Percentage Of Methylated Reference Research Articles

Hypermethylation of MDFI promoter with NSCLC is specific for females, non-smokers and people younger than 65.

Non-small cell lung carcinoma (NSCLC) is a major subtype of lung cancer. Aberrant DNA methylation has been frequently observed in NSCLC. The aim of the present study was to investigate the role of MyoD family inhibitor (MDFI) methylation in NSCLC. Formalin-fixed paraffin-embedded tumor tissues and adjacent non-cancerous tissues were collected from a total of 111 patients with NSCLC. A methylation assay was performed using the quantitative methylation-specific polymerase chain reaction method. The percentage of methylated reference was used to represent the methylation level of the MDFI promoter. Data mining of a dataset from The Cancer Genome Atlas (TCGA) demonstrated that MDFI promoter methylation levels were significantly increased in 830 tumor tissues compared with 75 non-tumor tissues (P=0.012). However, the results on tissues obtained in the present study indicated that the MDFI promoter methylation levels in tumor tissues were not significantly different compared with those in the adjacent non-tumor tissues (P=0.159). Subsequent breakdown analysis identified that higher MDFI promoter methylation levels were significantly associated with NSCLC in females (P=0.031), but not in males (P=0.832). Age-based subgroup analysis demonstrated that higher MDFI promoter methylation levels were significantly associated with NSCLC in younger patients (≤65 years; P=0.003), but not in older patients (P=0.327). In addition, the association of MDFI methylation with NSCLC was significant in non-smokers (P=0.014), but not in smokers (P=0.832). Similar results also have been determined from subgroup analysis of the TCGA datasets. The Gene Expression Omnibus database indicated MDFI expression restoration in partial lung cancer cell lines (H1299 and Hotz) following demethylation treatment. However, it was identified that MDFI promoter hypermethylation was not significantly associated with prognosis of NSCLC (P>0.05). In conclusion, the present study indicated that the association of higher methylation of the MDFI promoter with NSCLC may be specific to females, non-smokers and people aged ≤65.

Quantitative DNA methylation analysis of paired box gene 1 and LIM homeobox transcription factor 1 α genes in cervical cancer.

DNA methylation is associated with tumorigenesis and may act as a potential biomarker for detecting cervical cancer. The aim of the present study was to explore the methylation status of the paired box gene 1 (PAX1) and the LIM homeobox transcription factor 1 α (LMX1A) gene in a spectrum of cervical lesions in an Eastern Chinese population. This single-center study involved 121 patients who were divided into normal cervix (NC; n=28), low-grade squamous intraepithelial lesion (LSIL; n=32), high-grade squamous intraepithelial lesion (HSIL; n=34) and cervical squamous cell carcinoma (CSCC; n=27) groups, according to biopsy results. Following extraction and modification of the DNA, quantitative assessment of the PAX1 and LMX1A genes in exfoliated cells was performed using pyrosequencing analysis. Receiver operating characteristic (ROC) curves were generated to calculate the sensitivity and specificity of each parameter and cut-off values of the percentage of methylation reference (PMR) for differentiation diagnosis. Analysis of variance was used to identify differences among groups. The PMR of the two genes was significantly higher in the HSIL and CSCC groups compared with that in the NC and LSIL groups (P<0.001). ROC curve analysis demonstrated that the sensitivity, specificity and accuracy for detection of CSCC were 0.790, 0.837 and 0.809, respectively, using PAX1; and 0.633, 0.357 and 0.893, respectively, using LMX1A. These results indicated that quantitative PAX1 methylation demonstrates potential for cervical cancer screening, while further investigation is required to determine the potential of LMX1A methylation.

Abstract 46: Validation of potential predictive DNA methylation biomarkers for head and neck squamous cell carcinoma anatomic subsite

