HPV Infection Leaves a DNA Methylation Signature in Oropharyngeal Cancer Affecting Both Coding Genes and Transposable Elements

HPV oncoproteins can modulate DNMT1 expression and activity, and previous studies have reported both gene-specific and global DNA methylation alterations according to HPV status in head and neck cancer. However, validation of these findings and a more detailed analysis of the transposable elements (TEs) are still missing. Here we performed pyrosequencing to evaluate a 5-CpG methylation signature and Line1 methylation in an oropharyngeal squamous cell carcinoma (OPSCC) cohort. We further evaluated the methylation levels of the TEs, their correlation with gene expression and their impact on overall survival (OS) using the TCGA cohort. In our dataset, the 5-CpG signature distinguished HPV-positive and HPV-negative OPSCC with 66.67% sensitivity and 84.33% specificity. Line1 methylation levels were higher in HPV-positive cases. In the TCGA cohort, Line1, Alu and long terminal repeats (LTRs) showed hypermethylation in a frequency of 60.5%, 58.9% and 92.3%, respectively. ZNF541 and CCNL1 higher expression was observed in HPV-positive OPSCC, correlated with lower methylation levels of promoter-associated Alu and LTR, respectively, and independently associated with better OS. Based on our findings, we may conclude that a 5-CpG methylation signature can discriminate OPSCC according to HPV status with high accuracy and TEs are differentially methylated and may regulate gene expression in HPV-positive OPSCC.

Pre-Operative Decitabine in Colon Cancer Patients: Analyses on WNT Target Methylation and Expression

DNA hypermethylation is common in colon cancer. Previously, we have shown that methylation of WNT target genes predicts poor prognosis in stage II colon cancer. The primary objective of this study was to assess whether pre-operative treatment with decitabine can decrease methylation and increase the expression of WNT target genes APCDD1, AXIN2 and DKK1 in colon cancer patients. A clinical study was conducted, investigating these potential effects of decitabine in colon cancer patients (DECO). Patients were treated two times with 25 mg/m2 decitabine before surgery. Methylation and expression of LINE1 and WNT target genes (primary outcome) and expression of endogenous retroviral genes (secondary outcome) were analysed in pre- and post-treatment tumour samples using pyrosequencing and rt-PCR. Ten patients were treated with decitabine and eighteen patients were used as controls. Decitabine treatment only marginally decreased LINE1 methylation. More importantly, no differences in methylation or expression of WNT target or endogenous retroviral genes were observed. Due to the lack of an effect on primary and secondary outcomes, the study was prematurely closed. In conclusion, pre-operative treatment with decitabine is safe, but with the current dosing, the primary objective, increased WNT target gene expression, cannot be achieved.

Association between Serum Vitamin B12 and Global DNA Methylation in Colorectal Cancer Patients

Vitamin B12 has been widely related to methionine metabolism, which is an essential component for biological methylation reactions, including DNA methylation. However, the relationship between vitamin B12 and DNA methylation is still controversial. In addition, there is increasing evidence for the association between vitamin B12 and the risk of colorectal cancer (CRC), although results of this association need to be assessed with caution. For this purpose, we hypothesized that serum vitamin B12 could be associated with global DNA methylation in the CRC context. To test this hypothesis, we studied the association between global DNA methylation through long interspersed nuclear element-1 (LINE1) in CRC patients under the 25th percentile of serum vitamin B12. We found that the high vitamin B12 group had low LINE1 methylation in both tumor area and peripheral blood mononuclear cells (PBMCs) than the low serum vitamin B12 group. LINE1 methylation levels were significantly lower in tumor area compared to the adjacent tumor-free area, only in the high vitamin B12 group. LINE1 methylation in visceral adipose tissue (VAT) and PBMCs were correlated with tumoral, inflammatory, and insulin metabolism markers. However, the interaction between LINE1 methylation and vitamin B12 levels was associated with neoadjuvant therapy in the regression analysis only in men, suggesting a beneficial relationship. In conclusion, our results reported an inverse association between DNA methylation and vitamin B12 in the CRC context, which suggests that vitamin B12 may be implicated in an epigenetic state or mediation in CRC.

