DNA Methylation In Tissues Research Articles

PSI-11 Anti-inflammatory treatment modifies epigenetics changes to muscle tissue caused by altered nutrient demand in early lactation dairy cows

Abstract Short-term treatment with non-steroidal anti-inflammatory drugs (NSAIDs) has been shown to alter whole-lactation milk yield; perhaps because epigenetic modifications are responsible for long-term effects, although mechanisms are unclear. Altered nutrient demand due to fasting or exercise in other species has been shown to affect DNA methylation in muscle tissue. Our objective was to determine if NSAID treatment or alterations to nutrient demand have epigenetic effects on muscle tissue in early lactation. In this study, 33 multiparous Holstein cows were enrolled at parturition and randomly assigned to milking frequency (MF; 1× or 3×/day), and either sodium salicylate (SS; 2.3 g/L administered via drinking water) or control (CTL; molasses carrier alone) treatment in a 2×2 factorial design, beginning ~24 h postpartum. Milking frequency treatments were designed to alter nutrient demand, and 3× milked increased milk yield by 24%. After 5 days of treatment, tissue biopsies were collected from the Longissimus dorsi muscle and snap-frozen. DNA was isolated and global methylation (GM) was assessed with a 5-methylcytosine enzyme-linked immunosorbent assay. An interaction between MF and SS treatment was detected (P = 0.02), with GM of muscle tissue decreased by more frequent milking only in the CTL cows (4.9 and 1.4 ± 1.0% of DNA methylated for 1× and 3×, respectively; P < 0.001). No effect of MF was detected in SS-treated cows (2.9 and 2.4 ± 1.0% of DNA methylated for 1× and 3×, respectively; P > 0.1). Observed changes to DNA methylation in muscle tissue due to altered nutrient supply are consistent with results reported after fasting and exercise. Additionally, increased demand for milk component precursors in 3×-milked cows may alter the availability of methyl donors for DNA methylation. Our data support a link between SS and epigenetic changes, but further research is needed to determine how SS may have altered the muscle DNA methylation response to nutrient demand.

Retention of paternal DNA methylome in the developing zebrafish germline

Two waves of DNA methylation reprogramming occur during mammalian embryogenesis; during preimplantation development and during primordial germ cell (PGC) formation. However, it is currently unclear how evolutionarily conserved these processes are. Here we characterise the DNA methylomes of zebrafish PGCs at four developmental stages and identify retention of paternal epigenetic memory, in stark contrast to the findings in mammals. Gene expression profiling of zebrafish PGCs at the same developmental stages revealed that the embryonic germline is defined by a small number of markers that display strong developmental stage-specificity and that are independent of DNA methylation-mediated regulation. We identified promoters that are specifically targeted by DNA methylation in somatic and germline tissues during vertebrate embryogenesis and that are frequently misregulated in human cancers. Together, these detailed methylome and transcriptome maps of the zebrafish germline provide insight into vertebrate DNA methylation reprogramming and enhance our understanding of the relationships between germline fate acquisition and oncogenesis.

Abstract 611: MYC DNA methylation in prostate tumor tissue is associated with tumor aggressiveness

