Unmethylated Group Research Articles

Abstract 907: Bioinformatic method to define epigenetically regulated enhancer elements associated with cancer

Abstract BACKGROUND: Several mechanisms involved in gene regulation are altered in cancer. Cataloging these alterations can lead to a better understanding of tumorigenesis. In addition, the alterations can be used to classify patients with similar clinical features and thereby lead to better targeted treatment. Epigenetics (e.g. DNA methylation) is the process by which cells define gene regulation and aberrant DNA methylation patterns have been observed in many cancer types. Alterations in non-promoter (intergenic regions) have been shown to be tightly associated with functional genomic elements such as enhancers or transcription factor binding. In order to identify altered candidate functional elements associated with specific gene or pathways, we developed a method to integrate enhancer, DNA methylation and gene expression data, using tumor and non-tumor data. METHOD: Using epigenome-wide platform (Illumina 850K), CpG probes were separated into promoters and intergenic regions. The intragenic CpGs were further filtered by overlapping with known functional enhancer database from multiple studies. The nearest genes to each CpG enhancer is further stratified based on differential gene expression. Each CpG/gene pair is classified as methylated or unmethylated by sample, using a 50% methylation cutoff. The mean expression of the methylated samples is calculated and pairs with lower than the bottom 10% (1.28 standard deviation) of the mean expression in the unmethylated group of samples are selected. Finally, CpG/gene pairs with at least 75% of the methylated samples have expression values lower than the mean expression in the unmethylated group of samples are classified as epigenetically silenced. CpG/gene pairs unmethylated and upregulated are called as epigenetically active. By separating samples into different epigenetically deregulated states (silenced or active), we can further characterize each sample by evaluating the association or enrichment for specific clinical features such as outcome, treatment, age at diagnosis, etc. RESULTS: As a proof of concept, we applied our method across the TCGA PanCan cohort to identify potential enhancers regulating genes encoding subunits of the SWI/SNF protein complex. Our method was able to detect several deregulated enhancers associated with SWI/SNF genes specifically altered in each tumor type, independent of mutation. We validated the results using Hi-C data from primary cancer cell lines. Citation Format: Thais S. Sabedot, Seth H. Cassel, Galen F. Gao, Caleb A. Lareau, Andrew Cherniack, Alexander Lazar, Cigall Kadoch, Houtan Noushmehr. Bioinformatic method to define epigenetically regulated enhancer elements associated with cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 907.

Predictive MGMT status in a homogeneous cohort of IDH wildtype glioblastoma patients

Methylation of the O(6)-Methylguanine-DNA methyltransferase (MGMT) promoter is predictive for treatment response in glioblastoma patients. However, precise predictive cutoff values to distinguish “MGMT methylated” from “MGMT unmethylated” patients remain highly debated in terms of pyrosequencing (PSQ) analysis. We retrospectively analyzed a clinically and molecularly very well-characterized cohort of 111 IDH wildtype glioblastoma patients, who underwent gross total tumor resection and received standard Stupp treatment. Detailed clinical parameters were obtained. Predictive cutoff values for MGMT promoter methylation were determined using ROC curve analysis and survival curve comparison using Log-rank (Mantel-Cox) test. MGMT status was analyzed using pyrosequencing (PSQ), semi-quantitative methylation specific PCR (sqMSP) and direct bisulfite sequencing (dBiSeq). Highly methylated (> 20%) MGMT correlated with significantly improved progression-free survival (PFS) and overall survival (OS) in our cohort. Median PFS was 7.2 months in the unmethylated group (UM, < 10% mean methylation), 10.4 months in the low methylated group (LM, 10-20% mean methylation) and 19.83 months in the highly methylated group (HM, > 20% mean methylation). Median OS was 13.4 months for UM, 17.9 months for LM and 29.93 months for HM. Within the LM group, correlation of PSQ and sqMSP or dBiSeq was only conclusive in 51.5% of our cases. ROC curve analysis revealed superior test precision for survival if additional sqMSP results were considered (AUC = 0.76) compared to PSQ (cutoff 10%) alone (AUC = 0.67). We therefore challenge the widely used, strict PSQ cutoff at 10% which might not fully reflect the clinical response to alkylating agents and suggest applying a second method for MGMT testing (e.g. MSP) to confirm PSQ results for patients with LM MGMT levels if therapeutically relevant.

ADAMTSL4, a Secreted Glycoprotein, Is a Novel Immune-Related Biomarker for Primary Glioblastoma Multiforme.