Fasting and fasting mimetic supplementation address sirtuin expression, miRNA and microbiota composition

Background: Fasting and fasting mimetics - bioactive compounds mimicking fasting effects, are of growing interest as potential means to slow down the aging process and increase health span. Sirtuins are known as enzymes that interfere with mitochondrial energy metabolism and molecular pathways involved in longevity. Although their activation is determined as a response to stress i.e. caloric restriction. Sirtuin activating nutraceuticals are believed to mimic the effects of nutrient deprivation, thus activating signaling pathways correlated to an improved health span. In this study, we compare 5 days periodic buchinger fasting intervention with 3 months shot supplementation, a drink formula, containing secondary plant ingredients considered to activate sirtuins.Methods: We analyzed pathways in response to fasting and a sirtuins activating drink. Genetic and epigenetic biomarkers including telomere length, LINE1 methylation, and a set of mRNAs and miRNAs were assessed using qPCR analysis. Gut composition and metabolites were compared using Illumnia sequencing and mass spectrometry.Results: Fasting, but also the fasting mimetic could increase expression of FoxO1, SIRT1, and MLH1 mRNA, all genes discussed in aspects of longevity. A positive correlation between telomere length and both SIRT1, and SIRT6 was observed. Furthermore, a significant change in the gut composition was measured. Actinobacteria increased in the supplementation group, whereas after buchinger fasting a rise in the distribution of Proteobacteria could be observed. Firmicutes/Bacteroidetes ratio decreased and correlated with the body mass index (BMI).Conclusions: Our results confirm the effects of fasting on longevity associated mechanisms but also suggest that SIRTFOOD shot intervention addresses some of these effects.

LINE1 Methylation is Associated With Lead Exposure and Certain Job-Tasks Performed by Electronic Waste Workers

Background: Electronic waste recycling processes such as dismantling with rudimentary tools and open-air burning result in the release of several toxic chemicals into the environment. Exposure to these toxic chemical mixtures has been associated with many adverse health outcomes affecting respiratory, cardiovascular, neurological, and reproductive systems. DNA methylation has been associated with exposure to toxic chemicals, including heavy metals in several epidemiological studies. DNA methylation profile due to exposure to toxic chemicals among e-waste recyclers has not been studied.Objective: This study assessed the associations between blood and urine levels of heavy metals; cadmium (Cd), lead (Pb), and arsenic (As) and methylation levels of the LINE1 gene among e-waste and control populations in Ghana.Methods: The study enrolled 100 male e-waste workers and 51 all-male non e-waste workers or controls. Body burden of Cd, Pb and As was measured in blood and urine using Inductively Coupled Plasma Mass Spectrometry, while LINE1 methylation levels were assessed by pyrosequencing of bisulfite-converted DNA extracted from whole blood.Results: There was no significant difference in LINE1 methylation between the e-waste and the non e-waste workers (85.16% ±1.32 vs 85.17% ±1.11, p = 0.950). However, CpG1 showed significantly lower mean methylation among controls, compared to e-waste workers (81.70% ±1.86 vs 82.48% ±2.20, p = 0.034). In linear regression models, blood lead (B-Pb) level was significantly inversely associated with overall LINE1 methylation (β = -0.004; 95%CI: -0.008, -0.0003; p = 0.034). Among e-waste recyclers, collectors showed significantly reduced LINE1 methylation levels (β = -0.889; 95%CI: -1.757, -0.021; p = 0.045). Conclusion: Continuous exposure to Pb may interfere with LINE1 methylation leading to epigenetic alteration, thus serve as an early epigenetic marker for future adverse health outcomes.

