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Methylome-wide association study of early life stressors and adult mental health.

Hum Mol Genet 2021 Sep 15. Epub 2021 Sep 15.

Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK.

The environment and events that we are exposed to in utero, during birth and in early childhood influence our future physical and mental health. The underlying mechanisms that lead to these outcomes are unclear, but long-term changes in epigenetic marks, such as DNA methylation, could act as a mediating factor or biomarker. DNA methylation data was assayed at 713522 CpG sites from 9537 participants of the Generation Scotland: Scottish Family Health Study, a family-based cohort with extensive genetic, medical, family history and lifestyle information. Read More

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September 2021

Magnetic systems for cancer immunotherapy.

Acta Pharm Sin B 2021 Aug 30;11(8):2172-2196. Epub 2021 Apr 30.

Department of Chemical & Biological Engineering, University of Colorado, Boulder, CO 80303, USA.

Immunotherapy is a rapidly developing area of cancer treatment due to its higher specificity and potential for greater efficacy than traditional therapies. Immune cell modulation through the administration of drugs, proteins, and cells can enhance antitumoral responses through pathways that may be otherwise inhibited in the presence of immunosuppressive tumors. Magnetic systems offer several advantages for improving the performance of immunotherapies, including increased spatiotemporal control over transport, release, and dosing of immunomodulatory drugs within the body, resulting in reduced off-target effects and improved efficacy. Read More

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A transcriptome-wide association study identifies novel candidate susceptibility genes for prostate cancer risk.

Int J Cancer 2021 Sep 14. Epub 2021 Sep 14.

Cancer Epidemiology Division, Population Sciences in the Pacific Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI, USA.

A large proportion of heritability for prostate cancer risk remains unknown. Transcriptome-wide association study combined with validation comparing overall levels will help to identify candidate genes potentially playing a role in prostate cancer development. Using data from the Genotype-Tissue Expression Project, we built genetic models to predict normal prostate tissue gene expression using the statistical framework PrediXcan, a modified version of the unified test for molecular signatures, and Joint-Tissue Imputation. Read More

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September 2021

Perinatal stress and methylation of the gene in newborns: Systematic Review.

Epigenetics 2021 Sep 14. Epub 2021 Sep 14.

D'Or Institute for Research and Education (IDOR), Rio de Janeiro, RJ, Brazil.

Adverse experiences in the perinatal period have been associated with the methylation of the human glucocorticoid receptor gene () and long-term diseases. We conducted a systematic review on the association between adversities in the perinatal period and DNA methylation in the 1 region of the gene in newborns. We explored the MEDLINE, Web of Science, Scopus, Scielo, and Lilacs databases without time or language limitations. Read More

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September 2021

DNA methylation landscapes of 1538 breast cancers reveal a replication-linked clock, epigenomic instability and cis-regulation.

Nat Commun 2021 Sep 13;12(1):5406. Epub 2021 Sep 13.

Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK.

DNA methylation is aberrant in cancer, but the dynamics, regulatory role and clinical implications of such epigenetic changes are still poorly understood. Here, reduced representation bisulfite sequencing (RRBS) profiles of 1538 breast tumors and 244 normal breast tissues from the METABRIC cohort are reported, facilitating detailed analysis of DNA methylation within a rich context of genomic, transcriptional, and clinical data. Tumor methylation from immune and stromal signatures are deconvoluted leading to the discovery of a tumor replication-linked clock with genome-wide methylation loss in non-CpG island sites. Read More

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September 2021

Follistatin supplementation induces changes in CDX2 CpG methylation and improves in vitro development of bovine SCNT preimplantation embryos.

Reprod Biol Endocrinol 2021 Sep 13;19(1):141. Epub 2021 Sep 13.

Laboratory of Mammalian Reproductive Biology and Genomics, Department of Animal Science, Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, MI, USA.

Caudal Type Homeobox 2 (CDX2) is a key regulator of trophectoderm formation and maintenance in preimplantation embryos. We previously demonstrated that supplementation of exogenous follistatin, during in vitro culture of bovine IVF embryos, upregulates CDX2 expression, possibly, via alteration of the methylation status of CDX2 gene. Here, we further investigated the effects of exogenous follistatin supplementation on developmental competence and CDX2 methylation in bovine somatic cell nuclear transfer (SCNT) embryos. Read More

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September 2021

Epigenome-wide analysis of DNA methylation and coronary heart disease: a nested case-control study.