Abstract We previously reported an increased risk of aggressive, but not non-aggressive, prostate cancer associated with pre-diagnostic blood DNA methylation levels in exon 3 of the MYC oncogene among Caucasian men in the Prostate, Lung, Colorectal and Ovarian Cancer Screening Trial. In the present study, we aimed to investigate MYC DNA methylation in prostate tissue in relation to tumor aggressiveness (based on Gleason score). We also aimed to investigate whether MYC methylation in prostate tissue is associated with race or tumor/normal status. We accessed formalin-fixed, paraffin-embedded prostate tumor and normal tissue from 50 Caucasian and 50 African American prostate cancer patients that underwent radical prostatectomy at the University of Maryland; for each race group, we selected 25 patients with a Gleason score of 7 and 25 with a Gleason score of 6. We systematically selected the most recent samples, and year of surgery for our patients ranged from 2001-2017. Age at surgery ranged from 42-75 years. We used pyrosequencing to measure DNA methylation at six CpG sites in MYC exon 3 (Chr8:128753145 - Chr8:128753221). We excluded 11 patients for whom the assays failed, resulting in a final sample size of 43 African American and 46 Caucasian men. The six CpG sites demonstrated moderate correlations with one another in tumor tissue (Spearman rho: 0.30-0.60, p-value<0.01 for all pairings). Correlations between the CpG sites were less pronounced in the normal tissue samples (Spearman rho: -0.08-0.57) and five pairs were no longer significantly correlated. We used paired t-tests to evaluate differences in MYC DNA methylation between tumor and normal samples from the same patients, and unpaired t-tests to evaluate differences by Gleason score and race. We observed significantly higher MYC DNA methylation for all six CpG sites in the normal compared to the tumor samples (p<0.05). The difference in mean percent methylation between normal and tumor for the six sites ranged from 2.3 to 16.3 percentage points. In the tumor samples, we also observed significantly higher MYC DNA methylation for patients with a Gleason score of 6 compared to those with a Gleason score of 7 for three of the CpG sites. These included Chr8:128753145 (mean percent methylation for Gleason 6 group=89.0%; mean for Gleason 7=83.6%; t-test p-value=0.002), Chr8:128753154 (mean for Gleason 6=87.7%; mean for Gleason 7=81.7%; t-test p-value=0.004) and Chr8:128753200 (mean for Gleason 6=82.6%; mean for Gleason 7=78.8%; t-test p-value=0.02). Also in tumor tissue, we observed borderline significantly higher DNAm at Chr8:128753151 for African American than Caucasian men (mean for African American men=79.1%; mean for Caucasian men=73.7%; t-test p-value=0.06); no other CpG sites displayed differences by race. Our results provide further evidence for a role of altered MYC DNA methylation in aggressive prostate cancer. Citation Format: Kathryn Hughes Barry, Kareshma Mohanty, Gary Rose, Ashley Cellini, Nicholas Ambulos, Jing Yin, Liying Yan, Matthew Poulin, Ann Meyer, Yuji Zhang, Søren Bentzen, Allen Burke, Arif Hussain, Sonja I. Berndt. MYC DNA methylation in prostate tumor tissue is associated with tumor aggressiveness [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 611.

Epigenome-wide skeletal muscle DNA methylation profiles at the background of distinct metabolic types and ryanodine receptor variation in pigs

BackgroundEpigenetic variation may result from selection for complex traits related to metabolic processes or appear in the course of adaptation to mediate responses to exogenous stressors. Moreover epigenetic marks, in particular the DNA methylation state, of specific loci are driven by genetic variation. In this sense, polymorphism with major gene effects on metabolic and cell signaling processes, like the variation of the ryanodine receptors in skeletal muscle, may affect DNA methylation.MethodsDNA-Methylation profiles were generated applying Reduced Representation Bisulfite Sequencing (RRBS) on 17 Musculus longissimus dorsi samples. We examined DNA methylation in skeletal muscle of pig breeds differing in metabolic type, Duroc and Pietrain. We also included F2 crosses of these breeds to get a first clue to DNA methylation sites that may contribute to breed differences. Moreover, we compared DNA methylation in muscle tissue of Pietrain pigs differing in genotypes at the gene encoding the Ca2+ release channel (RYR1) that largely affects muscle physiology.ResultsMore than 2000 differently methylated sites were found between breeds including changes in methylation profiles of METRNL, IDH3B, COMMD6, and SLC22A18, genes involved in lipid metabolism. Depending on RYR1 genotype there were 1060 differently methylated sites including some functionally related genes, such as CABP2 and EHD, which play a role in buffering free cytosolic Ca2+ or interact with the Na+/Ca2+ exchanger.ConclusionsThe change in the level of methylation between the breeds is probably the result of the long-term selection process for quantitative traits involving an infinite number of genes, or it may be the result of a major gene mutation that plays an important role in muscle metabolism and triggers extensive compensatory processes.

The Epigenetic Signature of Colonizing New Environments in Anolis Lizards

Founder populations often show rapid divergence from source populations after colonizing new environments. Epigenetic modifications can mediate phenotypic responses to environmental change and may be an important mechanism promoting rapid differentiation in founder populations. Whereas many long-term studies have explored the extent to which divergence between source and founder populations is genetically heritable versus plastic, the role of epigenetic processes during colonization remains unclear. To investigate epigenetic modifications in founding populations, we experimentally colonized eight small Caribbean islands with brown anole lizards (Anolis sagrei) from a common source population. We then quantitatively measured genome-wide DNA methylation in liver tissue using reduced representation bisulfite sequencing of individuals transplanted onto islands with high- versus low-habitat quality. We found that lizard sex and habitat quality explained a significant proportion of epigenetic variation. Differentially methylated cytosines mapped to genes that encode proteins with functions likely to be relevant to habitat change (e.g., signal transduction, immune response, circadian rhythm). This study provides experimental evidence of a relationship between epigenetic responses and the earliest stages of colonization of novel environments in nature and suggests that habitat quality influences the nature of these epigenetic modifications.

