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450K epigenome-wide scan identifies differential DNA methylation in newborns related to maternal smoking during pregnancy.

https://arctichealth.org/en/permalink/ahliterature122072
Source
Environ Health Perspect. 2012 Oct;120(10):1425-31
Publication Type
Article
Date
Oct-2012
Author
Bonnie R Joubert
Siri E Håberg
Roy M Nilsen
Xuting Wang
Stein E Vollset
Susan K Murphy
Zhiqing Huang
Cathrine Hoyo
Øivind Midttun
Lea A Cupul-Uicab
Per M Ueland
Michael C Wu
Wenche Nystad
Douglas A Bell
Shyamal D Peddada
Stephanie J London
Author Affiliation
Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina 27709, USA.
Source
Environ Health Perspect. 2012 Oct;120(10):1425-31
Date
Oct-2012
Language
English
Publication Type
Article
Keywords
Adult
Basic Helix-Loop-Helix Transcription Factors - genetics - metabolism
Biological Markers - blood
Chromatography, Liquid
Cohort Studies
Cotinine - blood
Cytochrome P-450 CYP1A1 - genetics - metabolism
DNA Methylation
DNA-Binding Proteins - genetics - metabolism
Epigenesis, Genetic
Female
Fetal Blood
Genome-Wide Association Study
Humans
Infant, Newborn
Male
Maternal Exposure
Norway - epidemiology
Pregnancy
Prenatal Exposure Delayed Effects - chemically induced - epidemiology - genetics
Repressor Proteins - genetics - metabolism
Tandem Mass Spectrometry
Tobacco Smoke Pollution - adverse effects
Transcription Factors - genetics - metabolism
United States - epidemiology
Abstract
Epigenetic modifications, such as DNA methylation, due to in utero exposures may play a critical role in early programming for childhood and adult illness. Maternal smoking is a major risk factor for multiple adverse health outcomes in children, but the underlying mechanisms are unclear.
We investigated epigenome-wide methylation in cord blood of newborns in relation to maternal smoking during pregnancy.
We examined maternal plasma cotinine (an objective biomarker of smoking) measured during pregnancy in relation to DNA methylation at 473,844 CpG sites (CpGs) in 1,062 newborn cord blood samples from the Norwegian Mother and Child Cohort Study (MoBa) using the Infinium HumanMethylation450 BeadChip (450K).
We found differential DNA methylation at epigenome-wide statistical significance (p-value
Notes
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Comment In: Environ Health Perspect. 2012 Oct;120(10):a40223026408
Erratum In: Environ Health Perspect. 2012 Dec;120(12):A455
PubMed ID
22851337 View in PubMed
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[Analysis of the most frequent mutations in girls with Rett syndrome]

https://arctichealth.org/en/permalink/ahliterature31968
Source
Cas Lek Cesk. 2001 Aug 2;140(15):473-6
Publication Type
Article
Date
Aug-2-2001
Author
R. Rosipal
J. Zeman
J. Hadac
N. Misovicová
S. Nevsímalová
P. Martásek
Author Affiliation
Klinika detského a dorostového lékarství a Centrum integrované genomiky 1. LF UK, Praha. rosipal@hotmail.com
Source
Cas Lek Cesk. 2001 Aug 2;140(15):473-6
Date
Aug-2-2001
Language
Czech
Publication Type
Article
Keywords
Adolescent
Adult
Child
Child, Preschool
Chromosomal Proteins, Non-Histone
CpG Islands - genetics
DNA-Binding Proteins - genetics
English Abstract
Female
Humans
Linkage (Genetics)
Methyl-CpG-Binding Protein 2
Mutation
Polymorphism, Restriction Fragment Length
Repressor Proteins - genetics
Research Support, Non-U.S. Gov't
Rett Syndrome - genetics
X Chromosome
Abstract
BACKGROUND: Rett syndrome is an X-linked dominant neurodevelopmental disorder affecting 1 from 10,000 to 15,000 females worldwide. The responsible gene, encoding methyl-CpG binding protein 2 was recently identified. Methyl-CpG binding protein 2 is thought to act as a global transcriptional repressor. In the methyl-CpG binding protein 2 gene are known 5 prevalent mutations that cause Rett syndrome. Four of them are detectable by restriction analysis. In this study we present the results of the molecular study of four prevalent mutations in the gene for methyl-CpG binding protein 2 in Czech and Slovak patients with Rett syndrome. METHODS AND RESULTS: 22 females with Rett syndrome were investigated by methods of molecular biology. Restriction analysis and direct sequencing of PCR products revealed in methyl-CpG binding protein 2 gene 3 different mutations (T158M, R168X, R270X) in six unrelated patients with Rett syndrome. Mutation R306C, frequent in Great Britain and Sweden, was not detected in our group of patients with Rett syndrome. CONCLUSIONS: The diagnosis of Rett syndrome and genetic counselling in affected families should go out from the close cooperation of the pediatric, neurologic, and genetic departments with the specialized laboratories dealing with the molecular biological diagnosis.
