Older age and dietary folate are determinants of genomic and p16-specific DNA methylation in mouse colon

Exploring the promising potential of induced pluripotent stem cells in cancer research and therapy

The advent of iPSCs has brought about a significant transformation in stem cell research, opening up promising avenues for advancing cancer treatment. The formation of cancer is a multifaceted process influenced by genetic, epigenetic, and environmental factors. iPSCs offer a distinctive platform for investigating the origin of cancer, paving the way for novel approaches to cancer treatment, drug testing, and tailored medical interventions. This review article will provide an overview of the science behind iPSCs, the current limitations and challenges in iPSC-based cancer therapy, the ethical and social implications, and the comparative analysis with other stem cell types for cancer treatment. The article will also discuss the applications of iPSCs in tumorigenesis, the future of iPSCs in tumorigenesis research, and highlight successful case studies utilizing iPSCs in tumorigenesis research. The conclusion will summarize the advancements made in iPSC-based tumorigenesis research and the importance of continued investment in iPSC research to unlock the full potential of these cells.

One-carbon metabolism-related nutrients intake is associated with lower risk of preeclampsia in pregnant women: a matched case-control study

Many studies have suggested that folate plays a role in preeclampsia (PE) risks, but few studies have assessed folate-related 1-carbon metabolism (OCM)-related nutrients with the risk of PE. We hypothesized that OCM-related nutrients are associated with PE. A 1:1 matched case-control study was conducted to explore the association between dietary OCM-related nutrients intake and the risk of PE in pregnant Chinese women. Four hundred and forty pairs of pregnant women with PE and hospital-based, healthy pregnant women, matched according to gestational week (±1 week) and age (±3 years), were recruited. Dietary intake was assessed using a validated 78-item semiquantitative food frequency questionnaire. Multivariate conditional logistic regression was used to estimate odds ratios (ORs) and 95% CIs. Restricted cubic splines were plotted to evaluate the dose-response relationship between dietary OCM-related nutrient intake and the risk of PE. Intake of folate, vitamin B₆, vitamin B₁₂, methionine, and total choline were inversely related to the risk of PE after adjustment for covariates (all P trend < .05). Adjusted ORs (95% CIs) for quartile 4 versus quartile 1 were 0.71 (0.55-0.93) for folate, 0.66 (0.50-0.87) for vitamin B₆, 0.68 (0.52-0.88) for vitamin B₁₂, 0.77 (0.60-0.81) for methionine, and 0.67 (0.51-0.87) for total choline. This study suggests that dietary OCM-related nutrients intake is associated with lower odds of PE in pregnant Chinese women.

Folic acid depletion as well as oversupplementation helps in the progression of hepatocarcinogenesis in HepG2 cells

Folate ingestion below and above the physiologic dose has been shown to play a tumorigenic role in certain cancers. Also, excessive folate supplementation after establishment of pre-established lesions led to an advancement in the growth of a few tumors. However, such information has not yet been achieved in the case of HCC. In our study, HepG2 cells were administered with three different concentrations of folic acid i.e. folic acid normal (FN) (2.27 µM), folic acid deficient (FD) (no folic acid), folic acid oversupplementation (FO) (100 µM) for 10 days. Intracellular folate levels were assayed by Elecsys Folate III kit based method. The migratory and invasive abilities were estimated by transwell migration and matrigel invasion methods respectively. FACS was done to evaluate cell viability and apoptosis. Agarose-coated plates were used to access cancer stem cells (CSCs) number. Quantitative RT-PCR and western blotting approaches were used for gene and protein expression of certain tumor suppressor genes (TSGs), respectively. FD cells depicted increased migration, invasion, apoptosis, necrosis and decreased cell viability, CSCs. On the other hand, FO cells showed increased migration, invasion, cell viability and number of CSCs and decreased apoptosis and necrosis. TSGs revealed diminished expression with both FA modulations with respect to FN cells. Thus, FA deficiency as well as abundance enhanced the HCC progression by adapting different mechanisms.

The epigenetic aging, obesity, and lifestyle

The prevalence of obesity has dramatically increased worldwide over the past decades. Aging-related chronic conditions, such as type 2 diabetes and cardiovascular disease, are more prevalent in individuals with obesity, thus reducing their lifespan. Epigenetic clocks, the new metrics of biological age based on DNA methylation patterns, could be considered a reflection of the state of one’s health. Several environmental exposures and lifestyle factors can induce epigenetic aging accelerations, including obesity, thus leading to an increased risk of age-related diseases. The insight into the complex link between obesity and aging might have significant implications for the promotion of health and the mitigation of future disease risk. The present narrative review takes into account the interaction between epigenetic aging and obesity, suggesting that epigenome may be an intriguing target for age-related physiological changes and that its modification could influence aging and prolong a healthy lifespan. Therefore, we have focused on DNA methylation age as a clinical biomarker, as well as on the potential reversal of epigenetic age using a personalized diet- and lifestyle-based intervention.

In utero exposure to endocrine-disrupting chemicals, maternal factors and alterations in the epigenetic landscape underlying later-life health effects

Widespread persistence of endocrine-disrupting chemicals (EDCs) in the environment has mandated the need to study their potential effects on an individual's long-term health after both acute and chronic exposure periods. In this review article a particular focus is given on in utero exposure to EDCs in rodent models which resulted in altered epigenetic programming and transgenerational effects in the offspring causing disrupted reproductive and metabolic phenotypes. The literature to date establishes the impact of transgenerational effects of EDCs potentially associated with epigenetic mediated mechanisms. Therefore, this review aims to provide a comprehensive overview of epigenetic programming and it's regulation in mammals, primarily focusing on the epigenetic plasticity and susceptibility to exogenous hormone active chemicals during the early developmental period. Further, we have also in depth discussed the epigenetic alterations associated with the exposure to selected EDCs such as Bisphenol A (BPA), di-2-ethylhexyl phthalate (DEHP) and vinclozlin upon in utero exposure especially in rodent models.

CXCL8 expression and methylation are correlated with anthropometric and metabolic parameters in childhood obesity

Childhood obesity is a global and increasing health issue. Inflammation and dysregulated adipose tissue secretion are common findings in obesity and have been related to poor metabolic function. Given that DNA methylation impacts gene expression and is responsive to environmental changes, we aimed, in addition to characterize the patients in anthropometric and biochemical terms, to determine the expression of cytokines and adipokines, assess the methylation on regulatory regions of the genes that code for these molecules, and investigate the association of the expression and gene methylation with anthropometric and biochemical parameters in childhood obesity. Obese children present dyslipidemia, dysregulated serum levels of adipokines and their ratios, altered leukocytic expression of cytokines, and higher methylation at the CXCL8 promoter as compared to the control group. However, no significant results were observed in the fasting plasma glucose levels or the methylation of TGFB1, LEP, and the enhancer region of ADIPOQ. We also found negative correlations of CXCL8 expression with anthropometric and biochemical parameters, and positive correlation of CXCL8 promoter methylation and the serum levels of hepatic enzymes. Our results indicate that changes in metabolic parameters observed in childhood obesity are associated with the expression of adipokines and cytokines, and the methylation status at the CXCL8 promoter. CXCL8 may be a key factor for these alterations, as it correlates with many of the parameters assessed in the present study.