Background Researches on immunotherapy of glioblastoma multiforme (GBM, WHO grade IV) have increased exponentially in recent years. As a targeted therapy, a series of biomarkers have been identified in local tumor tissue, while circulating marker which could be detected in the body fluids is still lacking. ADAMTSL4, a secreted glycoprotein, was earlier found to play a critical role in a prognostic signature for primary GBM (pGBM). We aimed to investigate the role of ADAMTSL4 at transcriptome level and its relationship with clinical practice in pGBM. Methods A cohort of 88 pGBM patients with RNA-seq data from the Chinese Glioma Genome Atlas (CGGA) was analyzed, and 168 pGBM patients from TCGA were included as validation. Several bioinformatic methods and predictive tools were applied to investigate the ADAMTSL4-associated immune microenvironment status. Results We found that ADAMTSL4 was enriched in GBM (WHO grade IV), especially for those with IDH1/2 wild-type and MGMT unmethylated groups. According to the TCGA classification scheme, ADAMTSL4 can act as a potential marker for subtypes with poorer prognosis. Bioinformatic analyses revealed that ADAMTSL4 was significantly correlated to the immune-related processes in GBM (WHO grade IV), especially representing the infiltration of immune cells and complicated tumor microenvironment. Clinically, high expression of ADAMTSL4 was an independent indicator for poor prognosis. Conclusion The expression of ADAMTSL4 is closely related to the clinicopathologic characteristics of pGBM. Meanwhile, it may play a critical role in immune-related processes. As a secreted glycoprotein, ADAMTSL4 is a promising circulating biomarker for pGBM, deserving further investigations.

CADD-50. AN OLD STORY (MGMT) IN AN EXPANDED CONTEXT (NATIONAL CANCER DATABASE)

O6-methylguanine-DNA methyltransferase (MGMT), a DNA repair protein, which is expressed in majority of cancers including glioblastoma multiforme (GBM), a predictive biomarker in the alkylator based treatment of gliomas. The objective of this study is to confirm the MGMT’s role as a predictive biomarker and to re-evaluate the potential MGMT, patient subset specific, prognostic role using the National Cancer Database (NCDB). METHOD: We used the NCDB to identify GBM patients with MGMT (N=5934) registered from 2010 through 2014 in which MGMT status was detected. Hyper methylation was detected in 40.65% patients while the remaining 59.35% were unmethylated (low methylation scores). The mean, and SD age of the patients was 60.8 ± 12.7 years. The patient population included 90.6% white, 4.95% black, 4.42% of other races (Hispanic and Asians), out of these, males 57.7% and females 43.3 %. The incidence of GBM was 11.5% in 2010 and 34.29% in 2014. Overall survival (OS) among GBM patients was higher among methylated patients regardless of therapeutic intervention (p <0.001). Unadjusted mortality risk was higher in unmethylated patients (HR=1.22; 1.09–1.34). However adjusted for other demographic and therapeutic factors the hazard ratio was further increased to 1.5 (95% CI; 1.43–1.61). The other predictors of mortality were male (HR=1.10; 1.04–1.17), white (HR=1.31; 1.12–1.52), and black vs others (HR=1.22; 1.00–1.52), 5-year increase in age (HR=1.17; 1.15–1.19), no surgical resection (HR=2.00; 1.81–2.20) and no radiation treatment (HR=2.16; 2.01–2.32). Mean survival for the methylated group was 24.22 months, whereas mean survival for the unmethylated group was 17.55 months. These results confirm that MGMT promoter methylation is the single most important factor affecting survival among GBM patients and MGMT promoter methylation was an independent indicator of better prognosis for GBM patients. The presence of a methylated MGMT promoter is a predictive biomarker for response to alkylator based therapies.

The study of GPX3 methylation in patients with Kashin-Beck Disease and its mechanism in chondrocyte apoptosis.

Selenium deficiency is a risk factor for Kashin-Beck Disease (KBD), an endemic osteoarthropathy. Although promoter hypermethylation of glutathione peroxidase 3 (GPX3) (a selenoprotein) has been identified in several cancers, little is known about promoter methylation and expression of GPX3 and their relation to selenium in KBD. The present study was thus conducted to investigate this research question. Methylation and expressions of GPX3 in whole blood drawn from 288 KBD patients and 362 healthy controls and in chondrocyte cell line were evaluated using methylation-specific PCR and qRT-PCR, respectively. The protein levels of PI3K/Akt/c-fos signaling in the whole blood and chondrocyte cell line were determined with Western blotting. Chondrocytes apoptosis were detected by Hoechst 33342 and Annexin V-FITC/PI staining. GPX3 methylation was increased, GPX3 mRNA was decreased, and protein levels in the PI3K/Akt/c-fos signaling pathway were up-regulated in the whole blood collected from KBD patients as compared with healthy controls. Similar results were obtained for chondrocytes injured by oxidative stress. There was a significant, decreasing trend in GPX3 expression across groups of unmethylation, partial methylation, and complete methylation for GPX3, in sequence. Compared with unmethylation group, protein levels in PI3K/Akt/c-fos pathway were enhanced in partial and complete methylation groups. Treatment of chondrocytes with sodium selenite resulted in reduced methylation and increased expression of GPX3 as well as down-regulated level of PI3K/Akt/c-fos proteins. The methylation and expression of GPX3 and expression of PI3K/Akt/c-fos pathway are altered in KBD and these changes are reversible by selenium supplementation.