Abstract Introduction: We previously identified by a genome-wide approach, differentially methylated genes in head and neck squamous cell carcinoma (HNSCC), including genes uniquely methylated in each HNSCC anatomic subsite. To define their potential prognostic value the validation of uniquely methylated genes in a cohort of HNSCC patients, according to the anatomic subsite, is warranted. Thus, here we present validation data of three potential DNA methylation biomarkers in a cohort comprising primary tumors of 54 HNSCC patients. Methods: Tumor DNA was extracted from HNSCC patients, stratified by the primary tumor anatomic subsite, which included 21 laryngeal cancers, 21 oral cavity cancer, and 12 pharyngeal cancers. The DNA methylation status of three candidate biomarkers, CDH1 for laryngeal cancer, PITX2 for oral cavity cancer, and SFRP1 for pharyngeal cancer were assessed. DNA methylation analysis was performed using qMSP MethyLight assay and quantitative methylation value for each gene was expressed as the Percentage of Methylation Reference (PMR). A PMR value cut-off was established to classify samples as positively or negatively methylated. PMR values &amp;lt;10 were classified as negatively methylated and PMR values of ≥10 were classified as positively methylated for each gene. Results: Positive methylation (PMR ≥10) was detected in 71% of laryngeal samples for CDH1 and, in pharyngeal cancer, 66% showed positive methylation for SFRP1. 90% of oral cavity samples showed positive methylation for PITX2. No association with clinicopathologic characteristics (stage, differentiation, recurrence) was found. However, high PMR values (PMR ≥20) were observed in early stage tumors (I and II) as for late stage tumors (III and IV) for all candidate genes tested. Conclusion: HNSCC subsites (larynx, oral cavity and pharynx) show differential DNA methylation patterns for selected genes. Aberrant methylation of CDH1, PITX2 and SFRP1 was established in a high percentage of tumors, suggesting these candidate genes might be useful as molecular classifiers for HNSCC subsite. In addition, aberrant methylation of CDH1, PITX2, and SFRP1 was detected in early stage tumors; which might be indicators of hypermethylation as an early event in HNSCC carcinogenesis, and in association to the anatomic subsite. Analysis of these unique DNA methylation biomarkers for HNSCC may be valuable for an accurate disease prognosis and for design of novel treatments. Citation Format: Bianca L. Rivera, Jaime Aponte, Sol Nadal, Sebastian Oliva, Sebastian Bravo, Rafael Guerrero, Juan Trinidad, Adriana Baez. Validation of potential predictive DNA methylation biomarkers for head and neck squamous cell carcinoma anatomic subsite [abstract]. In: Proceedings of the AACR-AHNS Head and Neck Cancer Conference: Optimizing Survival and Quality of Life through Basic, Clinical, and Translational Research; April 23-25, 2017; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2017;23(23_Suppl):Abstract nr 46.

Elevated UMOD methylation level in peripheral blood is associated with gout risk

Uromodulin (UMOD) encodes an uromodulin glycoprotein, and its mutation results in uromodulin glycoprotein dysfunction and the occurrence of gout. The aim of our study was to assess whether UMOD methylation could predict the risk of gout. A total of 89 sporadic gout cases and 103 age and gender-matched healthy controls were recruited in this study. UMOD methylation level was determined by quantitative methylation-specific PCR (qMSP) in peripheral blood, and the percentage of methylated reference (PMR) was described to represent the methylation level. Our results showed that UMOD methylation was significantly higher in gout cases than controls (median: 1.45 versus 0.75, P < 0.001). The area under curve (AUC) of UMOD methylation in gout was 0.764 (P = 2.90E-10) with a sensitivity of 65.2% and a specificity of 88.3%. UMOD methylation level was shown to be significantly correlated with the serum level of uric acid (UA) (r = −0.208, P = 0.035). Besides, the luciferase reporter assay showed that UMOD CpG island region was able to upregulate gene expression (fold change = 2, P = 0.004). In conclusion, UMOD methylation assessment might be used to predict the occurrence of gout.

AGTR1 promoter hypermethylation in lung squamous cell carcinoma but not in lung adenocarcinoma

Aberrant DNA methylation is associated with non-small cell lung cancer (NSCLC), suggesting that gene promoter methylation may be a potential biomarker for the detection or risk prediction of NSCLC. The present study aimed to evaluate the potential usage of angiotensin II receptor type 1 (AGTR1) methylation in two major pathologic subtypes: Lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC). Quantitative methylation-specific polymerase chain reaction was used to investigate the effect of AGTR1 promoter methylation in the tumor and the paired adjacent non-tumor tissue samples from 42 patients with LUSC, and 69 with LUAD. The percentage of methylated reference was calculated and presented as the median (interquartile range 25th-75th percentile). The results of the current study revealed that there was significantly increased AGTR1 promoter methylation in the tumor tissues compared with the paired adjacent non-tumor tissue [97.4 (57.22-130.5) vs. 85 (48.25-123); P=0.024]. Furthermore, higher AGTR1 promoter methylation was observed in patients with LUSC compared with LUAD (odds ratio=2.483; 95% confidence interval=1.125-5.480; P=0.023). Significant differences were identified in AGTR1 methylation between non-tumor and the tumor tissues in LUSC [113.5 (68.33-148.73) vs. 93.04 (45.94-140); P=0.008]. In addition, the Cancer Genome Atlas data of 378 patients with LUSC and 477 with LUAD revealed an inverse correlation between gene expression and the methylation status of AGTR1 promoter.. These data suggest that AGTR1 hypermethylation is a promising biomarker to assist in LUSC detection and diagnosis.