Elife 2021 Sep 13;10. Epub 2021 Sep 13.

Epidemiology and Biostatistics, Peking University, Beijing, China.

Identifying environmentally responsive genetic loci where DNA methylation is associated with coronary heart disease (CHD) may reveal novel pathways or therapeutic targets for CHD. We conducted the first prospective epigenome-wide analysis of DNA methylation in relation to incident CHD in the Asian population.

We did a nested case-control study comprising incident CHD cases and 1:1 matched controls who were identified from the 10-year follow-up of the China Kadoorie Biobank. Read More

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September 2021

Prenatal risk factors and neonatal DNA methylation in very preterm infants.

Clin Epigenetics 2021 Sep 10;13(1):171. Epub 2021 Sep 10.

Department of Psychiatry and Human Behavior, Alpert Medical School of Brown University, Providence, RI, USA.

Background: Prenatal risk factors are related to poor health and developmental outcomes for infants, potentially via epigenetic mechanisms. We tested associations between person-centered prenatal risk profiles, cumulative prenatal risk models, and epigenome-wide DNA methylation (DNAm) in very preterm neonates.

Methods: We studied 542 infants from a multi-center study of infants born < 30 weeks postmenstrual age. Read More

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September 2021

Integrating genome and methylome data to identify candidate DNA methylation biomarkers for pancreatic cancer risk.

Cancer Epidemiol Biomarkers Prev 2021 Sep 8. Epub 2021 Sep 8.

University of Hawaii at Manoa

Background The role of methylation in pancreatic cancer (PC) risk remains unclear. We integrated genome and methylome data to identify CpG sites (CpGs) with the genetically predicted methylation to be associated with PC risk. We also studied gene expression to understand the identified associations. Read More

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September 2021

Developmental programming of DNA methylation and gene expression patterns is associated with extreme cardiovascular tolerance to anoxia in the common snapping turtle.

Epigenetics Chromatin 2021 Sep 6;14(1):42. Epub 2021 Sep 6.

Division of Cardiovascular Sciences, School of Medical Sciences, University of Manchester, Manchester, M13 9NT, UK.

Background: Environmental fluctuation during embryonic and fetal development can permanently alter an organism's morphology, physiology, and behaviour. This phenomenon, known as developmental plasticity, is particularly relevant to reptiles that develop in subterranean nests with variable oxygen tensions. Previous work has shown hypoxia permanently alters the cardiovascular system of snapping turtles and may improve cardiac anoxia tolerance later in life. Read More

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September 2021

Fetal malnutrition is associated with impairment of endogenous melatonin synthesis in pineal via hyper-methylation of promoters of protein kinase C alpha and cAMP-response element-binding.

J Pineal Res 2021 Sep 6:e12764. Epub 2021 Sep 6.

National Key Discipline, Department of Nutrition and Food Hygiene, School of Public Health, Harbin Medical University, Harbin, Heilongjiang Province, 150081, P. R. China.

This study investigated whether and how fetal-malnutrition would influence endogenous melatonin synthesis, and whether such effect of fetal-malnutrition would transmit to the next generation. We enrolled 2466 participants and 1313 their offspring. The urine 6-hydroxymelatonin-sulfate and serum melatonin-rhythm were measured. Read More

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September 2021

The epigenetic DNA modification 5-carboxylcytosine promotes high levels of cyclobutane pyrimidine dimer formation upon UVB irradiation.

Genome Instab Dis 2021 Feb 2;2(1):59-69. Epub 2021 Jan 2.

Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, USA.

In mammals, DNA methyltransferases create 5-methylcytosines (5mC) predominantly at CpG dinucleotides. 5mC oxidases convert 5mC in three consecutive oxidation steps to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and then 5-carboxylcytosine (5caC). Upon irradiation with UV light, dipyrimidines containing C, 5mC and 5hmC are known to form cyclobutane pyrimidine dimers (CPDs) as major DNA photolesions. Read More

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February 2021

DNA methylation changes in African American women with a history of preterm birth from the InterGEN study.

