scholarly journals TCDD-induced multi- and transgenerational changes in the methylome of male zebrafish gonads

2020 ◽  
Vol 6 (1) ◽  
Author(s):  
Camille Akemann ◽  
Danielle N Meyer ◽  
Katherine Gurdziel ◽  
Tracie R Baker
Keyword(s):  
Dna Methylation ◽  
Skin Irritation ◽  
Epigenetic Mechanism ◽  
Endocrine Function ◽  
Reproductive Capacity ◽  
Transgenerational Effects ◽  
Endocrine Disrupting Chemical ◽  
Reproductive Effects ◽  
Aryl Hydrocarbon Receptor Agonist ◽  
Differentially Methylated Genes

Abstract The legacy endocrine disrupting chemical and aryl hydrocarbon receptor agonist, 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), is produced as a byproduct of industrial processes and causes adverse health effects ranging from skin irritation to cancer. TCDD endpoints are also observed in subsequent, unexposed generations; however, the mechanisms of these multi- and transgenerational effects are unknown. We hypothesized an epigenetic mechanism, specifically DNA methylation for the transgenerational, male-mediated reproductive effects of developmental TCDD exposure. Using whole genome bisulfite sequencing, we evaluated DNA methylation changes in three generations of zebrafish, the first of which was exposed to TCDD during sexual development at 50 ppt for 1 h at both 3- and 7-week post-fertilization. We discovered that TCDD induces multi- and transgenerational methylomic changes in testicular tissue from zebrafish with decreased reproductive capacity, but most significantly in the indirectly exposed F1 generation. In comparing differentially methylated genes to concurrent transcriptomic changes, we identified several genes and pathways through which transgenerational effects of low level TCDD exposure are likely inherited. These include significant differential methylation of genes involved in reproduction, endocrine function, xenobiotic metabolism, and epigenetic processing. Notably, a number of histone modification genes were both differentially methylated and expressed in all generations, and many differentially methylated genes overlapped between multiple generations. Collectively, our results suggest that DNA methylation is a promising mechanism to explain male-mediated transgenerational reproductive effects of TCDD exposure in zebrafish, and these effects are likely inherited through integration of multiple epigenetic pathways.

Genome-Wide Methylation Arrays Reveal Distinct Methylation Profiles in Prognostic Subsets of Chronic Lymphocytic Leukemia.

Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 364-364
Author(s):  
Nicola Cahill ◽  
Meena Kanduri ◽  
Hanna Göransson ◽  
Anders Isaksson ◽  
Camilla Enström ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Chronic Lymphocytic Leukemia ◽  
Tumor Suppressor ◽  
Methylation Status ◽  
Lymphocytic Leukemia ◽  
Epigenetic Mechanism ◽  
Absolute Difference ◽  
Global Methylation ◽  
Genome Wide ◽  
Differentially Methylated Genes