Global DNA Methylation in the Limbic System of Cattle.

To elucidate the extent to which DNA methylation varies across multiple tissues in the brain and between animals, we have quantified global DNA methylation in tissues comprising the limbic system for six Red Angus x Simmental steers. Global DNA methylation was measured in nine regions of the bovine brain: amygdala, the bed nucleus of the stria terminalis, cingulate gyrus, dorsal raphe, hippocampus, hypothalamus, nucleus accumbens, periaqueductal gray and prefrontal cortex. DNA methylation varies among animals for each tissue type and varies among tissue types for each animal. The highest amounts of DNA methylation were found in the amygdala, cingulate gyrus and dorsal raphe, while the bed nucleus of the stria terminalis, nucleus accumbens and periaqueductal gray had the lowest amounts of DNA methylation. A heatmap sorted by k-means clustering was generated to graphically display percent DNA methylation in relation to tissue type and animal number. This is the first study to report measures of DNA methylation in the limbic system of the bovine brain and can be used to inform the cattle genomics community of expected variation in cattle brain methylation.

Identification of DNA-Methylated CpG Islands Associated With Gene Silencing in the Adult Body Tissues of the Ogye Chicken Using RNA-Seq and Reduced Representation Bisulfite Sequencing.

DNA methylation is an epigenetic mark that plays an essential role in regulating gene expression. CpG islands are DNA methylations regions in promoters known to regulate gene expression through transcriptional silencing of the corresponding gene. DNA methylation at CpG islands is crucial for gene expression and tissue-specific processes. At the current time, a limited number of studies have reported on gene expression associated with DNA methylation in diverse adult tissues at the genome-wide level. Expression levels are rarely affected by DNA methylation in normal adult tissues; however, statistical differences in gene expression level correlated with DNA methylation have recently been revealed. In this study, we examined 20 pairs of DNA methylomes and transcriptomes from RNA-seq and reduced representation bisulfite sequencing (RRBS) data using adult Ogye chicken tissues. A total of 3,133 CpG islands were identified from 20 tissue data in a single chicken sample which could affect downstream genes. Analyzing these CpG island and gene pairs, 121 significant units were statistically correlated. Among them, six genes (CLDN3, DECR2, EVA1B, NME4, NTSR1, and XPNPEP2) were highly significantly changed by altered DNA methylation. Finally, our data demonstrated how DNA methylation correlated to gene expression in normal adult tissues. Our source codes can be found at https://github.com/wjlim/correlation-between-rna-seq-and-RRBS.

DNA methylation of dopamine-related gene promoters is associated with line bisection deviation in healthy adults

Handedness and language lateralization are the most investigated phenotypes among functional hemispheric asymmetries, i.e. differences in function between the left and the right half of the human brain. Both phenotypes are left hemisphere-dominant, while investigations of the molecular factors underlying right hemisphere-dominant phenotypes are less prominent. In the classical line bisection task, healthy subjects typically show a leftward attentional bias due to a relative dominance of the right hemisphere for visuospatial attention. Based on findings of variations in dopamine-related genes affecting performance in the line bisection task, we first tested whether DNA methylation in non-neuronal tissue in the promoter regions of DBH, SLC6A3, and DRD2 are associated with line bisection deviation. We replicated the typical behavioral pattern and found an effect of DNA methylation in the DBH promoter region on line bisection deviation in right-aligned trials. A second exploratory analysis indicated that an overall DNA methylation profile of genes involved in dopamine function predicts line bisection performance in right-aligned trials. Genetic variation in dopamine-related genes has been linked to attention deficit hyperactivity disorder (ADHD), a neurodevelopmental trait associated with rightward attentional bias. Overall, our findings point towards epigenetic markers for functional hemispheric asymmetries in non-neuronal tissue not only for left hemisphere-dominant, but also for right hemisphere-dominant phenotypes.

