DNA Methylation Processes Research Articles

Omega-3 Polyunsaturated Fatty Acids Inhibited Tumor Growth via Preventing the Decrease of Genomic DNA Methylation in Colorectal Cancer Rats

ABSTRACTOmge-3 polyunsaturated fatty acids (PUFAs) exhibited significant effect in inhibiting various tumors. However, the mechanisms of its anticancer role have not been fully demonstrated. The declination of 5-methylcytosine (5 mC) was closely associated with poor prognosis of tumors. To explore whether omega-3 PUFAs influences on DNA methylation level in tumors, colorectal cancer (CRC) rat model were constructed using N-methyl phosphite nitrourea and omega-3 PUFAs were fed to part of the rats during tumor induction. The PUFAs contents in the rats of 3 experimental groups were measured using gas chromatography and 5 mC level were detected by liquid chromatography tandem mass spectrometry. The results showed that tumor incidence in omega-3 treated rats was much lower than in CRC model rats, which confirmed significant antitumor role of omega-3 PUFAs. Six PUFA members categorized to omega-3 and omega-6 families were quantified and the ratio of omega-6/omega-3 PUFAs was remarkably lower in omega-3 PUFAs treatment group than in CRC model group. 5 mC content in omega-3 PUFAs treated rats was higher than in CRC model rats, suggesting omega-3 PUFAs promoted 5 mC synthesis. Therefore, omega-3 PUFAs probably inhibited tumor growth via regulating DNA methylation process, which provided a novel anticancer mechanism of omega-3 PUFAs from epigenetic view.

Genetics of Schizophrenia: Historical Insights and Prevailing Evidence.

Schizophrenia's (SZ's) heritability and familial transmission have been known for several decades; however, despite the clear evidence for a genetic component, it has been very difficult to pinpoint specific causative genes. Even so genetic studies have taught us a lot, even in the pregenomic era, about the molecular underpinnings and disease-relevant pathways. Recurring themes emerged revealing the involvement of neurodevelopmental processes, glutamate regulation, and immune system differential activation in SZ etiology. The recent emergence of epigeneticstudies aimed at shedding light on the biological mechanisms underlying SZ has provided another layer of information in the investigation of gene and environment interactions. However, this epigenetic insight also brings forth another layer of complexity to the (epi)genomic landscape such as interactions between genetic variants, epigenetic marks-including cross-talk between DNA methylation and histone modification processes-, gene expression regulation, and environmental influences. In this review, we seek to synthesize perspectives, including limitations and obstacles yet to overcome, from genetic and epigenetic literature on SZ through a qualitative review of risk factors and prevailing hypotheses. Encouraged by the findings of both genetic and epigenetic studies to date, as well as the continued development of new technologies to collect and interpret large-scale studies, we are left with a positive outlook for the future of elucidating the molecular genetic mechanisms underlying SZ and other complex neuropsychiatric disorders.

Global DNA methylation and related mRNA profiles in sheep oocytes and early embryos derived from pre-pubertal and adult donors

The developmental capacity of in vitro-matured oocytes and in vitro-fertilized embryos from pre-pubertal sheep is less than that of adult counterparts, and epigenetic mechanisms are thought to be involved. In the present study, germinal vesicle stage oocytes were collected by follicular aspiration from superovulated 4-week-old lambs and 2.5-year-old ewes. There were evaluations of the developmental potential of oocytes and embryos by in vitro culture and fertilization, global DNA methylation and hydroxymethylation patterns by immunofluorescence staining, and relative abundance of enzyme mRNA by quantitative real-time polymerase chain reaction analysis in pre-pubertal and adult sheep donors. The results showed that the rates of maturation and cleavage of oocytes as well as pregnancy and lambing rates from the transfer of 2-cell embryos collected from lambs were less than those from adults (P<0.05). The global DNA methylation and hydroxymethylation and relative abundance of Dnmt1, Dnmt3a, and Tet3 mRNA were less at all stages of oocytes, zygotes, and two-cell embryos from lambs compared with those from adults (P<0.05) with no difference in relative abundance of Dnmt3b mRNA. Thus, younger donor age was associated with disturbed DNA methylation processes due to insufficient methyltransferases during gametogenesis and early embryonic development, and this may be responsible for the lesser developmental potential of oocytes and early developing embryos when oocytes are collected from lambs.

