SOCS-1 and 5.0 % (1/20) for E-cadherin, MGMT, p73 as well as TIMP-2. There was no hypermethylation of p15, p16, RARbeta, DAP kinase 1, SOCS-3, hMLH1, TIMP-3 and RASSF1A. We detected at least one hypermethylated gene promoter region in 35.0 % (7/20) of the primary patient samples. Our data indicate that hypermethylation of tumor suppressor genes is a common event in CIMF. Epigenetic modification of genes regulating growth factor signaling, cell adhesion and DNA repair may, in addition to genetic aberrations, contribute to the malignant phenotype in CIMF. The exploration of our growing knowledge about epigenetic aberrations in tumorigenesis may help develop novel strategies in diagnosis and treatment of CIMF for the future.

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Expression of Sclerostin in Osteoporotic Fracture Patients Is Associated with DNA Methylation in the CpG Island of the SOST Gene

International Journal of Genomics ◽

10.1155/2019/7076513 ◽

2019 ◽

Vol 2019 ◽

pp. 1-8 ◽

Cited By ~ 1

Author(s):

Yanming Cao ◽

Bin Wang ◽

Ding Wang ◽

Dongxiang Zhan ◽

Caiyuan Mai ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Osteoporotic Fracture ◽

Cpg Island ◽

Epigenetic Modification ◽

Methylation Status ◽

Gene Promoter ◽

Primary Osteoporosis ◽

Sost Gene ◽

Fracture Bone

Purpose. SOST gene is one of the key factors in regulating bone absorption. Although there are reports showing diverse transcription factors, epigenetic modification could be responsible for regulating SOST gene expression. There is still little exploration on promoter methylation status of SOST gene in osteoporotic bone tissues. The aim of this study is to investigate the involvement of CpG methylation in regulation of SOST expression in patients with primary osteoporosis. Methods. The diagnosis of osteoporosis was established on the basis of dual energy X-ray absorptiometry to measure BMD. All femoral bone tissues were separated in surgeries. After extracting total RNA and protein, we checked the relative expression levels of SOST by quantitative real-time PCR and western blot. Also, immunohistochemical staining was performed to observe the expression of SOST protein in the bone samples. The genomic DNA of non-OPF (non-osteoporotic fracture bone tissues) and OPF (osteoporotic fracture bone tissues) were treated by bisulfite modification, and methylation status of CpG sites in the CpG island of SOST gene promoter was determined by DNA sequencing. Results. SOST gene expression in the non-OPF group was lower than that in OPF group. Bisulfite sequencing result showed that SOST gene promoter was slightly demethylated in the OPF group, as compared with non-OPF group. Conclusion. Our study demonstrated that DNA methylation influenced the transcriptional expression of SOST gene, which probably may play an important role in the pathogenesis of primary osteoporosis.

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DNA Methylation Levels of the TBX5 Gene Promoter Are Associated with Congenital Septal Defects in Mexican Paediatric Patients

Biology ◽

10.3390/biology11010096 ◽

2022 ◽

Vol 11 (1) ◽

pp. 96

Author(s):

Esbeidy García-Flores ◽

José Manuel Rodríguez-Pérez ◽

Verónica Marusa Borgonio-Cuadra ◽

Gilberto Vargas-Alarcón ◽

Juan Calderón-Colmenero ◽

...

Keyword(s):

Dna Methylation ◽

Heart Development ◽

Operating Characteristic ◽

Morphological Changes ◽

Heart Defects ◽

Gene Promoter ◽

Cpg Sites ◽

Septal Defects ◽

Average Methylation ◽

Tbx5 Gene

The TBX5 gene regulates morphological changes during heart development, and it has been associated with epigenetic abnormalities observed in congenital heart defects (CHD). The aim of this research was to evaluate the association between DNA methylation levels of the TBX5 gene promoter and congenital septal defects. DNA methylation levels of six CpG sites in the TBX5 gene promoter were evaluated using pyrosequencing analysis in 35 patients with congenital septal defects and 48 controls. Average methylation levels were higher in individuals with congenital septal defects than in the controls (p < 0.004). In five CpG sites, we also found higher methylation levels in patients than in the controls (p < 0.05). High methylation levels were associated with congenital septal defects (OR = 3.91; 95% CI = 1.02–14.8; p = 0.045). The analysis of Receiver Operating Characteristic (ROC) showed that the methylation levels of the TBX5 gene could be used as a risk marker for congenital septal defects (AUC = 0.68, 95% CI = 0.56–0.80; p = 0.004). Finally, an analysis of environmental factors indicated that maternal infections increased the risk (OR = 2.90; 95% CI = 1.01–8.33; p = 0.048) of congenital septal defects. Our data suggest that a high DNA methylation of the TBX5 gene could be associated with congenital septal defects.

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DNA Methylation and the Potential Role of Methyl-Containing Nutrients in Cardiovascular Diseases

Oxidative Medicine and Cellular Longevity ◽

10.1155/2017/1670815 ◽

2017 ◽

Vol 2017 ◽

pp. 1-7 ◽

Cited By ~ 3

Author(s):

Gang Liu ◽

Peng Bin ◽

Tianwei Wang ◽

Wenkai Ren ◽

Jin Zhong ◽

...