PubMed ID
11569169 View in PubMed
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Analysis of ZNF350/ZBRK1 promoter variants and breast cancer susceptibility in non-BRCA1/2 French Canadian breast cancer families.

https://arctichealth.org/en/permalink/ahliterature118982
Source
J Hum Genet. 2013 Feb;58(2):59-66
Publication Type
Article
Date
Feb-2013
Author
Karine V Plourde
Yvan Labrie
Sylvie Desjardins
Pascal Belleau
Geneviève Ouellette
Francine Durocher
Author Affiliation
Cancer Genomics Laboratory, Oncology and Molecular Endocrinology Research Centre, Centre Hospitalier Universitaire de Québec and Laval University, Québec City, QC, Canada.
Source
J Hum Genet. 2013 Feb;58(2):59-66
Date
Feb-2013
Language
English
Publication Type
Article
Keywords
Base Sequence
Breast Neoplasms - genetics
Canada
DNA Primers
Female
Genes, BRCA1
Genes, BRCA2
Genetic Predisposition to Disease
Haplotypes
Humans
Linkage Disequilibrium
Polymerase Chain Reaction
Promoter Regions, Genetic
Repressor Proteins - genetics
Abstract
ZNF350/ZBRK1 is a transcription factor, which associates with BRCA1 to co-repress GADD45A to regulate DNA damage repair, and the expression of ZNF350 is altered in different human carcinomas. In a previous study, we identified ZNF350 genomic variants potentially involved in breast cancer susceptibility in high-risk non-BRCA1/2 breast cancer individuals, which pointed toward a potential association for variants in the 5'-UTR and promoter regions. Therefore, direct sequencing was undertaken and identified 12 promoter variants, whereas haplotype analyses put in evidence four common haplotypes with a frequency>2%. However, based on their frequency observed in breast cancer and unrelated healthy individuals, these are not statistically associated with breast cancer risk. Luciferase promoter assays in two breast cancer cell lines identified two haplotypes (H11 and H12) stimulating significantly the expression of ZNF350 transcript compared with the common haplotype H8. The high expression of the H11 allele was associated with the variant c.-874A. Using MatInspector and Transcription Element Search softwares, in silico analyses predicted that the variant c.-874A created a binding site for the factors c-Myc and myogenin. This study represents the first characterization step of the ZNF350 promoter. Additional studies in larger cohorts and other populations will be needed to further evaluate whether common and/or rare ZNF350 promoter variants and haplotypes could be associated with a modest risk of breast cancer.
Notes
Comment In: J Hum Genet. 2013 Feb;58(2):5823223009
PubMed ID
23151675 View in PubMed
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[Association of polymorphisms in toll-like receptor genes with atopic dermatitis in the Republic of Bashkortostan].