Correlation of commercially available quantitative MGMT (O-6-methylguanine-DNA methyltransferase) promoter methylation scores and GBM patient survival.

Between 2011 and 2016, O-6-methylguanine-DNA methyltransferase (MGMT) promoter methylation testing at University of California Los Angeles (UCLA) was performed through LabCorp, using a threshold of 2 to distinguish MGMT methylated from unmethylated tumors. In this study, we sought to determine whether the magnitude of the methylation score correlated with outcome. We identified 165 newly diagnosed glioblastoma (GBM) isocitrate dehydrogenase (IDH) wild-type and temozolomide-treated upfront patients at UCLA and Kaiser Permanente Los Angeles with LabCorp-derived quantitative MGMT scores obtained on pretreatment tissue samples. Using LabCorp's threshold, we found 102 unmethylated and 63 methylated patients. We then further substratified each group based on the magnitude of the score, and performed Kaplan-Meier and Cox regression analyses of overall survival (OS) and progression-free survival (PFS). We validated that the standard LabCorp threshold of 2 could separate our cohort by survival, showing longer OS and PFS for MGMT methylated patients vs unmethylated patients. Cox regression analysis confirmed that MGMT (<1) patients had worse outcome, with OS and PFS hazard ratios of 2.375 (P = .053) and 2.463 (P = .023), respectively, when compared to the MGMT (1-1.99) patients. Contrary to our expectation, when we substratified the ≥2 (methylated) group, we did not find a dose-dependent relationship between the magnitude of MGMT methylation and improved survival. The MGMT unmethylated group contains a partially methylated group (greater than 1) that shares survival benefits similar to the methylated group. However, we did not demonstrate an association of very high methylation scores with increased survival. These findings will require validation in additional independent clinical data sets.

Molecular classification of patients with grade II/III glioma using quantitative MRI characteristics.

Molecular markers of WHO grade II/III glioma are known to have important prognostic and predictive implications and may be associated with unique imaging phenotypes. The purpose of this study is to determine whether three clinically relevant molecular markers identified in gliomas-IDH, 1p/19q, and MGMT status-show distinct quantitative MRI characteristics on FLAIR imaging. Sixty-one patients with grade II/III gliomas who had molecular data and MRI available prior to radiation were included. Quantitative MRI features were extracted that measured tissue heterogeneity (homogeneity and pixel correlation) and FLAIR border distinctiveness (edge contrast; EC). T-tests were conducted to determine whether patients with different genotypes differ across the features. Logistic regression with LASSO regularization was used to determine the optimal combination of MRI and clinical features for predicting molecular subtypes. Patients with IDH wildtype tumors showed greater signal heterogeneity (p = 0.001) and lower EC (p = 0.008) within the FLAIR region compared to IDH mutant tumors. Among patients with IDH mutant tumors, 1p/19q co-deleted tumors had greater signal heterogeneity (p = 0.002) and lower EC (p = 0.005) compared to 1p/19q intact tumors. MGMT methylated tumors showed lower EC (p = 0.03) compared to the unmethylated group. The combination of FLAIR border distinctness, heterogeneity, and pixel correlation optimally classified tumors by IDH status. Quantitative imaging characteristics of FLAIR heterogeneity and border pattern in grade II/III gliomas may provide unique information for determining molecular status at time of initial diagnostic imaging, which may then guide subsequent surgical and medical management.

Interaction of DRD4 Methylation and Phthalate Metabolites Affects Continuous Performance Test Performance in ADHD

Objective: We investigated the interaction effect between the methylation of dopamine receptor D4 (DRD4) and phthalate exposure in ADHD on continuous performance test (CPT) variables. Method: Urine concentrations of mono-(2-ethyl-5-hydroxyhexyl) phthalate (MEHHP), mono-(2-ethyl-5-oxohexyl) phthalate (MEOHP), and mono-n-butyl phthalate (MBP) were tested. The methylation status was analyzed for CpG sites of DRD4. Multivariable linear regression models were applied to investigate the interaction effects of methylation and phthalate levels. Results: There was a significant interaction effect of the methylation of CpG26 and CpG28 with the MEHHP level on omission errors in ADHD patients, but not in controls. The post hoc analysis revealed a significant correlation between the MEHHP concentration and omission errors in the methylated group, but not in the unmethylated group. Conclusion: The interaction between the methylation status of CpG sites of DRD4, particularly CpG26 and CpG28, and phthalate metabolite levels affects the attention level in ADHD patients.

