Concordant methylation of the ER and N33 genes in glioblastoma multiforme

Genetic Prognostic Factors in Adult Diffuse Gliomas: A 10-Year Experience at a Single Institution

Gliomas are primary brain lesions involving cerebral structures without well-defined boundaries and constitute the most prevalent central nervous system (CNS) neoplasms. Among gliomas, glioblastoma (GB) is a glioma of the highest grade and is associated with a grim prognosis. We examined how clinical variables and molecular profiles may have affected overall survival (OS) over the past ten years. A retrospective study was conducted at Sina Hospital in Tehran, Iran and examined patients with confirmed glioma diagnoses between 2012 and 2020. We evaluated the correlation between OS in GB patients and sociodemographic as well as clinical factors and molecular profiling based on IDH1, O-6-Methylguanine-DNA Methyltransferase (MGMT), TERTp, and epidermal growth factor receptor (EGFR) amplification (EGFR-amp) status. Kaplan-Meier and multivariate Cox regression models were used to assess patient survival. A total of 178 patients were enrolled in the study. The median OS was 20 months, with a 2-year survival rate of 61.0%. Among the 127 patients with available IDH measurements, 100 (78.7%) exhibited mutated IDH1 (IDH1-mut) tumors. Of the 127 patients with assessed MGMT promoter methylation (MGMTp-met), 89 (70.1%) had MGMT methylated tumors. Mutant TERTp (TERTp-mut) was detected in 20 out of 127 cases (15.7%), while wildtype TERTp (wildtype TERTp-wt) was observed in 107 cases (84.3%). Analyses using multivariable models revealed that age at histological grade (p < 0.0001), adjuvant radiotherapy (p < 0.018), IDH1 status (p < 0.043), and TERT-p status (p < 0.014) were independently associated with OS. Our study demonstrates that patients with higher tumor histological grades who had received adjuvant radiotherapy exhibited IDH1-mut or presented with TERTp-wt experienced improved OS. Besides, an interesting finding showed an association between methylation of MGMTp and TERTp status with tumor location.

Do the indices of deprivation or smoking affect post-operative 1-year mortality in patients undergoing a craniotomy for a brain tumour in a public healthcare system?

OBJECTIVE

We sought to determine the 1-year survival following craniotomy for tumour resection in a public healthcare system and analyse the effect of indices of multiple deprivation (IMD) as well as smoking, alcohol, BMI, ASA grade and medical co-morbidities on post-operative morbidity and mortality.

METHODS

This is a retrospective, single-centre study in a high volume neurosurgical centre, over a 2-year period. All patients undergoing a craniotomy for a brain tumour were included. Data was collected from the neuro-oncology database and electronic patient records. Individual patient IMD data was obtained using their postcode from a national government database. Each English postcode being ranked from 1 to 32,844, with 1 being the most deprived and 32,844 the most affluent. Descriptive results are described along with further data analysis using multiple linear and logistic regression analyses.

RESULTS

630 patients underwent an elective or urgent craniotomy for tumour. 10% of all patients underwent urgent surgery. 68% (95% CI: 64 to 71%) survived at least 1-year post-surgery. Our study found that social deprivation (IMD postcode rank) was not associated with mortality at 1 year after adjusting for potential confounding factors. Those from decile 1 had the lowest risk of death at 12 months for all tumour types (p = 0.0070). Previous smokers carried an increased risk of death at 12 months when compared with people who had never smoked RR 1.40 CI 1.10-1.78 (p = 0.006) but this risk was not evident in current smokers RR 0.92 CI 0.65-1.31 (p = 0.64). Increasing age and male gender were also found to be associated with higher mortality at 1 year (p =  < 0.001).

CONCLUSIONS

In the UK despite the discrepancy in the health of the general population between the north and south, social deprivation does not appear to be detrimental to neurooncological outcomes although smoking status, advancing age and male sex are.