Altered metabolic and hormonal responses in male rats exposed to acute bright light-at-night associated with global DNA hypo-methylation

The association between light pollution and disruption of daily rhythms, metabolic and hormonal disorders, as well as cancer progression is well-recognized. These adverse effects could be due to nocturnal melatonin suppression. The signaling pathway by which light pollution affects metabolism and endocrine responses is unclear. We studied the effects of artificial light at night (ALAN11Artificial light at night.) on body mass, food and water intake, daily rhythms of body temperature, serum glucose and insulin in male rats. Daily rhythms of urine production and urinary 6-sulfatoxymelatonin (6-SMT226-sulfatoxymelatonin.), as well as global DNA methylation in pancreas and liver tissues were also assessed. Mass gain was higher in ALAN rats compared with controls. Food intake, water consumption, glucose, insulin, and 6-SMT levels markedly lessened in response to ALAN. Conversely, urine production and body temperature were elevated in ALAN rats compared with controls. Significant 24-h rhythms were detected for all variables that were altered in mesor, amplitude, and acrophase occurrences under ALAN conditions. DNA hypo-methylation was detected in ALAN pancreatic tissue compared with controls, but not in hepatic tissue. Overall, ALAN affects metabolic and hormonal physiology in different levels in which flexible crosstalk between melatonin and both epigenetics and metabolic levels expressed as body temperature rhythm, is suggested to mediate the environmental exposure at the molecular level and subsequently physiology is altered. The flexibility of epigenetic modifications provides a potential therapeutic target for rectifying ALAN adverse effects by epigenetic markers such as melatonin and behavioral lifestyle interventions for confining ALAN exposures as much as possible.

Variation in DNA methylation in the KvDMR1 (ICR2) region in first-trimester human pregnancies

To investigate the levels of DNA methylation in the KvDMR1 (KvLQT1 differentially methylated region 1) in embryonic and extra-embryonic tissues. Cross-sectional study. University medical center and clinical hospital. Embryonic and/or extraembryonic tissues (umbilical cord, chorionic villus, chorion, decidua, and/or amnion) collected from 27 first-trimester pregnancies (up to 12weeks of gestation, single embryos) from elective abortions, extravillous trophoblasts (EVTs) from the top of individual chorionic villi, and chorionic villi from 10 normal full-term placentas collected after birth. None. DNA methylation of the KvDMR1 region evaluated using quantitative analysis of DNA methylation followed by real-time polymerase chain reaction (qAMP) and bisulfite sequencing (bis-seq) analysis. The results showed variability in KvDMR1 DNA methylation in different tissues from the same pregnancy. The average of DNA methylation was not different between the embryo, umbilical cord, amnion, and chorionic villi, despite the relatively low level of methylation observed in the amnion (33.50% ± 14.48%). Chorionic villi from term placentas showed a normal methylation pattern at KvDMR1 (42.60% ± 6.08%). The normal methylation pattern at KvDMR1 in chorionic villi (as well as in EVTs) from first-trimester placentas was confirmed by bis-seq. Our results highlight an existing heterogeneity in DNA methylation of the KvDMR1 region during first trimester and a consistent hypomethylation in the amnion in this period of gestation.

Analyses of IGFBP2 DNA methylation and mRNA expression in visceral and subcutaneous adipose tissues of obese subjects

Insulin-like growth factor binding-protein 2 (IGFBP-2) is secreted by differentiating white adipocytes. Clinical studies demonstrate that circulating IGFBP-2 levels associated inversely with body mass index (BMI) and insulin resistance. To explore possible epigenetic changes of the IGFBP2 gene in obesity, we analyzed DNA methylation and mRNA expression in adipocytes from different depots. Healthy lean controls (BMI = 24.5 ± 0.3 kg/m2, n = 19) and obese subjects (BMI > 35 kg/m2, n = 24) were recruited. All subjects were Swedish Caucasian. Visceral abdominal adipose tissue (VAT) and subcutaneous adipose tissue (SAT) fragments were homogenized. Genomic DNA and total RNAs were extracted. Four CpG sites in the IGFBP2 gene promoter region were analyzed with bisulfite pyrosequencing. IGFBP2 gene expression at mRNA levels was determined with TaqMan real time RT-PCR. Serum samples were used for measurement of circulating IGFBP-2 and leptin levels. IGFBP2 DNA methylation levels in VAT were increased in obese subjects compared with controls (P < .05). By contrast, IGFBP2 mRNA expression levels in VAT were lower in obesity subjects than in controls (P < .05). In SAT, IGFBP2 DNA methylation and RNA expression levels were lower than in VAT, irrespective of obesity. Obese subjects demonstrated increased serum leptin levels (P < .001) and reduced serum IGFBP-2 levels compared to controls (P < .05). In conclusion, the current study demonstrates that IGFBP2 DNA methylation levels are increased in VAT from obese subjects. This suggests that IGFBP-2 is epigenetically regulated in abdominal obesity.

