Effects of Chronic Exposure to an Environmentally Relevant Mixture of Brominated Flame Retardants on the Reproductive and Thyroid System in Adult Male Rats

Brominated flame retardants (BFRs) are incorporated into a wide variety of consumer products, are readily released into home and work environments, and are present in house dust. Studies using animal models have revealed that exposure to polybrominated diphenyl ethers (PBDEs) may impair adult male reproductive function and thyroid hormone physiology. Such studies have generally characterized the outcome of acute or chronic exposure to a single BFR technical mixture or congener but not the impact of environmentally relevant BFR mixtures. We tested whether exposure to the BFRs found in house dust would have an adverse impact on the adult male rat reproductive system and thyroid function. Adult male Sprague Dawley rats were exposed to a complex BFR mixture composed of three commercial brominated diphenyl ethers (52.1% DE-71, 0.4% DE-79, and 44.2% decaBDE-209) and hexabromocyclododecane (3.3%), formulated to mimic the relative congener levels in house dust. BFRs were delivered in the diet at target doses of 0, 0.02, 0.2, 2, or 20 mg/kg/day for 70 days. Compared with controls, males exposed to the highest dose of BFRs displayed a significant increase in the weights of the kidneys and liver, which was accompanied by induction of CYP1A and CYP2B P450 hepatic drug–metabolizing enzymes. BFR exposure did not affect reproductive organ weights, serum testosterone levels, testicular function, or sperm DNA integrity. The highest dose caused thyroid toxicity as indicated by decreased serum thyroxine (T4) and hypertrophy of the thyroid gland epithelium. At lower doses, the thickness of the thyroid gland epithelium was reduced, but no changes in hormone levels (T4 and thyroid-stimulating hormone) were observed. Thus, exposure to BFRs affected liver and thyroid physiology but not male reproductive parameters

Developmental exposures to common environmental contaminants, DEHP and lead, alter adult brain and blood hydroxymethylation in mice

Introduction: The developing epigenome changes rapidly, potentially making it more sensitive to toxicant exposures. DNA modifications, including methylation and hydroxymethylation, are important parts of the epigenome that may be affected by environmental exposures. However, most studies do not differentiate between these two DNA modifications, possibly masking significant effects.Methods: To investigate the relationship between DNA hydroxymethylation and developmental exposure to common contaminants, a collaborative, NIEHS-sponsored consortium, TaRGET II, initiated longitudinal mouse studies of developmental exposure to human-relevant levels of the phthalate plasticizer di(2-ethylhexyl) phthalate (DEHP), and the metal lead (Pb). Exposures to 25 mg DEHP/kg of food (approximately 5 mg DEHP/kg body weight) or 32 ppm Pb-acetate in drinking water were administered to nulliparous adult female mice. Exposure began 2 weeks before breeding and continued throughout pregnancy and lactation, until offspring were 21 days old. At 5 months, perinatally exposed offspring blood and cortex tissue were collected, for a total of 25 male mice and 17 female mice (n = 5–7 per tissue and exposure). DNA was extracted and hydroxymethylation was measured using hydroxymethylated DNA immunoprecipitation sequencing (hMeDIP-seq). Differential peak and pathway analysis was conducted comparing across exposure groups, tissue types, and animal sex, using an FDR cutoff of 0.15.Results: DEHP-exposed females had two genomic regions with lower hydroxymethylation in blood and no differences in cortex hydroxymethylation. For DEHP-exposed males, ten regions in blood (six higher and four lower) and 246 regions (242 higher and four lower) and four pathways in cortex were identified. Pb-exposed females had no statistically significant differences in blood or cortex hydroxymethylation compared to controls. Pb-exposed males, however, had 385 regions (all higher) and six pathways altered in cortex, but no differential hydroxymethylation was identified in blood.Discussion: Overall, perinatal exposure to human-relevant levels of two common toxicants showed differences in adult DNA hydroxymethylation that was specific to sex, exposure type, and tissue, but male cortex was most susceptible to hydroxymethylation differences by exposure. Future assessments should focus on understanding if these findings indicate potential biomarkers of exposure or are related to functional long-term health effects

The SEQC2 epigenomics quality control (EpiQC) study

Correction: Volume22, Issue1 Article Number350 DOI10.1186/s13059-021-02573-y PublishedDEC 23 2021 Publisher Copyright: © 2021, The Author(s).Background: Cytosine modifications in DNA such as 5-methylcytosine (5mC) underlie a broad range of developmental processes, maintain cellular lineage specification, and can define or stratify types of cancer and other diseases. However, the wide variety of approaches available to interrogate these modifications has created a need for harmonized materials, methods, and rigorous benchmarking to improve genome-wide methylome sequencing applications in clinical and basic research. Here, we present a multi-platform assessment and cross-validated resource for epigenetics research from the FDA’s Epigenomics Quality Control Group. Results: Each sample is processed in multiple replicates by three whole-genome bisulfite sequencing (WGBS) protocols (TruSeq DNA methylation, Accel-NGS MethylSeq, and SPLAT), oxidative bisulfite sequencing (TrueMethyl), enzymatic deamination method (EMSeq), targeted methylation sequencing (Illumina Methyl Capture EPIC), single-molecule long-read nanopore sequencing from Oxford Nanopore Technologies, and 850k Illumina methylation arrays. After rigorous quality assessment and comparison to Illumina EPIC methylation microarrays and testing on a range of algorithms (Bismark, BitmapperBS, bwa-meth, and BitMapperBS), we find overall high concordance between assays, but also differences in efficiency of read mapping, CpG capture, coverage, and platform performance, and variable performance across 26 microarray normalization algorithms. Conclusions: The data provided herein can guide the use of these DNA reference materials in epigenomics research, as well as provide best practices for experimental design in future studies. By leveraging seven human cell lines that are designated as publicly available reference materials, these data can be used as a baseline to advance epigenomics research.Peer reviewe