The Prognostic Impact of Gender, Therapeutic Strategies, Molecular Background, and Tumor-Infiltrating Lymphocytes in Glioblastoma: A Still Unsolved Jigsaw

Despite the adoption of novel therapeutical approaches, the outcomes for glioblastoma (GBM) patients remain poor. In the present study, we investigated the prognostic impact of several clinico-pathological and molecular features as well as the role of the cellular immune response in a series of 59 GBM. CD4+ and CD8+ tumor-infiltrating lymphocytes (TILs) were digitally assessed on tissue microarray cores and their prognostic role was investigated. Moreover, the impact of other clinico-pathological features was evaluated. The number of CD4+ and CD8+ is higher in GBM tissue compared to normal brain tissue (p < 0.0001 and p = 0.0005 respectively). A positive correlation between CD4+ and CD8+ in GBM is present (rs = 0.417-p = 0.001). CD4+ TILs are inversely related to overall survival (OS) (HR = 1.79, 95% CI 1.1-3.1, p = 0.035). The presence of low CD4+ TILs combined with low CD8+ TILs is an independent predictor of longer OS (HR 0.38, 95% CI 0.18-0.79, p = 0.014). Female sex is independently related to longer OS (HR 0.42, 95% CI 0.22-0.77, p = 0.006). Adjuvant treatment, methylguanine methyltransferase (MGMT) promoter methylation, and age remain important prognostic factors but are influenced by other features. Adaptive cell-mediated immunity can affect the outcomes of GBM patients. Further studies are needed to elucidate the commitment of the CD4+ cells and the effects of different TILs subpopulations in GBM.

The Impact of Extent of Resection on the Prognosis of Glioblastoma Multiforme: A Systematic Review and Meta-analysis

Purpose: To investigate the predictor factors of mortality describing the prognosis of primary surgical resection of Glioblastoma Multiforme (GBM). Materials and Methods: A systemic search was conducted from electronic databases (PubMed/Medline, Cochrane Library, and Google Scholar) from inception to 12th September 2021.  All statistical analysis was conducted in Review Manager 5.4.1. Studies meeting inclusion criteria were selected. A random-effect model was used when heterogeneity was seen to pool the studies, and the result were reported in the Hazards Ratio (HR) and corresponding 95% Confidence interval (CI). Result: Twenty-three cohort studies were selected for meta-analysis. There was statistically significant effect of extent of resection on prognosis of surgery in GBM patients (HR= 0.90 [0.86, 0.95]; p< 0.0001; I2= 96%), male gender (HR= 1.19 [1.06, 1.34]; p= 0.002; I2= 0%) and decrease Karnofsky Performance Status (HR= 0.97 [0.95, 0.99]; p= 0.003; I2= 90%). Age and tumor volume was also analyzed in the study. Conclusion: The results of our meta-analysis suggested that age, gender, pre-operative KPS score and extent of resection have significant effects on the post-surgical mortality rate, therefore, these factors can be used significant predictor of mortality in GBM patients.

Prognosis of Oligodendroglioma Patients Stratified by Age: A SEER Population-Based Analysis

Purpose

Glioma may affect patients of any age. So far, only a limited number of big data studies have been conducted concerning oligodendroglioma (OG) in diverse age groups. This study evaluated the risk factors for OG in different age groups using the Surveillance, Epidemiology, and End Results (SEER) database built by the National Cancer Institute, which is part of the National Institutes of Health.

Patients and Methods

A total of 5437 cases within the SEER database were included. These patients were divided into seven age groups. The Kaplan-Meier method was employed for survival analysis. The independent risk factors for the survival of OG patients were identified using the Cox regression model. A nomogram was drawn with R software based on the independent risk factors. The X-tile software was adopted to find the optimal age group at diagnosis.

Results

The all-cause mortality and the tumor-specific mortality increased with age. The univariate analysis showed that the patients' age, gender, primary lesion location, side affected by the primary lesion (left or right), surgery for the primary lesion, and tumor size were correlated with survival (P<0.05). Multivariate Cox regression analysis showed that age was an independent risk factor for the survival of OG patients (P<0.05). The optimal cutoff value of age in terms of overall survival (OS) and cause-specific survival (CSS) were identified as 48 and 61 years and 48 and 59 years, respectively.

Conclusion

The older the age, the worse the survival would be. That's, the mortality increased with age. In the clinic, healthcare professionals should be fully aware of the variability in the prognosis of OG patients in different age groups. Therefore, individualized treatments are recommended to OG patients in different age groups to optimize the prognosis.