BMC Genom Data 2021 Sep 5;22(1):30. Epub 2021 Sep 5.

Center for Research on People of Color, School of Nursing, Columbia University, 560 W 168th St, Room 605, New York, NY, 10032, USA.

Background: Preterm birth (< 37 weeks' gestation) is a common outcome of pregnancy that has been associated with increased risk of cardiovascular disease for women later in life. Little is known about the physiologic mechanisms underlying this risk. To date, no studies have evaluated if differences in DNA methylation (DNAm) among women who experience preterm birth are short-term or if they persist and are associated with subsequent cardiovascular sequelae or other health disorders. Read More

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September 2021

Methylation quantitative trait locus rs5326 is associated with susceptibility and effective dosage of methadone maintenance treatment for heroin use disorder.

Psychopharmacology (Berl) 2021 Sep 3. Epub 2021 Sep 3.

Key Laboratory of National Health Commission for Forensic Science, College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China.

Rationale: Opioid use disorder is a complicated brain disease with high heritability. The underlying mechanisms of the genetic underpinnings in the susceptibility and treatment response of opioid use disorder remain elusive.

Objectives: To reveal the potential associations of genotypes and gene methylations of dopaminergic system genes, as well as roles of them in opioid use disorder. Read More

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September 2021

Genome-wide sequencing-based identification of methylation quantitative trait loci and their role in schizophrenia risk.

Nat Commun 2021 09 2;12(1):5251. Epub 2021 Sep 2.

Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA.

DNA methylation (DNAm) is an epigenetic regulator of gene expression and a hallmark of gene-environment interaction. Using whole-genome bisulfite sequencing, we have surveyed DNAm in 344 samples of human postmortem brain tissue from neurotypical subjects and individuals with schizophrenia. We identify genetic influence on local methylation levels throughout the genome, both at CpG sites and CpH sites, with 86% of SNPs and 55% of CpGs being part of methylation quantitative trait loci (meQTLs). Read More

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September 2021

Infant RSV immunoprophylaxis changes nasal epithelial DNA methylation at 6 years of age.

Pediatr Pulmonol 2021 Sep 2. Epub 2021 Sep 2.

Department of Pediatric Pulmonology and Pediatric Allergy, Beatrix Children's Hospital, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.

Background: Respiratory syncytial virus (RSV) infection has been associated with childhood wheeze and asthma, and potential mechanisms include persistent epigenetic effects.

Methods: In the randomized, placebo-controlled MAKI trial, 429 preterm infants randomly received RSV immunoprophylaxis with palivizumab or placebo during their first RSV season. Children were followed until age 6 for asthma evaluation. Read More

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September 2021

Associations between childhood maltreatment and DNA methylation of the oxytocin receptor gene in immune cells of mother-newborn dyads.

Transl Psychiatry 2021 Sep 1;11(1):449. Epub 2021 Sep 1.

Clinical & Biological Psychology, Institute of Psychology and Education, Ulm University, Ulm, Germany.

The neuropeptide oxytocin (OXT) and its receptor (OXTR) modulate interpersonal relationships, particularly mother-child interactions. DNA methylation (DNAm) changes of the OXTR gene were observed in individuals who experienced Childhood Maltreatment (CM). A modulatory role of single nucleotide polymorphisms (SNP) within OXTR in association with CM on the regulation of OXTR was also postulated. Read More

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September 2021

MGMT promoter methylation testing to predict overall survival in people with glioblastoma treated with temozolomide: a comprehensive meta-analysis based on a Cochrane Systematic Review.

Neuro Oncol 2021 Sep;23(9):1457-1469

Bristol Medical School, Brain Tumour Research Centre, Population Health Sciences, University of Bristol, Bristol, UK.

Background: The DNA repair protein O6-methylguanine-DNA methyltransferase (MGMT) causes resistance of tumor cells to alkylating agents. It is a predictive biomarker in high-grade gliomas treated with temozolomide, however, there is no consensus on which test method, methylation sites, and cutoff values to use.