Tumor suppressor genes are differentially regulated with dietary folate modulations in a rat model of hepatocellular carcinoma

The current study evaluated the outcome of dietary folate modulations on the expression of tumor suppressor genes (TSGs) during developmental stages of hepatocellular carcinoma (HCC) in a Wistar rat model. In addition to dietary folate modulations, male rats were administered diethylnitrosamine (DEN) intraperitoneally once a week upto 18 weeks to induce HCC. Serum folate levels were found to be decreased and increased in folate deficiency (FD) and folate-oversupplemented (FO) groups respectively when compared to folate normal (FN) rats. Apoptosis was observed in FD in fibrosis and HCC stages. mRNA expression analysis by RT-PCR of TSGs (DPT, p16, RUNX3, RASSF1A and SOCS1) and protein expression by western blot (RASSF1A, RUNX3 and p16) depicted differential expression in FD and FO in various stages of HCC development. Bisulfite sequencing for p16 and RASSF1A promoter was performed. The promoter region of p16 gene was hypermethylated at 7th and that of RASSF1A was hypomethylated at 10th CpG in cirrhotic category in FD rats. Hyper and hypomethylation at 10th and 24th CpG respectively in RASSF1A promoter was observed in HCC category in both FD and FO groups. All TSGs showed differential expression at transcript and protein level. Increased expression of DPT, RASSF1A, SOCS1 and decreased expression of RUNX3 could be playing role in HCC development in FD rats. Reduced expression of RUNX3, RASSF1A and SOCS1 in HCC category was demonstrated in FO rats. Thus, the studied TSGs are differentially expressed with dietary folate modulations during the development of HCC in DEN-treated rat model and the promoter methylation might be a contributing mechanism under these conditions.

Association between the methylation of the STAT1 and SOCS3 in peripheral blood and gastric cancer

BACKGROUND AND AIM

DNA methylation is an important epigenetic modification that can promote the development of various cancers. The STAT1 and SOCS3 have been observed to be hypermethylated in tumor tissues and peripheral blood. This study aimed to explore the relationship between the methylation status of the STAT1 and SOCS3 in peripheral blood and gastric cancer (GC).

METHODS

This hospital-based case-control study involved 372 patients with GC and 379 controls. The methylation status of the STAT1 and SOCS3 was semiquantitatively determined using the methylation-sensitive high-resolution melting method. Logistic regression analysis was used to analyze the relationship between the STAT1 and SOCS3 methylation status and GC susceptibility. Moreover, propensity scores were used to control confounding factors.

RESULTS

Compared with negative methylation, the positive methylation of SOCS3 significantly increased the risk of GC (OR_a  = 1.820, 95% CI: 1.247-2.658, P = 0.002). This trend was also found via stratified analysis, and methylation positivity of the SOCS3 significantly increased the risk of GC in the < 60 years group, in the ≥ 60 years group, and in the positive Helicobacter pylori infection group (OR_a  = 1.654, 95% CI: 1.029-2.660, P = 0.038; OR_a  = 1.957, 95% CI: 1.136-3.376, P = 0.016; OR_a  = 2.084, 95% CI: 1.270-3.422, P = 0.004, respectively). Additionally, no significant association was found between STAT1 methylation and GC risk (OR_a  = 0.646, 95% CI: 0.363-1.147, P = 0.135). This study found that the interaction between the methylation status of STAT1 and SOCS3 and environmental factors did not have an impact on GC risk.

CONCLUSION

SOCS3 methylation may serve as a new potential biomarker for GC susceptibility.

Maternal Exposure to High-Fat Diet Induces Long-Term Derepressive Chromatin Marks in the Heart

Heart diseases are a leading cause of death. While the link between early exposure to nutritional excess and heart disease risk is clear, the molecular mechanisms involved are poorly understood. In the developmental programming field, increasing evidence is pointing out the critical role of epigenetic mechanisms. Among them, polycomb repressive complex 2 (PRC2) and DNA methylation play a critical role in heart development and pathogenesis. In this context, we aimed at evaluating the role of these epigenetic marks in the long-term cardiac alterations induced by early dietary challenge. Using a model of rats exposed to maternal high-fat diet during gestation and lactation, we evaluated cardiac alterations at adulthood. Expression levels of PRC2 components, its histone marks di- and trimethylated histone H3 (H3K27me2/3), associated histone mark (ubiquitinated histone H2A, H2AK119ub1) and target genes were measured by Western blot. Global DNA methylation level and DNA methyl transferase 3B (DNMT3B) protein levels were measured. Maternal high-fat diet decreased H3K27me3, H2Ak119ub1 and DNA methylation levels, down-regulated the enhancer of zeste homolog 2 (EZH2), and DNMT3B expression. The levels of the target genes, isl lim homeobox 1 (Isl1), six homeobox 1 (Six1) and mads box transcription enhancer factor 2, polypeptide C (Mef2c), involved in cardiac pathogenesis were up regulated. Overall, our data suggest that the programming of cardiac alterations by maternal exposure to high-fat diet involves the derepression of pro-fibrotic and pro-hypertrophic genes through the induction of EZH2 and DNMT3B deficiency.

Folic acid, but not folate, regulates different stages of neurogenesis in the ventral hippocampus of adult female rats

Folate is an important regulator of hippocampal neurogenesis, and folic acid is needed prenatally to reduce the risk of neural tube defects. Both high levels of folic acid and low levels of folate can be harmful to health because low levels of folate have been linked to several diseases while high folic acid supplements can mask a vitamin B₁₂ deficiency. Depressed patients exhibit folate deficiencies, lower levels of hippocampal neurogenesis, elevated levels of homocysteine and elevated levels of the stress hormone, cortisol, which may be inter-related. In the present study, we were interested in whether different doses of natural folate or synthetic folic acid diets can influence neurogenesis in the hippocampus, levels of plasma homocysteine and serum corticosterone in adult female rats. Adult female Sprague-Dawley rats underwent dietary interventions for 29 days. Animals were randomly assigned to six different dietary groups: folate deficient + succinylsulphathiazole (SST), low 5-methyltetrahydrofolate (5-MTHF), low 5-MTHF + (SST), high 5-MTHF + SST, low folic acid and high folic acid. SST was added to a subset of the 5-MTHF diets to eliminate folic acid production in the gut. Before and after dietary treatment, blood samples were collected for corticosterone and homocysteine analysis, and brain tissue was collected for neurogenesis analysis. High folic acid and low 5-MTHF without SST increased the number of immature neurones (doublecortin-expressing cells) within the ventral hippocampus compared to folate deficient controls. Low 5-MTHF without SST significantly increased the number of immature neurones compared to low and high 5-MTHF + SST, indicating that SST interfered with elevations in neurogenesis. Low folic acid and high 5-MTHF + SST reduced plasma homocysteine levels compared to controls, although there was no significant effect of diet on serum corticosterone levels. In addition, low folic acid and high 5-MTHF + SST reduced the number of mature new neurones in the ventral hippocampus (bromodeoxyuridine/NeuN-positive cells) compared to folate deficient controls. Overall, folic acid dose-dependently influenced neurogenesis with low levels decreasing but high levels increasing neurogenesis in the ventral hippocampus, suggesting that this region, which is important for regulating stress, is particularly sensitive to folic acid in diets. Furthermore, the addition of SST negated the effects of 5-MTHF to increase neurogenesis in the ventral hippocampus.

[Correlation between methylation level of CDKN2A and CDKN2B genes and aging in healthy individuals]

OBJECTIVE

To analyze the relationship between CDKN2A and CDKN2B gene methylation with aging in the general population.

METHODS

We collected peripheral blood samples from 284 male and 246 female healthy subjects for detection of methylation levels of CDKN2A and CDKN2B genes using quantitative methylation-specific PCR (qMSP). The relationship between the methylation levels of CDKN2A and CDKN2B genes and aging was analyzed using Spearman or Pearson correlation test.