Surgical outcome and molecular pattern characterization of recurrent glioblastoma multiforme: A single-center retrospective series

OBJECTIVE

Despite recent advances in diagnosis and treatment of the disease, the prognosis of patients with glioblastoma multiforme (GBM) remains poor. While the value of molecular pattern profiles at first diagnosis has been demonstrated, only few studies have examined these biomarkers at the time of recurrence. The aim of this study was to explore the impact of extent of resection at repeated craniotomy on overall survival (OS) of patients with recurrent GBM. In addition, we investigated the molecular pattern profiles at first and second surgery to evaluate possible temporal evolution of these patterns and to assess the effect of these modifications on OS.

METHODS

We conducted a retrospective cohort study of 63 patients (mean age 59.2 years) surgically treated at least two times for recurrent GBM between 2006 and 2020.

RESULTS

Median OS and progression-free survival (PFS) were 22 months (range 2-168 months) and 10 months (range 1-96 months), respectively. The OS following gross-total resection (GTR) at recurrence for patients with initial GTR (GTR/GTR) was significantly increased (42.6 months) compared with sub-total resection (STR) at reoperation after initial GTR (GTR/STR) (19 months) and with GTR at reoperation after initial STR (STR/GTR) (17 months) (p = 0.0004). Overall surgical morbidity resulted 12.7% and 11.1% at first and at second surgery, respectively. Changes in genetic profiles between first and second surgery of 1p/19q co-deletion, MGMT promoter methylation and p53 mutations occurred in 5.6%, 1.9% and 9.3% of cases, respectively. MGMT promoter methylation appeared to affect OS in univariate analysis at first (p = 0.038) and second surgery (p = 0.107), whereas p53 mutation appeared to affect OS only at second surgery (p = 0.01). In a multivariate analysis female sex (HR = 0.322, 95% CI 0.147-0.705; p = 0.005), PFS (HR = 0.959, 95% CI 0.934-0.986; p = 0.003), GTR at first and second surgery (HR = 0.195, 95% CI 0.091-0.419; p < 0.0001) and adjuvant chemotherapy at recurrence (HR = 0.407, 95% CI 0.206-0.809; p = 0.01) were associated with longer OS.

CONCLUSIONS

This study confirmed the role of extent of resection (EOR) at first and at recurrence as a significant predictor of outcome in patients with recurrent GBM. In addition, this study highlighted the concept of a dynamic evolution of GBM genome after initial surgical resection, supporting the need of further studies to investigate the clinical and therapeutic implications of the changes in genetic profiles after initial surgery.

Integration of genome-level data to allow identification of subtype-specific vulnerability genes as novel therapeutic targets

The identification of cancer-specific vulnerability genes is one of the most promising approaches for developing more effective and less toxic cancer treatments. Cancer genomes exhibit thousands of changes in DNA methylation and gene expression, with the vast majority likely to be passenger changes. We hypothesised that, through integration of genome-wide DNA methylation/expression data, we could exploit this inherent variability to identify cancer subtype-specific vulnerability genes that would represent novel therapeutic targets that could allow cancer-specific cell killing. We developed a bioinformatics pipeline integrating genome-wide DNA methylation/gene expression data to identify candidate subtype-specific vulnerability partner genes for the genetic drivers of individual genetic/molecular subtypes. Using acute lymphoblastic leukaemia as an initial model, 21 candidate subtype-specific vulnerability genes were identified across the five common genetic subtypes, with at least one per subtype. To confirm the approach was applicable across cancer types, we also assessed medulloblastoma, identifying 15 candidate subtype-specific vulnerability genes across three of four established subtypes. Almost all identified genes had not previously been implicated in these diseases. Functional analysis of seven candidate subtype-specific vulnerability genes across the two tumour types confirmed that siRNA-mediated knockdown induced significant inhibition of proliferation/induction of apoptosis, which was specific to the cancer subtype in which the gene was predicted to be specifically lethal. Thus, we present a novel approach that integrates genome-wide DNA methylation/expression data to identify cancer subtype-specific vulnerability genes as novel therapeutic targets. We demonstrate this approach is applicable to multiple cancer types and identifies true functional subtype-specific vulnerability genes with high efficiency.