CCL2 promoter hypomethylation is associated with gout risk in Chinese Han male population

ObjectivesC-C motif chemokine ligand 2 (CCL2) encodes a chemokine which amplifies and maintains inflammation through chemokine-cytokine networks. Gout is a type of painful inflammation arthritis in response to the deposition of monosodium urate (MSU) crystals in joints. The purpose of this study was to figure out the role of CCL2 promoter methylation in gout. MethodsA quantitative methylation-specific polymerase chain reaction (qMSP) was used to measure CCL2 promoter methylation in 93 gout patients and 101 healthy controls, respectively. All participants were Chinese Han males. The percent of methylated reference (PMR) was used to evaluate methylation level of each sample. ResultsIn the current study, we have found that CCL2 promoter methylation was significantly lower in gout than in healthy controls (24.95% versus 42.68%, P<0.001). CCL2 promoter hypermethylation was considered as a risk factor of gout [OR (95% CI)=3.59E-04 (5.67E-06, 0.023), P=1.79E-04]. Receiver operating characteristic (ROC) curve analysis showed there was a significant diagnostic value of CCL2 hypomethylation for gout (AUC=0.763, 95% CI=0.695-0.830, sensitivity=0.644, specificity=0.849). ConclusionsCCL2 promoter hypomethylation in peripheral blood could be a potential biomarker for the diagnosis of gout in Chinese Han males.

Detection of SPG20 gene promoter-methylated DNA, as a novel epigenetic biomarker, in plasma for colorectal cancer diagnosis using the MethyLight method.

Aberrant promoter methylation of genes is a common epigenetic alteration in colorectal cancer (CRC). In the present study, spastic paraplegia 20 (SPG20) promoter-methylated DNA, as a potential diagnostic biomarker, was investigated in plasma and tumor tissue samples from patients with CRC. To the best of our knowledge, the quantification of SPG20 promoter-methylated DNA in plasma samples remains unreported. SPG20 promoter methylation was investigated in 32 paired tumor and healthy adjacent tissues, 37 plasma samples from patients with CRC, and in 37 plasma samples from a healthy control group, using the MethyLight method. The percentage of methylated reference (PMR) values was determined for each sample, and the sensitivity and specificity of this unique biomarker were evaluated. PMR values were significantly higher in plasma samples from patients with CRC compared with in those from the control group (P<0.05). Plasma specimens from patients and healthy controls exhibited median PMR values of 7.7 (95% CI, 4.15-15.28) and 0.59 (95% CI, 0.14-1.12), respectively. Notably, the median PMR values were identified as 42.39 (95% CI, 27.69-72.26) and 3.61 (95% CI, 1.07-5.29) in tumor and adjacent healthy tissues, respectively. Using receiver-operating characteristics curve analysis, the area under curve (AUC) was demonstrated to be 0.984 for plasma samples, exhibiting a sensitivity of 81.1% and a specificity of 96.9%. Furthermore, the AUC was 0.996 for tissue samples, revealing a sensitivity of 93.8% and specificity of 99.96%. Results from the present study indicate that the identification of SPG20 promoter-methylated DNA in plasma is a potential diagnostic biomarker for the detection of CRC. Furthermore, the results demonstrate a satisfactory sensitivity and specificity, indicating the importance of SPG20 methylation as a novel noninvasive biomarker.