Abstract Abstract 364 Introduction: Aberrant DNA methylation has been shown to play a strong role in tumorogenesis, where genome-wide hypomethylation and regional hypermethylation of tumor suppressor gene (TGS) promoters are characteristic hallmarks of many cancers. In chronic lymphocytic leukemia (CLL), the epigenetic mechanism of gene regulation has thus far received limited attention, although promoter methylation and transcriptional silencing has been shown for certain individual genes, for example, DAPK1, ZAP70 and PEG10. To date, only the ‘Restriction Landmark Genomic Scanning' technique has been performed to assess the genome-wide methylation status in CLL. However, this technique spans only 3000 CpG islands and does not give a full coverage of the genome. Patients and methods: Here, we analyzed the global methylation profiles in CLL by applying high-resolution genome-wide methylation arrays from Illumina that cover 28,000 CpG sites, spanning 14,000 genes. Specifically, 23 CLL samples belonging to the immunoglobulin heavy-chain variable (IGHV) mutated (favorable prognostic) and IGHV unmutated/IGHV3-21 (poor-prognostic) subsets were analysed. The raw data was processed using the BeadStudio software followed by bioinformatic analysis where the arcsin transformed data was used in a moderated t-test to find differentially methylated genes. Only genes with a large absolute difference between the groups were included for further analysis. Methylation-specific PCR (MSP-PCR) and realtime-PCR (RQ-PCR) were performed on a selection of genes to confirm the array data. Additionally, bi-sulfite sequencing was employed on selected genes to confirm the degree of methylation. Moreover, CLL samples were treated with the DNA methyl transferase inhibitor 5-aza-2'-deoxycytidine combined with and without the histone deacetylase inhibitor (HDAC) trichostatin A to induce re-expression of selected methylated genes Results: Overall, we observed significant differences in methylation patterns between the CLL subgroups. Specifically, we identified TSGs that were preferentially methylated in the IGHV unmutated (7 genes, e.g. VHL, ABI3) and IGHV3-21(1 gene, SLC22A18) subgroups. We also identified 10 unmethylated and hence potentially expressed genes shown to be involved in activation of proliferative pathways such as the NFkB pathway (e.g. ADORA3), and the MAP/ERK kinase pathway (e.g. FABP7) in the IGHV unmutated and IGHV3-21 subgroups. In contrast, these latter genes were silenced by methylation in IGHV mutated patients. The methylation status was verified for 4 genes (BCL10, PRF1, ADORA3 and IGSF4) by MSP-PCR and the expression status of 7 genes (BCL10, PRF1, ADORA3, IGSF4, NGFR, ABI3 and VHL) was confirmed using RQ-PCR. Furthermore, bi-sulfite sequencing confirmed the degree of methylation for 2 methylated TSGs (VHL and ABI3) in unmutated CLL samples. Finally, the significance of DNA methylation in regulating gene promoters was shown by re-inducing 3 methylated TSGs ( VHL, ABI3 and IGSF4) in IGHV unmutated samples using the methyl-inhibitor 5-aza-2'-deoxycytidine. Conclusion: Taken together, our data for the first time reveals differences in global methylation profiles between prognostic subsets of CLL, which may unfold important epigenetic silencing mechanisms involved in CLL pathogenesis. Specific inhibition of expression of unmethylated genes involved in facilitating tumorogenesis and re-expression of methylated tumor suppressor genes within the poor-prognostic CLL subgroups may represent potential new drug therapy targets. Disclosures: No relevant conflicts of interest to declare.

Gestational Diabetes Alters Offspring DNA Methylation Profiles in Human and Rat: Identification of Key Pathways Involved in Endocrine System Disorders, Insulin Signaling, Diabetes Signaling, and ILK Signaling

Endocrinology ◽  
2015 ◽  
Vol 156 (6) ◽  
pp. 2222-2238 ◽  
Author(s):  
Sophie Petropoulos ◽  
Claire Guillemin ◽  
Zivanit Ergaz ◽  
Sergiy Dimov ◽  
Matthew Suderman ◽  
...  
Keyword(s):  
Metabolic Disease ◽  
Dna Methylation ◽  
Gestational Diabetes ◽  
Endocrine System ◽  
Maternal Diabetes ◽  
Endocrine Function ◽  
Diabetic Rat ◽  
Therapeutic Implications ◽  
Differentially Methylated Genes ◽  
Insulin Responses

Abstract Gestational diabetes is associated with risk for metabolic disease later in life. Using a cross-species approach in rat and humans, we examined the hypothesis that gestational diabetes during pregnancy triggers changes in the methylome of the offspring that might be mediating these risks. We show in a gestation diabetes rat model, the Cohen diabetic rat, that gestational diabetes triggers wide alterations in DNA methylation in the placenta in both candidate diabetes genes and genome-wide promoters, thus providing evidence for a causal relationship between diabetes during pregnancy and DNA methylation alterations. There is a significant overlap between differentially methylated genes in the placenta and the liver of the rat offspring. Several genes differentially methylated in rat placenta exposed to maternal diabetes are also differentially methylated in the human placenta of offspring exposed to gestational diabetes in utero. DNA methylation changes inversely correlate with changes in expression. The changes in DNA methylation affect known functional gene pathways involved in endocrine function, metabolism, and insulin responses. These data provide support to the hypothesis that early-life exposures and their effects on metabolic disease are mediated by DNA methylation changes. This has important diagnostic and therapeutic implications.