Epigenetic alterations in patients with type 2 diabetes mellitus.

Epigenetic changes, in particular DNA methylation processes, play a role in the pathogenesis and progression of type 2 diabetes mellitus (T2DM) linking genetic and environmental factors. To clarify this role, we have analyzed in patients with different duration of T2DM: (i) expression levels of methyl-CpG-binding domain protein 2 (MBD2) as marker of DNA methylation, and ii) methylation changes in 22 genes connected to cellular stress and toxicity. We have analyzed MBD2 mRNA expression levels in16 patients and 12 controls and the methylation status of stress and toxicity genes in four DNA pools: (i) controls; (ii) newly-diagnosed T2DM patients; (iii) patients with T2DM duration of <5 years and (iv) of >5 years. The MBD2 expression levels were 10.4-times increased on average in T2DM patients compared to controls. Consistent increase in DNA methylation fraction with the increase in T2DM duration was observed in Prdx2 and SCARA3 genes, connected to oxidative stress protection and in BRCA1 and Tp53 tumor-suppressor genes. In conclusion, increased MBD2 expression in patients indicated general dysregulation of DNA methylation in T2DM. The elevated methylation of Prdx2 and SCARA3 genes suggests disturbance in oxidative stress protection in T2DM. The increased methylation of BRCA1 and Tp53 genes unraveled an epigenetic cause for T2DM related increase in cancer risk.

DNA Methylation Dynamics During Differentiation, Proliferation, and Tumorigenesis in the Intestinal Tract

DNA methylation, an epigenetic control mechanism in mammals, is widely present in the intestinal tract during the differentiation and proliferation of epithelial cells. Cells in stem cell pools or villi have different patterns of DNA methylation. The process of DNA methylation is dynamic and occurs at many relevant regulatory elements during the rapid transition of stem cells into fully mature, differentiated epithelial cells. Changes in DNA methylation patterns most often take place in enhancer and promoter regions and are associated with transcription factor binding. During differentiation, enhancer regions associated with genes important to enterocyte differentiation are demethylated, activating gene expression. Abnormal patterns of DNA methylation during differentiation and proliferation in the intestinal tract can lead to the formation of aberrant crypt foci and destroy the barrier and absorptive functions of the intestinal epithelium. Accumulation of these epigenetic changes may even result in tumorigenesis. In the current review, we discuss recent findings on the association between DNA methylation and cell differentiation and proliferation in the small intestine and highlight the possible links between dysregulation of this process and tumorigenesis.

Differential expression of seven conserved microRNAs in response to abiotic stress and their regulatory network in Helianthus annuus.

Biotic and abiotic stresses affect plant development and production through alternation of the gene expression pattern. Gene expression itself is under the control of different regulators such as miRNAs and transcription factors (TFs). MiRNAs are known to play important roles in regulation of stress responses via interacting with their target mRNAs. Here, for the first time, seven conserved miRNAs, associated with drought, heat, salt and cadmium stresses were characterized in sunflower. The expression profiles of miRNAs and their targets were comparatively analyzed between leaves and roots of plants grown under the mentioned stress conditions. Gene ontology analysis of target genes revealed that they are involved in several important pathways such as auxin and ethylene signaling, RNA mediated silencing and DNA methylation processes. Gene regulatory network highlighted the existence of cross-talks between these stress-responsive miRNAs and the other stress responsive genes in sunflower. Based on network analysis, we suggest that some of these miRNAs in sunflower such as miR172 and miR403 may play critical roles in epigenetic responses to stress. It seems that depending on the stress type, theses miRNAs target several pathways and cellular processes to help sunflower to cope with drought, heat, salt and cadmium stress conditions in a tissue-associated manner.

Epigenetic modulation of DNA methylation by nutrition and its mechanisms in animals.

It is well known that phenotype of animals may be modified by the nutritional modulations through epigenetic mechanisms. As a key and central component of epigenetic network, DNA methylation is labile in response to nutritional influences. Alterations in DNA methylation profiles can lead to changes in gene expression, resulting in diverse phenotypes with the potential for decreased growth and health. Here, I reviewed the biological process of DNA methylation that results in the addition of methyl groups to DNA; the possible ways including methyl donors, DNA methyltransferase (DNMT) activity and other cofactors, the critical periods including prenatal, postnatal and dietary transition periods, and tissue specific of epigenetic modulation of DNA methylation by nutrition and its mechanisms in animals.

