DNA Methylation, Genomic Silencing, and Links to Nutrition and Cancer

Role of macronutrients, dairy products, fruits and vegetables in occurrence and progression of endometriosis: A summary of current evidence in a systematic review

Background

Current evidence on the role of macro- and micronutrients in the aetiopathogenesis of endometriosis is controversial.

Objectives

In this systematic review, we aimed to investigate the effect of macronutrients, dairy products, fruits, and vegetables on the occurrence and progression of endometriosis.

Materials and Methods

A systematic literature review of eligible articles retrieved from medical databases, including PubMed, Cochrane, and Academic Search, was performed from inception to May 2023.

Main outcome measures

The role of nutritional diet effects in endometriosis.

Results

Our search yielded 12 studies, including five prospective cohort trials and seven case-control studies. The analysis of this literature supports the idea that processed and unprocessed red meat increases the risk of endometriosis, while no conclusive evidence exists about the effects of other protein sources on the disease. Studies on total fat consumption, including monounsaturated, polyunsaturated, saturated, and trans-unsaturated fats, do not suggest a definitive association with endometriosis. Green leafy vegetables and fresh fruit consumption may reduce the risk of endometriosis. Furthermore, the evidence regarding fibre consumption is not conclusive. Dairy products were found to have a risk-reducing effect on the disease. However, there was no consensus about the role of vitamin D in endometriosis.

Conclusions

The certainty of the relationship between endometriosis and outcomes of nutritional factors was "very low" to "low," which limits current literature from being applied for conclusive interpretations. Further large-scale randomised trials and consequent meta-analyses are recommended for high-level evidence.

What is new?

This article presents an overview of evidence-based studies on the relationship between endometriosis and macronutrients. In addition, the possible influence of other nutritional variables on the development of endometriosis and the limitations of nutritional studies.

Cis-Acting Factors Causing Secondary Epimutations: Impact on the Risk for Cancer and Other Diseases

Epigenetics affects gene expression and contributes to disease development by alterations known as epimutations. Hypermethylation that results in transcriptional silencing of tumor suppressor genes has been described in patients with hereditary cancers and without pathogenic variants in the coding region of cancer susceptibility genes. Although somatic promoter hypermethylation of these genes can occur in later stages of the carcinogenic process, constitutional methylation can be a crucial event during the first steps of tumorigenesis, accelerating tumor development. Primary epimutations originate independently of changes in the DNA sequence, while secondary epimutations are a consequence of a mutation in a cis or trans-acting factor. Secondary epimutations have a genetic basis in cis of the promoter regions of genes involved in familial cancers. This highlights epimutations as a novel carcinogenic mechanism whose contribution to human diseases is underestimated by the scarcity of the variants described. In this review, we provide an overview of secondary epimutations and present evidence of their impact on cancer. We propose the necessity for genetic screening of loci associated with secondary epimutations in familial cancer as part of prevention programs to improve molecular diagnosis, secondary prevention, and reduce the mortality of these diseases.

Does Nutrition Affect Endometriosis?

Endometriosis is a hormone-related, chronic inflammation in women of childbearing age. The aetiology and pathogenesis of endometriosis are not yet fully understood. For other illnesses classed as lifestyle diseases, the link between nutrition and pathogenesis has already been researched and proven. With regard to these findings, the question continues to arise as to whether and how a specific diet and lifestyle could also influence pathogenesis and the progression of endometriosis. The aim of this review is to examine the data and determine what influence nutrition has on the development of endometriosis or on existing disease. The study results currently available do not permit a clear, scientific recommendation or indicate a detailed diet. In summary, it can be said that fish oil capsules in combination with vitamin B ₁₂ have been associated with a positive effect on endometriosis symptoms (particularly of dysmenorrhoea). Alcohol and increased consumption of red meat and trans fats are associated with a negative effect. The results of the studies listed with regard to fruit and vegetables, dairy products, unsaturated fats, fibre, soy products and coffee are not clear. Therefore, the general recommendations for a balanced and varied diet in line with the guidelines of the Deutsche Gesellschaft für Ernährung e. V. [German Nutrition Society] apply, along with the recommendation to cut out alcohol. In order to be able to derive more concrete recommendations, we require further studies to investigate the influence of nutrition on endometriosis.

Decision Analysis of Transplantation for Patients with Myelodysplasia: "Who Should We Transplant Today?"

PURPOSE OF REVIEW

Myelodysplastic syndrome (MDS) is a heterogeneous hematological disorder characterized by a spectrum of clinical presentation, cytogenetic, and somatic gene mutations and the risk of transformation to acute leukemia. Management options include observation, supportive care, blood transfusion, administration of growth factors and/or hypomethylating agents, and hematopoietic cell transplant (HCT) either upfront or after disease progression.

RECENT FINDINGS

Currently, HCT is the only curative therapy available for patients with MDS, with multiple factors such as donor availability, patient, and disease characteristics being involved in making the decision to proceed with transplant. In this article, we summarize (1) overall prognosis and natural history of MDS, (2) currently available non-HCT therapy with a focus on hypomethylating agents (HMA), (3) outcomes after HCT in patients with MDS, (4) factors to be considered to proceed to HCT for treatment of MDS, and (5) more recent/ongoing studies relevant to HCT decision-making processes.

Origin of Hypoglycemic Benefits of Probiotic-Fermented Carrot Pulp

It has been found that probiotic-fermented carrot pulp has a beneficial effect in reducing blood glucose, more so than unfermented pulp. This paper explores the reason for this by looking at fermentation-induced changes in nutritional components and hypoglycemic effects of its polysaccharides. Micronutrient content showed minor changes, except for titratable acidity. Fat and protein decreased, while total carbohydrates increased. These polysaccharides are pectinic, and the number of total polysaccharides rose after fermentation. Scanning electron microscopy showed that the morphology changed from filamentous solid to spiral. The molecular weight of water-soluble polysaccharide (WSP) diminished after fermentation, while those of acid- and alkali-soluble polysaccharides increased. WSP had stronger hydroxyl radical scavenging activity in vitro, and WSP from probiotic-fermented carrot pulps showed better hypoglycemic effects than WSP from non-fermented carrot pulps in animal experiments. Thus, the fermentation-induced improvement in diabetes control from fermented carrot pulp probably arises from its WSP.