DNA methylation in adipose tissue and the development of diabetes and obesity

Diabetes and obesity are complicated metabolic diseases which frequently occur together and are affected by environmental, hereditary and metabolic factors. Adipose tissue is involved in various physiological and pathological processes and plays an essential role as an endocrine organ which regulates the metabolic balance of the body. DNA methylation of some genes in adipose tissue may have an impact on its function. A growing body of evidence suggests that changes in DNA methylation may alter gene expression and lead to the development of diabetes and obesity in which adipose tissue function is imbalanced. This review discusses recent advances in alterations of DNA methylation in different types of adipose tissue in individuals with diabetes and obesity. This evidence may lead to a greater understanding of the pathogenesis of these diseases and lead to potential therapeutic interventions and management strategies for diabetes and obesity.

Human age prediction based on DNA methylation of non-blood tissues

Background and ObjectiveThe study of human aging contributes to disease prevention, treatment and life extension. Recently, epigenetics studies have evidenced that there is a close association between DNA methylation and human ages. A quantitatively statistical modeling between DNA methylation and ages could predict the person's age more accurately. MethodsWe propose a regression model to predict human age based on gradient boosting regressor (GBR). We collect a total of 1280 publicly available non-blood tissues samples with ages ranged from 0 to 90 years old. We calculate the Pearson correlation between CpG's DNA methylation level and age to select age-related CpGs. ResultsThirteen age-related CpG sites are selected. GBR has the smallest mean absolute deviation to the actual age comparing with other three different models including Bayesian ridge, multiple linear regression, and support vector regression. In the training datasets, the cross-validation results show that the correlation R2 between predicted age and DNA methylation is 0.89, and the mean absolute deviation is 4.66 years. In an independent testing set with 262 samples, the GBR achieves the mean absolute deviation of 6.08 years. Meanwhile we also briefly describe the function of the selected thirteen CpG sites. ConclusionsWe build an age predictor to study the association between ages and the DNA methylation of human non-blood tissues. Our new model provides a more accurate estimation of human ages which will be instrumental for understanding the regulation of DNA methylation on human aging and will accurately monitor the individual aging process.

The Effects of Low Selenium on DNA Methylation in the Tissues of Chickens.

DNA methylation is involved in epigenetic mechanisms associated with gene suppression, and its abnormalities lead to gene instability and disease development. As an essential trace element in humans and animals, selenium (Se) is also associated with abnormal changes in DNA methylation. However, the effect of low Se on DNA methylation in avian tissues has not been reported. In the current study, chickens were fed a low-Se diet (0.033mgSe/kg) or supplemented with 0.15mgSe/kg as selenite for up to 55days. DNA methylation levels were examined by high-performance liquid chromatography (HPLC). DNA methyltransferases (DNMTs) and methyl-DpG-binding domain protein 2 (MBD2) mRNA levels were examined through the applications of RT-PCR. The experiment aims to explore the relationship between low Se and DNA methylation. The results showed that total DNA methylation levels in the muscle tissues, brain, immune tissues, and liver of the low-selenium diet group were decreased compared with the control group. The degree of DNA methylation reduction in different tissues from largest to smallest was liver > cerebellum > thymus > brain > spleen ≥ leg muscles > pectoral muscles > bursa of Fabricius > thalamus > wing muscles. DNMT1, DNMT3A, and DNMT3B mRNA expression levels of the low-selenium diet group were decreased compared with those in the control group. The mRNA expression of the MBD2 gene was increased. The results indicate that low Se can reduce the DNA methylation levels of tissues, especially within the liver. These conclusions provide a basis for exploring the pathogenesis of selenium deficiency from the perspective of DNA methylation and create a new basis for comparative medicine.