RESULTS

We found a significant positive correlation between the methylation levels of the two genes in these subjects (P &lt; 0.05). In the overall population as well in the female subjects, CDKN2A methylation was found to be inversely correlated with age (P &lt; 0.05). The methylation levels of CDKN2A and CDKN2B genes were inversely correlated with TG, ApoE, Lp(a) and AST in the overall population (P &lt; 0.05). In both the female and male subjects, the methylation levels of the two genes were inversely correlated with Lp(a) (P &lt; 0.05). In the male subjects, CDKN2A methylation was inversely correlated with AST (P &lt; 0.05), while CDKN2B methylation was inversely correlated with HDL and ApoE (P &lt; 0.05). In the female subjects, CDKN2A methylation was positively correlated with LDL and inversely correlated with ApoE and AST (P &lt; 0.05).

CONCLUSIONS

The methylation levels of CDKN2A and CDKN2B are closely related to age and the levels of multiple proteins in healthy subjects.

A cross-talk between blood-cell neuroplasticity-related genes and environmental enrichment in working dogs

This study aims to identify a panel of blood-cell neuroplasticity-related genes expressed following environmental enrichment stimulation (EE). The Drug detection (DD) training course was an excellent model for the study of EE in the working dog. This research is divided into two experimental trials. In the First Trial, we identified a panel of blood-cell neuroplasticity related-genes associated with DD ability acquired during the training course. In the Second Trial, we assessed the EE additional factor complementary feeding effect on blood-cell neuroplasticity gene expressions. In the First and Second Trials, at different time points of the DD test, blood samples were collected, and NGF, BDNF, VEGFA, IGF1, EGR1, NGFR, and ICE2 blood-cell neuroplasticity related-genes were analyzed. As noted in the First Trial, the DD test in working dogs induced the transient up-regulation of VEGFA, NGF, NGFR, BDNF, and IGF, immediately after the DD test, suggesting the existence of gene regulations. On the contrary, the Second Trial, with feeding implementation, showed an absence of mRNA up-regulation after the DD test. We suppose that complementary feeding alters the systemic metabolism, which, in turn, changes neuroplasticity-related gene blood-cell mRNA. These findings suggested that, in working dogs, there is a cross-talk between blood-cell neuroplasticity-related genes and environmental enrichment. These outcomes could be used to improve future treatments in sensory implementation.

Methyl Donor Micronutrients that Modify DNA Methylation and Cancer Outcome

DNA methylation is an epigenetic mechanism that is essential for regulating gene transcription. However, aberrant DNA methylation, which is a nearly universal finding in cancer, can result in disturbed gene expression. DNA methylation is modified by environmental factors such as diet that may modify cancer risk and tumor behavior. Abnormal DNA methylation has been observed in several cancers such as colon, stomach, cervical, prostate, and breast cancers. These alterations in DNA methylation may play a critical role in cancer development and progression. Dietary nutrient intake and bioactive food components are essential environmental factors that may influence DNA methylation either by directly inhibiting enzymes that catalyze DNA methylation or by changing the availability of substrates required for those enzymatic reactions such as the availability and utilization of methyl groups. In this review, we focused on nutrients that act as methyl donors or methylation co-factors and presented intriguing evidence for the role of these bioactive food components in altering DNA methylation patterns in cancer. Such a role is likely to have a mechanistic impact on the process of carcinogenesis and offer possible therapeutic potentials.

Evaluation of Serum Trace Element and Vitamin Levels in Children With Cancer in the First 6 Months After Diagnosis

Adequate nutrient intake should be provided for the cure of children diagnosed with cancer. The aim of this study was to evaluate serum trace elements and vitamins of children with cancer at diagnosis and during treatment. Children with newly diagnosed cancer who were admitted to our center were evaluated for serum selenium, iron, ferritin, C-reactive protein, vitamin B12, folate, and 25-OH vitamin D levels at presentation, and at the third and sixth months of cancer treatment. Forty-two children (male/female: 15/27) with a median age of 8 years (range, 2 to 17) were included in the study. Mean serum B12, folate, and iron levels were within normal ranges, but selenium and 25-OH vitamin D were low at presentation and during the 6-month period. Serum ferritin levels were high in all 3 measures, but they decreased significantly at the sixth month (P=0.04). There was no relation between micronutrient deficiency and sex, or primary disease, or stage, or place of residence of the patient. In conclusion, serum trace element and vitamin deficiencies are common in children with cancer, and there is a need for further studies with larger patient series.

Modulation of dietary folate with age confers selective hepatocellular epigenetic imprints through DNA methylation

The present study has been designed to determine the effect of folate modulation (deficiency/supplementation) with aging on the promoter methylation of tumor suppressor and proto-oncogenes to understand the underlying mechanism of epigenetic alterations. Folate deficiency was induced for 3 and 5 months in weanling, young and adult groups, and after 3 months of folate deficiency, they were repleted with physiological folate (2 mg/kg diet) and folate oversupplementation (8 mg/kg diet) for another 2 months. The methylation facet in the present study revealed that the combined effect of folate deficiency and aging decreased the methylation index. Folate deficiency with age resulted in the up-regulation of proto-oncogenes (C-MYC and C-JUN) and cell cycle regulator gene Cyclin E as a result of promoter hypomethylation. However, in case of tumor suppressor genes (p53, p15ink4b and p16ink4a), the expression levels were found to be decreased at transcriptional level due to promoter hypermethylation. Upon repletion with physiological folate and folate oversupplementation, we found down-regulation of proto-oncogenes and up-regulation of tumor suppressor genes as a result of promoter hypermethylation and hypomethylation, respectively. Deregulation of these important genes due to folate deficiency may contribute toward the pathogenesis at cellular level.

Effects of Prenatal Nutrition and the Role of the Placenta in Health and Disease

Epidemiologic studies identified the linkage between exposures to stresses, including the type and plane of nutrition in utero with development of disease in later life. Given the critical roles of the placenta in mediating transport of nutrients between the mother and fetus and regulation of maternal metabolism, recent attention has focused on the role of the placenta in mediating the effect of altered nutritional exposures on the development of disease in later life. In this chapter we describe the mechanisms of nutrient transport in the placenta, the influence of placental metabolism on this, and how placental energetics influence placental function in response to a variety of stressors. Further the recent "recognition" that the placenta itself has a sex which affects its function may begin to help elucidate the mechanisms underlying the well-known dimorphism in development of disease in adult life.

p16 Tumor Suppressor Gene Methylation in Diffuse Large B Cell Lymphoma: A Study of 88 Cases at Two Hospitals in the East Coast of Malaysia

Introduction: p16 gene plays an important role in the normal cell cycle regulation. Methylation of p16 has been reported to be one of the epigenetic events contributing to the pathogenesis of diffuse large B-cell lymphoma (DLBCL) which occurring at varying frequency. DLBCL is an aggressive and high-grade malignancy which accounts for approximately 30% of all non-Hodgkin lymphoma cases. However, little is known regarding the epigenetic alterations of p16 gene in DLBCL cases in Malaysia. Therefore, the objective of this study was to examine the status of p16 methylation in DLBCL. Methods: A total of 88 formalin-fixed paraffin-embedded DLBCL tissues retrieved from two hospitals located in the east coast of Malaysia, namely Hospital Tengku Ampuan Afzan (HTAA) Pahang and Hospital Universiti Sains Malaysia (HUSM) Kelantan, were chosen for this study. DNA specimens were isolated and subsequently subjected to bisulfite treatment prior to methylation specific-PCR. Two pairs of primers were used to amplify methylated and unmethylated regions of p16 gene. The PCR products were then separated using agarose gel electrophoresis and visualised under UV illumination. SPSS version 12.0 was utilised to perform all statistical analysis. Result: p16 methylation was detected in 65 of 88 (74%) samples. There was a significant association between p16 methylation status and patients aged >50 years old (p=0.04). Conclusion: Our study demonstrated that methylation of p16 tumor suppressor gene in our DLBCL cases is common and significantly increased among patients aged 50 years and above. Aging is known to be an important risk factor in the development of cancers and we speculate that this might be due to the increased transformation of malignant cells in aging cell population. However, this has yet to be confirmed with further research and correlate the findings with clinicopathological parameters.

