5mC Levels Research Articles

Genome-wide discovery and validation of diagnostic DNA methylation-based biomarkers for hepatocellular cancer detection in circulating cell free DNA.

Hepatocellular carcinoma (HCC), the most prevalent form of liver cancer, is growing in incidence but treatment options remain limited, particularly for late stage disease. As liver cirrhosis is the principal risk state for HCC development, markers to detect early HCC within this patient population are urgently needed. Perturbation of epigenetic marks, such as DNA methylation (5mC), is a hallmark of human cancers, including HCC. Identification of regions with consistently altered 5mC levels in circulating cell free DNA (cfDNA) during progression from cirrhosis to HCC could therefore serve as markers for development of minimally-invasive screens of early HCC diagnosis and surveillance.Methods: To discover DNA methylation derived biomarkers of HCC in the background of liver cirrhosis, we profiled genome-wide 5mC landscapes in patient cfDNA using the Infinium HumanMethylation450k BeadChip Array. We further linked these findings to primary tissue data available from TCGA and other public sources. Using biological and statistical frameworks, we selected CpGs that robustly differentiated cirrhosis from HCC in primary tissue and cfDNA followed by validation in an additional independent cohort.Results: We identified CpGs that segregate patients with cirrhosis, from patients with HCC within a cirrhotic liver background, through genome-wide analysis of cfDNA 5mC landscapes. Lasso regression analysis pinpointed a panel of probes in our discovery cohort that were validated in two independent datasets. A panel of five CpGs (cg04645914, cg06215569, cg23663760, cg13781744, and cg07610777) yielded area under the receiver operating characteristic (AUROC) curves of 0.9525, 0.9714, and 0.9528 in cfDNA discovery and tissue validation cohorts 1 and 2, respectively. Validation of a 5-marker panel created from combining hypermethylated and hypomethylated CpGs in an independent cfDNA set by bisulfite pyrosequencing yielded an AUROC of 0.956, compared to the discovery AUROC of 0.996.Conclusion: Our finding that 5mC markers derived from primary tissue did not perform well in cfDNA, compared to those identified directly from cfDNA, reveals potential advantages of starting with cfDNA to discover high performing markers for liquid biopsy development.

Prostaglandin E2 induces DNA hypermethylation in gastric cancer in vitro and in vivo.

Rationale: Prostaglandin E2 (PGE2) is a pro-inflammatory eicosanoid up-regulated in gastric cancer (GC). However, its impact on epigenetic dysfunction in the process of gastric carcinogenesis is unknown. In this study, we investigate the role of PGE2 in DNA methylation in gastric epithelium in vitro, in mice, and humans.Methods: PGE2-induced DNMT3B and DNA methylation was determined in gastric cell lines and COX-2 transgenic mice. Effect of COX-2 inhibition on DNA methylation was evaluated in a randomized controlled trial. Efficacy of combined COX-2/PGE2 and DNMT inhibition on GC growth was examined in cell lines and mice models.Results: PCR array analysis of PGE2-treated GC cells revealed the up-regulation of DNMT3B, a de novo DNA methyltransferase. In GC cells, PGE2 induced DNMT3B expression and activity, leading to increased methylated cytosine (5mC) and promoter methylation of tumor suppressive genes (MGMT and CNR1). Consistently, Cox-2 (rate-limiting enzyme for PGE2 biosynthesis) transgenic expression in mice significantly induced Dnmt3b expression, increased 5mC content, and promoted Mgmt promoter methylation. We retrospectively analyzed the 5mC content of 42 patients with intestinal metaplasia (a precancerous lesion of GC) treated with a COX-2 specific inhibitor Rofecoxib or placebo for 2 years, revealing that the COX-2 inhibitor significantly down-regulated 5mC levels (N=42, P=0.009). Collectively, these data indicate that PGE2 is closely related to DNA hypermethylation in vitro and in vivo. Using genome-wide 450K methylation array, we identified chromosomal genes (POT1, ATM and HIST1H2AA) were preferentially methylated by PGE2. Biofunctional work revealed that POT1 functions as a tumor suppressor. Finally, we demonstrated that combinatorial inhibition of COX-2 and DNMT using Celecoxib and Decitabine synergistically inhibited GC growth in vitro and in vivo.Conclusion: This study suggested that PGE2 promotes DNA methylation in GC, and that co-targeting of PGE2 and DNMT inhibits GC.