https://arctichealth.org/en/permalink/ahliterature265137
Source
Mol Biol (Mosk). 2014 Mar-Apr;48(2):265-76
Publication Type
Article
Author
G F Gimalova
A S Karunas
Iu Iu Fedorova
É R Gumennaia
S V Levasheva
Z R Khismatullina
E. Prans
S. Koks
É I Étkina
É K Khusnutdinova
Source
Mol Biol (Mosk). 2014 Mar-Apr;48(2):265-76
Language
Russian
Publication Type
Article
Keywords
Adolescent
Adult
Alleles
Antigens, CD14 - genetics - immunology
Bashkiria
Case-Control Studies
Child
Child, Preschool
Chromosomes, Human, Pair 11
Dermatitis, Atopic - genetics - immunology - pathology
Female
Gene Expression
Gene Frequency
Gene-Environment Interaction
Genetic Loci
Genetic Predisposition to Disease
Humans
Male
Membrane Proteins - genetics - immunology
Middle Aged
Neoplasm Proteins - genetics - immunology
Nod1 Signaling Adaptor Protein - genetics - immunology
Nod2 Signaling Adaptor Protein - genetics - immunology
Nuclear Proteins - genetics - immunology
Polymorphism, Genetic
Repressor Proteins - genetics - immunology
Toll-Like Receptors - genetics - immunology
Abstract
Atopic dermatitis (AD) is a prevalent chronic inflammatory skin disease developing as a result of the interaction between genetic predisposition and environmental factors. Considerable role in allergic diseases development is played by polymorphisms of genes of pattern-recognition receptors (PRR) which are capable of recognizing conservative standard molecular structures (patterns) unique for large pathogen groups. In this study polymorphic variants of PRR genes--Toll-like receptors (TLR1, TLR2, TLR4, TLR5, TLR6, TLR9, TLR10), NOD-like receptors (NOD1, NOD2), lipopolysaccharide receptor CD14 gene, and C11orf30 and LRRC32 genes, located in 11q13.5 region, have been investigated in AD patients and control subjects from the Republic of Bashkortostan. An association of TLR1 (rs5743571 and rs5743604), TLR6 (rs5743794) and TLR10 (rs11466617) with AD was found. Our results confirm an important role of the innate immune system in the pathogenesis of AD and the significance of polymorphisms within the Toll-like receptor 2 subfamily genes in AD development.
PubMed ID
25850295 View in PubMed
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Associations between oxytocin-related genes and autistic-like traits.

https://arctichealth.org/en/permalink/ahliterature259494
Source
Soc Neurosci. 2014;9(4):378-86
Publication Type
Article
Date
2014
Author
Daniel Hovey
Anna Zettergren
Lina Jonsson
Jonas Melke
Henrik Anckarsäter
Paul Lichtenstein
Lars Westberg
Source
Soc Neurosci. 2014;9(4):378-86
Date
2014
Language
English
Publication Type
Article
Keywords
Antigens, CD38 - genetics
Aryl Hydrocarbon Receptor Nuclear Translocator - genetics
Basic Helix-Loop-Helix Transcription Factors - genetics
Child
Child Development Disorders, Pervasive - genetics - psychology
Female
Genotyping Techniques
Humans
Interviews as Topic
Language Development Disorders - genetics
Male
Membrane Glycoproteins - genetics
Oxytocin - genetics
Parents
Phenotype
Polymorphism, Single Nucleotide
Repressor Proteins - genetics
Social Behavior
Stereotyped Behavior
Sweden
Abstract
Oxytocin has repeatedly been shown to influence human behavior in social contexts; also, a relationship between oxytocin and the pathophysiology of autism spectrum disorder (ASD) has been suggested. In the present study, we investigated single-nucleotide polymorphisms (SNPs) in the oxytocin gene (OXT) and the genes for single-minded 1 (SIM1), aryl hydrocarbon receptor nuclear translocator 2 (ARNT2) and cluster of differentiation 38 (CD38) in a population of 1771 children from the Child and Adolescent Twin Study in Sweden (CATSS). Statistical analyses were performed to investigate any association between SNPs and autistic-like traits (ALTs), measured through ASD scores in the Autism-Tics, ADHD and other Co-morbidities inventory. Firstly, we found a statistically significant association between the SIM1 SNP rs3734354 (Pro352Thr) and scores for language impairment (p = .0004), but due to low statistical power this should be interpreted cautiously. Furthermore, nominal associations were found between ASD scores and SNPs in OXT, ARNT2 and CD38. In summary, the present study lends support to the hypothesis that oxytocin and oxytocin neuron development may have an influence on the development of ALTs and suggests a new candidate gene in the search for the pathophysiology of ASD.