One-carbon metabolism and epigenetics

The function of one-carbon metabolism is that of regulating the provision of methyl groups for biological methylation reactions including that of DNA and histone proteins. Methylation at specific sites into the DNA sequence and at histone tails are among the major epigenetic feature of mammalian genome for the regulation of gene expression. The enzymes within one-carbon metabolism are dependent from a number of vitamins or nutrients that serve either as co-factors or methyl acceptors or donors among which folate, vitamin B12, vitamin B6, betaine, choline and methionine have a major role. Several evidences show that there is a strict inter-relationship between one-carbon metabolism nutrients and epigenetic phenomena. Epigenetics is closely involved in gene transcriptional regulation through modifications super-imposed to the nucleotide sequence of DNA, such as DNA methylation, through chromatin remodeling systems that involves post-translational modifications of histones or through non-coding RNAs-based mechanisms. The epigenetic features of the genome are potentially modifiable by the action of several environmental factors among which nutrients cover a special place and interest considering their potential of influencing regulatory pathways at a molecular level by specific nutritional intervention and eventually influence disease prevention and outcomes. The present review will focus on the link between one-carbon nutrients and epigenetic phenomena based on the current knowledge from findings in cell culture, animal models and human studies.

The critical role of epigenetics in systemic lupus erythematosus and autoimmunity

One of the major disappointments in human autoimmunity has been the relative failure on genome-wide association studies to provide "smoking genetic guns" that would explain the critical role of genetic susceptibility to loss of tolerance. It is well known that autoimmunity refers to the abnormal state that the dysregulated immune system attacks the healthy cells and tissues due to the loss of immunological tolerance to self-antigens. Its clinical outcomes are generally characterized by the presence of autoreactive immune cells and (or) the development of autoantibodies, leading to various types of autoimmune disorders. The etiology and pathogenesis of autoimmune diseases are highly complex. Both genetic predisposition and environmental factors such as nutrition, infection, and chemicals are implicated in the pathogenic process of autoimmunity, however, how much and by what mechanisms each of these factors contribute to the development of autoimmunity remain unclear. Epigenetics, which refers to potentially heritable changes in gene expression and function that do not involve alterations of the DNA sequence, has provided us with a brand new key to answer these questions. In the recent decades, increasing evidence have demonstrated the roles of epigenetic dysregulation, including DNA methylation, histone modification, and noncoding RNA, in the pathogenesis of autoimmune diseases, especially systemic lupus erythematosus (SLE), which have shed light on a new era for autoimmunity research. Notably, DNA hypomethylation and reactivation of the inactive X chromosome are two epigenetic hallmarks of SLE. We will herein discuss briefly how genetic studies fail to completely elucidate the pathogenesis of autoimmune diseases and present a comprehensive review on landmark epigenetic findings in autoimmune diseases, taking SLE as an extensively studied example. The epigenetics of other autoimmune diseases such as rheumatic arthritis, systemic sclerosis and primary biliary cirrhosis will also be summarized. Importantly we emphasize that the stochastic processes that lead to DNA modification may be the lynch pins that drive the initial break in tolerance.

The Impact of External Factors on the Epigenome: In Utero and over Lifetime

Epigenetic marks change during fetal development, adult life, and aging. Some changes play an important role in the establishment and regulation of gene programs, but others seem to occur without any apparent physiological role. An important future challenge in the field of epigenetics will be to describe how the environment affects both of these types of epigenetic change and to learn if interaction between them can determine healthy and disease phenotypes during lifetime. Here we discuss how chemical and physical environmental stressors, diet, life habits, and pharmacological treatments can affect the epigenome during lifetime and the possible impact of these epigenetic changes on pathophysiological processes.

Methylation status of COX-2 in blood leukocyte DNA and risk of gastric cancer in a high-risk Chinese population

Background

Methylation is a common epigenetic modification which may play a crucial role in cancer development. To investigate the association between methylation of COX-2 in blood leukocyte DNA and risk of gastric cancer (GC), a nested case–control study was conducted in Linqu County, Shandong Province, a high risk area of GC in China.

Methods

Association between blood leukocyte DNA methylation of COX-2 and risk of GC was investigated in 133 GCs and 285 superficial gastritis (SG)/ chronic atrophic gastritis (CAG). The temporal trend of COX-2 methylation level during GC development was further explored in 74 pre-GC and 95 post-GC samples (including 31 cases with both pre- and post-GC samples). In addition, the association of DNA methylation and risk of progression to GC was evaluated in 74 pre-GC samples and their relevant intestinal metaplasia (IM)/dysplasia (DYS) controls. Methylation level was determined by quantitative methylation-specific PCR (QMSP). Odds ratios (ORs) and 95 % confidence intervals (CIs) were calculated by unconditional logistic regression analysis.

Results

The medians of COX-2 methylation levels were 2.3 % and 2.2 % in GC cases and controls, respectively. No significant association was found between COX-2 methylation and risk of GC (OR, 1.15; 95 % CI: 0.70-1.88). However, the temporal trend analysis showed that COX-2 methylation levels were elevated at 1–4 years ahead of clinical GC diagnosis compared with the year of GC diagnosis (3.0 % vs. 2.2 %, p = 0.01). Further validation in 31 GCs with both pre- and post-GC samples indicated that COX-2 methylation levels were significantly decreased at the year of GC diagnosis compared with pre-GC samples (1.5 % vs. 2.5 %, p = 0.02). No significant association between COX-2 methylation and risk of progression to GC was found in subjects with IM (OR, 0.50; 95 % CI: 0.18–1.42) or DYS (OR, 0.70; 95 % CI: 0.23–2.18). Additionally, we found that elder people had increased risk of COX-2 hypermethylation (OR, 1.55; 95 % CI: 1.02–2.36) and subjects who ever infected with H. pylori had decreased risk of COX-2 hypermethylation (OR, 0.54; 95 % CI: 0.34–0.88).

Conclusions

COX-2 methylation exists in blood leukocyte DNA but at a low level. COX-2 methylation levels in blood leukocyte DNA may change during GC development.

Environmental challenge, epigenetic plasticity and the induction of altered phenotypes in mammals

The level of transcriptional activity of a gene is regulated by epigenetic processes. There is compelling evidence that environmental challenges throughout the life course can induce phenotypic change. In this review, we summarize the current evidence, focusing specifically on the effects of nutrition and of environmental pollutants, that epigenetic processes underpin the induction by environmental change of altered phenotypic traits, emphasizing the implications for health outcomes. We also discuss whether epigenetic processes may be involved in the passage of induced traits between generations. Overall, current findings indicate that epigenetic processes may play an important role in determining disease risk, but there is a lack of studies that demonstrate causal links between epigenetic change and tissue function.

Environmental Epigenetics: Crossroad between Public Health, Lifestyle, and Cancer Prevention

Epigenetics provides the key to transform the genetic information into phenotype and because of its reversibility it is considered an ideal target for therapeutic interventions. This paper reviews the basic mechanisms of epigenetic control: DNA methylation, histone modifications, chromatin remodeling, and ncRNA expression and their role in disease development. We describe also the influence of the environment, lifestyle, nutritional habits, and the psychological influence on epigenetic marks and how these factors are related to cancer and other diseases development. Finally we discuss the potential use of natural epigenetic modifiers in the chemoprevention of cancer to link together public health, environment, and lifestyle.