Circulating cell-free DNA of methylated insulin-like growth factor-binding protein 7 predicts a poor prognosis in hepatitis B virus-associated hepatocellular carcinoma after hepatectomy

The initiation and progression of hepatocellular carcinoma (HCC) is a multistage process involving a variety of changes at the gene level. Methylation of insulin-like growth factor-binding protein 7 (IGFBP7) plays a crucial role in HCC development. The main purpose of this study was to investigate the relationship between oxidative stress, DNA methyltransferases (DNMTs) expression, and IGFBP7 methylation, and to evaluate the prognostic value of serum IGFBP7 methylation status in patients with HCC after hepatectomy. We enrolled 155 patients with HCC undergoing surgical resection. The IGFBP7 methylation status, DNMTs mRNA levels and malondialdehyde (MDA), xanthine oxidase (XOD), reduced glutathione hormone (GSH), and glutathione-S-transferases (GST) levels were detected. MDA and XOD levels were significantly higher in IGFBP7 methylated group than unmethylated group, while GSH level was lower in methylated group than unmethylated group. The DNMT1 and DNMT3a mRNA levels were higher in IGFBP7 methylated group than unmethylated group. Kaplan–Meier curve analysis revealed that IGFBP7 promoter methylation was significantly correlated with overall survival (OS) (p < .001). Moreover, IGFBP7 methylation was an independent prognostic predictor for OS (p = .000) and early tumour recurrence (ETR) (p = .008) in HCC after hepatectomy. Our results indicated that IGFBP7 promoter methylation was associated with oxidative stress and DNMTs expression. Meanwhile, IGFBP7 promoter methylation was associated with OS and ETR, indicating that it might serve as a potentially independent prognostic factor in patients with HCC after hepatectomy.

Prognostic Significance of MGMT Promoter Methylation in Egyptian GBM Patients: A Single-institution Experience

Background: Glioblastoma Multiforme (GBM) is the highest-mortality tumor of the central nervous system. Epigenetic silencing of the MGMT gene by promoter methylation is associated with loss of MGMT expression and deficiency in MGMT-mediated DNA repair, which is affiliated with improved survival in patients treated with alkylating agents such as TMZ.Purpose: This is a retrospective work, studying the MGMT promoter status in a group of GBM patients; correlating this status to time to progression (TTP) and overall survival (OS).Methods: Thirty-nine patients with GBM, treated in Kasr El-Ainy Center of Clinical Oncology and Nuclear Medicine (NEMROCK) between January 2014 and January 2015, were included in our study. The QIAamp DNA FFPE Tissue Kit (Qiagen, USA) was used for genomic DNA extraction from Formalin-fixed paraffin-embedded tumor tissues of the 39 patients. Bisulfite modification of DNA was performed for detecting methylation in MGMT promoter using EpiTect Bisulfite Kit (Qiagen, USA). Specific primers were used to match methylated &amp; un-methylated DNA that was visualized by loading its PCR products in gel electrophoresis system. All statistical analyses were carried out using SPSS version 20.0.Results: The mean age for our patients was 48 years; with a male to female ratio of 1.3:1. MGMT promoter methylation was found in 27 patients (69.2%) compared to 12 (30.8%) with un-methylation. TMZ was received in 71.8 % (28) of our patients throughout their treatment. The median OS for all patients was 20.03 months; while the median TTP 15.03 was months. Although the OS was statistically significantly higher for patients with the methylated promoter (p-value = 0.004) compared to the un-methylated group; yet the TTP difference did not reach a statistically significant value (p-value = 0.048). Conclusions: The epigenetic silencing of the MGMT gene by promoter methylation has been associated with longer OS &amp; TTP in patients with GBM.