Keyword(s):

Dna Methylation ◽

Folic Acid ◽

Cardiovascular Diseases ◽

Dna Methyltransferase ◽

Epigenetic Modification ◽

Nutritional Supplements ◽

Clinical Value ◽

Research Findings ◽

Therapeutic Measures ◽

The Impact

Patients suffering from cardiovascular diseases (CVDs) experience a low quality of life and increase pressure on healthcare systems both nationally and globally. DNA methylation, which refers to the pathway by which DNA methyltransferase facilitates the addition of a methyl group to DNA, is of critical importance in this respect primarily because the epigenetic modification is implicated in a range of serious conditions including atherosclerosis, CVDs, and cancer. Research findings indicate that the number of epigenetic alterations can be elicited (both in utero and in adults) through the administration of certain nutritional supplements, including folic acid and methionine; this is partly attributable to the effect employed by methyl-containing nutrients in DNA methylation. Thus, for the purpose of illuminating viable therapeutic measures and preventive strategies for CVDs, research should continue to explore the intricate associations that exist between epigenetic regulation and CVD pathogenesis. This review centers on an exposition of the mechanism by which DNA methylation takes place, the impact it has on a range of conditions, and the potential clinical value of nutrition, driven mainly by the observation that nutritional supplements such as folic acid can affect DNA methylation.

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The Pattern and Function of DNA Methylation in Fungal Plant Pathogens

Microorganisms ◽

10.3390/microorganisms8020227 ◽

2020 ◽

Vol 8 (2) ◽

pp. 227 ◽

Cited By ~ 2

Author(s):

Chang He ◽

Zhanquan Zhang ◽

Boqiang Li ◽

Shiping Tian

Keyword(s):

Dna Methylation ◽

Dna Sequences ◽

Plant Pathogens ◽

Epigenetic Modification ◽

Gene Promoter ◽

Pathogenic Fungi ◽

Dna Methyltransferases ◽

Phytopathogenic Fungi ◽

Fungal Plant Pathogens ◽

Wide Range

To successfully infect plants and trigger disease, fungal plant pathogens use various strategies that are dependent on characteristics of their biology and genomes. Although pathogenic fungi are different from animals and plants in the genomic heritability, sequence feature, and epigenetic modification, an increasing number of phytopathogenic fungi have been demonstrated to share DNA methyltransferases (MTases) responsible for DNA methylation with animals and plants. Fungal plant pathogens predominantly possess four types of DNA MTase homologs, including DIM-2, DNMT1, DNMT5, and RID. Numerous studies have indicated that DNA methylation in phytopathogenic fungi mainly distributes in transposable elements (TEs), gene promoter regions, and the repetitive DNA sequences. As an important and heritable epigenetic modification, DNA methylation is associated with silencing of gene expression and transposon, and it is responsible for a wide range of biological phenomena in fungi. This review highlights the relevant reports and insights into the important roles of DNA methylation in the modulation of development, pathogenicity, and secondary metabolism of fungal plant pathogens. Recent evidences prove that there are massive links between DNA and histone methylation in fungi, and they commonly regulate fungal development and mycotoxin biosynthesis.

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CAMP Gene Promoter Methylation Induces Chondrocyte Apoptosis By Inhibiting ROS Levels And Inflammatory Response

10.21203/rs.3.rs-139089/v1 ◽

2021 ◽

Author(s):

Guoliang Wang ◽

Yanlin Li ◽

Guang Yang ◽

Tengyun Yang ◽

Lu He ◽

...

Keyword(s):

Articular Cartilage ◽

Promoter Methylation ◽

Epigenetic Modification ◽

Gene Expression Pattern ◽

Gene Promoter ◽

Cartilage Tissue ◽

Inflammatory Factors ◽

Chondrocyte Apoptosis ◽

Gene Methylation ◽

Genetic And Environmental Factors

Abstract Objective: The occurrence of osteoarthritis is related to genetic and environmental factors. Among them, the change of chondrocyte gene expression pattern regulated by epigenetic modification is an important participant. This study analyzed the effect of CAMP gene methylation on the level of oxidative stress and inflammation of chondrocytes. Methods: We analyzed the changes of the transcriptome in the articular cartilage tissue of osteoarthritis patients (OA) from the GSE117999 dataset. The GSE48422 dataset was used to analyze the changes in the methylation level of osteoarthritis cells. MTT assay and flow cytometry analysis of short hairpin RNA (shRNA) silencing CAMP gene and 5μM 5-Aza-2’-Deoxycytidine (AZA) treatment on the proliferation and apoptosis of Human Chondrocytes Osteoarthritis (HC-OA) cells. The DCFH-DA assay was used to detect the level of reactive oxygen species (ROS), and the expression level of inflammatory factors was analyzed by Western Blot. Results: The expression of CAMP in cartilage tissue of OA patients was up-regulated, and the level of methylation was down-regulated. CAMP was highly expressed in osteoarthritis articular cartilage cells. Silencing CAMP inhibited the proliferation of HC-OA cells and promoted their apoptosis. CAMP gene methylation inhibited ROS levels and TNF-α expression levels in HC-OA cells, and promoted TGF-β expression. CAMP gene methylation inhibited the proliferation of HC-OA cells and promoted their apoptosis. Conclusion: CAMP gene promoter methylation induces chondrocyte apoptosis by inhibiting ROS levels and inflammation.

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