Identification the potential of stool-based SNCA methylation as a candidate biomarker for early colorectal cancer detection

Background: Stool-based DNA methylation are emerging as promising biomarkers for colorectal cancer (CRC), but their capability for detecting curable stages (adenomas) remains unclear. This study aims to explore the potential of selected candidate biomarkers (SNCA, SPG20 and FBN1) in stool samples for identifying patients with adenomas or CRC. Methods: Thirty-one patients with CRC, 49 patients with adenomas, and 64 normal controls were selected. Stool samples were processed by the stool intestinal mucosal cells collector and analyzed by quantitative methylation-specific polymerase chain reaction (qMSP). Results: Promoter methylation status of genes was denoted as percentage of methylated reference (PMR) values. The SNCA PMR values were significantly higher in CRC and adenomas groups than normal controls. The area under the ROC curve (AUC) for SNCA was 0.836 and 0.772 for detection of CRC and adenomas, respectively. The sensitivity of stool-based SNCA methylation was 83.9% for CRC and 75.5% for adenomas, with the specificity of 75% for both. The odds ratio (OR) for CRC and adenomas with stool SNCA hypermethylation was 11.291 and 9.234, respectively, after adjustment for patients’ age and sex. Though there was a trend of increase of SNCA promoter methylation with disease progression, the difference was not significant. No significant difference in stool-based SNCA methylation was found between proximal and distal lesions. SNCA methylation significantly reduced after tumor resection compared to the initial status. The SPG20 and FBN1 methylation status was not significantly different among groups. Conclusions: The results validated the capability of SNCA methylation in stool samples for the identification of patients with adenomas or CRC.

Experimental factors affecting the robustness of DNA methylation analysis

Diverging methylation frequencies are often reported for the same locus in the same disease, underscoring the need for limiting technical variability in DNA methylation analyses. We have investigated seven likely sources of variability at different steps of bisulfite PCR-based DNA methylation analyses using a fully automated quantitative methylation-specific PCR setup of six gene promoters across 20 colon cancer cell lines. Based on >15,000 individual PCRs, all tested parameters affected the normalized percent of methylated reference (PMR) differences, with a fourfold varying magnitude. Additionally, large variations were observed across the six genes analyzed. The highest variation was seen using single-copy genes as reference for normalization, followed by different amounts of template in the PCR, different amounts of DNA in the bisulfite reaction, and storage of bisulfite converted samples. Finally, when a highly standardized pipeline was repeated, the difference in PMR value for the same assay in the same cell line was on average limited to five (on a 0–100 scale). In conclusion, a standardized pipeline is essential for consistent methylation results, where parameters are kept constant for all samples. Nevertheless, a certain level of variation in methylation values must be expected, underscoring the need for careful interpretation of data.

High promoter methylation levels of glutathione-S-transferase M3 predict poor prognosis of acute-on-chronic hepatitis B liver failure.

This study aimed to evaluate the prognostic value of glutathione-S-transferase M3 (GSTM3) gene promoter methylation in patients with acute-on-chronic hepatitis B liver failure (ACHBLF). A total of 119 patients with ACHBLF, 60 patients with chronic hepatitis B and 30 healthy controls were enrolled. We used a quantitative methylation detection technique, MethyLight, to examine the methylation levels of GSTM3 in peripheral blood mononuclear cells. The GSTM3 methylation level was significantly higher in patients with ACHBLF than those in patients with chronic hepatitis B and healthy controls (both P <0.05). In patients with ACHBLF, GSTM3 methylation level percentage of methylated reference (PMR) positively correlated with total bilirubin, international normalized ratio, and Model for End-stage Liver Disease (MELD) score, and negatively correlated with prothrombin activity and albumin (all P <0.05). The PMR for GSTM3 of non-survivors was significantly increased compared to that of survivors (P < 0.05). Multivariate analysis indicated that GSTM3 methylation level was one of the independent prognostic factors for 3-month mortality of ACHBLF (P = 0.000). The area under the receiver-operator characteristic curve of PMR for GSTM3 in predicting 3-month mortality of ACHBLF was not statistically different from that of MELD score (0.798 vs. 0.716, P = 0.152). However, the area under the curve of PMR for GSTM3 was significantly higher than that of MELD score in predicting 1-month mortality (0.887 vs. 0.737, P = 0.020). Promoter methylation levels of GSTM3 in peripheral blood mononuclear cells closely correlated with disease severity and could be used to predict prognosis of patients with ACHBLF.