Endometriosis and food habits: Can diet make the difference?

Endometriosis is a chronic, inflammatory, estrogenic-dependent disease characterized by the presence of endometrial glands outside the uterine cavity, affecting approximately 2%–10% of women in reproductive age and 30%–50% of women in general. Despite the high prevalence of the disease, not much is known about etiology, possible risk factors, and an adequate and satisfactory therapy. In the past years, many studies have focused on food intake (nutrients and food groups) and on its possible correlation with endometriosis, demonstrating how diet could be identified as a possible risk factor. Comprehensive searches in the largest medical information databases (Medline-PubMed, Embase, Lilacs, and Cochrane Library) were conducted using the Medical Subject Heading terms “diet,” “food,” “nutrition,” “fatty acids,” vitamins,” “fruit,” “vegetables,” “coffee,” “caffeine,” “fish,” “soy food,” “dairy products,” “tea,” “curcumin” combined with “endometriosis.” Purpose of this review is to revise the literature, in order to determine potential modifiable risk factors of the disease.

Positional effects revealed in Illumina methylation array and the impact on analysis

AIM

We aimed to prove the existence of positional effects in the Illumina methylation beadchip data and to find an optimal correction method.

MATERIALS & METHODS

Three HumanMethylation450, three HumanMethylation27 datasets and two EPIC datasets were analyzed. ComBat, linear regression, functional normalization and single-sample Noob were used for minimizing positional effects. The corrected results were evaluated by four methods.

RESULTS

We detected 52,988 CpG loci significantly associated with sample positions, 112 remained after ComBat correction in the primary dataset. The pre- and postcorrection comparisons indicate the positional effects could alter the measured methylation values and downstream analysis results.

CONCLUSION

Positional effects exist in the Illumina methylation array and may bias the analyses. Using ComBat to correct positional effects is recommended.

Role of genetic and environmental factors in DNA methylation of lipid metabolism

A number of recent studies revealed that DNA methylation plays a central role in the regulation of lipid metabolism. DNA methylation modifications are important regulators of transcriptional networks that do not affect the DNA sequence and can translate genetic variants and environmental factors into phenotypic traits. Therefore, elucidating the factors that underlie inter-individual DNA methylation variations gives us an opportunity to predict diseases and interfere with the establishment of aberrant DNA methylation early. In this review, we summarize the findings of DNA methylation-related studies focused on unravelling the potential role of genetic and environmental factors in DNA methylation and the regulatory effect of DNA methylation on gene expression in lipid metabolism.

Diagnostic accuracy of DNA methylation in detection of gastric cancer: a meta-analysis

Emerging studies demonstrate the diagnostic utility of DNA methylation-based blood test for gastric cancer. The aim of the meta-analysis is to evaluate the accuracy of blood DNA methylation markers for detecting patients with gastric cancer. A systematic literature search to November 2016 that evaluated DNA methylation markers utilizing blood specimen to detect gastric cancer were selected to derive pooled sensitivities and specificities. 32 studies including 4,172 patients (gastric cancer (N = 2,098), control (N = 2,074)) met the study criteria. Overall sensitivity of DNA methylation-based blood test for detecting gastric cancer was 57% (95% CI 50–63%); specificity was 97% (95% CI 95–98%). Among patients who received plasma-based testing, sensitivity was 71% (95% CI 59–81%); specificity was 89% (95% CI 78–94%). Among patients who received serum-based testing, sensitivity was 50% (95% CI 43–58%); specificity was 98% (95% CI 96–99%). Using multiple methylated genes had sensitivity of 76% (95% CI 64–84%); specificity of 85% (95% CI 65–95%). DNA methylation test had sensitivity of 55% (95% CI 47–64%) and specificity of 96% (95% CI 92–98%) for detecting TNM stage I+II gastric cancer. In conclusion, blood-based DNA methylation test had high specificity but modest sensitivity for detecting gastric cancer. Evaluating multiple methylated genes or using plasma sample may improve the diagnostic sensitivity.

Nutrients and the Pancreas: An Epigenetic Perspective

Pancreatic cancer is the fourth most common cause of cancer-related deaths with a dismal average five-year survival rate of six percent. Substitutional progress has been made in understanding how pancreatic cancer develops and progresses. Evidence is mounting which demonstrates that diet and nutrition are key factors in carcinogenesis. In particular, diets low in folate and high in fruits, vegetables, red/processed meat, and saturated fat have been identified as pancreatic cancer risk factors with a proposed mechanism involving epigenetic modifications or gene regulation. We review the current literature assessing the correlation between diet, epigenetics, and pancreatic cancer.

Greek pregnant women demonstrate inadequate micronutrient intake despite supplement use

BACKGROUND/AIM

Maternal diet is important in the outcome of pregnancy and the health of the children. The present cross-sectional study aimed to assess the use of dietary supplements during pregnancy and define the maternal characteristics associated with supplement use.

METHODS

The diet of 100 childbearing women was recorded for three consecutive days and micronutrient supplementation was added to the dietary intake and the median values were used in the analyses.

RESULTS

The majority of the participants (92%) consumed at least one supplement. Supplementation of folic acid (FA) was significantly lower during the third trimester compared to the second (p ≤ .007). Higher intake of Ca and Fe supplements was observed in the second trimester (p ≤ .001). The use of supplements contributed to an attenuated consumption of all reported micronutrients (Mg, Ca, FA, and Fe, p ≤ .001). The principal components analysis revealed that the most important factor contributing to supplementation was primiparity.

CONCLUSIONS

Overall, a high prevalence of micronutrient supplementation during pregnancy was observed without ensuring adequacy in the micronutrient intake. The increased rates of supplement users might be the result of an act for balancing diet in unplanned pregnancies.