Placenta Lactate Is Inversely Associated with Birth Weight: Threshold Effects of Maternal Methyl Donor Status on Fetal Lactate Metabolism in Taiwanese Mother-Newborn Pairs

Objectives We examined associations between maternal methyl donor status with lymphocytic epigenetic markers at third trimester, fetal fuel metabolism in placenta and neonatal birth weight (BW). Methods This study included seventy-eight healthy mother-newborn pairs with placenta samples and newborn growth data from the Taiwan Pregnancy-Newborn Epigenetics cohort. Maternal plasma methyl donors (folate/free choline/betaine) and lymphocytic epigenetic marks (DNA methylation of LINE1 and H19 imprinted gene) at the third trimester were measured. Placenta fuel metabolites (glucose/lactate/folate), expressions of glycolytic enzymes (hexokinase II: HK-II and lactate dehydrogenase: LDH) and the metabolic signaling AMP-activated protein kinase (AMPK) were assayed. Associations with BW were analyzed by multiple linear regression. Results Both maternal LINE1 methylation (β: −0.289, P = 0.044) and placenta lactate level (β: −0.262, P = 0.034) predicted neonatal BW variance. Maternal RBC folate level predicted LINE1 methylation (β: 0.300, P = 0.048). The significance of fetal lactate-prediction on neonatal BW variance was negated by adjustment for placenta glucose, maternal methyl donor status (folate/free choline/betaine), and maternal prepregnancy BMI. Further adjustment for maternal epigenetic marks (LINE1 and H19 methylation) resumed the prediction power (β: −0.366, P = 0.039). By stratification of maternal and fetal methyl donor status, the significant fetal lactate-BW prediction only displayed in mothers with high plasma folate levels (>10.2 ng/mL) (β: −0.371, P = 0.037), low free choline levels (<12.9 μM) (β: −0.444, P = 0.038) and low betaine levels (<13.4 μM) (β: −0.536, P = 0.010). As maternal plasma folate significantly predicted placenta folate (β: 0.283, P = 0.014), high placenta folate levels (>17.5 ng/g) markedly strengthen the fetal lactate-BW prediction (β: −0.657, P = 0.001), which coincided with higher expression of placenta AMPK levels. Conclusions Our data highlights the inverse association between placenta lactate and birth weight. Maternal third trimester and placental methyl donor status may affect neonatal birth weight variance through their threshold effects on fetal lactate metabolism. Funding Sources This study was supported by a grant from the Ministry of Science and Technology, Taiwan.