Methods: We performed a Cochrane Review to examine studies using different techniques to measure MGMT and predict survival in glioblastoma patients treated with temozolomide. Read More

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September 2021

TANC1 methylation as a novel biomarker for the diagnosis of patients with anti-tuberculosis drug-induced liver injury.

Sci Rep 2021 Aug 31;11(1):17423. Epub 2021 Aug 31.

School of Public Health, North China University of Science and Technology, Tangshan, 063210, China.

We aimed to elucidate the differences in genomic methylation patterns between ADLI and non-ADLI patients to identify DNA methylation-based biomarkers. Genome-wide DNA methylation patterns were obtained using Infinium MethylationEPIC (EPIC) BeadChip array to analyze 14 peripheral blood samples (7 ADLI cases, 7 non-ADLI controls). Changes in the mRNA and DNA methylation in the target genes of another 120 peripheral blood samples (60 ADLI cases, 60 non-ADLI controls) were analyzed by real-time polymerase chain reaction and pyrosequencing, respectively. Read More

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Mutational Signatures: From Methods to Mechanisms.

Annu Rev Biomed Data Sci 2021 07 11;4:189-206. Epub 2021 May 11.

National Center of Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA; email:

Mutations are the driving force of evolution, yet they underlie many diseases, in particular, cancer. They are thought to arise from a combination of stochastic errors in DNA processing, naturally occurring DNA damage (e.g. Read More

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IUSMMT: Survival mediation analysis of gene expression with multiple DNA methylation exposures and its application to cancers of TCGA.

PLoS Comput Biol 2021 Aug 31;17(8):e1009250. Epub 2021 Aug 31.

Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, Jiangsu, China.

Effective and powerful survival mediation models are currently lacking. To partly fill such knowledge gap, we particularly focus on the mediation analysis that includes multiple DNA methylations acting as exposures, one gene expression as the mediator and one survival time as the outcome. We proposed IUSMMT (intersection-union survival mixture-adjusted mediation test) to effectively examine the existence of mediation effect by fitting an empirical three-component mixture null distribution. Read More

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The potential positive epigenetic effects of various mind-body therapies (MBTs): a narrative review.

J Complement Integr Med 2021 Jun 22. Epub 2021 Jun 22.

Division of Behavioral Medicine, Cooper University Hospital, Cooper Medical School of Rowan University, Camden, NJ, USA.

Mind-Body Therapies (MBTs), such as mindfulness, meditation, yoga, and tai-chi, are said to improve quality of life by contributing to positive thinking and reducing overall distress. MBTs not only play a role in reducing stress and anxiety, but they are also found to epigenetically affect genes and other areas in our genomes that are implicated in inflammation, stress, and distress. This review analyzes the role of MBTs in reducing the epigenetic changes as reported in five previously conducted controlled studies found in the NCBI PubMed database. Read More

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Association between dietary patterns reflecting one-carbon metabolism nutrients intake before pregnancy and placental DNA methylation.

Epigenetics 2021 Aug 31:1-16. Epub 2021 Aug 31.

Université De Paris, Cress, Inserm, Inrae, Paris, France.

The preconception period represents an important window for foetal and epigenetic programming. Some micronutrients (B vitamins, choline, betaine, methionine) implicated in one-carbon metabolism (OCM) are essential for major epigenetic processes that take place in early pregnancy. However, few studies have evaluated the implication of the micronutrients in placental DNA methylation. Read More

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Human non-CpG methylation patterns display both tissue-specific and inter-individual differences suggestive of underlying function.

Epigenetics 2021 Aug 30:1-12. Epub 2021 Aug 30.

MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK.

DNA methylation (DNAm) in mammals is mostly examined within the context of CpG dinucleotides. Non-CpG DNAm is also widespread across the human genome, but the functional relevance, tissue-specific disposition, and inter-individual variability has not been widely studied. Our aim was to examine non-CpG DNAm in the wider methylome across multiple tissues from the same individuals to better understand non-CpG DNAm distribution within different tissues and individuals and in relation to known genomic regulatory features. Read More

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Origins of nonsense mutations in human tumor suppressor genes.