PD46-07 URINARY DNA METHYLATION BIOMARKERS: A NON-INVASIVE METHOD FOR PROSTATE CANCER MONITORING

INTRODUCTION AND OBJECTIVES: The majority of men with prostate cancer (PCa) are diagnosed with low-risk disease given effective PSA screening. To avoid over-treatment, men with low-risk PCa are encouraged to be followed on an Active Surveillance (AS) protocol in which repeated blood tests, digital rectal examinations (DRE) and prostate biopsies are utilized to monitor disease progression. Aberrant DNA methylation is a common feature in a variety of tumours. Tumour-specific gene methylation would be an ideal biomarker since only minute amounts of DNA are required which could be extracted from post-DRE urine samples, thus being a much less invasive method for PCa screening as compared to frequent biopsies. Our group previously identified and validated a panel of DNA methylation biomarkers that predicted the presence of high risk disease and/or post treatment biochemical recurrence in radical prostatectomy samples. In the current study, we investigated if this same panel of biomarkers can be detected in post-DRE urine samples of PCa patients participating in an AS program, and whether methylation of these biomarkers could have prognostic value in predicting development of high-risk PCa. METHODS: We collected post DRE urine samples from PCa patients with lowand intermediate-risk PCa patients followed in an AS program. DNA extracted from urine cell pellets was analyzed for selected methylation biomarkers by multiplex MethyLight, a highly sensitive, methylation specific qPCR assay. Patients were stratified using Chi-square analysis by the percent of methylated reference (PMR). Correlative studies were performed on methylation data and clinical variables such as Gleason score and clinical stage. RESULTS: DNA extracted from DRE urine cell pellets of 142 patients was analyzed for the presence of 9 DNA methylation biomarkers. DNA methylation in one or more biomarkers was seen in 73% of patients. Methylation of 3 independent biomarkers was able to distinguish between low(GS6) and intermediate-risk (GS7) PCa (p<0.05). Multigene analysis showed that methylation in a combination of any 3 genes was able to stratify between GS6 and GS7 patients (p<0.05). CONCLUSIONS: We have demonstrated that our panel of DNA methylation biomarkers can be detected in DRE urine samples of PCa patients. These markers have prognostic value in distinguishing low-risk vs intermediate risk PCa. The promising results from this study may help establish a less invasive method for PCa monitoring for patients in AS programs, resulting in better management and treatment for PCa patients.

Detection of methylated septin 9 in tissue and plasma of colorectal patients with neoplasia and the relationship to the amount of circulating cell-free DNA.

BackgroundDetermination of methylated Septin 9 (mSEPT9) in plasma has been shown to be a sensitive and specific biomarker for colorectal cancer (CRC). However, the relationship between methylated DNA in plasma and colon tissue of the same subjects has not been reported.MethodsPlasma and matching biopsy samples were collected from 24 patients with no evidence of disease (NED), 26 patients with adenoma and 34 patients with CRC. Following bisulfite conversion of DNA a commercial RT-PCR assay was used to determine the total amount of DNA in each sample and the fraction of mSEPT9 DNA. The Septin-9 protein was assessed using immunohistochemistry.ResultsThe percent of methylated reference (PMR) values for SEPT9 above a PMR threshold of 1% were detected in 4.2% (1/24) of NED, 100% (26/26) of adenoma and 97.1% (33/34) of CRC tissues. PMR differences between NED vs. adenoma and NED vs. CRC comparisons were significant (p<0.001). In matching plasma samples using a PMR cut-off level of 0.01%, SEPT9 methylation was 8.3% (2/24) of NED, 30.8% (8/26) of adenoma and 88.2% (30/34) of CRC. Significant PMR differences were observed between NED vs. CRC (p<0.01) and adenoma vs. CRC (p<0.01). Significant differences (p<0.01) were found in the amount of cfDNA (circulating cell-free DNA) between NED and CRC, and a modest correlation was observed between mSEPT9 concentration and cfDNA of cancer (R2 = 0.48). The level of Septin-9 protein in tissues was inversely correlated to mSEPT9 levels with abundant expression in normals, and diminished expression in adenomas and tumors.ConclusionsMethylated SEPT9 was detected in all tissue samples. In plasma samples, elevated mSEPT9 values were detected in CRC, but not in adenomas. Tissue levels of mSEPT9 alone are not sufficient to predict mSEPT9 levels in plasma. Additional parameters including the amount of cfDNA in plasma appear to also play a role.