Abstract LB-A05: Utilizing methylation and expression signatures to construct predictive models and personalized cancer treatments

Abstract Background: Data from high-throughput genomic arrays available through The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) have been helpful in elucidating the role of methylome and transcriptome level variations in the oncogenesis and progression of various cancers. Methylome remodeling has been observed across most cancers, and several studies have revealed a novel role for methylation in regulating alternative splicing. Alternative splicing contributes to the malignancy and aggressiveness of cancers, and intragenic methylation of alternatively spliced exons (ASEs) can serve as an effective biomarker for prognosis and personalized treatment. This study focuses on identifying and exploiting clinically relevant intragenic methylation signatures in cancer. Methods: In this study, methylation beta values from the Illumina HumanMethylation450 (HM450) platform, exon expression values from the Illumina HiSeq 2000 platform and patient survival data were downloaded from TCGA. Values were then sorted into methylated and unmethylated groups at each intragenic HM450 probe using an algorithm for dichotomizing microarray data. Probes were selected if their methylation status significantly affected both exon expression and patient mortality and sorted by the difference in patient mortality between the two groups. Biomarkers with beta values falling within the lower mortality group were considered “positive biomarkers.” A series of univariate analyses were used to determine groupings of patients with similar outcomes based on the total number of positive biomarkers in a sample. This methodology was applied to multiple TCGA cohorts including breast cancer, non-small cell lung cancer (NSCLC) and metastatic melanoma. Prognostic models were constructed using multivariate regressions for each TCGA cohort and independently validated with data from GEO. Using clinical data from TCGA and Broad GDAC Firehose, each group of patients was also analyzed based on treatment including surgery, radiation and chemotherapy. Results: In each type of cancer, an unweighted index was created from the top biomarkers. In breast cancer nine probes were included in the index. Patients with seven to nine positive biomarkers had similar overall survivals (HR=1.000), as did patients with four to six positive biomarkers (HR=2.336, 95% CI=1.507-3.621) and zero to three positive biomarkers (HR=8.223, 95% CI=4.103-16.482). Benefits of radiation therapy were seen in the group with four to six positive biomarkers (p&amp;lt;.01). On average, normal breast tissue had more positive biomarkers than tumor tissue (p&amp;lt;.0001). In NSCLC, shorter survival rates were associated with patients in the top biomarker group treated with radiation therapy (p&amp;lt;.05). Patients in the second NSCLC group responded best to cisplatin (p&amp;lt;.05) while patients in the third group responded best to carboplatin (p&amp;lt;.05). The full results of the study will be made available online through an interactive web tool for physicians and researchers. Conclusions: This study has identified biomarkers of genes and pathways involved in alternative splicing in various cancers. These biomarkers are powerful predictors of prognosis and therapeutic response in the tested cohorts and may ultimately be useful for predicting personalized patient prognosis and guiding effective therapy. Citation Format: Caleb Reagor, Rebecca Conway. Utilizing methylation and expression signatures to construct predictive models and personalized cancer treatments [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2017 Oct 26-30; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Ther 2018;17(1 Suppl):Abstract nr LB-A05.

Estrogen receptor-α promoter methylation is a biomarker for outcome prediction of cisplatin resistance in triple-negative breast cancer.

A number of previous studies have indicated the presence of a link between estrogen receptor-α (ERα) methylation and triple-negative breast cancer (TNBC). However, the association between ERα methylation and drug resistance during the treatment of TNBC remains unclear. Methylation-specific polymerase chain reaction was used to investigate the methylation of ERα in the genomic DNA of 35 patients with TNBC who were defined as cisplatin-based chemotherapy-resistant using chemosensitivity testing. Survival probabilities by covariates were assessed using Kaplan-Meier estimator survival analysis and Cox's proportional hazards models, adjusting for age, menopausal status, tumor size, lymph node metastasis and ERα promoter DNA methylation. Of the 35 patients with TNBC analyzed, 8 exhibited ERα promoter DNA methylation. Cisplatin resistance was confirmed to be overwhelmingly associated with ERα methylation by univariate and multivariate analysis. Even in a limited analysis in patients with ERα methylation, the results generated from methylated tumor tissue and unmethylated tumor tissue revealed that expression of breast cancer type 1/2 susceptibility proteins was increased in ERα-methylated breast tumor tissue compared with in unmethylated tissue. The ERα methylation group tended to have significantly shorter progression-free (P=0.010) and overall (P=0.023) survival times compared with those in the unmethylated group. Similarly, shorter progression-free (P=0.024) and overall (P=0.018) survival times were observed in the cisplatin-resistant group compared with the cisplatin-non-resistant group. ERα methylation predicts a poor clinical outcome for patients with TNBC. The results of the present study indicated that ERα methylation may be a candidate surrogate biomarker for outcome prediction and cisplatin resistance in TNBC. Further investigation is required to identify potential biomarkers in a larger cohort in a prospective study.

The Initial Area Under the Curve Derived from Dynamic Contrast-Enhanced MRI Improves Prognosis Prediction in Glioblastoma with Unmethylated MGMT Promoter.