Impact of folic acid fortification on global DNA methylation and one-carbon biomarkers in the Women's Health Initiative Observational Study cohort

DNA methylation is an epigenetic mechanism that regulates gene expression and can be modified by one-carbon nutrients. The objective of this study was to investigate the impact of folic acid (FA) fortification of the US food supply on leukocyte global DNA methylation and the relationship between DNA methylation, red blood cell (RBC) folate, and other one-carbon biomarkers among postmenopausal women enrolled in the Women's Health Initiative Observational Study. We selected 408 women from the highest and lowest tertiles of RBC folate distribution matching on age and timing of the baseline blood draw, which spanned the pre- (1994-1995), peri- (1996-1997), or post-fortification (1998) periods. Global DNA methylation was assessed by liquid chromatography-tandem mass spectrometry and expressed as a percentage of total cytosine. We observed an interaction (P = 0.02) between fortification period and RBC folate in relation to DNA methylation. Women with higher (vs. lower) RBC folate had higher mean DNA methylation (5.12 vs. 4.99%; P = 0.05) in the pre-fortification period, but lower (4.95 vs. 5.16%; P = 0.03) DNA methylation in the post-fortification period. We also observed significant correlations between one-carbon biomarkers and DNA methylation in the pre-fortification period, but not in the peri- or post-fortification period. The correlation between plasma homocysteine and DNA methylation was reversed from an inverse relationship during the pre-fortification period to a positive relationship during the post-fortification period. Our data suggest that (1) during FA fortification, higher RBC folate status is associated with a reduction in leukocyte global DNA methylation among postmenopausal women and; (2) the relationship between one-carbon biomarkers and global DNA methylation is dependent on folate availability.

The E2F1/DNMT1 axis is associated with the development of AR negative castration resistant prostate cancer

BACKGROUND

Research on castration resistant prostate cancer (CRPC) has focused primarily on functional alterations of the androgen receptor (AR). However, little is known about the loss of AR gene expression itself and the possible contribution of AR negative cells to CRPC.

METHODS

Human and murine prostate cancer tissue microarrays (TMAs) were evaluated with antibodies specific for E2F1, DNA methyltransferase 1 or AR. The human prostate cancer TMA consisted of clinical samples ranging from normal tissue to samples of metastatic disease. The murine TMA was comprised of benign, localized or metastatic prostate cancer acquired from TRAMP mice treated with castration and/or 5'-Aza-2'-deoxycytidine (5Aza).

RESULTS

Immunohistochemical analysis revealed increased nuclear DNMT1 staining in localized PCa (P < 0.0001) and metastatic PCa (P < 0.0001) compared to normal tissue. Examination of specific diagnoses revealed that Gleason seven tumors exhibited greater nuclear DNMT1 staining than Gleason six tumors (P < 0.05) and that metastatic tissue exhibited greater levels of nuclear DNMT1 than Gleason seven tumors (P < 0.01). Evaluation of the murine tissue cores revealed that 8.2% and 8.1% of benign tissue cores stained positive for E2F1 and DNMT1 respectively, while 97.0% were AR positive. Conversely, 81% and 100% of tumors were positive for E2F1 and DNMT1 respectively. This was in stark contrast to only 18% of tumors positive for AR. Treatment of mice with 5Aza reduced DNMT1 staining by 30%, while AR increased by 27%.

CONCLUSIONS

These findings demonstrate that the E2F1/DNMT1 inhibitory axis of AR transcription is activated during the emergence of CRPC.

A potential role of probiotics in colorectal cancer prevention: review of possible mechanisms of action

A number of investigations, mainly using in vitro and animal models, have demonstrated a wide range of possible mechanisms, by which probiotics may play a role in colorectal cancer (CRC) prevention. In this context, the most well studied probiotics are certain strains from the genera of lactobacilli and bifidobacteria. The reported anti-CRC mechanisms of probiotics encompass intraluminal, systemic, and direct effects on intestinal mucosa. Intraluminal effects detailed in this review include competitive exclusion of pathogenic intestinal flora, alteration of intestinal microflora enzyme activity, reduction of carcinogenic secondary bile acids, binding of carcinogens and mutagens, and increasing short chain fatty acids production. Reduction of DNA damage and suppression of aberrant crypt foci formation have been well demonstrated as direct anti-CRC effects of probiotics on intestinal mucosa. Existing evidence clearly support a multifaceted immunomodulatory role of probiotics in CRC, particularly its ability to modulate intestinal inflammation, a well known risk factor for CRC. The effectiveness of probiotics in CRC prevention is dependent on the strain of the microorganism, while viability may not be a prerequisite for certain probiotic anticancer mechanisms, as indicated by several studies. Emerging data suggest synbiotic as a more effective approach than either prebiotics or probiotics alone. More in vivo especially human studies are warranted to further elucidate and confirm the potential role of probiotics (viable and non-viable), prebiotics and synbiotics in CRC chemoprevention.

Association between DNA methyltransferases 3B gene polymorphisms and the susceptibility to acute myeloid leukemia in Chinese Han population

DNMT3B plays a crucial role in the generation of aberrant methylation during carcinogenesis. Polymorphisms in the DNMT3B gene may influence the DNA methylation enzymatic activity of DNMT3B, thereby modulating the susceptibility to AML. Thus, we investigated the association between SNPs in the DNMT3Bgene and their haplotypes with the risk of AML in the Chinese Han population. The DNMT3B genotype was determined by HRM in 317 de novo AML patients and 406 healthy control subjects matched for age and gender. Among the 5 SNPs investigated in this study, rs2424913 demonstrated no polymorphisms in the Chinese Han populations, rs1569686 and rs2424908 were significantly associated with AML risk. The GG genotype of rs1569686 was associated with increased AML risk (OR: 5.76; 95%CI: 2.60-12.73; P<0.01) compared with the TT genotype, and individuals with a G allele had a significantly increased risk (OR: 1.89; 95%CI: 1.41-2.52; P<0.01) for AML compared with those harboring a C allele, this polymorphism can predict the risk of AML in a minority of patients. While the CC genotype of rs2424908 appeared to reduce the AML risk (OR: 0.57; 95%CI: 0.36-0.91; P=0.01) compared with the TT genotype, individuals with a C allele were associated with a lower risk (OR: 0.79, 95%CI: 0.64-0.97, P=0.03) for developing AML compared with those harboring a T allele. The other 2 SNPs, rs6087990 and rs6119954, had no significant association with AML risk in the study population. The CGGT, CTAT, TGAT, and CGAT haplotypes of rs6087990, rs1569686, rs6119954, and rs2424908 appeared to significantly increase the AML risk, and the TTGC haplotype appeared to significantly reduce the risk. These results suggest that DNMT3B polymorphisms may contribute to the genetic susceptibility to AML; in particular, the G allele of rs1569686 serves as a risk factor for AML, whereas the C allele of rs2424908 represents a potential protective factor.