Effects of bisphenol-A and folic acid on growth, reproductive development, and DNA methylation in snapdragons (Antirrhinum majus)

Bisphenol-A (BPA), used in the production of polycarbonate plastics, exerts complex effects on the development of organisms and on their epigenomes as a methylation disruptor. BPA is of concern due to its ubiquity in the environment. In contrast, folic acid can promote plant growth and has been shown to correct the methyl-disrupting effects of BPA in mice. We investigated the effects of prolonged exposure to BPA and folic acid on plant height, dry mass, and DNA methylation of floral tissues of Antirrhinum majus L. (snapdragons) from seedling to floral senescence. At low and medium concentrations (5 and 25 mg/L), BPA had a growth-promoting effect early in development and appeared to accelerate floral development compared with the controls. At senescence, plants treated with the low and medium concentrations of BPA had decreased dry mass compared with the controls. Folic acid promoted growth early through mid-vegetative development and also promoted early flowering. In general, the acceleration of floral development associated with the low concentration of BPA and folic acid correlated with higher DNA methylation percentages. These data suggest that prolonged exposure to BPA influences plant growth and floral development, and causes epigenetic modifications that may potentially be alleviated through the application of folic acid, thus suggesting the significance of folic acid for environmental protection.

Hormone therapy use and breast tissue DNA methylation: analysis of epigenome wide data from the normal breast study

ABSTRACTHormone therapy (HT) is associated with increased risk of breast cancer, strongly dependent on type, duration, and recency of use. HT use could affect cancer risk by changing breast tissue transcriptional programs. We hypothesize that these changes are preceded by changes in DNA methylation. To explore this hypothesis we used histologically normal-appearing breast tissue from the Normal Breast Study (NBS). DNA methylation β-values were obtained using the Illumina HumanMethylation 450 BeadChips for 90 samples including all NBS-participants who used HT within 5 y before surgery. Data were analyzed using the reference-free cell mixture method. Cancer Genome Atlas (TCGA) mRNA-Seq data were used to assess correlation between DNA methylation and gene expression. We identified 527 CpG sites in 403 genes that were associated with ever using HT at genome wide significance (FDR q < 0.05), of these, 68 sites were also significantly associated with duration of use or recency of use. Twelve sites reached significance in all analyses one of which was cg01382688 in ARHGEF4 (p < 1.2x10−7). Mutations in ARHGEF4 have been reported in breast tumors, but this is the first report of possible breast cancer-related DNA methylation changes. In addition, 22 genes included more than one significant CpG site and a majority of these sites were significantly correlated with gene expression. Although based on small numbers, these findings support the hypothesis that HT is associated with epigenetic alterations in breast tissue, and identifies genes with altered DNA methylation states which could be linked to breast cancer development.

Association between serum 25-hydroxyvitamin D and global DNA methylation in visceral adipose tissue from colorectal cancer patients

BackgroundVisceral adipose tissue (VAT) has been identified as the essential fat depot for pathogenetic theories that associateobesity and colon cancer. LINE-1 hypomethylation has been mostly detected in tumor colon tissue, but less is known about the epigenetic pattern in surrounding tissues. The aim was to analyze for the first time the potential relationship between serum vitamin D, obesity and global methylation (LINE-1) in the visceral adipose tissue (VAT) from patients with and without colorectal cancer.MethodsA total of 55 patients with colorectal cancer and 35 control subjects participated in the study. LINE-1 DNA methylation in VAT was measured by pyrosequencing. Serum 25(OH)D levels were determined by ELISA.ResultsCancer patients had lower levels of LINE-1 methylation in VAT compared with the control group. In the subjects with colorectal cancer, LINE-1 DNA methylation levels were associated positively with vitamin D levels (r = 0,463; p < 0.001) and negatively with BMI (r = − 0.334, p = 0.01) and HOMA insulin resistance index (r = − 0.348, p = 0.01). Serum vitamin D was the main variable explaining the LINE-1% variance in the cancer group (β = 0.460, p < 0.001). In a multivariate analysis, subjects with higher LINE-1 methylation values had lower risk of developing colorectal cancer (OR = 0.53; IC95% =0.28–0.99) compared with the control group.ConclusionsWe showed for the first time an association between LINE-1 DNA methylation in VAT and vitamin D levels in subjects with colorectal cancer, highlighting the importance of VAT from cancer patients, which could be modified epigenetically compared to healthy subjects.

Altered Adipose Tissue DNA Methylation Status in Metabolic Syndrome: Relationships Between Global DNA Methylation and Specific Methylation at Adipogenic, Lipid Metabolism and Inflammatory Candidate Genes and Metabolic Variables.