A lifelong exposure to a Western-style diet, but not aging, alters global DNA methylation in mouse colon

BACKGROUND/OBJECTIVES

Previous studies have indicated that when compared to young mice, old mice have lower global DNA methylation and higher p16 promoter methylation in colonic mucosa, which is a common finding in colon cancer. It is also known that a Western-style diet (WSD) high in fat and calories, and low in calcium, vitamin D, fiber, methionine and choline (based on the AIN 76A diet) is tumorigenic in colons of mice. Because DNA methylation is modifiable by diet, we investigate whether a WSD disrupts DNA methylation patterns, creating a tumorigenic environment.

SUBJECTVIES/METHODS

We investigated the effects of a WSD and aging on global and p16 promoter DNA methylation in the colon. Two month old male C57BL/6 mice were fed either a WSD or a control diet (AIN76A) for 6, 12 or 17 months. Global DNA methylation, p16 promoter methylation and p16 expression were determined by LC/MS, methyl-specific PCR and real time RT-PCR, respectively.

RESULTS

The WSD group demonstrated significantly decreased global DNA methylation compared with the control at 17 months (4.05 vs 4.31%, P = 0.019). While both diets did not change global DNA methylation over time, mice fed the WSD had lower global methylation relative to controls when comparing all animals (4.13 vs 4.30%, P = 0.0005). There was an increase in p16 promoter methylation from 6 to 17 months in both diet groups (P < 0.05) but no differences were observed between diet groups. Expression of p16 increased with age in both control and WSD groups.

CONCLUSIONS

In this model a WSD reduces global DNA methylation, whereas aging itself has no affect. Although the epigenetic effect of aging was not strong enough to alter global DNA methylation, changes in promoter-specific methylation and gene expression occurred with aging regardless of diet, demonstrating the complexity of epigenetic patterns.

DNA methylation and gene expression profiles show novel regulatory pathways in hepatocellular carcinoma

Background

Alcohol is a well-known risk factor for hepatocellular carcinoma (HCC), but the mechanisms underlying the alcohol-related hepatocarcinogenesis are still poorly understood. Alcohol alters the provision of methyl groups within the hepatic one-carbon metabolism, possibly inducing aberrant DNA methylation. Whether specific pathways are epigenetically regulated in alcohol-associated HCC is, however, unknown. The aim of the present study was to investigate the genome-wide promoter DNA methylation and gene expression profiles in non-viral, alcohol-associated HCC. From eight HCC patients undergoing curative surgery, array-based DNA methylation and gene expression data of all annotated genes were analyzed by comparing HCC tissue and homologous cancer-free liver tissue.

Results

After merging the DNA methylation with gene expression data, we identified 159 hypermethylated-repressed, 30 hypomethylated-induced, 49 hypermethylated-induced, and 56 hypomethylated-repressed genes. Notably, promoter DNA methylation emerged as a novel regulatory mechanism for the transcriptional repression of genes controlling the retinol metabolism (ADH1A, ADH1B, ADH6, CYP3A43, CYP4A22, RDH16), iron homeostasis (HAMP), one-carbon metabolism (SHMT1), and genes with a putative, newly identified function as tumor suppressors (FAM107A, IGFALS, MT1G, MT1H, RNF180).

Conclusions

A genome-wide DNA methylation approach merged with array-based gene expression profiles allowed identifying a number of novel, epigenetically regulated candidate tumor-suppressor genes in alcohol-associated hepatocarcinogenesis. Retinol metabolism genes and SHMT1 are also epigenetically regulated through promoter DNA methylation in alcohol-associated HCC.

Due to the reversibility of epigenetic mechanisms by environmental/nutritional factors, these findings may open up to novel interventional strategies for hepatocarcinogenesis prevention in HCC related to alcohol, a modifiable dietary component.

Electronic supplementary material

The online version of this article (doi:10.1186/s13148-015-0077-1) contains supplementary material, which is available to authorized users.

Epigenetics: Its Understanding Is Crucial to a Sustainable Healthcare System

Understanding the molecular impact of lifestyle factors has never been so important; a period in time where there are so many adults above retirement age has been previously unknown. As a species, our life expectancy is increasing yet the period of our lives where we enjoy good health is not expanding proportionately. Over the next 50 years we will need to almost double the percentage of GDP spent on health care, largely due to the increasing incidence of obesity related chronic diseases. A greater understanding and implementation of an integrated approach to health is required. Research exploring the impact of nutritional and exercise intervention on the epigenetically flexible genome is up front in terms of addressing healthy aging. Alongside this, we need a greater understanding of the interaction with our immune and nervous systems in preserving and maintaining health and cognition.

Folates Induce Colorectal Carcinoma HT29 Cell Line Proliferation Through Notch1 Signaling

Folic acid (FA) consumption at high levels has been associated with colon cancer risk. Several mechanisms have been proposed to explain this association. The Notch signal pathway has been implicated in the regulation of cellular proliferation. Our aim was to demonstrate that high concentrations of FA or its reduced form, 5-methyltetrahydrofolic acid (5-MTHF), increase colorectal carcinoma HT29 cell proliferation through an increase of Notch1 activation and to prove if the inhibition of Notch1 activation by gamma secretase inhibitor, reduce the effect of folic acid. HT29 cells were cultured in high (400 nM), low (20 nM), or 0 nM FA or 5-MTHF concentrations during 96 h with or without DAPT (gamma secretase inhibitor). Cell proliferation was determined by the methylthiazole tetrazolium method, and Notch1-intracellular domain (NICD) was analyzed by flow cytometry. HT29 cells exposed to 400 nM FA or 5-MTHF showed higher proliferation rate than those exposed to 20 nM of FA or 5-MTHF (P < 0.01) during 96 h. NICD expression increased at higher FA or 5-MTHF concentrations compared with lower concentrations (P < 0.01). This effect on proliferation was partially reversible when we blocked Notch1 activation with the inhibitor of γ-secretase (P < 0.05).These data suggest that high concentration of FA and 5-MTHF induce HT29 cell proliferation activating Notch1 pathway.

One-Carbon Metabolism and Colorectal Cancer: Potential Mechanisms of Chemoprevention

For many years folic acid has been evaluated for its utility as a chemopreventive agent due to its position at the center of the one-carbon metabolic network. This network is responsible for generating precursors to nucleotide synthesis as well as the one-carbon moieties used in DNA methylation reactions, two mechanisms which are frequently disrupted during carcinogenesis. While the use of folic acid for the chemoprevention of colorectal cancer is still controversial, there is evidence that folic acid intake has significant influence on these fundamental cellular mechanisms. Folic acid has a dual role with regards to nucleotide synthesis and colorectal cancer (CRC) prevention; in a healthy colon, adequate folate status is important for nucleotide metabolism homeostasis and the maintenance of DNA integrity, however in a colon harboring premalignant lesions lowered folate status may help to eliminate transformed cells. In addition, folic acid is important for the generation of the one-carbon groups used in DNA methylation reactions, and modulation of folic acid metabolism may be useful in combating the aberrant DNA methylation during carcinogenesis. Interestingly, it has been revealed that decreased folic acid intake can dampen the inflammatory response, which has recently been a popular strategy for colorectal cancer chemoprevention. In this review we discuss the molecular mechanisms influenced by folic acid intake and how they might be relevant to cancer chemoprevention in greater detail.

DNA methylation, ageing and the influence of early life nutrition

It is well established that genotype plays an important role in the ageing process. However, recent studies have suggested that epigenetic mechanisms may also influence the onset of ageing-associated diseases and longevity. Epigenetics is defined as processes that induce heritable changes in gene expression without a change in the DNA nucleotide sequence. The major epigenetic mechanisms are DNA methylation, histone modification and non-coding RNA. Such processes are involved in the regulation of tissue-specific gene expression, cell differentiation and genomic imprinting. However, epigenetic dysregulation is frequently seen with ageing. Relatively little is known about the factors that initiate such changes. However, there is emerging evidence that the early life environment, in particular nutrition, in early life can induce long-term changes in DNA methylation resulting in an altered susceptibility to a range of ageing-associated diseases. In this review, we will focus on the changes in DNA methylation that occur during ageing; their role in the ageing process and how early life nutrition can modulate DNA methylation and influence longevity. Understanding the mechanisms by which diet in early life can influence the epigenome will be crucial for the development of preventative and intervention strategies to increase well-being in later life.