PubMed ID
24635660 View in PubMed
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A case of Rett syndrome from Ukraine--clinical diagnosis confirmed by mutation analysis of the MECP2 gene.

https://arctichealth.org/en/permalink/ahliterature58208
Source
Bratisl Lek Listy. 2004;105(9):299-302
Publication Type
Article
Date
2004
Author
V. Bzduch
D. Zahorakova
E. Grechanina
E P Zdibskaja
I G Goldfarb
J. Zeman
P. Martasek
Author Affiliation
First Department of Pediatrics, Comenius University Children's Hospital, Bratislava, Slovakia.
Source
Bratisl Lek Listy. 2004;105(9):299-302
Date
2004
Language
English
Publication Type
Article
Keywords
Chromosomal Proteins, Non-Histone - genetics
CpG Islands - genetics
DNA-Binding Proteins - genetics
Female
Frameshift Mutation
Genetic markers
Humans
Infant
Methyl-CpG-Binding Protein 2
Mutation
Repressor Proteins - genetics
Research Support, Non-U.S. Gov't
Rett Syndrome - diagnosis - epidemiology - genetics
Ukraine - epidemiology
Abstract
Rett syndrome (RTT) is an X-linked disorder caused by mutations in the methyl-CpG-binding protein 2 gene (MECP2). The incidence is 1:10,000-1:15,000 females worldwide. To date, the mutational spectrum of MECP2 in the Ukrainian population is not known. Here we present first Ukrainian girl with classic clinical signs of RTT, in whom mutation of MECP2 gene was detected. Total genomic DNA was extracted from a dry blood spot using the QIAamp DNA Mini Kit (Qiagen) according to the manufacturer's protocol. Genomic DNA was used to amplify coding sequence and exon/intron borders of MECP2 gene. Products were examined by restriction analysis and automatic direct sequencing. The sequencing analysis of our patient revealed a small deletion of 4 bases AAAG at position 856-859 in exon 4 of MECP2 gene (856-859del4). This mutation leads to a frameshift (K286fs) and a premature stop codon. The creation of premature stop codon results in synthesis of truncated MeCP2 protein. Localization of the mutation into the transcription repression domain (TRD) probably affects the function of MECP2 protein in the process of transcriptional repression. To our knowledge this is the first case from Ukraine, in whom clinical diagnosis of RTT was confirmed by mutation analysis of MECP2 gene. Mutation analyses of further patients are needed to establish the spectrum of MECP2 mutations in the Ukrainian population. (Tab. 1, Fig. 3, Ref. 22.)
PubMed ID
15633890 View in PubMed
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Clinical features of Clostridium difficile infection and molecular characterization of the isolated strains in a cohort of Danish hospitalized patients.