Effect of DNA Methylation in Various Diseases and the Probable Protective Role of Nutrition: A Mini-Review.

DNA methylation, a process of adding a methyl group to DNA done by a DNA methyltransferase is a heritable (epigenetic) alteration leading to cancer, atherosclerosis, nervous disorders (Imprinting disorders), and cardiovascular diseases. The role of nutrition in DNA methylation is revealed by identification of methyl variable positions (MVP) on DNA. These regions are more susceptible to DNA methylations. Nutritional supplementation of folic acid and methionine in utero and in adults decreased epigenetic modifications due to its role in DNA metabolism (one carbon metabolism). Thus, in utero and adult supplementation of folic acid and methionine may reduce DNA methylation. This review attempts to highlight the process of DNA methylation, its effect on various diseases, and the probable protective role of nutrition.

Abstract 4571: Chronic oxidative stress increases resistance in renal carcinoma cells to doxorubicin-induced cytotoxicity potentially through epigenetic mechanism

Abstract Human renal cell carcinoma (RCC) is the most common form of kidney cancer. Regardless of therapeutic advancement, patients with metastatic RCC are failed to clinical treatment due to rapidly developing resistance. Resistance to chemotherapy can be of innate or acquired overtime following exposure to drug and can arise through a number of different intrinsic and extrinsic factors and their interactions. While some reports suggest role of ROS in developing drug resistance, response of cancer cells with chronic exposure to oxidative stress to chemotherapeutic drugs is not known. Hence, the objective of this study was to evaluate the impact of chronic exposure to elevated levels of oxidative stress in human kidney cancer cells. Caki-1 human renal carcinoma cells were given chronic (6 months) exposure to direct ROS source hydrogen peroxide (25 μM and 200 μM). Using these cells the effect of oxidative stress on sensitivity to doxorubicin-induced cytotoxicity was measured by MTT assay. The result was further confirmed by anchorage independent growth on soft agar and cell cycle analysis using flow cytometer. To understand the molecular mechanism, the expression of genes involved in drug resistance, cell survival, and DNA repair dependent apoptosis were measured by qRT- PCR. Results of MTT, soft agar assay, and cell cycle analysis showed that doxorubicin-induced cytotoxicity was significantly less in Caki-1 cells chronically exposed to H2O2 when compare to H2O2 unexposed control cells. The alterations in the expression of genes involved in drug transport further confirmed the increased resistance to doxorubicin-induced cytotoxicity in cells exposed to oxidative stress. Decreased expression of MSH2 gene in cells exposed to H2O2-induced oxidative stress suggests that loss of DNA repair-dependent apoptosis could be a potential mechanism for increased resistance to doxorubicin-induced cytotoxicity. To further evaluate the role of epigenetic process of DNA methylation in oxidative stress-induced drug resistance, cells were pretreated with demethylating agent 5-aza-2′ deoxycytidine (5-aza 2dC), and then treated with doxorubicin. The pretreatment with 5-aza 2dC significantly resensitized the chronic ROS adapted Caki-1 cells to doxorubicin-induced cytotoxicity and restored the expression of MSH2 gene in these cells. This suggests that epigenetic silencing of MSH2 and therefore DNA repair-dependent apoptosis could be a potential mechanism for oxidative stress-induced resistance to chemotherapeutic drugs in renal cancer cells. In summary, this study for the first time provides direct evidence for the role of oxidative stress in chemoresistance in renal carcinoma cells. Additionally, the findings of this study also suggest that epigenetic therapy may be a useful strategy in re-sensitizing the chemotherapeutic resistant RCC cells. Citation Format: Logeswari Ponnusamy, PrathapKumar S. Mahalingaiah, Kamaleshwar P. Singh. Chronic oxidative stress increases resistance in renal carcinoma cells to doxorubicin-induced cytotoxicity potentially through epigenetic mechanism. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4571. doi:10.1158/1538-7445.AM2015-4571

Parallel action of AtDRB2 and RdDM in the control of transposable element expression