Although perfusion and permeability MR parameters have known to have prognostic value, they have reproducibility issues. Our aim was to evaluate whether the initial area under the time-to-signal intensity curve (IAUC) derived from dynamic contrast-enhanced MR imaging can improve prognosis prediction in patients with glioblastoma with known MGMT status. We retrospectively examined 88 patients with glioblastoma who underwent preoperative dynamic contrast-enhanced MR imaging. The means of IAUC values at 30 and 60 seconds (IAUC30mean and IAUC60mean) were extracted from enhancing tumors. The prognostic values of IAUC parameters for overall survival and progression-free survival were assessed with log-rank tests, according to the MGMT status. Multivariate overall survival and progression-free survival models before and after adding the IAUC parameters as covariates were explored by net reclassification improvement after receiver operating characteristic analysis for 1.5-year overall survival and 1-year progression-free survival and by random survival forest. High IAUC parameters were associated with worse overall survival and progression-free survival in the unmethylated MGMT group, but not in the methylated group. In the unmethylated MGMT group, 1.5-year overall survival and 1-year progression-free survival prediction improved significantly after adding IAUC parameters (overall survival area under the receiver operating characteristic curve, 0.86; progression-free survival area under the receiver operating characteristic curve, 0.74-0.76) to the model with other prognostic factors (overall survival area under the receiver operating characteristic curve, 0.81; progression-free survival area under the receiver operating characteristic curve, 0.69; P < .05 for all) except in the case of IAUC60mean for 1-year progression-free survival prediction (P = .059). Random survival forest models indicated that the IAUC parameters were the second or most important predictors in the unmethylated MGMT group, except in the case of the IAUC60mean for progression-free survival. IAUC can be a useful prognostic imaging biomarker in patients with glioblastoma with known MGMT status, improving prediction of glioblastoma prognosis with the unmethylated MGMT promoter status.

MGMT promoter methylation status as a prognostic factor for the outcome of gamma knife radiosurgery for recurrent glioblastoma.

We conducted this study to determine whether the methylation status of the O6-methylguanine-DNA methyltransferase (MGMT) promoter was a prognostic marker for positive outcomes of gamma knife radiosurgery (GKS) for recurrent glioblastoma (GBM). We retrospectively examined 61 patients, who underwent GKS for local recurrent GBM between 2004 and 2015; in all patients, the methylation status of the MGMT promoter was identified via methylation-specific quantitative real-time polymerase chain reaction. All patients underwent surgical resection and were diagnosed histopathologically with GBM. Prognostic factors associated with progression-free survival (PFS) and overall survival (OS) were identified in univariate and multivariate analyses. Twenty-five (41%) had a methylated MGMT promoter, and 36 (59%) had an unmethylated MGMT promoter. The median age at GKS was 58 years. The median tumor volume at GKS was 7.0cm3, and the median marginal dose was 16Gy. The median follow-up period after GKS was 7.5 months. The median PFS time after GKS was 8.9 months (95% CI 4.3-13.5 months) in the methylated and 4.6 months (95% CI 3.7-5.5 months) in the unmethylated group (P = 0.016). The median OS time after GKS was 14.0 months (95% CI 9.3-18.7 months) in the methylated group and 9.0 months (95% CI 6.5-11.5 months) in the unmethylated group (P = 0.026). Methylation of the MGMT promoter correlated with better PFS and OS after GKS for recurrent GBM. Prospective comparative studies are required to determine whether MGMT methylation directly affects the efficiency of GKS.

Hypermethylation of the N-Myc Downstream-Regulated Gene 2 Promoter in Peripheral Blood Mononuclear Cells is Associated with Liver Fibrosis in Chronic Hepatitis B.

DNA methylation is a fundamental epigenetic modification to regulate gene expression. N-Myc downstream-regulated gene (NDRG) 2 is a cytoplasmic protein and participates in the pathogenesis of liver fibrosis. In this study, the mRNA expression and methylation status of NDRG2 was evaluated in patients with chronic hepatitis B (CHB). The study included 143 CHB patients and 65 normal controls (NC). The mRNA expression of NDRG2 in peripheral blood mononuclear cells (PBMCs) was detected by quantitative real-time polymerase chain reaction. The methylation status of the NDRG2 promoter in PBMCs was detected by methylation-specific polymerase chain reaction. The NDRG2 mRNA level was lower in the CHB group than in the NC group (p < 0.001). Methylation frequency of the NDRG2 promoter was significantly higher in CHB patients than in the NC group (52.44% vs. 26.15%, p < 0.001). Importantly, the relative expression levels of NDRG2 mRNA were significantly lower in the methylated group than in the unmethylated group in both CHB patients and NC (p < 0.001). Furthermore, a lower mRNA level and hypermethylation of NDRG2 were associated with liver fibrosis and inflammation grade in CHB. The aspartate aminotransferase-to-platelet ratio index (APRI) score is widely used to predict liver fibrosis. The mRNA expression levels and methylation status of NDRG2 showed a better score compared to APRI for discriminating the severity of liver fibrosis. In conclusion, hypermethylation of NDRG2 in PBMCs was correlated with decreased mRNA expression and with liver fibrosis. The methylation status of the NDRG2 promoter in PBMCs is a potential noninvasive biomarker to predict the severity of liver fibrosis.