Oral Vitamin C Supplementation to Azacitidine in Patients with Myeloid Cancer: Normalization of Plasma Vitamin C Induces Epigenetic Changes

▪IntroductionHematological cancer patients are often vitamin C deficient, and vitamin C is essential for the TET induced conversion of 5-methylcytosine (5mC) to 5-hydroxymethylsytosine (5hmC); the first step in active DNA demethylation. In tissue culture, we have shown that restoration of vitamin C to normal concentrations can potentiate the effect of DNA methyltransferase inhibitors (DNMTis) by activation of DNA demethylation and induction of genes in the viral defense pathway, so called ‘viral mimicry’ (Liu et al. PNAS 2016). Here, we investigated whether oral vitamin C supplementation can correct vitamin C deficiency, enhance the efficacy of active DNA demethylation and induce upregulation of genes in the viral defense pathway in patients with myeloid cancers treated with the DNMTi 5-azacytidine.Study Design and MethodsA randomized, placebo-controlled clinical trial of myelodysplastic syndrome (MDS; n=9), chronic myelomonocytic leukemia (CMML; n=4) and acute myeloid leukemia (AML; n=7) patients was performed during 3 cycles/12 weeks of DNMTi treatment (5-azacytidine, 100mg/m2 day 1 to 5 in a 4-week cycle) supplemented by oral dose of 500mg vitamin C (n=10) or placebo (n=10) daily during the last 8 weeks (Figure 1). Blood samples were drawn on day 1 and 5 of each treatment cycle before 5-azacytidine was administered and on day 28 of the third treatment cycle. Total plasma vitamin C was measured by HPLC in samples that had been acidified by 10% meta-phosphoric acid immediately after blood drawn. Mutational status of the 20 most commonly mutated genes in MDS were conducted by targeted next-generation sequencing. Global levels of 5mC and 5hmC were measured with LC-MS/MS in DNA extracted from MACS-sorted malignant cells and quoted relative to total levels of deoxyguanine. Total RNA-seq was performed on 20 RNA samples from 6 patients; cDNA libraries were prepared using KAPA RNA HyperPrep Kits and sequencing on a NextSeq 500 instrument (Illumina).ResultsFourteen patients were deficient in plasma vitamin C (<23 µM) and 4 of the remaining 6 patients took vitamin supplement at inclusion. Global DNA methylation was significantly higher in patients with severe vitamin C deficiency (<11.4 µM; P=0.004) and borderline significantly higher in DNMTi naïve (n=11) compared to non-naïve patients (P=0.095). At baseline, global 5hmC/5mC levels were lower in the 7 patients with TET2 mutations (n=7; P= 0.013). Oral supplementation restored plasma vitamin C levels to the normal range in all patients in the vitamin C arm (P<0.0005). We show for the first time that active DNA demethylation, estimated as the change in global 5hmC/5mC levels, was significantly increased in patients receiving vitamin C compared to placebo (P=0.041). Preliminary RNA sequencing data show increased upregulation of genes involved in the viral defense pathway, including IRF7 and IFIT1, in vitamin C supplemented patients that were DNMTi naïve at study inclusion.ConclusionsThe increase in active DNA demethylation, indicated by the elevation of 5hmC/5mC levels in myeloid cells from vitamin C supplemented patients compared to placebos, plus the increased expression of viral defense genes in vitamin C treated DNMTi naïve patients, suggest that the efficacy of 5-azacytidine might be increased by oral supplementation of vitamin C. We suggest that normalization of plasma vitamin C by oral supplementation may enhance the biological effects of DNMTis in patients and prompts the investigation of the clinical relevance of vitamin C supplementation to DNMTis in a large randomized placebo controlled trial.Figure 1. Study design. Days 1, 5, and 28: before vitamin C/placebo exposure. Day 32: after short-term vitamin C/placebo exposure. Days 56, 60, and 84: after longer-term vitamin C/placebo exposure. C = cycle, D = day in cycle. [Display omitted] DisclosuresJones:ZYMO Corporation: Consultancy. Grønbæk:Celgene: Membership on an entity's Board of Directors or advisory committees; Otsuka Pharma: Membership on an entity's Board of Directors or advisory committees; Janssen Pharma: Membership on an entity's Board of Directors or advisory committees.

Prediction of modulus of elasticity of poplar wood using ultrasonic technique by applying empirical correction factors

In this research, dynamic modulus of elasticity (MOE) of poplar wood was predicted under two different levels of moisture content, two different specimen dimensions, and three different transducer directions by ultrasonic technique. The main goal of this research was evaluate five correlations for the prediction of MOE and finding the best model based on a correction factor. Ultrasonic velocity in the wood was measured using Sylvatest Duo 9906-015 device. Dynamic MOE was calculated using measured ultrasonic wave velocity and density in different transducer directions and compared to static MOE. Static MOE was directly measured using Instron-4486 universal testing machine. Results generally showed that only two correlations had acceptable errors in the range of 5.8%–10.4% for all levels of moisture content. The results also showed that the ultrasonic technique is a suitable and accurate method for the prediction of MOE of poplar wood using models 2 and 3 (with around 7% relative error), especially in lower level of MC. Transducer direction B give the best outcomes along with minimum relative error (6.7%) among the other transducer directions. The empirical correction factors have an impressive effect on the reduction of relative error.