Transcriptional Differences between Rhesus Embryonic Stem Cells Generated from <em>In Vitro</em> and <em>In Vivo</em> Derived Embryos

<div><p>Numerous studies have focused on the transcriptional signatures that underlie the maintenance of embryonic stem cell (ESC) pluripotency. However, it remains unclear whether ESC retain transcriptional aberrations seen in <em>in vitro</em> cultured embryos. Here we report the first global transcriptional profile comparison between ESC generated from either <em>in vitro</em> cultured or <em>in vivo</em> derived primate embryos by microarray analysis. Genes involved in pluripotency, oxygen regulation and the cell cycle were downregulated in rhesus ESC generated from <em>in vitro</em> cultured embryos (<em>in vitro</em> ESC). Significantly, several gene differences are similarly downregulated in preimplantation embryos cultured <em>in vitro</em>, which have been associated with long term developmental consequences and disease predisposition. This data indicates that prior to derivation, embryo quality may influence the molecular signature of ESC lines, and may differentially impact the physiology of cells prior to or following differentiation.</p> </div

Epigenetic mechanisms underlying the association between maternal climate stress and child growth: characterizing severe drought and its impact on a Kenyan community engaging in a climate change-sensitive livelihood

Pastoralists in East Africa are among the world’s most vulnerable communities to climate change, already living near their upper thermal limits and engaging in a climate-sensitive livelihood in a climate change global hot spot. Pregnant women and children are even more at risk. Here, we report the findings of a study characterizing Samburu pastoralist women’s experiences of severe drought and outcomes in their children (N = 213, 1.8–9.6 y). First, we examined potential DNA methylation (DNAm) differences between children exposed to severe drought in utero and same-sex unexposed siblings. Next, we performed a high-dimensional mediation analysis to test whether DNAm mediated associations of exposure to severe drought with body weight and adiposity. DNAm was measured using the Infinium MethylationEPIC BeadChip array. After quality control; batch, chip, and genomic inflation corrections; covariate adjustment; and multiple testing correction, 16 CpG sites were differentially methylated between exposed and unexposed children, predominantly in metabolism and immune function pathways. We found a significant indirect effect of drought exposure on child body weight through cg03771070. Our results are the first to identify biological mediators linking severe drought to child growth in a low-income global hot spot for climate change. A better understanding of the mechanisms underlying the association between drought exposure and child growth is important to increasing climate change resilience by identifying targets for intervention

Functional classification and hierarchical clustering of 3881 significantly different transcripts in rhesus ESC.

<p><b>A:</b> Pie charts representing up- and down-regulated biological functions of 3881 differentially expression genes in ESC. Numbers represent percentages of 560 up- and 3321 down-regulated genes in ESC generated from <i>in vitro</i> cultured embryos, compared with ESC generated from <i>in vivo</i> derived embryos. <b>B:</b> Combination Venn diagram of shared and specific genes expressed in ESC originating from <i>in vitro</i> or <i>in vivo</i> derived embryos. The region of overlap between all areas represents the number of genes expressed in ESC from either origin. Regions not overlapping reflect genes expressed specifically in <i>in vitro</i> or <i>in vivo</i> ESC. There are 11521 genes categorized as present (dChip). Of the 3881 genes identified as significant genes from ChipInspector, 2955 genes are considered as present by dChip, the remaining 926 genes as absent. Of the 2955 genes, 2,524 are down-regulated and 431 are up-regulated; on the 926 absent genes, 797 are down-regulated, 129 are up-regulated. <b>C:</b> Dendrogram representing 3881 significantly different transcripts and hierarchical clustering of biological replicates. Colors indicate relative expression level of each gene in all analyzed samples, with red indicating higher expression and green indicating lower expression.</p

Bibliosphere analysis of transcripts where two genes are co-cited and restricted to sentences with gene+function word+gene.

<p>sentences with expert curated information. Each rectangle depicts a single gene. Red indicates the gene is unregulated, blue downregulated. Arrows between two genes shows regulatory mechanisms: green indicates a transcription factor binding site match in the target promoter; open arrowhead indicates regulation; filled arrowhead indicates activation; blocked arrowhead indicates inhibition; blue dot on the edge indicates that the connection has been annotated by experts; <b>A:</b> Associations present between HIF1A and other genes at the expert level; <b>B:</b> Associations present between SMAD2 and other genes at the expert level. IN: gene is an input gene; TF: gene's product is a transcription factor; ST: gene product is part of signal transduction pathway.</p

Differentially expressed transcripts that display altered expression patterns following <i>in vitro</i> embryo culture.

<p>The q-value is calculated as log2 fold change.</p