scholarly journals Comparative Transcriptome and DNA Methylation Analysis of Phenotypic Plasticity in the Pacific Abalone (Haliotis discus hannai)

2021 ◽  
Vol 12 ◽  
Author(s):  
Zekun Huang ◽  
Qizhen Xiao ◽  
Feng Yu ◽  
Yang Gan ◽  
Chengkuan Lu ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Phenotypic Plasticity ◽  
Large Scale ◽  
Southern China ◽  
Epigenetic Mechanism ◽  
Adaptive Plasticity ◽  
Haliotis Discus Hannai ◽  
Pacific Abalone ◽  
Differentially Methylated Genes ◽  
Haliotis Discus

Phenotypic plasticity is an adaptive mechanism used by organisms to cope with environmental fluctuations. Pacific abalone (Haliotis discus hannai) are large-scale farmed in the temperate area of northern China and in the warmer waters of southern China. RNA-seq and comparative transcriptomic analysis here were performed to determine if the northern and southern populations have evolved divergent plasticity and if functional differences are associated with protein synthesis and growth-related biological progress. The DNA methylation (5mC) landscape of H. discus hannai from the two populations using whole genomic bisulfite sequencing (WGBS), exhibited different epigenetic patterns. The southern population had significant genomic hypo-methylation that may have resulted from long-term acclimation to heat stress. Combining 790 differentially expressed genes (DEGs) and 7635 differentially methylated genes (DMGs), we found that methylation within the gene body might be important in predicting abalone gene expression. Genes related to growth, development, transduction, and apoptosis may be regulated by methylation and could explain the phenotypic divergence of H. discus hannai. Our findings not only emphasize the significant roles of adaptive plasticity in the acclimation of H. discus hannai to high temperatures but also provide a new understanding of the epigenetic mechanism underlying the phenotypic plasticity in adaptation to climate change for marine organisms.

scholarly journals DNA methylome signatures of prenatal exposure to synthetic glucocorticoids in hippocampus and peripheral whole blood of female guinea pigs in early life

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Aya Sasaki ◽  
Margaret E. Eng ◽  
Abigail H. Lee ◽  
Alisa Kostaki ◽  
Stephen G. Matthews
Keyword(s):  
Dna Methylation ◽  
Whole Blood ◽  
Guinea Pigs ◽  
Critical Role ◽  
Methylation Status ◽  
Peripheral Tissues ◽  
Epigenetic Biomarkers ◽  
Differentially Methylated Genes ◽  
Increased Risk ◽  
Synthetic Glucocorticoids

AbstractSynthetic glucocorticoids (sGC) are administered to women at risk of preterm delivery, approximately 10% of all pregnancies. In animal models, offspring exposed to elevated glucocorticoids, either by administration of sGC or endogenous glucocorticoids as a result of maternal stress, show increased risk of developing behavioral, endocrine, and metabolic dysregulation. DNA methylation may play a critical role in long-lasting programming of gene regulation underlying these phenotypes. However, peripheral tissues such as blood are often the only accessible source of DNA for epigenetic analyses in humans. Here, we examined the hypothesis that prenatal sGC administration alters DNA methylation signatures in guinea pig offspring hippocampus and whole blood. We compared these signatures across the two tissue types to assess epigenetic biomarkers of common molecular pathways affected by sGC exposure. Guinea pigs were treated with sGC or saline in late gestation. Genome-wide modifications of DNA methylation were analyzed at single nucleotide resolution using reduced representation bisulfite sequencing in juvenile female offspring. Results indicate that there are tissue-specific as well as common methylation signatures of prenatal sGC exposure. Over 90% of the common methylation signatures associated with sGC exposure showed the same directionality of change in methylation. Among differentially methylated genes, 134 were modified in both hippocampus and blood, of which 61 showed methylation changes at identical CpG sites. Gene pathway analyses indicated that prenatal sGC exposure alters the methylation status of gene clusters involved in brain development. These data indicate concordance across tissues of epigenetic programming in response to alterations in glucocorticoid signaling.