Epigenetic variation at the SLC6A4 gene promoter in mother–child pairs with major depressive disorder

BackgroundGenetic and epigenetic variations of the serotonin transporter gene (SLC6A4) have been related to the etiology of depression. The 5-HTTLPR polymorphism at the SLC6A4 promoter region has two variants, a short allele (S) and a long allele (L), in which the S allele results in lower gene transcription and has been associated with depression. The short S-allele of 5-HTTLPR polymorphism of this gene has been associated with depression. In addition to molecular mechanisms, exposure to early life risk factors such as maternal depression seems to affect the development of depression in postnatal life. The present study investigated the association of 5-HTTLPR polymorphism and CpG DNA methylation (5mC) levels of an AluJb repeat element at the SLC6A4 promoter region in mother–child pairs exposed to maternal depression. MethodsWe analyzed DNA samples from 60 subjects (30 mother–child pairs) split into three groups, with and without major depression disorder (DSM-IV) among children and mothers. The genotyping of 5-HTTLPR polymorphism and quantification of 5mC levels was performed by qualitative PCR and methylation-sensitive restriction enzyme digestion, and real-time quantitative PCR (MSRED-qPCR), respectively. ResultsThe sample analyzed presented a higher frequency of S allele of 5-HTTLPR (67.5%). Despite the high frequency of this allele, we did not find statistically significant differences between individuals carrying at least one S allele between the depression and healthy control subjects, or among the mother–child pair groups with different patterns of occurrence of depression. In the group where the mother and child were both diagnosed with depression, we found a statistically significant decrease of the 5mC level at the SLC6A4 promoter region. LimitationsThe limitations are the relatively small sample size and lack of gene expression data available for comparison with methylation data. ConclusionIn this study, we demonstrated a repeat element specific 5mC level reduction in mother–child pairs, concordant for the diagnosis of depression.

342 - Ascorbate supplementation increases 5-hydroxymethylcytosine in brain cerebellum DNA of ascorbate knockout mice

5-Hydroxymethylcytosine (5hmC) is a newly characterized epigenetic mark arising from the enzymatic oxidation of 5-methylcytosine (5mC) in DNA by the ten eleven translocation (TET) family enzymes. Whereas 5mC supresses gene expression, the presence of 5hmC correlates with the upregulation of certain genes. Using LC-MS/MS, we compared the global levels of genomic 5mC, 5hmC and 5-formylcytosine (5fC) in the brains of 4-month-old wild-type mice on a standard diet without ascorbate in comparison with Gulo-/- ascorbate knockout mice on a standard diet plus 0, 0.1, and 4.0 g/L ascorbate supplements. In addition, these modifications were measured in 20-month-old wild-type mice. Four regions of the brain were examined, which included cerebellum, cortex, hippocampus and striatum. The total brain weight and particularly the cerebellum weight of Gulo-/- mice were lower than those of wild-type mice. There was also a reduction of both epigenetic marks (5mC and 5hmC) in the cerebellum of Gulo-/- compared to wild-type mice. In contrast, weight, 5mC, 5hmC did not significantly change in other regions of the brain between the age-matched ascorbate deficient Gulo-/- mice. Loss of 5hmC in the cerebellum was increased in going from extreme deficiency (no ascorbate) to ascorbate supplements (4.0 g/L) in Gulo-/- mice. Lastly, similar decreases in weight and the level of 5mC and 5hmC were observed with age when comparing 4-month-old to 20-month-old wild-type mice. These results demonstrate that ascorbate modulates 5hmC in vivo and that the cerebellum is the most sensitive region affected by brain ascorbate deficiency. This work links dietary ascorbate to the epigenetic regulation of pathways that may be involved in a variety of neurological disorders.

335 - Modulation of dynamic mitochondria by epigenetics in diabetic retinopathy

Introduction Mitochondria are highly dynamic, and they continually fuse and divide. Fusion mixes the contents of two mitochondria, and dilutes injured mitochondrial proteins and DNA. Outer membrane fusion is mediated by fusion proteins, mitofusins (Mfn), and Mfn2 itself is sufficient to modulate mitochondrial metabolism. In the pathogenesis of diabetic retinopathy, mitochondrial structure and DNA are damaged, oxygen consumption is decreased and Mfn2 levels are decreased, and damaged mitochondria accelerates capillary cell apoptosis. Gene expression is also regulated by epigenetic modifications, and these modifications are implicated in the development of diabetic retinopathy. Aim of this study is to investigate the role of epigenetic modifications in the regulation of Mfn2 in diabetic retinopathy. Methods In human retinal endothelial cells, incubated in normal (5mM) or high glucose (20mM) for four days, in the presence/absence of DNA methyltransferase (Dnmt) inhibitors (5-Azacytidine or Dnmt1-siRNA), methylated cytosine (5mC) levels at Mfn2 promoter were quantified by immunecapturing method. Mitochondrial stability was evaluated by measuring membrane permeability, complex-III activity and transcription of mtDNA (cytochrome b, Cytb), and cell apoptosis was quantified by ELISA method using monoclonal antibodies against DNA and histones. Key parameters were evaluated in the retinal microvessels from streptozotocin-induced diabetic mice receiving intravitreal administration of Dnmt1-siRNA. Results Cells exposed to high glucose had increased 5mC levels at Mfn2 promoter. Dnmt inhibition ameliorated increase in 5mC levels, decrease in Mfn2 expression, and protected mitochondrial stability. In the same cells, glucose-induced increase in apoptosis was also ameliorated. Similarly, Dnmt1-siRNA prevented diabetes-induced increase in 5mC at Mfn2 promoter and decrease in its expression. Conclusions DNA methylation of Mfn2 promoter in diabetes, impairs mitochondrial stability, leading to accelerated apoptosis. Thus, targeting Mfn2 DNA methylation could help maintain mitochondrial homeostasis, and halt/retard the development of diabetic retinopathy.