BackgroundIn plants and animals, a large number of double-stranded RNA binding proteins (DRBs) have been shown to act as non-catalytic cofactors of DICERs and to participate in the biogenesis of small RNAs involved in RNA silencing. We have previously shown that the loss of Arabidopsis thaliana’s DRB2 protein results in a significant increase in the population of RNA polymerase IV (p4) dependent siRNAs, which are involved in the RNA-directed DNA methylation (RdDM) process.ResultsSurprisingly, despite this observation, we show in this work that DRB2 is part of a high molecular weight complex that does not involve RdDM actors but several chromatin regulator proteins, such as MSI4, PRMT4B and HDA19. We show that DRB2 can bind transposable element (TE) transcripts in vivo but that drb2 mutants do not have a significant variation in TE DNA methylation.ConclusionWe propose that DRB2 is part of a repressive epigenetic regulator complex involved in a negative feedback loop, adjusting epigenetic state to transcription level at TE loci, in parallel of the RdDM pathway. Loss of DRB2 would mainly result in an increased production of TE transcripts, readily converted in p4-siRNAs by the RdDM machinery.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0455-z) contains supplementary material, which is available to authorized users.

Mechanisms and Αpplications of Ιnterleukins in Cancer Immunotherapy

Over the past years, advances in cancer immunotherapy have resulted in innovative and novel approaches in molecular cancer diagnostics and cancer therapeutic procedures. However, due to tumor heterogeneity and inter-tumoral discrepancy in tumor immunity, the clinical benefits are quite restricted. The goal of this review is to evaluate the major cytokines-interleukins involved in cancer immunotherapy and project their basic biochemical and clinical applications. Emphasis will be given to new cytokines in pre-clinical development, and potential directions for future investigation using cytokines. Furthermore, current interleukin-based approaches and clinical trial data from combination cancer immunotherapies will also be discussed. It appears that continuously increasing comprehension of cytokine-induced effects, cancer stemness, immunoediting, immune-surveillance as well as understanding of molecular interactions emerging in the tumor microenvironment and involving microRNAs, autophagy, epithelial-mesenchymal transition (EMT), inflammation, and DNA methylation processes may hold much promise in improving anti-tumor immunity. To this end, the emerging in-depth knowledge supports further studies on optimal synergistic combinations and additional adjuvant therapies to realize the full potential of cytokines as immunotherapeutic agents.

Sperm epigenetic profile and risk of cancer

Introduction and objective. The integrity, stability and composition of sperm chromatin are of great importance in the fertilizing potential of male gametes and their capacity to support normal embryonic development. In this study, the author presents the current state of knowledge about the sperm epigenetic profile and risk of cancer. Abbreviated description of the state of knowledge. The obtaining of pregnancy and the state of health of the baby depends on the quality of the genetic material of both the female and the male. Health behaviours and environmental factors directly affect the quality of sperm, as well as the human egg cell and, consequently, on the reproductive capabilities, the course of pregnancy and the state of the newborn. There exist two thoroughly investigated epigenetic modifications: DNA methylation and histone modifications. The process of DNA methylation can be also a fundamental factor contributing to the development of cancer, where epigenotype undergoes significant modifications. When considering numerous DNA aberrations in the male gamete, the most commonly encountered is DNA fragmentation, particularly in infertile subjects. Surprisingly, an intracytoplasmatic sperm injection study of mice oocytes, using spermatozoa with a high DNA Fragmentation Index (DFI), revealed that a considerable percentage of adults born as a result of this method, showed a significant increase in the incidence of abnormal behavioural tests, malformations, cancer and signs of premature aging. Summary. The issue of assisted procreation raises the need to look for an appropriate treatment for males with sperm chromatin abnormalities. As a result, the fight against smoking addiction becomes the obvious necessity. Moreover, the reasonable solution nowadays seems to be supplementation with micronutrients and folic acid. It has been proved that the process of DNA fragmentation is a phenomenon that intensifies over time. Therefore, there should be a pursuance for, as close as possible, to the moment of ejaculation, application of semen to reproductive techniques. Finally, epigenetic changes are suspected of being one of the factors responsible for the deterioration of male sperm parameters observed in recent decades.