scholarly journals Salivary DNA Methylation as an Epigenetic Biomarker for Head and Neck Cancer. Part I: A Diagnostic Accuracy Meta-Analysis

2021 ◽  
Vol 11 (6) ◽  
pp. 568
Author(s):  
Óscar Rapado-González ◽  
Cristina Martínez-Reglero ◽  
Ángel Salgado-Barreira ◽  
Laura Muinelo-Romay ◽  
Juan Muinelo-Lorenzo ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Head And Neck Cancer ◽  
Diagnostic Accuracy ◽  
Head And Neck ◽  
Likelihood Ratio ◽  
Neck Cancer ◽  
Meta Analysis ◽  
Positive Likelihood Ratio ◽  
Epigenetic Mechanism ◽  
Cochrane Library

DNA hypermethylation is an important epigenetic mechanism for gene expression inactivation in head and neck cancer (HNC). Saliva has emerged as a novel liquid biopsy representing a potential source of biomarkers. We performed a comprehensive meta-analysis to evaluate the overall diagnostic accuracy of salivary DNA methylation for detecting HNC. PubMed EMBASE, Web of Science, LILACS, and the Cochrane Library were searched. Study quality was assessed by the Quality Assessment for Studies of Diagnostic Accuracy-2, and sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), diagnostic odds ratio (dOR), and their corresponding 95% confidence intervals (CIs) were calculated using a bivariate random-effect meta-analysis model. Meta-regression and subgroup analyses were performed to assess heterogeneity. Eighty-four study units from 18 articles with 8368 subjects were included. The pooled sensitivity and specificity of salivary DNA methylation were 0.39 and 0.87, respectively, while PLR and NLR were 3.68 and 0.63, respectively. The overall area under the curve (AUC) was 0.81 and the dOR was 8.34. The combination of methylated genes showed higher diagnostic accuracy (AUC, 0.92 and dOR, 36.97) than individual gene analysis (AUC, 0.77 and dOR, 6.02). These findings provide evidence regarding the potential clinical application of salivary DNA methylation for HNC diagnosis.

scholarly journals Exploring Differentially Methylated Genes in Vulvar Squamous Cell Carcinoma

Cancers ◽  
2021 ◽  
Vol 13 (14) ◽  
pp. 3580
Author(s):  
Shatavisha Dasgupta ◽  
Patricia C. Ewing-Graham ◽  
Sigrid M. A. Swagemakers ◽  
Thierry P. P. van den Bosch ◽  
Peggy N. Atmodimedjo ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Squamous Cell ◽  
Dna Sequences ◽  
Cpg Island ◽  
Epigenetic Modification ◽  
Vulvar Squamous Cell Carcinoma ◽  
Differentially Methylated Genes ◽  
Methylation Profiling