338 - Mitochondrial DNA damage in diabetic retinopathy: role of epigenetics

Purpose Diabetes dysfunctions retinal mitochondria and increases base pair mismatches in mitochondrial DNA (mtDNA), and damaged mtDNA impairs the electron transport chain system. A mismatch repair system actively repairs the uncomplimentary base pairs, but in diabetes, the enzyme responsible for cutting the base-mismatches, MutL homolog 1 (Mlh1), is also compromised, which further adds to the damage of mtDNA. In diabetes, retinal DNA methylation machinery is also altered, and the activity of DNA methyl transferases (Dnmts) is significantly increased. Since Mlh1 promoter has over 50 CpG sites, making it a good target for DNA methylation, our aim was to investigate the role of DNA methylation in mtDNA damage in the development of diabetic retinopathy. Methods Retinal microvessels from streptozotocin-induced diabetic mice, with or without Dnmt inhibitor 5-azacytidine (Aza, 2.5mg/kg, intraperitoneal), were analyzed for methylated cytosine (5mC) levels using immuno-capture method and Mlh1 promoter- specific primers. Base-mismatch was quantified by digesting mtDNA amplicons using mismatch specific surveyor endonuclease, followed by DNA fragmentation analysis. Similar experiments were performed in retinal microvessels prepared from human donors with documented diabetic retinopathy. Results Compared to normal mice, retinal microvessels from diabetic mice had decreased Mlh1 expression and increased Dnmt1 and 5mC levels at Mlh1 promoter. In the same mice, base-mismatches in their mtDNA were also increased. Administration of Aza ameliorated diabetes-induced decrease in Mlh1 expression, and prevented increase in Dnmt1 and DNA methylation of Mlh1 promoter. Similarly, compared to age-matched non diabetic human donors, retinal microvessels from donors with established diabetic retinopathy had decreased levels of Mlh1 and increased levels of Dnmt1 and 5mC at Mlh1 promoter. Conclusions Thus, DNA methylation of Mlh1 promoter has a major role in impaired mtDNA damage. Therapies targeted to halt DNA methylation could have potential to prevent/halt mtDNA damage, and the development of diabetic retinopathy.

Superovulation Influences Methylation Reprogramming and Delays Onset of DNA Replication in Both Pronuclei of Mouse Zygotes

Although an essential component of assisted reproductive technologies, ovarian stimulation, or superovulation, may interfere with the epigenetic reprogramming machinery during early embryogenesis and gametogenesis. To investigate the possible impact of superovulation particularly on the methylation reprogramming process directly after fertilization, we performed immunofluorescence staining of pronuclear (PN) stage embryos with antibodies against 5mC and 5hmC. PN stage embryos obtained by superovulation displayed an increased incidence of abnormal methylation and hydroxymethylation patterns in both maternal and paternal pronuclear DNA. Subsequent single-cell RT-qPCR analyses of the Tet1, Tet2, and Tet3 genes revealed no significant expression differences between PN stage embryos from spontaneously and superovulated matings that could be causative for the abnormal methylation and hydroxymethylation patterns. To analyze the possible contribution of TET-independent replication-associated demethylation mechanisms, we then determined the 5mC and 5hmC levels of PN stage mouse embryos using immunofluorescence analyses after inhibition of DNA replication with aphidicolin. Inhibition of DNA replication had no effect on abnormal methylation and hydroxymethylation patterns that still persisted in the superovulated group. Interestingly, the onset of DNA replication, which was also analyzed in these experiments, was remarkably delayed in the superovulated group. Our findings imply an impact of superovulation on both replication-dependent and -independent or yet unknown demethylation mechanisms in PN stage mouse embryos. In addition, they reveal for the first time a negative effect of superovulation on the initiation of DNA replication in PN stage mouse embryos.

Epigenetic Changes Associated with Early Life Experiences: Saliva, A Biospecimen for DNA Methylation Signatures.