Real-time dynamics of methyl-CpG-binding domain protein 3 and its role in DNA demethylation by fluorescence correlation spectroscopy

With unprecedented development in technology, epigenetics is recognized as a substantial and flexible regulatory pathway for phenotyping. Cytosine methylation and its subsequent oxidization have attracted significant attention due to their direct impact on gene regulation, in association with methyl-CpG-binding domain proteins (MBDs) and transcription related factors. In this study we record the dynamics of DNA demethylation using the recombinant MBD3-GFP protein in living cells under hypoxia and Decitabine treatment using Fluorescence Correlation Spectroscopy (FCS) by monitoring the diffusion dynamics of MBD3. Our study shows a DNA-replication-independent decrease of 5-methylcytosine (5mC)/5-hydroxymethylcytosine (5hmC) under hypoxia vs. a dependent decrease under Decitabine treatment. Further, we define a significantly faster diffusion of MBD3 in the nucleus as a precursory event for active demethylation rather than the Decitabine induced passive demethylation. By monitoring the diffusion of bound and unbound MBD3 in the nucleus we were able to identify and characterize hypoxia-sensitive cells from insensitive/tolerant cells, as well as the respective contribution to active demethylation in a time-dependent manner. Last, we quantitatively describe the concurrent decreasing trend in all of the three oxidized products of 5mC, which points to the potential involvement of ten-eleven-translocation proteins (TETs) in hypoxia induced active demethylation. Overall, for the first time we correlate the dynamic process of DNA demethylation with the biophysical properties of the corresponding DNA binding proteins in live single cells by single molecule spectroscopy.

Folate and fetal programming: a play in epigenomics?

Folate plays a key role in the interactions between nutrition, fetal programming, and epigenomics. Maternal folate status influences DNA methylation, inheritance of the agouti phenotype, expression of imprinting genes, and the effects of mycotoxin FB1 on heterochromatin assembly in rodent offspring. Deficiency in folate and other methyl donors increases birth defects and produces visceral manifestations of fetal programming, including liver and heart steatosis, through imbalanced methylation and acetylation of PGC1-α and decreased SIRT1 expression, and produces persistent cognitive and learning disabilities through impaired plasticity and hippocampal atrophy. Maternal folate supplementation also produces long-term epigenomic effects in offspring, some beneficial and others negative. Deciphering these mechanisms will help understanding the discordances between experimental models and population studies of folate deficiency and supplementation.

Decitabine, a DNA methyltransferases inhibitor, induces cell cycle arrest at G2/M phase through p53-independent pathway in human cancer cells

Decitabine (5-aza-2'-deoxycytidine), an inhibitor of DNA methyltransferases, has a wide range of anti-metabolic and anti-cancer activities. Decitabine also induces cell cycle arrest at G2/M phase and apoptosis in human cancer cells. However, the cellular and molecular mechanisms of this cell cycle arrest are poorly understood. In the present study, we investigated the roles of the tumor suppressor p53 and the cyclin-dependent kinase (Cdk) inhibitor p21 following decitabine-induced G2/M arrest in human cancer cells. DNA flow cytometric analyses indicated that decitabine induced a G2/M arrest in AGS gastric and A549 lung carcinoma cell lines, which have wild type p53. Western blot analyses using whole cell lysates from AGS cells demonstrated that decitabine treatment did not change the steady-state level of Cdks and Cdk inhibitor p27, but it partially inhibited expression of cyclin A, cyclin B1, and Cdc25C proteins. However, similar results were found using the A549 cell line, where decitabine induced a dramatic up-regulation of both p53 and p21 expression, and the increased levels of p21 were associated with increased binding of p21 with Cdks, cyclin A, and cyclin B1. Knockdown of p53 by small interfering RNA (siRNA) markedly abolished p53 induction by decitabine in AGS cells, yet p53 siRNA had no attenuating effect on p21 induction. In addition, depletion of p21 expression with siRNA, but not p53, significantly attenuated decitabine-induced G2/M arrest. We also observed that decitabine strongly induced G2/M arrest associated with p21 induction in both p53 allele-null (-/-) HCT116 and wild type p53 (+/+) HCT116 cell lines. Therefore, our data indicated that p21 plays a crucial role in decitabine-induced G2/M arrest and operates in a p53-independent manner.

Diet and endometriosis risk: a literature review

A connection between dietary factors and endometriosis onset has become a topic of interest mostly due to the observation that physiological and pathological processes of the disease can be influenced by diet. This paper systematically reviews prior publications dealing with this aspect in order to identify potentially modifiable risk factors. Comprehensive searches in the electronic databases MEDLINE, EMBASE and Science Citation Index Expanded were conducted to identify published studies evaluating the association between food intake (nutrients and food groups) and endometriosis. Eleven studies were identified: 10 case-control and one cohort study. Information on diet was collected using food frequency questionnaires in seven studies, while in one study the questionnaire focused on caffeine and alcohol intake. Women with endometriosis seem to consume fewer vegetables and omega-3 polyunsaturated fatty acids and more red meat, coffee and trans fats but these findings could not be consistently replicated. Most data have also been discussed herein in light of the available experimental and animal model results. At present, evidence supporting a significant association between diet and endometriosis is equivocal. Further studies are needed to clarify the role of diet on endometriosis risk and progression.