DNA methylation is the most widely studied mechanism of epigenetic modification, which can influence gene expression without alterations in DNA sequences. Aberrations in DNA methylation are known to play a role in carcinogenesis, and methylation profiling has enabled the identification of biomarkers of potential clinical interest for several cancers. For vulvar squamous cell carcinoma (VSCC), however, methylation profiling remains an under-studied area. We sought to identify differentially methylated genes (DMGs) in VSCC, by performing Infinium MethylationEPIC BeadChip (Illumina) array sequencing, on a set of primary VSCC (n = 18), and normal vulvar tissue from women with no history of vulvar (pre)malignancies (n = 6). Using a false-discovery rate of 0.05, beta-difference (Δβ) of ± 0.5, and CpG-island probes as cut-offs, 199 DMGs (195 hyper-methylated, 4 hypo-methylated) were identified for VSCC. Most of the hyper-methylated genes were found to be involved in transcription regulator activity, indicating that disruption of this process plays a vital role in VSCC development. The majority of VSCCs harbored amplifications of chromosomes 3, 8, and 9. We identified a set of DMGs in this exploratory, hypothesis-generating study, which we hope will facilitate epigenetic profiling of VSCCs. Prognostic relevance of these DMGs deserves further exploration in larger cohorts of VSCC and its precursor lesions.

scholarly journals Epigenome-wide associations between observed maternal sensitivity and offspring DNA methylation: a population-based prospective study in children

2020 ◽  
pp. 1-11
Author(s):  
Lorenza Dall’ Aglio ◽  
Jolien Rijlaarsdam ◽  
Rosa H. Mulder ◽  
Alexander Neumann ◽  
Janine F. Felix ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Stress Responses ◽  
Association Studies ◽  
Maternal Sensitivity ◽  
Population Based ◽  
Epigenetic Mechanism ◽  
Developmental Problems ◽  
Maternal Caregiving ◽  
Typical Variation

Abstract Background Experimental work in animals has shown that DNA methylation (DNAm), an epigenetic mechanism regulating gene expression, is influenced by typical variation in maternal care. While emerging research in humans supports a similar association, studies to date have been limited to candidate gene and cross-sectional approaches, with a focus on extreme deviations in the caregiving environment. Methods Here, we explored the prospective association between typical variation in maternal sensitivity and offspring epigenome-wide DNAm, in a population-based cohort of children (N = 235). Maternal sensitivity was observed when children were 3- and 4-years-old. DNAm, quantified with the Infinium 450 K array, was extracted at age 6 (whole blood). The influence of methylation quantitative trait loci (mQTLs), DNAm at birth (cord blood), and confounders (socioeconomic status, maternal psychopathology) was considered in follow-up analyses. Results Genome-wide significant associations between maternal sensitivity and offspring DNAm were observed at 13 regions (p < 1.06 × 10−07), but not at single sites. Follow-up analyses indicated that associations at these regions were in part related to genetic factors, confounders, and baseline DNAm levels at birth, as evidenced by the presence of mQTLs at five regions and estimate attenuations. Robust associations with maternal sensitivity were found at four regions, annotated to ZBTB22, TAPBP, ZBTB12, and DOCK4. Conclusions These findings provide novel leads into the relationship between typical variation in maternal caregiving and offspring DNAm in humans, highlighting robust regions of associations, previously implicated in psychological and developmental problems, immune functioning, and stress responses.

scholarly journals Cellular Heterogeneity–Adjusted cLonal Methylation (CHALM) improves prediction of gene expression

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Jianfeng Xu ◽  
Jiejun Shi ◽  
Xiaodong Cui ◽  
Ya Cui ◽  
Jingyi Jessica Li ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Cellular Heterogeneity ◽  
Biological Functions ◽  
Global Correlation ◽  
Differentially Methylated Genes ◽  
Promoter Dna Methylation ◽  
Functional Consequences ◽  
Promoter Dna ◽  
Underlying Mechanisms

AbstractPromoter DNA methylation is a well-established mechanism of transcription repression, though its global correlation with gene expression is weak. This weak correlation can be attributed to the failure of current methylation quantification methods to consider the heterogeneity among sequenced bulk cells. Here, we introduce Cell Heterogeneity–Adjusted cLonal Methylation (CHALM) as a methylation quantification method. CHALM improves understanding of the functional consequences of DNA methylation, including its correlations with gene expression and H3K4me3. When applied to different methylation datasets, the CHALM method enables detection of differentially methylated genes that exhibit distinct biological functions supporting underlying mechanisms.