Background: Adverse Childhood Experiences (ACEs), which include traumatic injury, are associated with poor health outcomes in later life, yet the biological mechanisms mediating this association are unknown. Neurocircuitry, immune system and hormone regulation differ from normal in adults reporting ACEs. These systems could be affected by epigenetic changes, including methylation of cytosine (5mC) in genomic DNA, activated by ACEs. Since 5mC levels influence gene expression and can be long-lasting, altered 5mC status at specific sites or throughout the genome is hypothesized to influence mental and physical outcomes after ACE(s). Human and animal studies support this, with animal models allowing experiments for attributing causality. Here we provide a lengthy introduction and background on 5mC and the impact of early life adversity.Objective: Next we address the issue of a mixture of cell types in saliva, the most accessible biospecimen for 5mC analysis. Typical human bio-specimens for 5mC analysis include saliva or buccal swabs, whole blood or types of blood cells, tumors and post-mortem brain. In children saliva is the most accessible biospecimen, but contains a mixture of keratinocytes and white blood cells, as do buccal swabs. Even in saliva from the same individual at different time points, cell composition may differ widely. Similar issues affect analysis in blood, where nucleated cells represent a wide array of white blood cell types. Unless variations in ratios of these cells between each sample are included in the analysis, results can be unreliable.Methods: Several different biochemical assays are available to test for site-specific methylation levels genome-wide, each producing different information, with high-density arrays being the easiest to use, and bisulfite whole genome sequencing the most comprehensive. We compare results from different assays and use high-throughput computational processing to deconvolve cell composition in saliva samples.Results: Here we present examples demonstrating the critical importance of determining the relative contribution of blood cells versus keratinocytes to the 5mC profile found in saliva. We further describe a strategy to perform a reference-based computational correction for cell composition, and therefore to identify differential methylation patterns due to experience, or for the diagnosis of phenotypes that correlate between traits, such as hormone levels, trauma status and various mental health outcomes.Conclusion: Specific sites that respond to adversity with altered methylation levels in either blood cells, keratinocytes or both can be identified by this rigorous approach, which will then be useful as diagnostic biomarkers and therapeutic targets.

Impact of Global DNA Methylation in Treatment Outcome of Colorectal Cancer Patients.

Background: Global DNA methylation has an impact in cancer pathogenesis and progression. This study aimed at investigating the impact of global DNA methylation in treatment outcome of Colorectal Cancer (CRC).Patients and Methods: Global DNA methylation was measured by LC/MS/MS in peripheral blood leucocytes of 102, 48, and 32 Egyptian CRC patients at baseline and after 3 and 6 months of Fluoropyrimidine (FP) therapy respectively, in addition to 32 normal healthy matched in age and sex. The genetic expressions of DNA methyl transferases (DNMTs) were determined and correlated with patients‘ survival using univariate and multivariate methods of analyses.Results: Egyptian CRC patients had significant global hypomethylation of 5mC level and 5mC % with overexpression of DNMT3A and DNMT3B. Significant higher 5mC levels were shown in patients > 45 years, male gender, T2 tumors, stage II, negative lymph nodes, and absence of metastasis. FP therapy significantly reduced DNA methylation particularly in the subgroups of patients with high DNA methylation level at baseline and good prognostic features. After 3 years of follow up, patients with 5mC % > 8.02% had significant poor overall survival (OS) while, significant better event-free survival (EFS) was found in patients with 5mC level > 0.55. High initial CEA level and presence of metastasis were significantly associated with hazards of disease progression and death.Conclusion: Global DNA methylation has a significant impact on the treatment outcome and survival of Egyptian CRC patients treated with FP- based therapy.

Epigenetics and Regulation of Oxidative Stress in Diabetic Retinopathy.

PurposeOxidative stress plays a central role in the development of diabetic retinopathy, and in the pathogenesis of this blinding disease, activation of NADPH oxidase 2 (Nox2)-mediated cytosolic reactive oxygen species (ROS) production precedes mitochondrial damage. The multicomponent cytosolic Nox2 has an obligatory component, Ras-related C3 botulinum toxin substrate 1 (Rac1); in diabetes, Rac1 is functionally and transcriptionally active. Diabetes also facilitates many epigenetic modifications, and activates both DNA methylating (Dnmts) and hydroxymethylating (Tets) enzymes. Our aim was to investigate the role of epigenetics in Rac1 regulation in diabetes.MethodsUsing human retinal endothelial cells, exposed to high glucose, 5-methyl cytosine (5mC) and 5-hydroxy methyl cytosine (5hmC) levels, and binding of Dnmt and Tets were quantified at the Rac1 promoter. The effect of inhibition of Dnmts/Tets (pharmacological inhibitors or short interfering RNA [siRNA]) on glucose-induced activation of Rac1-ROS production was evaluated. Results were confirmed in retinal microvessels from streptozotocin-induced diabetic mice receiving intravitreally Dnmt1-siRNA.ResultsDespite high glucose-induced increased binding of Dnmt1, 5mC levels remained subnormal at Rac1 promoter. But, at the same site, 5hmC levels and transcription factor nuclear factor (NF)-kB binding were increased. Inhibition of Dnmts/Tets prevented increase in 5hmC and NF-kB binding, and attenuated Rac1 activation. Similarly, in mouse retinal microvessels, Dnmt1-siRNA ameliorated diabetes-induced increase in Rac1 transcripts and activity, and decreased ROS levels.ConclusionsThus, despite Dnmts activation, concomitant increase in Tets rapidly hydroxymethylates 5mC, allowing NF-κB to bind and activate Rac1. These results imply a critical role of an active DNA methylation in cytosolic ROS regulation in the development of diabetic retinopathy.

Effects of ten-eleven translocation 1 (Tet1) on DNA methylation and gene expression in chicken primordial germ cells.