Brain-derived neurotrophic factor (BDNF)—Epigenetic regulation in unipolar and bipolar affective disorder

BackgroundAlterations of brain-derived neurotrophic factor (BDNF) DNA methylation at specific BDNF promoters and corresponding gene expressions are associated with pathology and the response to antidepressant (AD) therapy in affective disorders such as major depressive disorder (MDD) and bipolar disorder (BD). MethodsGenomic DNA was derived from peripheral blood mononuclear cells (PBMCs) and was bisulfite converted. Percentage of methylated reference (PMR) was calculated based on results from quantitative real-time PCR following the MethyLight protocol. For statistical analysis parametric procedures were performed as appropriate. ResultsIn this study 544 subjects were included, 207 MDD subjects, 59 BD subjects and 278 control subjects. The BDNF exon I promoter methylation resulted to be significantly increased in MDD subjects compared to BD subjects (p=0.0089) and control subjects (p<0.001). Furthermore, the increase of methylation in MDD subjects was significantly associated with AD therapy (p=0.0019) but not to the clinical features of depression such as the severity of symptoms (p=n.s.). None of the 12 investigated single nucleotide polymorphisms (SNP) showed significant genotype–methylation interactions. LimitationsAlthough based on previous findings, the DNA methylation was evaluated within only one CpG island of the different alternative BDNF gene transcripts. ConclusionsThe results suggest that the methylation status might not only be affected by the disease phenotype but might also be further influenced by pharmacological treatment, therefore harbouring the possibility of identifying new insights for treatment options.

Clinical significance of ID4 methylation detection by quantitative methylation-specific PCR in acute leukemia

The advances of treatment improved the prognosis of the patients with acute leukemia (AL) in the last decade, but the lack of general biomarker for predicting relapse in AL, which is one of the most important factors influencing the survival and prognosis. DNA methylation of ID4 gene promoter occurred frequently in patients with AL and was found to be highly related to the tumor progression. Based on the previous work of the setup of methylation-specific quantitative PCR system for ID4 gene, this study was designed to investigate the relation between the quantitative indicator of methylation density, percentage of methylation reference(PMR) value, and different disease status of AL. PMR of ID4 was detected by MS-PCR in bone marrow (BM) samples of 17 healthy persons and 54 AL patients in the status of newly diagnosis, complete remission and disease relapse. The results showed that at different disease status, PMR value in newly diagnosed group was significantly lower than that in complete remission group (P = 0.031). Among serial samples, PMR value remained very low at the status of patients with continuous complete remission (<1.5‰), and increased along with the accumulation of tumor cells at relapse. In 1 relapse case, the abnormal rise of PMR value occurred prior to morphological relapse. PMR value seemed to be related to body tumor cell load. It is concluded that the quantitative indicator of methylation density and PMR value may reflect the change of tumor cell load in acute leukemia patients. Dynamic monitoring of PMR maybe predict leukemia relapse.

Correlation of HOXD3 promoter hypermethylation with clinical and pathologic features in screening prostate biopsies.

BACKGROUNDMolecular markers that can discriminate indolent cancers from aggressive ones may improve the management of prostate cancer and minimize unnecessary treatment. Aberrant DNA methylation is a common epigenetic event in cancers and HOXD3 promoter hypermethylation (H3PH) has been found in prostate cancer. Our objective was to evaluate the relationship between H3PH and clinicopathologic features in screening prostate biopsies.METHODSNinety-two patients who underwent a prostate biopsy at our institution between October 2011 and May 2012 were included in this study. The core with the greatest percentage of the highest grade disease was analyzed for H3PH by methylation-specific PCR. Correlational analysis was used to analyze the relationship between H3PH and various clinical parameters. Chi-square analysis was used to compare H3PH status between benign and malignant disease.RESULTSOf the 80 biopsies with HOXD3 methylation status assessable, 66 sets were confirmed to have cancer. In the 14 biopsies with benign disease there was minimal H3PH with the mean percentage of methylation reference (PMR) of 0.7%. In contrast, the HOXD3 promoter was hypermethylated in 16.7% of all cancers and in 50% of high risk tumors with an average PMR of 4.3% (P = 0.008). H3PH was significantly correlated with age (P = 0.013), Gleason score (P = 0.031) and the maximum involvement of the biopsy core (P = 0.035).CONCLUSIONSH3PH is associated with clinicopathologic features. The data indicate that H3PH is more common in older higher risk patients. More research is needed to determine the role of this marker in optimizing management strategies in men with newly diagnosed prostate cancer. Prostate 74:714–721, 2014. © 2014 The Authors. The Prostate published by Wiley Periodicals, Inc.