Distinctive Klf4 mutants determine preference for DNA methylation status.

Reprogramming of mammalian genome methylation is critically important but poorly understood. Klf4, a transcription factor directing reprogramming, contains a DNA binding domain with three consecutive C2H2 zinc fingers. Klf4 recognizes CpG or TpG within a specific sequence. Mouse Klf4 DNA binding domain has roughly equal affinity for methylated CpG or TpG, and slightly lower affinity for unmodified CpG. The structural basis for this key preference is unclear, though the side chain of Glu446 is known to contact the methyl group of 5-methylcytosine (5mC) or thymine (5-methyluracil). We examined the role of Glu446 by mutagenesis. Substituting Glu446 with aspartate (E446D) resulted in preference for unmodified cytosine, due to decreased affinity for 5mC. In contrast, substituting Glu446 with proline (E446P) increased affinity for 5mC by two orders of magnitude. Structural analysis revealed hydrophobic interaction between the proline's aliphatic cyclic structure and the 5-methyl group of the pyrimidine (5mC or T). As in wild-type Klf4 (E446), the proline at position 446 does not interact directly with either the 5mC N4 nitrogen or the thymine O4 oxygen. In contrast, the unmethylated cytosine's exocyclic N4 amino group (NH2) and its ring carbon C5 atom hydrogen bond directly with the aspartate carboxylate of the E446D variant. Both of these interactions would provide a preference for cytosine over thymine, and the latter one could explain the E446D preference for unmethylated cytosine. Finally, we evaluated the ability of these Klf4 mutants to regulate transcription of methylated and unmethylated promoters in a luciferase reporter assay.

Effect of MTHFR C677T Polymorphism on Methylation Status of E-Cadherin in Gastric Cancer

Background: MTHFR gene is one of the main and effective factors in genes methylation. This gene has a common polymorphism in cordon 677, which can affect its activity. Changing activity rate of this gene can affect methylation rate of tumor suppressor genes and cell membrane proteins and other genes in addition to their expression rate. Therefore, it can be considered as one of the effective factors on producing cancer. Methods: In this descriptive-cross sectional study, 34 cancer and non-cancer tissue samples were studied. Initially, DNA was extracted from samples and then E-cadherin and MTHFR c677t polymorphism were amplified by the polymerase chain reaction (PCR). Methylation status of E-cadherin was evaluated by adding methylation restriction enzyme HpaII and polymorphism of MTHFR c677t was assessment by the restriction fragment length polymorphism (RFLP) method. Results: Methylation status of E-cadherin gene numbers of methylated cases in the cancer group were equal to one and unmethylated cases equal to 33 and numbers of unmethylated cases in the non-cancer group was equal to 34 while there were no methylated cases. In assessment of methylation status of E-cadherin and different genotypes of MTHFR in codon number 677 in cancer samples, number of CC, CT and TT genotypes were equal to 0, 1 and 0 in the methylated group and equal to 6, 27 and 1 in the unmethylated group, respectively. Conclusions: According to this observation, another factor such as oncogenes activity may cause cancer in samples but CT genotype of MTHFR can be considered as an effective factor in creating cancer.

Phase 1 Study of Preoperative Chemoradiation Therapy With Temozolomide and Capecitabine in Patients With Locally Advanced Rectal Cancer