High-temperature effect on genes engaged in DNA methylation and affected by DNA methylation in Arabidopsis

Along with its essential role in the maintenance of genome integrity, DNA methylation takes part in regulation of genes which are important for plant development and stress response. In plants, DNA methylation process can be directed by small RNAs in process known as RNA-directed DNA methylation (RdDM) involving two plant-specific RNA polymerases – PolIV and PolV. The aim of the present study was to investigate the effect of heat stress on the expression of genes encoding key players in DNA methylation – DNA methyltransferase (MET1, CMT3, and DRM2), the largest subunits of PoIIV and PolV (NRPD1 and NRPE1 respectively) and the DNA demethylase ROS1. We also examined the high-temperature effect on two protein-coding genes – At3g50770 and At5g43260 whose promoters contain transposon insertions and are affected by DNA-methylation, as well as on the AtSN1, a SINE-like retrotransposon. To assess the involvement of PolIV and PolV in heat stress response, the promoter methylation status and transcript levels of these genes were compared between wild type and double mutant lacking NRPD1 and NRPE1. The results demonstrate coordinated up-regulation of the DRM2, NRPD1 and NRPE1 in response to high temperature and suggest that PolIV and/or PolV might be required for the induction of DRM2 expression under heat stress. The ROS1 expression was confirmed to be suppressed in the mutant lacking active PolIV and PolV that might be a consequence of abolished DNA methylation. The increased expression of At3g50770 in response to elevated temperature correlated with reduced promoter DNA methylation, while the stress response of At5g43260 did not show inverse correlation between promoter methylation and gene expression. Our results also imply that PolIV and/or PolV could regulate gene expression under stress conditions not only through RdDM but also by acting in other regulatory processes.

Mechanisms of superoxide signaling in epigenetic processes: relation to aging and cancer.

Superoxide is a precursor of many free radicals and reactive oxygen species (ROS) in biological systems. It has been shown that superoxide regulates major epigenetic processes of DNA methylation, histone methylation, and histone acetylation. We suggested that superoxide, being a radical anion and a strong nucleophile, could participate in DNA methylation and histone methylation and acetylation through mechanism of nucleophilic substitution and free radical abstraction. In nucleophilic reactions superoxide is able to neutralize positive charges of methyl donors S-adenosyl-L-methionine (SAM) and acetyl-coenzyme A (AcCoA) enhancing their nucleophilic capacity or to deprotonate cytosine. In the reversed free radical reactions of demethylation and deacetylation superoxide is formed catalytically by the (Tet) family of dioxygenates and converted into the iron form of hydroxyl radical with subsequent oxidation and final eradication of methyl substituents. Double role of superoxide in these epigenetic processes might be of importance for understanding of ROS effects under physiological and pathological conditions including cancer and aging.