Ten-eleven translocation 1 (Tet1) is involved in DNA demethylation in primordial germ cells (PGCs); however, the precise regulatory mechanism remains unclear. In the present study the dynamics of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) in developing PGCs and the role of Tet1 in PGC demethylation were analysed. Results show that 5mC levels dropped significantly after embryonic Day 4 (E4) and 5hmC levels increased reaching a peak at E5-E5.5. Interestingly, TET1 protein was highly expressed during E5 to E5.5, which showed a consistent trend with 5hmC. The expression of pluripotency-associated genes (Nanog, PouV and SRY-box 2 (Sox2)) and germ cell-specific genes (caveolin 1 (Cav1), piwi-like RNA-mediated gene silencing 1 (Piwi1) and deleted in azoospermia-like (Dazl)) was upregulated after E5, whereas the expression of genes from the DNA methyltransferase family was decreased. Moreover, the Dazl gene was highly methylated in early PGCs and then gradually hypomethylated. Knockdown of Tet1 showed impaired survival and proliferation of PGCs, as well as increased 5mC levels and reduced 5hmC levels. Further analysis showed that knockdown of Tet1 led to elevated DNA methylation levels of Dazl and downregulated gene expression including Dazl. Thus, this study reveals the dynamic epigenetic reprogramming of chicken PGCs invivo and the molecular mechanism of Tet1 in regulating genomic DNA demethylation and hypomethylation of Dazl during PGC development.

Malignant Peripheral Nerve Sheath Tumors Show Decreased Global DNA Methylation.

Malignant peripheral nerve sheath tumors (MPNST) are aggressive spindle cell neoplasms that may occur sporadically, often in association with radiation exposure, or in the clinical context of Neurofibromatosis type 1. MPNST are known to harbor genetic alterations affecting the function of polycomb repressive complex 2 (PRC2), resulting in profound changes to global H3K27me3 levels. Recent evidence suggests a link between the polycomb complex and DNA methylation. Given the established epigenetic alterations found in MPNST, we aimed to further explore global methylation changes including 5-methylcystosine (5mC), 5-hydroxymethylcytosine (5hmC), and H3K27me3 levels using previously validated immunolabeling protocols in a representative cohort of 28 peripheral nerve sheath tumors (MPNST [n = 8], localized cutaneous neurofibroma [n = 10], and plexiform neurofibroma [n = 10]). MPNST showed significantly decreased levels of H3K27me3 (p < 0.0002) and 5mC (p = 0.0001) with levels of 5hmC showing borderline statistical significance (p = 0.05) when compared to localized and plexiform neurofibromas. Immunohistochemical findings of decreased H3K27me3 and 5mC further our understanding of global epigenetic alterations observable in MPNST and may provide insight into the basis of tumor progression as well as prognostic and treatment implications in the future.

New Insights into the Epigenetic Activities of Natural Compounds

Background: With their varied pharmacophores, natural products are interesting tools to open the drug discovery pipeline. Several plant secondary metabolites belong to our diet and have conflictual documented epigenetic activities which need clarification. Methods: Seventy-one different natural products plus 17 controls were assembled for screening. First localized DNA methylation (DNAm) was studied on a stretch of the Retinoic Acid Receptor geneRAR followed then by a wider measure of all genomic 5 methylated Cytosine (5mC) by High Performance Liquid Chromatography tandem Mass Spectrometry (HPLC-MS/MS). DNA Methyl Transferase 1 (DNMT1) enzymatic activity was measured for selected compounds. Levels of Histone H3 trimethylation at lysine 9 and 27 (me3H3K9 and me3H3K27) were measured by Western blot. Global histone deacetylase inhibition (HDAC) was assayed first via a Bioluminescent Resonance Energy Transfer-based (BRET) assay and then with enzymatic fluorescence based-assays for HDAC class 1: 1, 2 and 3. As for HDAC6 inhibition, it was measured by Western blot screening. Sirtuine 2 (Sirt) inhibition was assessed first by a thermal shift assay and then by enzymatic assays for Sirt 1 and 2 using the SIRTainty™ Class III HDAC assay. Results: Several compounds decreased RAR methylation levels; but only Curcumin and (-) -Epigallocatechin gallate (EGCG) inhibited the DNMT1 catalytic activity; most other compounds worked probably, as S-Adenosyl-L-homocysteine (SAH) producers, with different potency under the assay conditions used here. Localized DNA demethylation was not mirrored by the global measure of 5mC levels. D-Glucuronic acid and anthraquinones decreased the level of me3H3K9 and 27 by un-deciphered mechanisms. When screening for HDAC class 1 inhibition, most flavonoids were emissive for enzymatic assays (excitation (Exec) = 340-360 nm and emission (Em) =440-465 nm). It was also the case when screening for Sirt activity by thermal shift (Exec= 365 nm and Em= 460 nm). This was overrun by the SIRTainty™ Class III HDAC (Exec= 420 nm and Em= 450 nm) assays by opposition to the FLUOR DE LYS® HDAC assay (Exec=360 nm and Em=460 nm). Within such limitations, we found that alkaloids like Brucine and Papaverin and anthraquinones are new epigenetic modifiers; this opens the epigenetic chemical space. Conclusions: To study diversity compound libraries, high through-put alpha screens are used at first. To study DNAm, they have large pitfalls. Indeed, finding unmethylated RARalleles does not indicate what a given compound is doing at the level of the entire genome for a given lapse of time and a given dose of compound. The measure of the DNMT1 enzymatic activity is not useful since most natural compounds are not direct enzymatic inhibitors. When studying histone methylation, Western blot is laborious but remains a cheap functional assay when several histone methylases (KDMs) or demethylases could be at the basis of histones methylation level decreases. Genome reversible epigenetic modifications remain desirable targets for nutrition oriented preventive strategies. However, reliable HDAC inhibition assays remain necessary before claiming that flavanols have true HDAC modulating activities.