Preoperative chemoradiation therapy (CRT) with capecitabine is a standard treatment strategy in patients with locally advanced rectal cancer (LARC). Temozolomide improves the survival of patients with glioblastoma with hypermethylated O(6)-methylguanine DNA methyltransferase (MGMT); MGMT hypermethylation is one of the colorectal carcinogenesis pathways. We aimed to determine the dose-limiting toxicity (DLT) and recommended dose (RD) of temolozomide in combination with capecitabine-based preoperative CRT for LARC. Radiation therapy was delivered with 45Gy/25 daily fractions with coned-down boost of 5.4Gy/3 fractions. Concurrent chemotherapy comprised fixed and escalated doses of capecitabine and temozolomide, respectively. The MGMT hypermethylation was evaluated in pretreatment tumor samples. This trial is registered with ClinicalTrials.gov with the number NCT01781403. Twenty-two patients with LARC of cT3-4N0 or cTanyN1-2 were accrued. Dose level 3 was chosen as the RD because DLT was noticeably absent in 10 patients treated up to dose level 3. An additional 12 patients were recruited in this group. Grade III adverse events were noted, and pathologic complete response (pCR) was observed in 7 patients (31.8%); MGMT hypermethylation was detected in 16. The pCR rate was 37.5% and 16.7% in the hypermethylated and unmethylated MGMT groups, respectively (P=.616). There was a tendency toward higher pCR rates in patients with hypermethylated MGMT. Future randomized studies are therefore warranted.

Different diagnostic values of imaging parameters to predict pseudoprogression in glioblastoma subgroups stratified by MGMT promoter methylation

The aim of this study was to determine whether diffusion and perfusion imaging parameters demonstrate different diagnostic values for predicting pseudoprogression between glioblastoma subgroups stratified by O6-mythylguanine-DNA methyltransferase (MGMT) promoter methylation status. We enrolled seventy-five glioblastoma patients that had presented with enlarged contrast-enhanced lesions on magnetic resonance imaging (MRI) one month after completing concurrent chemoradiotherapy and undergoing MGMT promoter methylation testing. The imaging parameters included 10 or 90% histogram cutoffs of apparent diffusion coefficient (ADC10), normalized cerebral blood volume (nCBV90), and initial area under the time signal-intensity curve (IAUC90). The results of the areas under the receiver operating characteristic curve (AUCs) with cross-validation were compared between MGMT methylation and unmethylation groups. MR imaging parameters demonstrated a trend toward higher accuracy in the MGMT promoter methylation group than in the unmethylation group (cross-validated AUCs = 0.70-0.95 and 0.56-0.87, respectively). The combination of MGMT methylation status with imaging parameters improved the AUCs from 0.70 to 0.75-0.90 for both readers in comparison with MGMT methylation status alone. The probability of pseudoprogression was highest (95.7%) when nCBV90 was below 4.02 in the MGMT promoter methylation group. MR imaging parameters could be stronger predictors of pseudoprogression in glioblastoma patients with the methylated MGMT promoter than in patients with the unmethylated MGMT promoter. • The glioblastoma subgroup was stratified according to MGMT promoter methylation status. • Diagnostic values of diffusion and perfusion parameters for predicting pseudoprogression were compared. • Imaging parameters showed higher diagnostic accuracy in the MGMT promoter methylation group. • Imaging parameters were independent to MGMT promoter methylation status for predicting pseudoprogression. • Imaging biomarkers might demonstrate different diagnostic values according to MGMT promoter methylation.

Demethylation of tumor necrosis factor-α converting enzyme predicts poor prognosis in acute-on-chronic hepatitis B liver failure

Tumor necrosis factor-α converting enzyme (TACE) has been demonstrated to be involved in liver inflammation. However, the significance of TACE methylation in acute-on-chronic hepatitis B liver failure (ACHBLF) has not been demonstrated. This study aims to evaluate TACE methylation status in ACHBLF and determine its predictive value for prognosis. Forty-five patients with ACHBLF, 80 with chronic hepatitisB (CHB) and 54 healthy controls (HCs) were enrolled. The methylation status of TACE promoter was determined by methylation-specific polymerase chain reaction. The TACE mRNA expression was determined by quantitative real-time polymerase chain reaction. The plasma levels of TACE, TNF-α, sTNFRI, sTNFRII were measured by enzyme-linked immunosorbent assay. TACE methylation was significantly lower in patients with ACHBLF than those with CHB (χ(2)=24.69, P<0.01) and HCs (χ(2)=35.93, P<0.01). Meanwhile, TACE methylation was significantly lower in CHB patients than HCs (χ(2)=4.03, P<0.05). TACE methylation was significantly inversely associated with its mRNA expression (r=-0.68; P<0.01). The plasma levels of TACE, TNF-α, sTNFRI, sTNFRII were significantly higher in patients with ACHBLF than those with CHB (P<0.05, respectively) and HCs (P<0.05, respectively). In patients with ACHBLF, significantly higher prothrombin activity, lower total bilirubin and MELD score were found in TACE methylated group than unmethylated group (P<0.05). ACHBLF patients with methylated TACE showed significantly better survival than those without (P<0.01). This study showed that demethylation of TACE promoter occurred in ACHBLF and might serve as a potential prognostic marker.