Association between hypermethylation of DNA repetitive elements in white blood cell DNA and early-onset colorectal cancer

Changes in the methylation levels of DNA from white blood cells (WBCs) are putatively associated with an elevated risk for several cancers. The aim of this study was to investigate the association between colorectal cancer (CRC) and the methylation status of three DNA repetitive elements in DNA from peripheral blood. WBC DNA from 539 CRC cases diagnosed before 60 years of age and 242 sex and age frequency-matched healthy controls from the Australasian Colorectal Cancer Family Registry were assessed for methylation across DNA repetitive elements Alu, LINE-1 and Sat2 using MethyLight. The percentage of methylated reference (PMR) of cases and controls was calculated for each marker. Odds ratios (ORs) and 95% confidence intervals (CIs) were estimated using multivariable logistic regression adjusted for potential confounders. CRC cases demonstrated a significantly higher median PMR for LINE-1 (p < 0.001), Sat2 (p < 0.001) and Alu repeats (p = 0.02) when compared with controls. For each of the DNA repetitive elements, individuals with PMR values in the highest quartile were significantly more likely to have CRC compared with those in the lowest quartile (LINE-1 OR = 2.34, 95%CI = 1.48–3.70; p < 0.001, Alu OR = 1.83, 95%CI = 1.17–2.86; p = 0.01, Sat2 OR = 1.72, 95%CI = 1.10–2.71; p = 0.02). When comparing the OR for the PMR of each marker across subgroups of CRC, only the Alu marker showed a significant difference in the 5-fluoruracil treated and nodal involvement subgroups (both p = 0.002). This association between increasing methylation levels of three DNA repetitive elements in WBC DNA and early-onset CRC is novel and may represent a potential epigenetic biomarker for early CRC detection.

Genome-Wide Identification and Validation of a Novel Methylation Biomarker, SDC2, for Blood-Based Detection of Colorectal Cancer

Aberrant DNA methylation has shown promise as a biomarker for the early detection of cancer. To discover novel genes frequently methylated at an early stage in colorectal cancer (CRC), DNA microarray analysis coupled with enriched methylated DNA was performed in primary tumors and compared with adjacent nontumor tissues of 12 patients with CRC at stages I to IV. Stepwise filtering for candidate selection in microarray data analysis yielded a set of genes that are highly methylated across all CRC tumors and that can be used as a composite biomarker for CRC detection. Verification assay identified the SDC2 gene as a potential methylation biomarker for early CRC detection. In clinical validation in tissues from 139 CRC patients, a much higher level of aberrant SDC2 methylation was measured in most primary tumors (97.8%), compared with corresponding nontumor tissue of CRC patients, irrespective of clinical stage. Clinical validation of SDC2 methylation in serum DNA from CRC patients (n = 131) at stages I to IV and from healthy individuals (n = 125) by quantitative methylation-specific PCR demonstrated a high sensitivity of 87.0% (95% CI, 80.0% to 92.3%) in detecting cancers, with a specificity of 95.2% (95% CI, 89.8% to 98.2%). Importantly, sensitivity at stage I was 92.3%, indicating the potential of SDC2 methylation as a blood-based DNA test for early detection of CRC.

Novel Application of Structural Equation Modeling to Correlation Structure Analysis of CpG Island Methylation in Colorectal Cancer

The CpG island methylator phenotype (CIMP-high, CIMP1) is a distinct phenotype associated with microsatellite instability (MSI) and BRAF mutation in colon cancer. Recent evidence suggests the presence of KRAS mutation-associated CIMP subtype (CIMP-low, CIMP2). We used cluster analysis, principal component analysis (PCA), and structural equation modeling (SEM), a novel strategy, to decipher the correlation structure of CpG island hypermethylation. Using a database of 861 colon and rectal cancers, DNA methylation at 16 CpG islands [CACNA1G, CDKN2A (p16/ink4a), CHFR, CRABP1, HIC1, IGF2, IGFBP3, MGMT, MINT-1, MINT-31, MLH1, NEUROG1, p14 (CDKN2A/arf), RUNX3, SOCS1, and WRN] was quantified by real-time PCR. Tumors were categorized into three groups: Group 1 with wild-type KRAS/BRAF (N = 440); Group 2 with mutant KRAS and wild-type BRAF (N = 308); and Group 3 with wild-type KRAS and mutant BRAF (N = 107). Tumors with mutant KRAS/BRAF (N = 6) were excluded. In unsupervised hierarchical clustering analysis, all but six markers (CACNA1G, IGF2, RUNX3, MGMT, MINT-1, and SOCS1) were differentially clustered with CIMP-high and CIMP-low according to KRAS and BRAF status. In SEM, the correlation structures between CIMP, locus-specific CpG island methylation, and MSI differed according to KRAS and BRAF status, which was consistent with PCA results. In conclusion, KRAS and BRAF mutations appear to differentially influence correlation structure of CpG island methylation. Our novel data suggest two distinct perturbations, resulting in differential locus-specific propensity of CpG methylation.