Abstract B075: The role of TET1 and hydroxymethylation in high-risk prostate cancer

Abstract The Ten-eleven translocation (TET) proteins are dioxygenases that catalyze the oxidation of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) as part of the DNA demethylation pathway. Gene silencing through cytosine methylation contributes to cancer formation, but how hydroxymethylation affects gene expression is largely unknown. In this work, TET1 and genomic hydroxymethylation were investigated in a high-risk prostate cancer cohort for which exome sequencing data are available (1). Immunohistochemical analysis of tumor versus nontumor prostate biopsies from high-risk prostate cancer showed a strong reduction of genome-wide 5hmC and milder but still significant reduction of 5mC levels in prostate cancer tissue compared to control tissue. Copy number analysis of high-risk prostate cancer showed a loss of the TET1 genomic region in 6 out of 39 samples of our cohort. As expected, the mRNA levels of TET1 were decreased in these tumor samples. Recently, an alternative promoter of TET1 was discovered. This promoter generates a novel isoform lacking the CXXC-domain, which is called TET1ALT (2). We therefore performed functional analyses of the two TET1 promoters in prostate cancer cells. Interestingly, the promoter controlling expression of the endogenous full-length TET1 is less active in prostate cancer cell line PC-3, while the alternative promoter generating TET1ALT is more active in these cells. This is shown by luciferase constructs driven by the two promoter regions. In conclusion, our findings indicate that there is a drop in (hydroxy)methylation levels in high-risk prostate cancer that correlates with decreased TET1 expression levels and in some cases by a copy number loss of TET1. We are currently working on a more detailed analysis of TET1 promoter usage and control. This will unravel the regulation of hydroxymethylation in prostate cancer, which is crucial for the understanding of prostate cancer development and progression.

Dysregulation and prognostic potential of 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) levels in prostate cancer

BackgroundPrognostic tools for prostate cancer (PC) are inadequate and new molecular biomarkers may improve risk stratification. The epigenetic mark 5-hydroxymethylcytosine (5hmC) has recently been proposed as a novel candidate prognostic biomarker in several malignancies including PC. 5hmC is an oxidized derivative of 5-methylcytosine (5mC) and can be further oxidized to 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). The present study is the first to investigate the biomarker potential in PC for all four DNA methylation marks in parallel. Thus, we determined 5mC, 5hmC, 5fC, and 5caC levels in non-malignant (NM) and PC tissue samples from a large radical prostatectomy (RP) patient cohort (n = 546) by immunohistochemical (IHC) analysis of serial sections of a tissue microarray. Possible associations between methylation marks, routine clinicopathological parameters, ERG status, and biochemical recurrence (BCR) after RP were investigated.Results5mC and 5hmC levels were significantly reduced in PC compared to NM prostate tissue samples (p ≤ 0.027) due to a global loss of both marks specifically in ERG− PCs. 5fC levels were significantly increased in ERG+ PCs (p = 0.004), whereas 5caC levels were elevated in both ERG− and ERG+ PCs compared with NM prostate tissue samples (p ≤ 0.019). Positive correlations were observed between 5mC, 5fC, and 5caC levels in both NM and PC tissues (p < 0.001), while 5hmC levels were only weakly positively correlated to 5mC in the PC subset (p = 0.030). There were no significant associations between 5mC, 5fC, or ERG status and time to BCR in this RP cohort. In contrast, high 5hmC levels were associated with BCR in ERG− PCs (p = 0.043), while high 5caC levels were associated with favorable prognosis in ERG+ PCs (p = 0.011) and were borderline significantly associated with worse prognosis in ERG− PCs (p = 0.058). Moreover, a combined high-5hmC/high-5caC score was a significant adverse predictor of post-operative BCR beyond routine clinicopathological variables in ERG− PCs (hazard ratio 3.18 (1.54–6.56), p = 0.002, multivariate Cox regression).ConclusionsThis is the first comprehensive study of 5mC, 5hmC, 5fC, and 5caC levels in PC and the first report of a significant prognostic potential for 5caC in PC.