DNA sequence context as a marker of CpG methylation instability in normal and cancer tissues

DNA methylation alterations are related to multiple molecular mechanisms. The DNA context of CpG sites plays a crucial role in the maintenance and stability of methylation patterns. The quantitative relationship between DNA composition and DNA methylation has been studied in normal as well as pathological conditions, showing that DNA methylation status is highly dependent on the local sequence context. In this work, we describe this relationship by analyzing the DNA sequence context associated to methylation profiles in both physiological and pathological conditions. In particular, we used DNA motifs to describe methylation stability patterns in normal tissues and aberrant methylation events in cancer lesions. In this manuscript, we show how different groups of DNA sequences can be related to specific epigenetic events, across normal and cancer tissues, and provide a thorough structural and functional characterization of these sequences.

Association Between RASSF2 Methylation and Gastric Cancer: A PRISMA-Compliant Systematic Review and Meta-Analysis

RASSF2 is a tumor suppressor gene closely related to gastric cancer. This meta-analysis was designed to assess the quality in the previous studies and establish the value of RASSF2 methylation in the prediction and prognosis of gastric cancer. The eligible literatures with publication deadline of May 3, 2019 were collected from PubMed, EMBASE, CNKI, Wanfang, and CNVIP databases. The correlation between RASSF2 methylation level and gastric cancer was estimated by odds ratio and 95% confidence interval (OR and 95% CI) values. A total of eight articles were included in the study. A total of 517 gastric cancer tissue samples and 517 adjacent nontumor tissue samples were included. The results of the analysis showed that RASSF2 had a significantly higher level of methylation in gastric cancer (OR = 17.56, 95% CI = 7.11-43.35, p-value = 0.009). Meanwhile, we tested whether there was association of RASSF2 methylation with tumor metastasis, and we also analyzed whether there was a gender difference in RASSF2 methylation. However, our results showed no statistical significance of the two aforementioned tests (p > 0.1). Our study suggested that RASSF2 methylation could predict the risk of gastric cancer. However, it might not be feasible for the prediction of tumor metastasis.

Impact of gender on the survival of patients with glioblastoma

Background: Preclinical models have suggested a role for sex hormones in the development of glioblastoma multiforme (GBM). However, the impact of gender on the survival time of patients with GBM has not been fully understood. The objective of the present study was to clarify the association between gender and survival of patients with GBM by analyzing population-based data.Methods: We searched the Surveillance, Epidemiology, and End-Results database who were diagnosed with GBM between 2000 and 2008 and were treated with surgery. Five-year cancer specific survival data were obtained. Kaplan-Meier methods and multivariable Cox regression models were used to analyze long-term survival outcomes and risk factors.Results: A total of 6586 patients were identified; 61.5% were men and 38.5% were women. The 5-year cancer-specific survival (CSS) rates in the male and female groups were 6.8% and 8.3%, respectively (P=0.002 by univariate and P<0.001 by multivariate analysis). A stratified analysis showed that male patients always had the lowest CSS rate across localized cancer stage and different age subgroups.Conclusions: Gender has prognostic value for determining GBM risk. The role of sex hormones in the development of GBM warrants further investigation.

Genome-wide analysis of DNA methylation in bronchial washings

Background

The objective of this study was to discover DNA methylation biomarkers for detecting non-small lung cancer (NSCLC) in bronchial washings and understanding the association between DNA methylation and smoking cessation.

Methods

DNA methylation was analyzed in bronchial washing samples from 70 NSCLCs and 53 hospital-based controls using Illumina HumanMethylation450K BeadChip. Methylation levels in these bronchial washings were compared to those in 897 primary lung tissues of The Cancer Genome Atlas (TCGA) data.

Results

Twenty-four CpGs (p < 1.03E−07) were significantly methylated in bronchial washings from 70 NSCLC patients compared to those from 53 controls. The CpGs also had significant methylation in the TCGA cohort. The 123 participants were divided into a training set (N = 82) and a test set (N = 41) to build a classification model. Logistic regression model showed the best performance for classification of lung cancer in bronchial washing samples: the sensitivity and specificity of a marker panel consisting of seven CpGs in TFAP2A, TBX15, PHF11, TOX2, PRR15, PDGFRA, and HOXA11 genes were 87.0 and 83.3% in the test set, respectively. The area under the curve (AUC) was equal to 0.87 (95% confidence interval = 0.73–0.96, p < 0.001). Methylation levels of two CpGs in RUNX3 and MIR196A1 genes were inversely associated with duration of smoking cessation in the controls, but not in NSCLCs, after adjusting for pack-years of smoking.