https://arctichealth.org/en/permalink/ahliterature133080
Source
Eur J Clin Microbiol Infect Dis. 2012 Feb;31(2):185-92
Publication Type
Article
Date
Feb-2012
Author
L M Søes
I. Brock
S. Persson
J. Simonsen
K E Pribil Olsen
M. Kemp
Author Affiliation
Department of Microbiological Diagnostics, Statens Serum Institut, Bldg. 43/317, Artillerivej 5, 2300 Copenhagen S, Denmark. lms@ssi.dk
Source
Eur J Clin Microbiol Infect Dis. 2012 Feb;31(2):185-92
Date
Feb-2012
Language
English
Publication Type
Article
Keywords
Adolescent
Adult
Aged
Bacterial Proteins - genetics
Bacterial Toxins - genetics
Child
Child, Preschool
Clostridium Infections - microbiology - pathology
Clostridium difficile - classification - genetics - isolation & purification
Cohort Studies
Community-Acquired Infections - microbiology - pathology
Cross Infection - microbiology - pathology
Denmark
Enterocolitis, Pseudomembranous - microbiology - pathology
Female
Hospitalization
Humans
Male
Middle Aged
Repressor Proteins - genetics
Severity of Illness Index
Young Adult
Abstract
The purpose of this study was to compare clinical features of Clostridium difficile infection (CDI) to toxin gene profiles of the strains isolated from Danish hospitalized patients. C. difficile isolates were characterized by PCR based molecular typing methods including toxin gene profiling and analysis of deletions and truncating mutations in the toxin regulating gene tcdC. Clinical features were obtained by questionnaire. Thirty percent of the CDI cases were classified as community-acquired. Infection by C. difficile with genes encoding both toxin A, toxin B and the binary toxin was significantly associated with hospital-acquired/healthcare-associated CDI compared to community-acquired CDI. Significantly higher leukocyte counts and more severe clinical manifestations were observed in patients infected by C. difficile containing genes also encoding the binary toxin together with toxin A and B compared to patients infected by C. difficile harbouring only toxin A and B. In conclusion, infection by C. difficile harbouring genes encoding both toxin A, toxin B and the binary toxin were associated with hospital acquisition, higher leukocyte counts and severe clinical disease.
PubMed ID
21744281 View in PubMed
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A common variant upstream of the PAX6 gene influences islet function in man.

https://arctichealth.org/en/permalink/ahliterature131235
Source
Diabetologia. 2012 Jan;55(1):94-104
Publication Type
Article
Date
Jan-2012
Author
Ahlqvist E
Turrini F
Lang ST
Taneera J
Zhou Y
Almgren P
Hansson O
Isomaa B
Tuomi T
Eriksson K
Eriksson JG
Lyssenko V
Groop L
Author Affiliation
Department of Clinical Sciences, Diabetes and Endocrinology, Lund University, CRC at Skåne University Hospital, 205 02 Malmö, Sweden. Emma.Ahlqvist@med.lu.se
Source
Diabetologia. 2012 Jan;55(1):94-104
Date
Jan-2012
Language
English
Publication Type
Article
Keywords
Adolescent
Adult
Aged
Cohort Studies
Diabetes Mellitus, Type 2 - genetics - metabolism - physiopathology
Down-Regulation
Eye Proteins - genetics - metabolism
Female
Finland
Genetic Association Studies
Homeodomain Proteins - genetics - metabolism
Humans
Insulin Resistance
Islets of Langerhans - metabolism - physiopathology
Linkage Disequilibrium
Male
Middle Aged
Oligonucleotide Array Sequence Analysis
Paired Box Transcription Factors - genetics - metabolism
Polymorphism, Single Nucleotide
Proprotein Convertase 1 - genetics - metabolism
RNA, Messenger - metabolism
Repressor Proteins - genetics - metabolism
Tissue Culture Techniques
Young Adult
Abstract
Impaired glucose tolerance and impaired insulin secretion have been reported in families with PAX6 mutations and it is suggested that they result from defective proinsulin processing due to lack of prohormone convertase 1/3, encoded by PCSK1. We investigated whether a common PAX6 variant would mimic these findings and explored in detail its effect on islet function in man.
