title: Lead exposure induces changes in 5-hydroxymethylcytosine clusters in CpG islands in human embryonic stem cells and umbilical cord blood.
abstract: Prenatal exposure to neurotoxicants such as lead (Pb) may cause stable changes in the DNA methylation (5mC) profile of the fetal genome. However, few studies have examined its effect on the DNA de-methylation pathway, specifically the dynamic changes of the 5-hydroxymethylcytosine (5hmC) profile. Therefore, in this study, we investigate the relationship between Pb exposure and 5mC and 5hmC modifications during early development. To study the changes in the 5hmC profile, we use a novel modification of the Infinium™ HumanMethylation450 assay (Illumina, Inc.), which we named HMeDIP-450K assay, in an in vitro human embryonic stem cell model of Pb exposure. We model Pb exposure-associated 5hmC changes as clusters of correlated, adjacent CpG sites, which are co-responding to Pb. We further extend our study to look at Pb-dependent changes in high density 5hmC regions in umbilical cord blood DNA from 48 mother-infant pairs from the Early Life Exposure in Mexico to Environmental Toxicants (ELEMENT) cohort. For our study, we randomly selected umbilical cord blood from 24 male and 24 female children from the 1st and 4th quartiles of Pb levels. Our data show that Pb-associated changes in the 5hmC and 5mC profiles can be divided into sex-dependent and sex-independent categories. Interestingly, differential 5mC sites are better markers of Pb-associated sex-dependent changes compared to differential 5hmC sites. In this study we identified several 5hmC and 5mC genomic loci, which we believe might have some potential as early biomarkers of prenatal Pb exposure.
authors.affiliation: a Institute of Environmental Health Sciences; Wayne State University ; Detroit , MI , USA.
authors.forename: Arko
authors.initials: A
authors.lastname: Sen
authors.forename: Pablo
authors.initials: P
authors.lastname: Cingolani
authors.forename: Marie-Claude
authors.initials: MC
authors.lastname: Senut
authors.forename: Susan
authors.initials: S
authors.lastname: Land
authors.forename: Adriana
authors.initials: A
authors.lastname: Mercado-Garcia
authors.forename: Martha M
authors.initials: MM
authors.lastname: Tellez-Rojo
authors.forename: Andrea A
authors.initials: AA
authors.lastname: Baccarelli
authors.forename: Robert O
authors.initials: RO
authors.lastname: Wright
authors.forename: Douglas M
authors.initials: DM
authors.lastname: Ruden
mesh_terms: D044503:5-Methylcytosine / Q000031:analogs & derivatives; D002460:Cell Line; D018899:CpG Islands / Q000187:drug effects*; D003596:Cytosine / Q000031:analogs & derivatives* / Q000737:chemistry / Q000378:metabolism; D019175:DNA Methylation / Q000187:drug effects; D004781:Environmental Exposure / Q000009:adverse effects*; D005312:Fetal Blood / Q000187:drug effects; D000066449:Human Embryonic Stem Cells / Q000187:drug effects*; D006801:Humans; D007854:Lead / Q000009:adverse effects*; D008800:Mexico; D017422:Sequence Analysis, DNA; D012737:Sex Factors; D014470:Umbilical Cord / Q000187:drug effects*
chemical_list: C011865:5-hydroxymethylcytosine; D007854:Lead; D044503:5-Methylcytosine; D003596:Cytosine
keywords: 5-hydroxymethylcytosine; 5-methylcytosine; A-clustering approach for grouping HM450K CpG sites into clusters based on correlations; Aclust; CpG island, CpG islands are usually in the promoter and 5' untranslated regions of genes; CpG islands; CpG, sites, CG dinucleotide methylation site in the genome corresponding with probes on HM450K; DMRs, Differentially methylated regions (clusters) identified by GEE; DhMRs, Differentially Hydroxymethylated regions (clusters) identified by GEE; ELEMENT, Early Life Exposure in Mexico to Environmental Toxicants; GEE, Generalized Estimating Equations, used to measure the estimated change in DNA methylation in co-regulated regions of the genome; HM450K; HM450K, Infinium Human Methylation 450K BeadChip array from Illumina; HMeDIP-450K; HMeDIP-450K, Infinium Human Methylation 450K BeadChip array from Illumina coupled with immunoprecipitation with 5hmC antibodies; LINE-1, Long Interspersed Element 1, a common retrotransposon in humans; MRs, Methylation regions (clusters) identified by A-clustering; clusters; hMRs, Hydroxymethylated regions (clusters) identified by A-clustering; lead; umbilical cord blood