scholarly journals Genome-Wide DNA Methylation Pattern of Cancer Stem Cells in Esophageal Cancer

2020 ◽  
Vol 19 ◽  
pp. 153303382098379
Author(s):  
Xiying Yu ◽  
Ying Teng ◽  
Xingran Jiang ◽  
Hui Yuan ◽  
Wei Jiang
Keyword(s):  
Dna Methylation ◽  
Stem Cells ◽  
Esophageal Cancer ◽  
Cancer Stem Cells ◽  
Side Population ◽  
Methylation Status ◽  
Methylation Profile ◽  
Cpg Dinucleotides ◽  
Genome Wide ◽  
Differentially Methylated Genes

Background: Cancer stem cells (CSCs) are considered the main cause of cancer recurrence and metastasis, and DNA methylation is involved in the maintenance of CSCs. However, the methylation profile of esophageal CSCs remains unknown. Methods: Side population (SP) cells were isolated from esophageal squamous cell carcinoma (ESCC) cell lines KYSE150 and EC109. Sphere-forming cells were collected from human primary esophageal cancer cells. SP cells and sphere-forming cells were used as substitutes for cancer stem-like cells. We investigated the genome-wide DNA methylation profile in esophageal cancer stem-like cells using reduced representation bisulfite sequencing (RRBS). Results: Methylated cytosine (mC) was found mostly in CpG dinucleotides, located mostly in the intronic, intergenic, and exonic regions. Forty intersected differentially methylated regions (DMRs) were identified in these 3 groups of samples. Thirteen differentially methylated genes with the same alteration trend were detected; these included OTX1, SPACA1, CD163L1, ST8SIA2, TECR, CADM3, GRM1, LRRK1, CHSY1, PROKR2, LINC00658, LOC100506688, and NKD2. DMRs covering ST8SIA2 and GRM1 were located in exons. These differentially methylated genes were involved in 10 categories of biological processes and 3 cell signaling pathways. Conclusions: When compared to non-CSCs, cancer stem-like cells have a differential methylation status, which provides an important biological base for understanding esophageal CSCs and developing therapeutic targets for esophageal cancer.

scholarly journals Global DNA methylation was changed by a maternal high-lipid, high-energy diet during gestation and lactation in male adult mice liver

2015 ◽  
Vol 113 (7) ◽  
pp. 1032-1039 ◽  
Author(s):  
Huan-Ling Yu ◽  
Shan Dong ◽  
Li-Fang Gao ◽  
Li Li ◽  
Yuan-Di Xi ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Maternal Diet ◽  
High Energy ◽  
Methylation Pattern ◽  
Epigenetic Mechanism ◽  
Chow Diet ◽  
Mrna Levels ◽  
Promoter Regions ◽  
Male Adult ◽  
High Lipid

An epigenetic mechanism has been suggested to explain the effects of the maternal diet on the development of disease in offspring. The present study aimed to observe the effects of a maternal high-lipid, high-energy (HLE) diet on the DNA methylation pattern of male offspring in mice. Female C57BL/6J mice were fed an HLE diet during gestation and lactation. The genomic DNA methylations at promoter sites of genes in the liver, mRNA and protein levels of selected genes related to lipid and glucose metabolism were measured by microarray, real-time PCR and Western blot. The results indicated that the percentage of methylated DNA in offspring from dams that were fed an HLE diet was significantly higher than that from dams that were fed a chow diet, and most of these genes were hypermethylated in promoter regions. The nuclear protein content and mRNA levels of hypermethylated genes, such as PPARγ and liver X receptor α (LXRα), were decreased significantly in offspring in the HLE group. The results suggested that the DNA methylation profile in adult offspring livers was changed by the maternal HLE diet during gestation and lactation.

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