Promoter methylation of CDKN2A and lack of p16 expression characterize patients with hepatocellular carcinoma.

BackgroundThe product of CDKN2A, p16 is an essential regulator of the cell cycle controlling the entry into the S-phase. Herein, we evaluated CDKN2A promoter methylation and p16 protein expression for the differentiation of hepatocellular carcinoma (HCC) from other liver tumors.MethodsTumor and corresponding non-tumor liver tissue samples were obtained from 85 patients with liver tumors. CDKN2A promoter methylation was studied using MethyLight technique and methylation-specific PCR (MSP). In the MethyLight analysis, samples with ≥ 4% of PMR (percentage of methylated reference) were regarded as hypermethylated. p16 expression was evaluated by immunohistochemistry in tissue sections (n = 148) obtained from 81 patients using an immunoreactivity score (IRS) ranging from 0 (no expression) to 6 (strong expression).ResultsHypermethylation of the CDKN2A promoter was found in 23 HCCs (69.7%; mean PMR = 42.34 ± 27.8%), six (20.7%; mean PMR = 31.85 ± 18%) liver metastases and in the extralesional tissue of only one patient. Using MSP, 32% of the non-tumor (n = 85), 70% of the HCCs, 40% of the CCCs and 24% of the liver metastases were hypermethylated. Correspondingly, nuclear p16 expression was found immunohistochemically in five (10.9%, mean IRS = 0.5) HCCs, 23 (92%; mean IRS = 4.9) metastases and only occasionally in hepatocytes of non-lesional liver tissues (mean IRS = 1.2). The difference of CDKN2A-methylation and p16 protein expression between HCCs and liver metastases was statistically significant (p < 0.01, respectively).ConclusionPromoter methylation of CDKN2A gene and lack of p16 expression characterize patients with HCC.

Quantitative DNA methylation analysis detects cervical intraepithelial neoplasms type 3 and worse

DNA methylation may be used a potential biomarker for detecting cervical cancer. The authors of this report used quantitative methylation analysis of 4 genes in a full spectrum of cervical lesions to test its potential clinical application. This hospital-based, retrospective, case-control study was conducted in 185 patients and included patients who had a normal uterine cervix (n = 53), cervical intraepithelial neoplasm type 1 (CIN1) (n = 37), CIN2 (n = 22), CIN3 (n = 24), carcinoma in situ (CIS) (n = 22), squamous cell carcinoma (SCC, n = 20), and adenocarcinoma (AC) (n = 7). Methylation levels of the genes sex-determining region Y, box 1 (SOX1); paired box gene 1 (PAX1); LIM homeobox transcription factor 1α (LMX1A), and NK6 transcription factor-related locus 1 (NKX6-1) were determined by using real-time methylation-specific polymerase chain reaction (PCR) amplification. Cutoff values of the percentage of methylation reference (PMR) for different diagnoses were determined to test the sensitivity and specificity and to generate receiver operating characteristic (ROC) curves. Two-sided Mann-Whitney U tests were used to test differences in PMR between groups. The PMRs of the 4 genes were significantly higher in CIN3 and worse (CIN3+) lesions than the PMRs in specimens of normal cervix and CIN1 or CIN2 (P < .001). ROC curve analysis demonstrated that the sensitivity, specificity, and accuracy for detecting CIN3+ lesions were 0.88, 0.82, and 0.95, respectively, for SOX1; 0.78, 0.91, and 0.89, respectively, for PAX1; 0.77, 0.88, and 0.90, respectively, for LMX1A; and 0.93, 0.97, and 0.97, respectively, for NKX6-1. The current results indicated that quantitative PCR-based testing for DNA methylation of 4 genes holds great promise for cervical cancer screening and warrants further population-based studies using standardized DNA methylation testing.