Mutat Res 2021 Aug 16;823:111761. Epub 2021 Aug 16.

Department of Pharmaceutical Sciences, University of Pittsburgh, Salk Hall, Pittsburgh, PA, 15261, United States. Electronic address:

Understanding the origins of mutations in tumor suppressor genes and oncogenes associated with cancers in different tissues is critical to the development of potential prevention strategies. Analysis of >10,000 nonsense mutations in 63 tumor suppressor genes based on the ratio of the number of nonsense mutations per codon type is reported for each gene. The ratio for C•G→T•A nonsense mutations at Arg CGA codons to the number of CGA codons in all cancers is 23 (3088 total nonsense mutations for 134 CGA codons in the 63 suppressor genes). Read More

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Effect of Naoluoxintong on the NogoA/RhoA/ROCK pathway by down-regulating DNA methylation in MCAO rats.

J Ethnopharmacol 2021 Aug 28;281:114559. Epub 2021 Aug 28.

School of Pharmacy, Anhui University of Chinese Medicine, Hefei, Anhui, 230012, China.

Ethnopharmacological Relevance: Naoluoxintong (NLXT) is a traditional Chinese Medicine (TCM) prescription that is clinically used in the treatment of ischemic stroke (IS). However, its therapeutic mechanism remains unclear.

Aim Of The Study: To obtain the mechanism of NLXT by observing the protective effects of NLXT on the NogoA/RhoA/Rock pathway in a rat model of IS by regulating DNA methylation. Read More

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Molecular characterization of SARS-CoV-2 from Bangladesh: implications in genetic diversity, possible origin of the virus, and functional significance of the mutations.

Heliyon 2021 Aug 21;7(8):e07866. Epub 2021 Aug 21.

Communicable Disease Control, Directorate General of Health Services, Mohakhali, Dhaka, 1212, Bangladesh.

In a try to understand the pathogenesis, evolution and epidemiology of the SARS-CoV-2 virus, scientists from all over the world are tracking its genomic changes in real-time. Genomic studies can be helpful in understanding the disease dynamics. We have downloaded 324 complete and near complete SARS-CoV-2 genomes submitted in GISAID database from Bangladesh which were isolated between 30 March to 7 September, 2020. Read More

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Characterization, expression and CpG methylation analysis of Dmrt1 and its response to steroid hormone in blotched snakehead (Channa maculata).

Comp Biochem Physiol B Biochem Mol Biol 2021 Aug 26;257:110672. Epub 2021 Aug 26.

Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China. Electronic address:

Dmrt1 is an important transcriptional regulator that plays critical role in male gonadogenesis, testicular differentiation and development. In this study, Dmrt1 was cloned from blotched snakehead (Channa maculata), which is designated as CmDmrt1. CmDmrt1 encoded a putative protein with 293 amino acids and presented an extremely conserved DM domain. Read More

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Longitudinal analysis of individual cfDNA methylome patterns in metastatic prostate cancer.

Clin Epigenetics 2021 Aug 28;13(1):168. Epub 2021 Aug 28.

Cancer Biology and Therapeutics Laboratory, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland.

Background: Disease progression and therapeutic resistance are hallmarks of advanced stage prostate cancer (PCa), which remains a major cause of cancer-related mortality around the world. Longitudinal studies, coupled with the use of liquid biopsies, offer a potentially new and minimally invasive platform to study the dynamics of tumour progression. Our aim was to investigate the dynamics of personal DNA methylomic profiles of metastatic PCa (mPCa) patients, during disease progression and therapy administration. Read More

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EGFR DNA Methylation Correlates With EGFR Expression, Immune Cell Infiltration, and Overall Survival in Lung Adenocarcinoma.

Front Oncol 2021 10;11:691915. Epub 2021 Aug 10.

Department of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China.

Background: The epidermal growth factor receptor (EGFR) is a primary target of molecular targeted therapy for lung adenocarcinoma (LUAD). The mechanisms that lead to epigenetic abnormalities of EGFR in LUAD are still unclear. The purpose of our study was to evaluate the abnormal methylation of EGFR CpG sites as potential biomarkers for LUAD. Read More

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