The multi-functional roles of GNMT in toxicology and cancer

Although glycine N-methyltransferase (GNMT) has been discovered for five decades, its function was not elucidated until recently. In this review, we discuss the multiple roles of GNMT in toxicology and cancer. Besides catalyzing the production of methylglycine (sarcosine) in one carbon metabolism pathway, GNMT was found to be able to bind a number of polycyclic aromatic hydrocarbons and inhibit DNA adducts formation. Moreover, GNMT exerts protective effects against the cytotoxicity and carcinogenicity of benzo(a)pyrene and aflatoxin B(1) in vitro and in vivo. Occupational study showed that workers who had genotypes with higher GNMT promoter activity may have lower content of oxidative damaged DNA products in their urine. In terms of cancer, recent studies using GNMT knockout mouse models demonstrated that GNMT deficiency has high penetrance in inducing the development of steatohepatitis and hepatocellular carcinoma. In terms of the mechanism, besides dysregulation of epigenetic modification, insights have been provided by recent identification of two novel proteins interacting with GNMT-DEPTOR and NPC2. These studies suggest that GNMT not only is involved in mTOR signaling pathway, but also plays an important role in the intracellular trafficking of cholesterol. The implication of these findings to the preventive medicine and translational research will be discussed.

Alcohol-associated folate disturbances result in altered methylation of folate-regulating genes

Folate plays a critical role in maintaining normal metabolic, energy, differentiation and growth status of all mammalian cells. The steady-state accumulation of folate seems to depend on the activity of two enzymes: folylpolyglutamate synthetase (FPGS), which adds glutamate residues, and gamma-glutamyl hydrolase (GGH), which removes them, enabling it to be transported across the biological membranes. Overexpression of GGH and downregulation of FPGS would be expected to decrease intracellular folate in its polyglutamylated form, thereby increasing efflux of folate and its related molecules, which might lead to resistance to drugs or folate deficiency. The study was sought to delineate the activity of GGH and expression FPGS in tissues involved in folate homeostasis during alcoholism and the epigenetic regulation of these enzymes and transporters regulating intracellular folate levels. We determined the activity of GGH and expression of FPGS in tissues after 3 months of ethanol feeding to rats at 1 g/kg body weight/day. The results showed that there was not any significant change in the activity of folate hydrolyzing enzyme GGH in ethanol-fed rats while there was significant down regulation in the expression of FPGS. Ethanol feeding decreased the total as well as polyglutamated folate levels. There was tissue-specific hyper/hypo methylation of folate transporter genes viz. PCFT and RFC by chronic ethanol feeding. Moreover, hypermethylation of FPGS gene was observed in intestine and kidney without any change in methylation levels of GGH in the ethanol-fed rats. In conclusion, the initial deconjugation of polyglutamylated folate by GGH was not impaired in ethanol-fed rats while the conversion of monoglutamylated folate to polyglutamylated form might be impaired. There was tissue-specific altered methylation of folate transporter genes by chronic ethanol feeding.

Biochemical and molecular mechanisms of folate transport in rat pancreas; interference with ethanol ingestion

Folic acid is an essential nutrient that is required for one-carbon biosynthetic processes and for methylation of biomolecules. Deficiency of this micronutrient leads to disturbances in normal physiology of cell. Chronic alcoholism is well known to be associated with folate deficiency which is due, in part to folate malabsorption. The present study deals with the mechanistic insights of reduced folate absorption in pancreas during chronic alcoholism. Male Wistar rats were fed 1 g/kg body weight/day ethanol (20% solution) orally for 3 months and the mechanisms of alcohol associated reduced folate uptake was studied in pancreas. The folate transport system in the pancreatic plasma membrane (PPM) was found to be acidic pH dependent one. The transporters proton coupled folate transporter (PCFT) and reduced folate carrier (RFC) are involved in folate uptake across PPM. The folate transporters were found to be associated with lipid raft microdomain of the PPM. Ethanol ingestion decreased the folate transport by reducing the levels of folate transporter molecules in lipid rafts at the PPM. The decreased transport efficiency of the PPM was reflected as reduced folate levels in pancreas. The chronic ethanol ingestion led to decreased pancreatic folate uptake. The decreased levels of PCFT and RFC expression in rat PPM were due to decreased association of these proteins with lipid rafts (LR) at the PPM.

Effects of altered maternal folic acid, vitamin B12 and docosahexaenoic acid on placental global DNA methylation patterns in Wistar rats

Potential adverse effects of excess maternal folic acid supplementation on a vegetarian population deficient in vitamin B(12) are poorly understood. We have previously shown in a rat model that maternal folic acid supplementation at marginal protein levels reduces brain omega-3 fatty acid levels in the adult offspring. We have also reported that reduced docosahexaenoic acid (DHA) levels may result in diversion of methyl groups towards DNA in the one carbon metabolic pathway ultimately resulting in DNA methylation. This study was designed to examine the effect of normal and excess folic acid in the absence and presence of vitamin B(12) deficiency on global methylation patterns in the placenta. Further, the effect of maternal omega 3 fatty acid supplementation on the above vitamin B(12) deficient diets was also examined. Our results suggest maternal folic acid supplementation in the absence of vitamin B(12) lowers plasma and placental DHA levels (p<0.05) and reduces global DNA methylation levels (p<0.05). When this group was supplemented with omega 3 fatty acids there was an increase in placental DHA levels and subsequently DNA methylation levels revert back to the levels of the control group. Our results suggest for the first time that DHA plays an important role in one carbon metabolism thereby influencing global DNA methylation in the placenta.

An emerging role for epigenetic dysregulation in arsenic toxicity and carcinogenesis

BACKGROUND

Exposure to arsenic, an established human carcinogen, through consumption of highly contaminated drinking water is a worldwide public health concern. Several mechanisms by which arsenical compounds induce tumorigenesis have been proposed, including oxidative stress, genotoxic damage, and chromosomal abnormalities. Recent studies have suggested that epigenetic mechanisms may also mediate toxicity and carcinogenicity resulting from arsenic exposure.

OBJECTIVE

We examined the evidence supporting the roles of the three major epigenetic mechanisms-DNA methylation, histone modification, and microRNA (miRNA) expression-in arsenic toxicity and, in particular, carcinogenicity. We also investigated future research directions necessary to clarify epigenetic and other mechanisms in humans.

DATA SOURCES AND SYNTHESIS

We conducted a PubMed search of arsenic exposure and epigenetic modification through April 2010 and summarized the in vitro and in vivo research findings, from both our group and others, on arsenic-associated epigenetic alteration and its potential role in toxicity and carcinogenicity.