Effects of resveratrol on the expression and DNA methylation of cytokine genes in diabetic rat aortas

This paper studies the expression of proinflammatory cytokines such as IL-1β, IL-6, TNF-α, and IFN-γ and anti-inflammatory cytokines such as IL-10 in diabetic rat aortas, the effects of resveratrol on these cytokines, and the potential epigenetic mechanisms involved. The experiment was performed on rats divided into four groups: normal group (NC), normal interventional group (NB), diabetic group (DM), and diabetic interventional group (DB). The NB and DB groups were treated with resveratrol. After more than 3 months, the rats' aortas were removed and analyzed for cytokines by using immunohistochemistry, Western blotting, real-time PCR, and methylation-specific PCR. Histological localization of these cytokines was mainly found in the arterial intima of diabetic rats. The protein and mRNA expression levels of IL-1β, IL-6, TNF-α, and IFN-γ were significantly higher in the DM group than in the NC group (p < 0.05), whereas in the resveratrol-treated groups (NB and DB), the levels were relatively lower than those in the corresponding groups. The DM group showed reduced levels of DNA methylation at the specific cytosine phosphate guanosine sites of IL-1β, IL-6, TNF-α, and IFN-γ, relative to those in the NC group (p < 0.01), and these levels were increased by resveratrol. In contrast, IL-10 was dramatically methylated and showed decreased expression in response to high glucose, and resveratrol reversed this effect. These results demonstrate that the inflammatory response is involved in diabetic macroangiopathy. Resveratrol inhibits the expression of proinflammatory cytokines and thus may have a protective effect on the aorta in hyperglycemia. Thus, DNA methylation, an epigenetic gene silencing signal, may be responsible for these two phenomena.

Effect of maternal and postweaning folic acid supplementation on global and gene-specific DNA methylation in the liver of the rat offspring

SCOPE

Intrauterine and early-life exposure to folic acid has significantly increased in North America owing to folic acid fortification, widespread supplemental use, and periconceptional supplementation. We investigated the effect of maternal and postweaning folic acid supplementation on DNA methylation in the rat offspring.

METHODS AND RESULTS

Female rats were placed on a control or folic acid-supplemented diet during pregnancy and lactation. At weaning, pups from each maternal diet group were randomized to the control or supplemented diet for 11 weeks. At weaning, maternal folic acid supplementation significantly decreased global (p < 0.001) and site-specific DNA methylation of the Ppar-γ, ER-α, p53, and Apc genes (p < 0.05) in the liver. At 14 weeks of age, postweaning, but not maternal, folic acid supplementation significantly decreased global DNA methylation (p < 0.05). At 14 weeks of age, both maternal and postweaning folic acid supplementation significantly increased DNA methylation of the Ppar-γ, p53, and p16 genes (p < 0.05) whereas only postweaning FA supplementation significantly increased DNA methylation of the ER-α and Apc genes (p < 0.05).

CONCLUSION

Our data suggest that maternal and postweaning folic acid supplementation can significantly modulate global and gene-specific DNA methylation in the rat offspring. The functional ramifications of the observed DNA methylation changes need to be determined in future studies.

Exercise induces age-dependent changes on epigenetic parameters in rat hippocampus: a preliminary study

Regular exercise improves learning and memory, including during aging process. Interestingly, the imbalance of epigenetic mechanisms has been linked to age-related cognitive deficits. However, studies about epigenetic alterations after exercise during the aging process are rare. In this preliminary study we investigated the effect of aging and exercise on DNA methyltransferases (DNMT1 and DNMT3b) and H3-K9 methylation levels in hippocampus from 3 and 20-months aged Wistar rats. The animals were submitted to two exercise protocols: single session or chronic treadmill protocol. DNMT1 and H3-K9 methylation levels were decreased in hippocampus from aged rats. The single exercise session decreased both DNMT3b and DNMT1 levels in young adult rats, without any effect in the aged group. Both exercise protocols reduced H3-K9 methylation levels in young adult rats, while the single session reversed the changes on H3-K9 methylation levels induced by aging. Together, these results suggest that an imbalance on DNMTs and H3-K9 methylation levels might be linked to the brain aging process and that the outcome to exercise seems to vary through lifespan.

Shifts in developmental timing, and not increased levels of experience-dependent neuronal activity, promote barrel expansion in the primary somatosensory cortex of rats enucleated at birth

Birth-enucleated rodents display enlarged representations of whiskers (i.e., barrels of the posteromedial subfield) in the primary somatosensory cortex. Although the historical view maintains that barrel expansion is due to incremental increases in neuronal activity along the trigeminal pathway during postnatal development, recent evidence obtained in experimental models of intramodal plasticity challenges this view. Here, we re-evaluate the role of experience-dependent neuronal activity on barrel expansion in birth-enucleated rats by combining various anatomical methods and sensory deprivation paradigms. We show that barrels in birth-enucleated rats were already enlarged by the end of the first week of life and had levels of metabolic activity comparable to those in control rats at different ages. Dewhiskering after the postnatal period of barrel formation did not prevent barrel expansion in adult, birth-enucleated rats. Further, dark rearing and enucleation after barrel formation did not lead to expanded barrels in adult brains. Because incremental increases of somatosensory experience did not promote barrel expansion in birth-enucleated rats, we explored whether shifts of the developmental timing could better explain barrel expansion during the first week of life. Accordingly, birth-enucleated rats show earlier formation of barrels, accelerated growth of somatosensory thalamocortical afferents, and an earlier H4 deacetylation. Interestingly, when H4 deacetylation was prevented with a histone deacetylases inhibitor (valproic acid), barrel specification timing returned to normal and barrel expansion did not occur. Thus, we provide evidence supporting that shifts in developmental timing modulated through epigenetic mechanisms, and not increased levels of experience dependent neuronal activity, promote barrel expansion in the primary somatosensory cortex of rats enucleated at birth.

Promoter and histone methylation and p16(INK4A) gene expression in colon cancer

The inactivation of the cyclin-dependent kinase inhibitor p16^INK4A gene by hypermethylation is observed in numerous types of cancer. New findings indicate that DNA and histone methylation act in concert in gene silencing. In this study, we investigated the methylation status of the p16^INK4A gene promoter and the histone 3 lysine 9 residue in the tumors and matched normal tissue samples from patients with colorectal cancer and analyzed their association with gene expression. The methylation and expression of the p16^INK4A gene were analyzed by real-time PCR, and histone methylation was analyzed by chromatin immunoprecipitation followed by real-time PCR. p16^INK4A expression was significantly higher in the tumors compared to normal tissue. Mono-, di- and trimethylation levels of the H3K9 residue were similar in the tumor and normal tissue samples. We did not observe any significant correlation between p16^INK4A methylation or expression and clinical parameters. Our results suggest that epigenetic modifications of the p16^INK4A gene and histone lysine methylation do not play a major role in colon carcinogenesis.