A PAX6 candidate single nucleotide polymorphism (rs685428) was associated with fasting insulin levels in the Diabetes Genetics Initiative genome-wide association study. We explored its potential association with glucose tolerance and insulin processing and secretion in three Scandinavian cohorts (N?=?8,897 individuals). In addition, insulin secretion and the expression of PAX6 and transcriptional target genes were studied in human pancreatic islets.
rs685428 G allele carriers had lower islet mRNA expression of PAX6 (p?=?0.01) and PCSK1 (p?=?0.001) than AA homozygotes. The G allele was associated with increased fasting insulin (p (replication)?=?0.02, p (all)?=?0.0008) and HOMA-insulin resistance (p (replication)?=?0.02, p (all)?=?0.001) as well as a lower fasting proinsulin/insulin ratio (p (all)?=?0.008) and lower fasting glucagon (p?=?0.04) and gastric inhibitory peptide (GIP) (p?=?0.05) concentrations. Arginine-stimulated (p?=?0.02) insulin secretion was reduced in vivo, which was further reflected by a reduction of glucose- and potassium-stimulated insulin secretion (p?=?0.002 and p?=?0.04, respectively) in human islets in vitro.
A common variant in PAX6 is associated with reduced PAX6 and PCSK1 expression in human islets and reduced insulin response, as well as decreased glucagon and GIP concentrations and decreased insulin sensitivity. These findings emphasise the central role of PAX6 in the regulation of islet function and glucose metabolism in man.
PubMed ID
21922321 View in PubMed
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DNA methylation of the cancer-related genes F2RL3 and AHRR is associated with occupational exposure to polycyclic aromatic hydrocarbons.

https://arctichealth.org/en/permalink/ahliterature297917
Source
Carcinogenesis. 2018 07 03; 39(7):869-878
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Date
07-03-2018
Author
Ayman Alhamdow
Christian Lindh
Jessika Hagberg
Pål Graff
Håkan Westberg
Annette M Krais
Maria Albin
Per Gustavsson
Håkan Tinnerberg
Karin Broberg
Author Affiliation
Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.
Source
Carcinogenesis. 2018 07 03; 39(7):869-878
Date
07-03-2018
Language
English
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Keywords
Adult
Aged
Basic Helix-Loop-Helix Transcription Factors - genetics
Biomarkers, Tumor - genetics
Carcinogens - toxicity
Creosote - adverse effects
DNA Methylation - drug effects
DNA, Mitochondrial - genetics
Humans
Lung Neoplasms - chemically induced - genetics
Male
Middle Aged
Occupational Exposure - adverse effects
Polycyclic Aromatic Hydrocarbons - adverse effects
Receptors, Thrombin - genetics
Repressor Proteins - genetics
Sweden
Young Adult
Abstract
Some polycyclic aromatic hydrocarbons (PAH) are known carcinogens and workplace PAH exposure may increase the risk of cancer. Monitoring early cancer-related changes can indicate whether the exposure is carcinogenic. Here, we enrolled 151 chimney sweeps, 152 controls and 19 creosote-exposed male workers from Sweden. We measured urinary PAH metabolites using LC/MS/MS, the cancer-related markers telomere length (TL) and mitochondrial DNA copy number (mtDNAcn) using qPCR, and DNA methylation of lung cancer-related genes F2RL3 and AHRR using pyrosequencing. The median 1-hydroxypyrene (PAH metabolite) concentrations were highest in creosote-exposed workers (8.0 µg/g creatinine) followed by chimney sweeps (0.34 µg/g creatinine) and controls (0.05 µg/g creatinine). TL and mtDNAcn did not differ between study groups. Chimney sweeps and creosote-exposed workers had significantly lower methylation of AHRR CpG site cg05575921 (88.1 and 84.9%, respectively) than controls (90%). Creosote-exposed workers (73.3%), but not chimney sweeps (76.6%) had lower methylation of F2RL3 cg03636183 than controls (76.7%). Linear regression analyses showed that chimney sweeps had lower AHRR cg05575921 methylation (B = -2.04; P
PubMed ID
29722794 View in PubMed
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39 records – page 1 of 4.