CONCLUSIONS

Arsenic exposure has been shown to alter methylation levels of both global DNA and gene promoters; histone acetylation, methylation, and phosphorylation; and miRNA expression, in studies analyzing mainly a limited number of epigenetic end points. Systematic epigenomic studies in human populations exposed to arsenic or in patients with arsenic-associated cancer have not yet been performed. Such studies would help to elucidate the relationship between arsenic exposure, epigenetic dysregulation, and carcinogenesis and are becoming feasible because of recent technological advancements.

Pre- and postnatal health: evidence of increased choline needs

Choline, a micronutrient found in food, serves as the starting material for several important metabolites that play key roles in fetal development, particularly the brain. Although human beings' requirement for choline is unknown, an Adequate Intake level of 425 mg/day was established for women with upward adjustments to 450 and 550 mg/day during pregnancy and lactation, respectively. The importance of choline in human development is supported by observations that a human fetus receives a large supply of choline during gestation; pregnancy causes depletion of hepatic choline pools in rats consuming a normal diet; human neonates are born with blood levels that are three times higher than maternal blood concentrations; and large amounts of choline are present in human milk. The development of the central nervous system is particularly sensitive to choline availability with evidence of effects on neural tube closure and cognition. Existing data show that the majority of pregnant (and presumably lactating) women are not achieving the target intake levels and that certain common genetic variants may increase requirements for choline beyond current recommendations. Because choline is not found in most varieties of prenatal vitamins (or regular multivitamins), increased consumption of choline-rich foods may be needed to meet the high pre- and postnatal demands for choline.

Choline intake exceeding current dietary recommendations preserves markers of cellular methylation in a genetic subgroup of folate-compromised men

Severe choline deficiency adversely affects cellular methylation and DNA integrity, with potentially serious implications for disease risk. As part of a 12-wk controlled choline intervention study conducted in folate-compromised Mexican-American men (n = 60; 18-55 y) differing in the methylenetetrahydrofolate reductase (MTHFR) C677T genotype (21 677CC, 29 677TT), this study evaluated the effects of varied choline intakes (300, 550, 1100, and 2200 mg/d) on the change (i.e. wk 12-0) in markers of cellular methylation and DNA integrity. Choline intake affected the change in plasma S-adenosylmethionine (P = 0.044), with decreases tending to be greater (P < or = 0.08) in the 300 and 550 mg/d groups than in the 2200 mg/d group. Choline intake also interacted with the MTHFR C677T genotype to affect the change in genomic DNA methylation and DNA damage. In men with the MTHFR 677CC genotype, choline intake affected (P = 0.007) the change in DNA methylation, with a greater decrease (P < 0.02) in the 300 mg/d group than in the 1100 and 2200 mg/d groups. In men with the MTHFR 677CC genotype, choline intake also affected (P = 0.047) the change in DNA damage, with the increase tending to be greater (P = 0.07) in the 550 mg/d group than in the 2200 mg/d group. Choline intake did not affect these variables in men with the MTHFR 677TT genotype. Overall, these data suggest that choline intake exceeding current dietary recommendations preserves markers of cellular methylation and attenuates DNA damage in a genetic subgroup of folate-compromised men.

Folate bioavailability: implications for establishing dietary recommendations and optimizing status

The addition of folic acid to the US food supply, along with the critical role of folate in certain health outcomes, has intensified worldwide interest in the bioavailability of folate. Bioavailability is a function of absorptive and postabsorptive processes, which in turn are influenced by diet, individuality, and complex diet-host interactions. As such, it is unlikely that a single bioavailability figure will accurately reflect food folate bioavailability from every diet for every person. Although there is broad agreement that naturally occurring food folate is not as bioavailable as folic acid, questions remain as to the extent of these differences, particularly within the context of a whole diet. This article 1) summarizes and integrates bioavailability estimates derived from studies that use whole-diet approaches; 2) highlights the influences of genetics, ethnicity-race, and sex as postabsorptive bioavailability modifiers; and 3) discusses the adequacy of the US folate Recommended Dietary Allowance in achieving folate sufficiency in select subpopulations.

Cellular mechanisms of tumour suppression by the retinoblastoma gene

The retinoblastoma (RB) tumour suppressor gene is functionally inactivated in a broad range of paediatric and adult cancers, and a plethora of cellular functions and partners have been identified for the RB protein. Data from human tumours and studies from mouse models indicate that loss of RB function contributes to both cancer initiation and progression. However, we still do not know the identity of the cell types in which RB normally prevents cancer initiation in vivo, and the specific functions of RB that suppress distinct aspects of the tumorigenic process are poorly understood.

Expression of methylation-related genes is associated with overall survival in patients with non-small cell lung cancer

The abnormality of DNA methylation is involved in tumour progression, and thus has a modulating effect on clinical outcome of cancer patients. In this study, we measured the mRNA expression levels of three methylation-regulating genes (DNMT1, DNMT3b, and MBD2) in 148 tumour samples from patients with non-small cell lung cancer (NSCLC) using quantitative real-time polymerase chain reaction and then determined their prognostic values. Our data showed that the high level of DNMT1 expression was significantly associated with an increased risk of death in all NSCLC patients (hazard ratio (HR), 1.74; 95% confidence interval (95% CI), 1.04-2.90). However, the high level of DNMT3b expression was significantly associated with poor prognosis only in young patients (<65 years). The high level of MBD2 expression had a significantly reduced risk for death only in male patients and in squamous cell lung carcinoma (SQLC) patients. All three combination groups with DNMT1 and DNMT3b, DNMT1 and MBD2 or DNMT3b and MBD2 revealed significant combined effects in male patients and SQLC patients. Our results suggest that DNMT1, DNMT3b, and MBD2 may play important roles in modulating NSCLC patient survival and thus be useful for identifying NSCLC patients who would benefit most from aggressive therapy.

Is folic acid good for everyone?