Metabolic, hormonal and immunological associations with global DNA methylation among postmenopausal women

DNA methylation is an epigenetic modification essential for the regulation of gene expression that has been implicated in many diseases, including cancer. Few studies have investigated the wide range of potential predictors of global DNA methylation, including biomarkers. Here, we investigated associations between DNA methylation and dietary factors, sex-steroid hormones, metabolic, lipid, inflammation, immune and one-carbon biomarkers. Data and baseline biomarker measurements were obtained from 173 overweight/obese postmenopausal women. Global DNA methylation in lymphocyte DNA was measured using the pyrosequencing assay for LINE-1 repeats. We used correlations and linear regression analyses to investigate associations between continuous data and DNA methylation, while t-tests were used for categorical data. Secondary analyses stratified by serum folate levels and multivitamin use were also conducted. There was little variability in LINE-1 methylation (66.3-79.5%). Mean LINE-1 methylation was significantly higher among women with elevated glucose levels. Mean LINE-1 methylation was also higher among women with high CD4+/CD8+ ratio, and lower among women with elevated vitamin B6, but neither reached statistical significance. In analyses stratified by folate status, DNA methylation was negatively associated with sex hormone concentrations (estrone, estradiol, testosterone and sex hormone binding globulin) among women with low serum folate levels (n = 53). Conversely, among women with high serum folate levels (n = 53), DNA methylation was positively associated with several immune markers (CD4/CD8 ratio, NK1656/lymphocytes and IgA). Results from this screening suggest that global DNA methylation is generally stable, with differential associations for sex hormones and immune markers depending on one-carbon status.

Pretreatment dietary intake is associated with tumor suppressor DNA methylation in head and neck squamous cell carcinomas

Diet is associated with cancer prognosis, including head and neck cancer (HNC), and has been hypothesized to influence epigenetic state by determining the availability of functional groups involved in the modification of DNA and histone proteins. The goal of this study was to describe the association between pretreatment diet and HNC tumor DNA methylation. Information on usual pretreatment food and nutrient intake was estimated via food frequency questionnaire (FFQ) on 49 HNC cases. Tumor DNA methylation patterns were assessed using the Illumina Goldengate Methylation Cancer Panel. First, a methylation score, the sum of individual hypermethylated tumor suppressor associated CpG sites, was calculated and associated with dietary intake of micronutrients involved in one-carbon metabolism and antioxidant activity, and food groups abundant in these nutrients. Second, gene specific analyses using linear modeling with empirical Bayesian variance estimation were conducted to identify if methylation at individual CpG sites was associated with diet. All models were controlled for age, sex, smoking, alcohol and HPV status. Individuals reporting in the highest quartile of folate, vitamin B12 and vitamin A intake, compared with those in the lowest quartile, showed significantly less tumor suppressor gene methylation, as did patients reporting the highest cruciferous vegetable intake. Gene specific analyses identified differential associations between DNA methylation and vitamin B12 and vitamin A intake when stratifying by HPV status. These preliminary results suggest that intake of folate, vitamin A and vitamin B12 may be associated with the tumor DNA methylation profile in HNC and enhance tumor suppression.

The quiescent cellular state is Arf/p53-dependent and associated with H2AX downregulation and genome stability

Cancer is a disease associated with genomic instability and mutations. Excluding some tumors with specific chromosomal translocations, most cancers that develop at an advanced age are characterized by either chromosomal or microsatellite instability. However, it is still unclear how genomic instability and mutations are generated during the process of cellular transformation and how the development of genomic instability contributes to cellular transformation. Recent studies of cellular regulation and tetraploidy development have provided insights into the factors triggering cellular transformation and the regulatory mechanisms that protect chromosomes from genomic instability.

Demethylation of the FCER1G promoter leads to FcεRI overexpression on monocytes of patients with atopic dermatitis

BACKGROUND

Overexpression of the high-affinity receptor for immunoglobulin E on atopic monocytes and dendritic cells is known to contribute to the pathogenesis of atopic dermatitis (AD). However, it remains unclear what is the underlying mechanism of FcεRI deregulation. It has been speculated that epigenetic deregulation may play a role.

METHODS

Global DNA methylation levels of monocytes from 10 AD patients and 10 healthy controls were measured using a global DNA methylation kit. Bisulfite sequencing was performed to determine the methylation status of the FCER1G promoter region. FcεRIγ mRNA and FcεRI protein levels were detected by real-time RT-PCR, Western blotting, and flow cytometry, respectively. Patch methylation and the demethylating agent, 5-azacytidine, were used to determine the functional significance of methylation changes on FcεRI expression.

RESULTS

Monocytes from AD patients show a global hypomethylation, as well as a locus-specific hypomethylation at FCER1G promoter, as compared to healthy controls. Furthermore, this hypomethylation of FCER1G is inversely correlated with its expression. Patch methylation in combination with luciferase reporter assay confirmed the direct relationship between methylation and expression. Moreover, treating healthy monocytes with 5-azacytidine caused a reduction in methylation levels and an induction in FcεRIγ transcription and surface expression of FcεRI.

CONCLUSION

Demethylation of specific regulatory elements within the FCER1G locus contributes to FcεRI overexpression on monocytes from patients with AD.

The epigenome and cancer prevention: A complex story of dietary supplementation

Epigenetic changes have been implicated in virtually all types of human malignancies. In contrast to genetic changes, epigenetic changes occur in a gradual manner during the tumorigenic process and they are potentially reversible. Because epigenetic changes have frequently been detected in high-risk populations, they are attractive targets to prevent the initiation of premalignant lesions or their advance to a malignant stage. A wide range of chemical entities has been found capable of altering the epigenome in animal models and humans. Epidemiological and laboratory-based studies suggested that these agents may have an anti-neoplastic effect against different cancer types. Several of these agents have been tested as dietary supplements, often with conflicting results. In this review, we discuss recent developments in our understanding of agents capable of modulating the epigenome and their potential to prevent human cancer when administered as dietary supplements.

Dietary and lifestyle factors of DNA methylation

Lifestyle factors, such as diet, smoking, physical activity, and body weight management, are known to constitute the majority of cancer causes. Epigenetics has been widely proposed as a main mechanism that mediates the reversible effects of dietary and lifestyle factors on carcinogenesis. This chapter reviews human studies on potential dietary and lifestyle determinants of DNA methylation. Apart from a few prospective investigations and interventions of limited size and duration, evidence mostly comes from cross-sectional observational studies and supports some associations. Studies to date suggest that certain dietary components may alter genomic and gene-specific DNA methylation levels in systemic and target tissues, affecting genomic stability and transcription of tumor suppressors and oncogenes. Most data and supportive evidence exist for folate, a key nutritional factor in one-carbon metabolism that supplies the methyl units for DNA methylation. Other candidate bioactive food components include alcohol and other key nutritional factors of one-carbon metabolism, polyphenols and flavonoids in green tea, phytoestrogen, and lycopene. Some data also support a link of DNA methylation with physical activity and energy balance. Effects of dietary and lifestyle exposures on DNA methylation may be additionally modified by common genetic variants, environmental carcinogens, and infectious agents, an aspect that remains largely unexplored. In addition, growing literature supports that the environmental conditions during critical developmental stages may influence later risk of metabolic disorders in part through persistent programming of DNA methylation. Further research of these modifiable determinants of DNA methylation will improve our understanding of cancer etiology and may present certain DNA methylation markers as attractive surrogate endpoints for prevention research. Considering the plasticity of epigenetic marks and correlated nature of lifestyle factors, more longitudinal studies of healthy individuals of varying age, sex, and ethnic groups are warranted, ideally with comprehensive data collection on various lifestyle factors.

Diet, epigenetics, and cancer

Cancer encompasses a highly heterogeneous group of diseases. It has been thought that transition from promotion to progression in carcinogenesis may be driven primarily by epigenetic abnormalities. Diet is known to play crucial roles in cancer etiology and has an important role in epigenetics. Current knowledge in the interrelationship among cancer, nutrition and epigenetics is reviewed.