Age-related epigenome-wide DNA methylation and hydroxymethylation in longitudinal mouse blood

ABSTRACTDNA methylation at cytosine-phosphate-guanine (CpG) dinucleotides changes as a function of age in humans and animal models, a process that may contribute to chronic disease development. Recent studies have investigated the role of an oxidized form of DNA methylation – 5-hydroxymethylcytosine (5hmC) – in the epigenome, but its contribution to age-related DNA methylation remains unclear. We tested the hypothesis that 5hmC changes with age, but in a direction opposite to 5-methylcytosine (5mC), potentially playing a distinct role in aging. To characterize epigenetic aging, genome-wide 5mC and 5hmC were measured in longitudinal blood samples (2, 4, and 10 months of age) from isogenic mice using two sequencing methods – enhanced reduced representation bisulfite sequencing and hydroxymethylated DNA immunoprecipitation sequencing. Examining the epigenome by age, we identified 28,196 unique differentially methylated CpGs (DMCs) and 8,613 differentially hydroxymethylated regions (DHMRs). Mouse blood showed a general pattern of epigenome-wide hypermethylation and hypo-hydroxymethylation with age. Comparing age-related DMCs and DHMRs, 1,854 annotated genes showed both differential 5mC and 5hmC, including one gene – Nfic – at five CpGs in the same 250 bp chromosomal region. At this region, 5mC and 5hmC levels both decreased with age. Reflecting these age-related epigenetic changes, Nfic RNA expression in blood decreased with age, suggesting that age-related regulation of this gene may be driven by 5hmC, not canonical DNA methylation. Combined, our genome-wide results show age-related differential 5mC and 5hmC, as well as some evidence that changes in 5hmC may drive age-related DNA methylation and gene expression.

Abstract 3246: Association between colorectal cancer and red or processed meat among Korean diet: A molecular approach

Abstract To study whether red or processed meat cause colorectal cancer in non- western population, we performed a pilot study in Korean people (N=30, case, 15 vs. control 15, mean of age=59.7 yrs) with biological monitoring of exposure and response biomarkers, i.e. metabolites of polycyclic aromatic hydrocarbons and heterocyclic amine (1-OHP, PhIP, and MeIQx), their DNA-adducts (dG-C8-MeIQx), and homocysteine, malondialdehyde (MDA), C-reactive protein and epigenetic alteration (5mC). The subjects also filled out daily consumption of food before diagnoses. As results, they averagely consumed 59.89 g/day and 2.47 g/day of red and processed meat, respectively. There were positive associations among consumption of Kimch(g), folate (ug) and fruits(g). The consumption of red meat was not associated with the cancer and the control even showed higher processed meat (g). From biomonitoring, the average levels of urinary 1-OHP, PhIP, and MeIQx, blood-dG-C8-MeIQx and 5mC were 0.13 ppb, 9.9 ppt, 14.63 ppt, 5.23 ppt/1.8 ug of DNA, and 5.3%, respectively. We found younger people more consumed processed meat or beverage and showed higher urinary levels of MeIQx than elderly people. The urinary levels of PhIP were negatively associated with folate consumption. The cases showed higher levels of LDL-cholesterol, homocysteine, urinary 1-OHP and dG-C8-MeIQx than controls. There were positive associations among levels of MeIQx, MDA, and 1-OHP. In addition, levels of dG-C8-MeIQx were positively associated with those of 1-OHP and total cholesterol. The levels of global methylation of 5mC (%) were higher in well done meat consumers than others. In conclusion, the Korean subjects might consume less volume of red or processed meat than western people. From questionnaire (FFQ), we could not find association between red or processed meat and colorectal cancer. However, biological monitoring showed the Korean colorectal cancer could be affected by red or processed meat, due to association with exposure or response biomarkers, particularly long term exposure biomarkers, such as dG-C8-MeIQx. This molecular epidemiological approach provides more reliable evidences to overcome limitation of case-control studies. Citation Format: Mihi Yang, Jeongseon Kim, Jong Y. Park. Association between colorectal cancer and red or processed meat among Korean diet: A molecular approach [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3246.

Diesel exhaust and house dust mite allergen lead to common changes in the airway methylome and hydroxymethylome.

Exposures to diesel exhaust particles (DEP) from traffic and house dust mite (HDM) allergens significantly increase risks of airway diseases, including asthma. This negative impact of DEP and HDM may in part be mediated by epigenetic mechanisms. Beyond functioning as a mechanical barrier, airway epithelial cells provide the first line of immune defense towards DEP and HDM exposures. To understand the epigenetic responses of airway epithelial cells to these exposures, we exposed human bronchial epithelial cells to DEP and HDM and studied genome-wide 5-methyl-cytosine (5mC) and 5-hydroxy-methylcytosine (5hmC) at base resolution. We found that exposures to DEP and HDM result in elevated TET1 and DNMT1 expression, associated with 5mC and 5hmC changes. Interestingly, over 20% of CpG sites are responsive to both exposures and changes in 5mC at these sites negatively correlated with gene expression differences. These 5mC and 5hmC changes are located in genes and pathways related to oxidative stress responses, epithelial function and immune cell responses and are enriched for binding sites of transcription factors (TFs) involved in these pathways. Histone marks associated with promoters, enhancers and actively transcribed gene bodies were associated with exposure-induced DNA methylation changes. Collectively, our data suggest that exposures to DEP and HDM alter 5mC and 5hmC levels at regulatory regions bound by TFs, which coordinate with histone marks to regulate gene networks of oxidative stress responses, epithelial function and immune cell responses. These observations provide novel insights into the epigenetic mechanisms that mediate the epithelial responses to DEP and HDM in airways.