Fortification of food with folic acid to reduce the number of neural tube defects was introduced 10 y ago in North America. Many countries are considering whether to adopt this policy. When fortification is introduced, several hundred thousand people are exposed to an increased intake of folic acid for each neural tube defect pregnancy that is prevented. Are the benefits to the few outweighed by possible harm to some of the many exposed? In animals, a folic acid-rich diet can influence DNA and histone methylation, which leads to phenotypic changes in subsequent generations. In humans, increased folic acid intake leads to elevated blood concentrations of naturally occurring folates and of unmetabolized folic acid. High blood concentrations of folic acid may be related to decreased natural killer cell cytotoxicity, and high folate status may reduce the response to antifolate drugs used against malaria, rheumatoid arthritis, psoriasis, and cancer. In the elderly, a combination of high folate levels and low vitamin B-12 status may be associated with an increased risk of cognitive impairment and anemia and, in pregnant women, with an increased risk of insulin resistance and obesity in their children. Folate has a dual effect on cancer, protecting against cancer initiation but facilitating progression and growth of preneoplastic cells and subclinical cancers, which are common in the population. Thus, a high folic acid intake may be harmful for some people. Nations considering fortification should be cautious and stimulate further research to identify the effects, good and bad, caused by a high intake of folic acid from fortified food or dietary supplements. Only then can authorities develop the right strategies for the population as a whole.

Genomic methylation of leukocyte DNA in relation to colorectal adenoma among asymptomatic women

BACKGROUND & AIMS

Systemic inhibition of DNA methylation causes cancers in animals, in part by inducing genetic instability. Epidemiologic evidence linking low genomic methylation in systemic blood DNA to carcinogenesis is limited, however, specifically to the colorectum, in which genetic instability is a primary etiologic factor. We examined genomic methylation of leukocyte DNA in relation to colorectal adenoma (CRA) among asymptomatic women (40-79 years of age) participating in a multicenter colonoscopy screening study (CONCeRN Study, 2000-2002).

METHODS

Of all participants who completed self-administered risk factor and food frequency questionnaires, peripheral blood donation, and colonoscopy, 115 pairs of CRA cases and controls with matching age and month of blood draw were studied. Genomic methylation of leukocyte DNA was determined by liquid chromatography mass spectrometry. Conditional logistic regression was used to estimate odds ratios (OR) and 95% confidence intervals (CI).

RESULTS

Compared with women in the lowest tertile of genomic methylation, women in the second (OR, 0.72; 95% CI: 0.34-1.52) and third tertiles (OR, 0.17; 95% CI: 0.06-0.49) had lower risk of CRA (P trend = .002). The inverse relationship was stronger for nonadvanced than for advanced adenoma and, less notably, for proximal than for distal adenoma. The association was also moderately more protective with low rather than high total folate intake but did not differ by other nutrients involved in 1-carbon metabolism or colorectal cancer risk factors.

CONCLUSIONS

Our findings regarding asymptomatic CRA implicate systemic genomic methylation as a potential etiologic factor for an early stage of CRA.

Cobalamin potentiates vinblastine cytotoxicity through downregulation of mdr-1 gene expression in HepG2 cells

BACKGROUND

P-glycoprotein (Pgp), produced by multidrug resistance-1 gene (mdr-1), is a main mechanism developed by cancer cells to guard against anti-cancer drugs. Alterations of DNA methylation of the mdr-1 gene promoter are known to be linked to mdr-1 gene expression and are probably related to intracellular S-adenosyl-methionine. We here used HepG2 cells to determine the role of the methionine cycle (through the use of the Methionine-Synthase (MS) cofactor, cobalamin) on mdr-1 gene expression.

METHODS

Semiquantitative RT-PCR of mdr-1 gene, cellular retention of rhodamine-123, and vinblastine cytotoxicity were carried out on cells cultivated with and without cobalamin. Methylation status of the mdr-1 gene promoter was determined by methylation-specific PCR.

RESULTS

Addition of cobalamin to the cells led to an increase in MS activity, to a significant decrease in mdr-1 gene expression which is correlated to an increase in retention of the Pgp substrate Rhodamine 123. Furthermore, cobalamin potentiated cell sensitivity to vinblastine to the same range as that of the Pgp blocker verapamil and prevented methotrexate-induced up-regulation of mdr-1 gene expression. However, no modification in methylation of the mdr-1 gene promoter was observed.

CONCLUSION

Cobalamin downregulates mdr-1 gene expression, as well as Pgp expression and function, and significantly increases cytotoxicity of vinblastine. The identification of this novel way of diminishing cellular resistance to the chemotherapeutic agent vinblastine holds promises of leading to better treatments for cancer patients.

Region-specific DNA methylation in the preimplantation embryo as a target for genomic plasticity

It has been long known that the unique genetic sequence each embryo inherits is not the sole determinant of phenotype. However, only recently have epigenetic modifications to DNA been implicated in providing potential developmental plasticity to the embryonic and fetal genome, with environmental influences directly altering the epigenetic modifications that contribute to tissue-specific gene regulation. Most is known about the potential environmental regulation of DNA methylation, epigenetic addition of methyl groups to cytosine residues in DNA that acts in the long-term silencing of affected sequences. While most attention has been paid to the methylation of imprinted gene sequences, in terms of developmental plasticity there are many more parts of the genome that are methylated and that could be affected. This review explores the distribution of cytosine methylation in the genome and discusses the potential effects of regional plasticity on subsequent development. Widening our consideration of potentially plastic regions is likely to greatly enhance our understanding of how individuals are shaped not only by DNA sequence, but by the environment in which pluripotent embryonic cells are transformed into the many cell types of the body.

The MTHFR 677TT genotype and folate intake interact to lower global leukocyte DNA methylation in young Mexican American women

DNA methylation is an epigenetic feature that is associated with X chromosome inactivation, genomic imprinting, transcriptional silencing of genes and genomic stability. Folate provides a labile source of methyl groups which may be used for cellular methylation reactions including DNA methylation. The methylenetetrahydrofolate reductase (MTHFR) 677C-->T variant is an important determinant of folate nutriture and may influence DNA methylation. This study sought to assess the influence of the MTHFR C677T genotype on global leukocyte DNA methylation in young (18-45y) Mexican American women (n=43; 14 CC, 12 CT and 17 TT). Subjects consumed a folate restricted diet (135 mug DFE/d) for 7 wk followed by folate treatment with 400 or 800 mug DFE/d for 7 wk. Global leukocyte DNA methylation was assessed via the cytosine extension assay at week 0, week 7 (after folate restriction) and week 14 (after folate treatment). No main effects of MTHFR C677T genotype or folate intake were detected at any time point during the study. However, at the end of folate treatment (wk 14), DNA methylation was lower (P<0.05) in women with the MTHFR 677TT genotype relative to the CT or CC genotype. Because it is unlikely that folate treatment would result in methyl group loss, we suggest that there was a delay in DNA methylation response to folate intake. Overall, these data suggest that the MTHFR 677TT genotype and folate interact to lower global leukocyte DNA methylation patterns in young Mexican American women.