DNA Demethylation By Activation-Induced Cytidine Deaminase in B Cell Lymphoma

DNA methylation and demethylation at cytosine residues are epigenetic modifications that regulate gene expression associated with early cell development, somatic cell differentiation, cellular reprogramming and malignant transformation. While the process of DNA methylation and maintenance by DNA methyltransferases is well described, the nature of DNA demethylation remains poorly understood. The current model of DNA demethylation proposes modification of 5-methylcytosine followed by DNA repair-dependent cytosine substitution. Although there is debate on the extent of its involvement in DNA demethylation, activation-induced cytidine deaminase (AID) has recently emerged as an enzyme that is capable of deaminating 5-methylcytosine to thymine, creating a T:G mismatch which can be repaired back to cytosine through DNA repair pathways. AID is expressed at low levels in many tissue types but is most highly expressed in germinal center B cells where it deaminates cytidine to uracil during somatic hypermutation and class switch recombination of the immunoglobulin genes. In addition to this critical role in immune diversification, aberrant targeting of AID contributes to oncogenic point mutations and chromosome translocations associated with B cell malignancies. Thus, to explore a role for AID in DNA demethylation in B cell lymphoma, we performed genome-wide methylation profiling in BL2 and AID-deficient (AID-/-) BL2 cell lines (Burkitt lymphoma that can be induced to express high levels of AID). Using Illumina’s Infinium II DNA Methylation assay combined with the Infinium Human Methylation 450 Bead Chip, we analyzed over 450,000 methylation (CpG) sites at single nucleotide resolution in each line. BL2 AID-/- cells had a median average beta value (ratio of the methylated probe intensity to overall intensity) of 0.76 compared with 0.73 in AID-expressing BL2 cells (P < 0.00001), indicating a significant reduction in global methylation in the presence of AID. Using a delta average beta value of ≥ 0.3 (high stringency cut-off whereby a difference of 0.3 or more defines a CpG site as hypomethylated), we identified 5883 CpG sites in 3347 genes that were hypomethylated in BL2 versus BL2 AID-/- cells. Using the Illumina HumanHT-12 v4 Expression BeadChip and Genome Studio software, we then integrated gene expression and methylation profiles from both lines to generate a list of genes that met the following criteria: 1) contained at least 4 methylation sites within the first 1500 bases downstream of the primary transcriptional start site (TSS 1500; AID is most active in this region during somatic hypermutation); 2) average beta value increased by >0.1 in the TSS 1500 region in BL2 compared with BL2 AID-/- cells; and 3) down-regulated by >50% in BL2 compared with BL2 AID-/- cells. This analysis identified 31 candidate genes targeted for AID-dependent demethylation with consequent changes in gene expression. Interestingly, 15 of these genes have been reported to be bound by AID in association with stalled RNA polymerase II in activated mouse B cells. After validating methylation status in a subset of genes (APOBEC3B, BIN1, DEM1, GRN, GNPDA1) through bisulfite sequencing, we selected DEM1 for further analysis. DEM1 encodes an exonuclease involved in DNA repair and contains 16 CpG sites within its TSS1500, with only one site >50% methylated in BL2 cells compared with 8 of 16 in BL2 AID-/- cells. To assess a direct role for AID in DEM1 methylation status, a retroviral construct (AIDΔL189-L198ER) driving tamoxifen-inducible expression of a C-terminal deletion mutant of AID (increases time spent in the nucleus) was introduced into BL2 AID-/- cells. BL2, BL2 AID-/-, and BL2 AIDΔL189-L198ER cells were cultured continuously for 21 days in the presence of tamoxifen, 100 nM. Bisulfite sequencing of DEM1 TSS 1500 did not demonstrate any significant changes in methylation at day 7. However, at day 21, 13 of the 16 DEM1 TSS 1500 methylation sites in BL2 AIDΔL189-L198ER cells were found to have an increase in the ratio of unmethylated to methylated clones ~10-25% above that of BL2 AID-/- cells. By qPCR, this correlated with a 1.75-fold increase in DEM1 gene expression to levels that were equivalent to that seen in BL2 cells (P = 0.003). Although further investigations are needed, this data supports the notion that AID is able to regulate target gene expression in B cell malignancy through active DNA demethylation. DisclosuresNo relevant conflicts of interest to declare.

The role of DNA methylation in the mechanisms of memory reconsolidation and development of amnesia

Current considerations suggest that the mechanisms of long term memory are based on the changes of the neuronal genetic algorithms. Process of the enzyme DNA methylation have great importance to the differential genes expression, and is likely to be one of the key mechanisms of the consolidation and memory storage. The present study aimed to investigate the DNA methylation processes role in the mechanisms of the conditioned food aversion memory reconsolidation and also in the amnesia development mechanisms, caused by disturbances of the reconsolidation in Helix lucorum. It was found that DNA–methyltransferase inhibitors zebularine and RG108 had no influence on the memory reconsolidation. We investigated the effects of the DNA–methyltransferase inhibitors on different amnesia stage. The amnesia was induced by NMDA glutamate receptors antagonists. At the early stage of amnesia (3rd day after its induction) injections of the DNA–methyltransferase inhibitors in combination with reminder by conditioned food stimuli led to memory recall. Memory was recovered by the DNA–methyltransferase inhibitors injections before the reminder and also 3h, but not 9h after the reminder. In case when enzyme inhibitors or reminders were applied separately, no effect on memory was revealed. At the late stage of amnesia (10th day) the DNA–methyltransferase inhibitors didn’t affects amnesia development. It might be hypothesized that presentation of reminding stimuli result in the reactivation/reconsolidation of molecular processes, involved in amnesia development, one of the key mechanisms of which could be the DNA methylation/demethylation of neural cells.

A genome-wide association study for the incidence of persistent bovine viral diarrhea virus infection in cattle.