Efficacy of OR21, a Novel Oral Demethylating Agent in Chronic Myeloid Leukemia

Chronic myeloid leukemia (CML) is a clonal hematopoietic stem cell disease induced by t(9;22)(q34;q11) translocation. The prognosis of patients with CML has dramatically improved since tyrosine kinase inhibitors (TKIs) were introduced, and recent studies show that approximately 40 to 50 % of CML patients achieved deep molecular response (DASISION and ENESTnd trial) within several years. However, therapeutic options for patients with CML who are resistant for TKIs are limited. Besides BCR-ABL kinase domain mutation, somatic mutations associated with epigenetic gene alteration (e.g. TET, DNMT3A) are reportedly involved in TKI resistance and disease progression. Thus, we investigated the efficacy of DNA demethylating agents in CML. Azacitidine (AZA) and decitabine (DAC), currently available as DNA demethylating agents, have low bioavailability for oral administration because they are easily degraded by cytidine deaminase. Then, we are developing a novel demethylating agent, OR21, with possible oral absorbability as a prodrug of DAC. In vivo analysis using cynomolgus monkeys, the area under the curve of DAC after intraduodenally administration of DAC (1.5mg/kg, 6.6µmol/kg) or OR21 (2.25mg/kg, 6.6µmol/kg) was 0.01 µM·h, 0.298 µM·h respectively, indicating OR21 have high oral absorbability. To assess the demethylating activity of OR21 for CML, we performed western blot analysis and bisulfite pyrosequencing assay to measure LINE1 methylation, using CML cell-lines (K562, BV173). OR21 decreased DNMT1 protein level as a result of demethylating and LINE1 methylation in K562 and BV173 comparable to DAC. Next, we performed cell growth inhibition and cell apoptosis assay after 72 hours exposure of OR21 to assess anti-tumor effect in vitro. OR21 inhibited cell growth comparable to DAC in CML cell-lines (K562, BV173, KCL22, MYL) in a dose-dependent manner. Notably, OR21 inhibited the cell growth and apoptosis against BV173 with an extremely low concentration (IC50; 5nM) than that of AZA (IC50; 122nM) via significant accumulation of reactive oxygen species. Whereas, OR21 weakly induced cell apoptosis against K562. OR21 induced G2/M phase cell-cycle arrest in CML cell-lines except for BV173 via pRb downregulation. These results indicated mechanisms of anti-tumor effect in OR21 were induction of cell apoptosis (BV173) or cell cycle arrest (K562, KCL22, MYL). Because of the different mechanism of action, we assessed whether OR21 and TKIs combination can enhance the anti-tumor effect of CML. We investigated the combination effects of OR21 with imatinib (IM) or dasatinib (DAS) in K562. Combination index values at IC80 calculated by Calucusyn software showed 0.642±0.129 (with IM), 1.182±0.2 (with DAS), respectively. Accordingly, OR21 combined with TKIs showed at least additive or synergistic effect for K562. TKI resistance, which can be associated with somatic mutations leading to epigenetic gene alteration or loss of function of p53, is an obstacle for molecular remission in patients with CML, thus we examined the effects of OR21 in TKI resistant cell lines or efficacy on p53 mutational status. OR21 inhibited the cell growth in IM-resistant cell-line MYL-R, a derivative of MYL, which had overexpression of Lyn, and Ba/F3 BCR-ABLT315I, which exogenously expressed Bcr-Abl (T315I), indicating OR21 could overcome TKI resistance in CML. OR21 or cytarabine did not enhance cell apoptosis against K562, MYL and KCL22 (p53 deficient or mutant cell lines) combination with nutlin-3a (MDM-2 inhibitor), while increased cell apoptosis was observed in BV173 (p53 wild type) treated with cytarabine and nutlin-3a, but not with OR21 and nutlin-3a. These results suggested the effects of OR21 did not depend on p53 mutational status. Finally, we used a mouse xenograft model to evaluate anti-tumor effect of OR21 in vivo. BALB/c Rag-2/JAK3 double-deficient (BRJ) mice were injected intravenously via tail vein with 5 ×106 BV173 cells. OR21 were administered at a dose of 2.7mg/kg (equivalent to DAC 1.0mg/kg in AUC) and PBS (vehicle) twice weekly. OR21 significantly prolonged survival in a xenograft mice model (median 35 days vs not reached, P<0.01). In conclusion, a novel orally available demethylating agent OR21 is effective for CML cells including TKI resistant clones. The efficacy and safety of OR21 for CML is expected to be verified by early-phase clinical trials. Disclosures Kamachi: Ohara Pharmaceutical Co.: Research Funding. Ureshino:OHARA Pharmaceutical Co.: Research Funding. Yoshida:OHARA Pharmaceutical Co., Ltd.: Research Funding. Kurahashi:Ohara Pharmaceutical Co.: Employment. Watanabe:Ohara Pharmaceutical Co.: Research Funding. Okada:Japan Agency for Medical Research and Development: Research Funding; Bristol-Myers Squibb: Research Funding. Kimura:Ohara Pharmaceutical Co.: Research Funding; Novartis: Honoraria, Research Funding.

Lower LINE-1 methylation is associated with promoter hypermethylation and distinct molecular features in gastric cancer

Aim: To investigate the associations between LINE1 methylation, an indicator for genome-wide hypomethylation, molecular and clinicopathological characteristics of gastric cancer (GC) patients. Patients & methods: LINE1 methylation statuses were examined in paired cancerous, non-neoplastic mucosa from 217 GC and gastric mucosa from separate group of 224 noncancer patients. CpG island methylator phenotype, TP53 and KRAS mutation, MLH1 methylation status and promoter hypermethylation of GC related and H. pylori-related genes were examined. Results: Lower LINE1 methylation was observed in primary GC compared with non-neoplastic gastric mucosa and associated with CpG island methylator phenotype, TP53 mutation, MLH1 methylation and promoter hypermethylation of GC related and H. pylori-related genes. Conclusion: Lower LINE1 methylation correlates specific molecular subtypes and promoter hypermethylation in GC.