Metabolic syndrome (MetS) has been postulated to increase the risk for type 2 diabetes, cardiovascular disease and cancer. Adipose tissue (AT) plays an important role in metabolic homeostasis, and AT dysfunction has an active role in metabolic diseases. MetS is closely related to lifestyle and environmental factors. Epigenetics has emerged as an interesting landscape to evaluate the possible interconnection between AT and metabolic disease, since it can be modulated by environmental factors and metabolic status. The aim of this study was to determine whether MetS has an impact on the global DNA methylation pattern and the DNA methylation of several genes related to adipogenesis (PPARG, PPARA), lipid metabolism (RXRA, SREBF2, SREBF1, SCD, LPL, LXRb), and inflammation (LRP1 C3, LEP and TNF) in visceral adipose tissue. LPL and TNF DNA methylation values were significantly different in the control-case comparisons, with higher and lower methylation respectively in the MetS group. Negative correlations were found between global DNA methylation (measured by LINE-1 methylation levels) and the metabolic deterioration and glucose levels. There were associations among variables of MetS, BMI, and HOMA-IR with DNA methylation at several CpG positions for the studied genes. In particular, there was a strong positive association between serum triglyceride levels (TG) with PPARA and LPL methylation levels. TNF methylation was negatively associated with the metabolic worsening and could be an important factor in preventing MetS occurrence according to logistic regression analysis. Therefore, global DNA methylation and methylation at specific genes related to adipogenesis, lipid metabolism and inflammation are related to the etiology of MetS and might explain in part some of the features associated to metabolic disorders.

DNA methylation and histone post-translational modification stability in post-mortem brain tissue

BackgroundEpigenetic (including DNA and histone) modifications occur in a variety of neurological disorders. If epigenetic features of brain autopsy material are to be studied, it is critical to understand the post-mortem stability of the modifications.MethodsPig and mouse brain tissue were formalin-fixed and paraffin-embedded, or frozen after post-mortem delays of 0, 24, 48, and 72 h. Epigenetic modifications frequently reported in the literature were studied by DNA agarose gel electrophoresis, DNA methylation enzyme-linked immunosorbent assays, Western blotting, and immunohistochemistry. We constructed a tissue microarray of human neocortex samples with devitalization or death to fixation times ranging from < 60 min to 5 days.ResultsIn pig and mouse brain tissue, we found that DNA cytosine modifications (5mC, 5hmC, 5fC, and 5caC) were stable for ≥ 72 h post-mortem. Histone methylation was generally stable for ≥ 48 h (H3K9me2/K9me3, H3K27me2, H3K36me3) or ≥ 72 h post-mortem (H3K4me3, H3K27me3). Histone acetylation was generally less stable. The levels of H3K9ac, H3K27ac, H4K5ac, H4K12ac, and H4K16ac declined as early as ≤ 24 h post-mortem, while the levels of H3K14ac did not change at ≥ 48 h. Immunohistochemistry showed that histone acetylation loss occurred primarily in the nuclei of large neurons, while immunoreactivity in glial cell nuclei was relatively unchanged. In the human brain tissue array, immunoreactivity for DNA cytosine modifications and histone methylation was stable, while subtle changes were apparent in histone acetylation at 4 to 5 days post-mortem.ConclusionWe conclude that global epigenetic studies on human post-mortem brain tissue are feasible, but great caution is needed for selection of post-mortem delay matched controls if histone acetylation is of interest.

Highly variant DNA methylation in normal tissues identifies a distinct subclass of cancer patients.

The "CpG Island Methylator Phenotype" (CIMP) has been found to be a useful concept in stratifying several types of human cancer into molecularly and clinically distinguishable subgroups. We have identified an additional epigenetic stratification category, the "Outlier Methylation Phenotype" (OMP). Whereas CIMP is defined on the basis of hyper-methylation in tumor genomes, OMP is defined on the basis of highly variant (either or both hyper- and hypo-methylation) methylation at many sites in normal tissues. OMP was identified and defined, originally, as being more common among low birth weight individuals conceived in vitro but we have also identified OMP individuals among colon cancer patients profiled by us, as well as multiple types of cancer patients in the TCGA database. The cause(s) of OMP are unknown, as is whether these individuals identify a clinically useful subgroup of patients, but both the causes of, and potential consequences to, this epigenetically distinct group are of great interest.