Bovine viral diarrhea viruses (BVDV) comprise a diverse group of viruses that cause disease in cattle. BVDV may establish both transient and persistent infections depending on the developmental stage of the animal at exposure. The objective was to determine whether genomic regions harboring single nucleotide polymorphisms (SNPs) could be associated with the presence or absence of persistent BVDV infection. A genome-wide association approach based on 777,000 SNP markers was used. Samples of animals identified as positive (n = 1200) or negative (n = 1200) for the presence of BVDV in skin samples (n = 1200) were used. DNA samples were combined in 24 pools (100 animals per pool). One SNP, significant at the 5 percent genome-wide level (P = 9.41 × 10(-8) ), was detected on chromosome 14, located at position 80 675 176 bp. Fifteen SNPs, residing on chromosomes 1, 2, 6, 8, 10, 15 and 18, were moderately associated (P < 1 × 10(-5) ) with persistent BVDV infection. Results show that genes harboring or neighboring significant SNPs are involved in leucopenia, signal transduction, RNA splicing and DNA methylation processes.

Cancer epigenetics: an introduction.

Epigenetic and genetic alterations contribute to cancer initiation and progression. Epigenetics refers to the study of heritable changes in gene expression without alterations in DNA sequences. Epigenetic changes are reversible and include key processes of DNA methylation, chromatin modifications, nucleosome positioning, and alterations in noncoding RNA profiles. Disruptions in epigenetic processes can lead to altered gene function and cellular neoplastic transformation. Epigenetic modifications precede genetic changes and usually occur at an early stage in neoplastic development. Recent technological advances offer a better understanding of the underlying epigenetic alterations during carcinogenesis and provide insight into the discovery of putative epigenetic biomarkers for detection, prognosis, risk assessment, and disease monitoring. In this chapter we provide information on various epigenetic mechanisms and their role in carcinogenesis, in particular, epigenetic modifications causing genetic changes and the potential clinical impact of epigenetic research in the future.

Epigenetic mechanisms underlying arsenic-associated lung carcinogenesis.

Arsenic is an established human carcinogen, but the mechanisms through which it contributes to for instance lung cancer development are still unclear. As arsenic is methylated during its metabolism, it may interfere with the DNA methylation process, and is therefore considered to be an epigenetic carcinogen. In the present study, we hypothesize that arsenic is able to induce DNA methylation changes, which lead to changes in specific gene expression, in pathways associated with lung cancer promotion and progression. A549 human adenocarcinoma lung cells were exposed to a low (0.08µM), intermediate (0.4µM) and high (2µM) concentration of sodium arsenite for 1, 2 and 8weeks. DNA was isolated for whole-genome DNA methylation analyses using NimbleGen 2.1M deluxe promoter arrays. In addition, RNA was isolated for whole-genome transcriptomic analysis using Affymetrix microarrays. Arsenic modulated DNA methylation and expression levels of hundreds of genes in a dose-dependent and time-dependent manner. By combining whole-genome DNA methylation and gene expression data with possibly involved transcription factors, a large molecular interaction network was created based on transcription factor-target gene pairs, consisting of 216 genes. A tumor protein p53 (TP53) subnetwork was identified, showing the interactions of TP53 with other genes affected by arsenic. Furthermore, multiple other new genes were discovered showing altered DNA methylation and gene expression. In particular, arsenic modulated genes which function as transcription factor, thereby affecting target genes which are known to play a role in lung cancer promotion and progression.

Exposure to arsenic via drinking water induces 5-hydroxymethylcytosine alteration in rat

Arsenic exposure has been implicated to alter DNA methylation process in vitro and in vivo, but it remains obscure whether it disrupts DNA demethylation process, which is pivotal for epigenetic regulation. The objective of this descriptive study was to investigate the relationship between arsenic exposure and 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC) alterations in various organs. In this study, we exposed male Sprague–Dawley rats to sodium arsenite (0.5, 2 or 10ppm) via drinking water for 8 weeks. Spleen accumulated 2- to 3-fold higher arsenic levels than liver and heart. Lower arsenic levels were observed in the kidney, pancreas and lung. No significant arsenic-induced global 5mC alterations were observed in the majority of investigated organs. However, arsenic induced organ-specific alterations of 5hmC and/or 5hmC/5mC in some investigated organs, i.e. lung, heart, kidney, pancreas and spleen. Our observations suggest that 5hmC is a more sensitive biomarker of arsenic-induced impacts on epigenetic processes than 5mC. Moreover, demethylation via hydroxylation of 5mC appears to play a central role in the toxic mechanism of arsenic.