Nutritional influences on epigenetics and age-related disease

Nutritional epigenetics has emerged as a novel mechanism underlying gene-diet interactions, further elucidating the modulatory role of nutrition in aging and age-related disease development. Epigenetics is defined as a heritable modification to the DNA that regulates chromosome architecture and modulates gene expression without changes in the underlying bp sequence, ultimately determining phenotype from genotype. DNA methylation and post-translational histone modifications are classical levels of epigenetic regulation. Epigenetic phenomena are critical from embryonic development through the aging process, with aberrations in epigenetic patterns emerging as aetiological mechanisms in many age-related diseases such as cancer, CVD and neurodegenerative disorders. Nutrients can act as the source of epigenetic modifications and can regulate the placement of these modifications. Nutrients involved in one-carbon metabolism, namely folate, vitamin B12, vitamin B6, riboflavin, methionine, choline and betaine, are involved in DNA methylation by regulating levels of the universal methyl donor S-adenosylmethionine and methyltransferase inhibitor S-adenosylhomocysteine. Other nutrients and bioactive food components such as retinoic acid, resveratrol, curcumin, sulforaphane and tea polyphenols can modulate epigenetic patterns by altering the levels of S-adenosylmethionine and S-adenosylhomocysteine or directing the enzymes that catalyse DNA methylation and histone modifications. Aging and age-related diseases are associated with profound changes in epigenetic patterns, though it is not yet known whether these changes are programmatic or stochastic in nature. Future work in this field seeks to characterise the epigenetic pattern of healthy aging to ultimately identify nutritional measures to achieve this pattern.

Promoter methylation of E-cadherin, p16, and RAR-β(2) genes in breast tumors and dietary intake of nutrients important in one-carbon metabolism

Aberrant DNA methylation plays a critical role in carcinogenesis, and the availability of dietary factors involved in 1-carbon metabolism may contribute to aberrant DNA methylation. We investigated the association of intake of folate, vitamins B(2), B(6), B(12), and methionine with promoter methylation of E-cadherin, p16, and RAR-β(2) genes in archived tumor tissues from incident, primary breast cancer cases in a population-based case-control study. Real-time methylation-specific PCR was performed on 803 paraffin-embedded samples; usual dietary intake was queried from a food frequency questionnaire. Unconditional logistic regression was used to derive adjusted odds ratios and 95% confidence intervals for likelihood of promoter methylation for high compared to low intake of those 1-carbon nutrients. Overall, in case-case comparisons, dietary intakes of folate, vitamins B(2), B(6), B(12), and methionine were not associated with likelihood of promoter methylation of E- cadherin, p16, and RAR-β(2) for all cases combined or within strata defined by menopausal status and estrogen receptor status in this study. This finding, however, does not exclude the possibility that intake of such nutrients might have the ability to modulate promoter methylation in normal or premalignant (dysplastic) breast tissue.

Dietary patterns are associated with levels of global genomic DNA methylation in a cancer-free population

Animal studies have provided direct evidence that dietary factors induce changes in DNA methylation patterns. In humans, studies on diet and DNA methylation have yielded inconsistent findings. Because humans tend to consume foods and nutrients that are highly interrelated, study of dietary patterns may have improved the power of detecting the effect of diet on DNA methylation. Using data collected from 149 participants aged 45-75 y in the North Texas Healthy Heart Study, we examined the relationship between dietary patterns and levels of genomic DNA methylation in peripheral blood leukocytes. Dietary data were collected from study participants using the Block FFQ. Genomic DNA methylation was measured using bisulfite conversion of DNA and real-time PCR (MethyLight) for LINE-1. Two dietary patterns were identified using factor analysis: a "prudent" dietary pattern characterized by a high intake of vegetables and fruits, and a "Western" dietary pattern characterized by a high intake of meats, grains, dairy, oils, and potatoes. The prudent dietary pattern was associated with a lower prevalence of DNA hypomethylation (Q(4) vs. Q(1); OR = 0.33, 95% CI: 0.12-0.92) and the association was dose dependent (P-trend = 0.04). There was no apparent association between the Western dietary pattern and global leukocyte DNA methylation (Q(4) vs. Q(1); OR = 1.28, 95% CI: 0.47-3.47; P-trend = 0.55). Thus, a dietary pattern characterized by a high intake of vegetables and fruits may protect against global DNA hypomethylation. Future studies with a larger sample size need to confirm that this association holds longitudinally.

Genetics, cytogenetics, and epigenetics of colorectal cancer

Most of the colorectal cancer (CRC) cases are sporadic, only 25% of the patients have a family history of the disease, and major genes causing syndromes predisposing to CRC only account for 5-6% of the total cases. The following subtypes can be recognized: MIN (microsatellite instability), CIN (chromosomal instability), and CIMP (CpG island methylator phenotype). CIN occurs in 80-85% of CRC. Chromosomal instability proceeds through two major mechanisms, missegregation that results in aneuploidy through the gain or loss of whole chromosomes, and unbalanced structural rearrangements that lead to the loss and/or gain of chromosomal regions. The loss of heterozygosity that occur in the first phases of the CRC cancerogenesis (in particular for the genes on 18q) as well as the alteration of methylation pattern of multiple key genes can drive the development of colorectal cancer by facilitating the acquisition of multiple tumor-associated mutations and the instability phenotype.

Epigenetics: A New Bridge between Nutrition and Health

Nutrients can reverse or change epigenetic phenomena such as DNA methylation and histone modifications, thereby modifying the expression of critical genes associated with physiologic and pathologic processes, including embryonic development, aging, and carcinogenesis. It appears that nutrients and bioactive food components can influence epigenetic phenomena either by directly inhibiting enzymes that catalyze DNA methylation or histone modifications, or by altering the availability of substrates necessary for those enzymatic reactions. In this regard, nutritional epigenetics has been viewed as an attractive tool to prevent pediatric developmental diseases and cancer as well as to delay aging-associated processes. In recent years, epigenetics has become an emerging issue in a broad range of diseases such as type 2 diabetes mellitus, obesity, inflammation, and neurocognitive disorders. Although the possibility of developing a treatment or discovering preventative measures of these diseases is exciting, current knowledge in nutritional epigenetics is limited, and further studies are needed to expand the available resources and better understand the use of nutrients or bioactive food components for maintaining our health and preventing diseases through modifiable epigenetic mechanisms.

p16INK4a hypermethylation and p53, p16 and MDM2 protein expression in esophageal squamous cell carcinoma

BACKGROUND

Tumor suppressor genes p53 and p16INK4a and the proto-oncogene MDM2 are considered to be essential G1 cell cycle regulatory genes whose loss of function is associated with ESCC carcinogenesis. We assessed the aberrant methylation of the p16 gene and its impact on p16INK4a protein expression and correlations with p53 and MDM2 protein expressions in patients with ESCC in the Golestan province of northeastern Iran in which ESCC has the highest incidence of cancer, well above the world average.

METHODS

Cancerous tissues and the adjacent normal tissue obtained from 50 ESCC patients were assessed with Methylation-Specific-PCR to examine the methylation status of p16. The expression of p16, p53 and MDM2 proteins was detected by immunohistochemical staining.

RESULTS

Abnormal expression of p16 and p53, but not MDM2, was significantly higher in the tumoral tissue. p53 was concomitantly accumulated in ESCC tumor along with MDM2 overexpression and p16 negative expression. Aberrant methylation of the p16INK4a gene was detected in 31/50 (62%) of esophageal tumor samples, while two of the adjacent normal mucosa were methylated (P < 0.001). p16INK4a aberrant methylation was significantly associated with decreased p16 protein expression (P = 0.033), as well as the overexpression of p53 (P = 0.020).

CONCLUSIONS

p16 hypermethylation is the principal mechanism of p16 protein underexpression and plays an important role in ESCC development. It is associated with p53 protein overexpression and may influence the accumulation of abnormally expressed proteins in p53-MDM2 and p16-Rb pathways, suggesting a possible cross-talk of the involved pathways in ESCC development.