S-Adenosylmethionine: jack of all trades and master of everything?

SAM (S-adenosylmethionine, also known as AdoMet) is well known as the methyl donor for the majority of methyltransferases that modify DNA, RNA, histones and other proteins, dictating replicational, transcriptional and translational fidelity, mismatch repair, chromatin modelling, epigenetic modifications and imprinting, which are all topics of great interest and importance in cancer research and aging. In total, 15 superfamilies of SAM-binding proteins have been identified, with many additional functions varying from methylation of phospholipids and small molecules such as arsenic to synthesis of polyamines or radical formation. SAM is regenerated from demethylated SAM via the methionine cycle, which involves folate. Imbalance of this cycle in humans, e.g. through folate shortage via dietary insufficiency, alcohol abuse, arsenic poisoning or hereditary factors, leads to depletion of SAM and human disease. In addition to its role as a methyl donor to modification enzymes that protect bacterial DNA against cognate restriction, SAM also serves as a co-factor for nucleases such as the type I restriction enzyme EcoKI, which is unable to restrict DNA in the absence of SAM. Finally, on a completely different tack, SAM can bind to certain RNA structures called riboswitches that control transcription or translation. In this way, expression of multiple genes can be regulated in a SAM-dependent manner, an unexpected finding that opens up new avenues into gene control. This minireview discusses some of these diverse and amazing roles of this small metabolite.

The LTR promoter of the rat oncomodulin gene is regulated by cell-line specific accessibility in the LTR U3 region

By germline insertion, a long terminal repeat (LTR) of an intracisternal A-particle type IAP retrovirus has overtaken the transcriptional control of the rat oncomodulin (OM) gene, which codes for a high affinity Ca2+-binding protein with modulatory capacity. In order to get insights into regulatory mechanisms of LTR directed OM gene expression we tested promoter activity of this LTR by transient transfection of transformed rat fibroblasts with this sequence placed 5' of the human growth hormone hGH reporter gene. The OM LTR is a strong promoter but does not follow an expression pattern similar to the one of the OM gene. Genomic sequencing showed a good correlation between CpG hypomethylation in the OM LTR and OM transcription among various cell lines and tissues. DNase I mapping of a 18 kb fragment containing the OM gene and 5' flanking sequences revealed cell-line specific hypersensitivity sites located within the U3 region of the LTR element. Several cis-elements in the OM LTR promoter exhibiting cell-line specific occupancy were identified by in vivo DMS-footprinting. Detailed analysis of protein interactions with two such sequence elements in vitro revealed binding of ubiquitously expressed nuclear factors within an AP-1 (activator protein 1) and a intracisternal A-particle upstream enhancer recognition sequence. Protein occupancy to the latter sequence is significantly reduced by CpG methylation. These results indicate that cell-line specificity of OM expression is dictated by factor accessibility to the LTR promoter.

The glycine N-methyltransferase (GNMT) 1289 C->T variant influences plasma total homocysteine concentrations in young women after restricting folate intake

Glycine N-methyltransferase (GNMT) is a key regulatory protein in folate metabolism, methionine availability, and transmethylation reactions. Perturbations in GNMT may lead to aberrations in homocysteine metabolism, a marker of numerous pathologies. The primary objective of this study was to examine the influence of the GNMT 1289 C-->T alone, and in combination with the methylenetetrahydrofolate reductase (MTHFR) 677 C-->T variant, on plasma total homocysteine concentrations in healthy young women (n = 114). Plasma total homocysteine was measured at baseline (wk 0) and after 2 wk of controlled folate restriction (135 microg/d as dietary folate equivalents). Plasma homocysteine concentrations did not differ among the GNMT C1289T genotypes at baseline. However, after folate restriction, women with the GNMT 1289 TT genotype (n = 16) had higher (P = 0.019) homocysteine concentrations than women with the CT (n = 51) or CC (n = 47) genotype. The influence of the GNMT 1289 C-->T variant on homocysteine was dependent on the MTHFR C677T genotype. In subjects with the MTHFR 677 CC genotype, homocysteine was greater (P < or = 0.05) for GNMT 1289 TT subjects relative to 1289 CT or CC subjects. However, in subjects with the MTHFR 677 TT genotype, plasma homocysteine concentrations did not differ among the GNMT C1289T genotypes. Overall, these data suggest that the GNMT 1289 C-->T polymorphism influences plasma homocysteine and is responsive to folate intake.

A long-term controlled folate feeding study in young women supports the validity of the 1.7 multiplier in the dietary folate equivalency equation

The presence of folic acid in enriched cereal grain products and the higher bioavailability of folic acid than food folate led to the expression of the 1998 folate RDA, 400 microg/d, as dietary folate equivalents (DFE). DFE are defined as: mug natural food folate + 1.7 x microg synthetic folic acid. The 1.7 multiplier was based on assumptions that added folic acid was 85% available and food folate was 50% available. The 85/50 ratio also inferred that the bioavailability of food folate was approximately 60% relative to added folic acid. The objective of this long-term controlled feeding study was to assess the dietary folate equivalency of folic acid. After a 2-wk period of folate restriction, women (n = 42, 18-45 y old) consumed either 400 or 800 microg DFE/d derived from various combinations of food folate and folic acid for 12 wk. Folic acid was converted to DFE using the 1.7 multiplier from the DFE calculation and was consumed with a meal throughout the treatment period. Folate status response to the various treatments was assessed during wk 12-14. Serum folate, RBC folate, and plasma total homocysteine did not differ among the 400 microg DFE/d groups or among the 800 microg DFE/d groups. In contrast, consumption of 800 microg DFE/d led to higher (P </= 0.05) serum and RBC folate than consumption of 400 microg DFE/d. These data support the validity of the 1.7 multiplier in the DFE equation and suggest that food folate bioavailability is approximately 60% that of added folic acid when consumed as part of a mixed diet.