Conclusions

The present study suggests that NSCLC may be detected by analyzing methylation changes of seven CpGs in bronchial washings. Furthermore, smoking cessation may lead to decreased DNA methylation in nonmalignant bronchial epithelial cells in a gene-specific manner.

Electronic supplementary material

The online version of this article (10.1186/s13148-018-0498-8) contains supplementary material, which is available to authorized users.

TUSC3: functional duality of a cancer gene

Two decades ago, following a systematic screening of LOH regions on chromosome 8p22, TUSC3 has been identified as a candidate tumor suppressor gene in ovarian, prostate and pancreatic cancers. Since then, a growing body of evidence documented its clinical importance in various other types of cancers, and first initial insights into its molecular function and phenotypic effects have been gained, though the precise role of TUSC3 in different cancers remains unclear. As a part of the oligosaccharyltransferase complex, TUSC3 localizes to the endoplasmic reticulum and functions in final steps of N-glycosylation of proteins, while its loss evokes the unfolded protein response. We are still trying to figure out how this mechanistic function is reconcilable with its varied effects on cancer promotion. In this review, we focus on cancer-related effects of TUSC3 and envisage a possible role of TUSC3 beyond endoplasmic reticulum.

TUSC3 promotes colorectal cancer progression and epithelial-mesenchymal transition (EMT) through WNT/β-catenin and MAPK signalling

Colorectal cancer (CRC) is one of the most common malignancies and is the second leading cause of cancer death in humans. Tumour suppressor candidate 3 (TUSC3) plays an important role in embryogenesis and metabolism. Deletion of TUSC3 often causes non-syndromic mental retardation. Even though TUSC3 deregulation is frequently observed in epithelial cancers, the function of TUSC3 in CRC has remained unknown. In this study, we observed greater expression of TUSC3 at the mRNA and protein level in clinical colorectal tumour samples compared with paired normal tissues. Gain- and loss-of-function analyses were performed to evaluate the functional significance of TUSC3 in CRC initiation and progression. Immunoblotting, immunofluorescence, and co-immunoprecipitation analyses were used to identify potential pathways with which TUSC3 might be involved. Overexpression of TUSC3 in CRC cells induced epithelial-mesenchymal transition (EMT) in CRC cells, accompanied by down-regulation of the epithelial marker, E-cadherin, and up-regulation of the mesenchymal marker, vimentin. Increased proliferation, migration, and invasion, as well as accelerated xenograft tumour growth, were observed in TUSC3-overexpressing CRC cells, while opposite effects were achieved in TUSC3-silenced cells. In conclusion, our study demonstrated the oncogenic role of TUSC3 in CRC and showed that TUSC3 may be responsible for alternations in the proliferation ability, aggressiveness, and invasive/metastatic potential of CRC through regulating the MAPK, PI3K/Akt, and Wnt/β-catenin signalling pathways.

CpG island methylator phenotype in colorectal cancer

Colorectal cancer (CRC) is one of the most common malignancies worldwide and is caused by accumulation of genetic and epigenetic changes. With the discovery of CpG island methylator phenotype (CIMP), more and more studies have focused on epigenetic modifications in CRC. CIMP is found in a subset of CRC with an exceptionally high frequency of methylated genes. Current research shows that CIMP has several molecular characteristics and is significantly associated with multiple clinicopathological features, but the mechanim of CIMP is still unclear. The prognosis and treatment response in CRC with CIMP are largely different form those of other CRCs, however, the absence of widely accepted CIMP biomarkers has prevented the clinical applications of CIMP to guide the personalized therapy of CRC.

CpG island hypermethylation as a biomarker for the early detection of lung cancer

Lung cancer is the most frequent cause of cancer-related deaths and causes over one million deaths worldwide each year. Despite significant strides in the diagnosis and treatment of lung cancer, the prognosis is extremely poor, with the overall 5-year survival rates still remaining around 15 %. This is largely due to occult metastatic dissemination, which appears in approximately two-thirds of patients at the time of detection. Thus, the development of efficient diagnostic methods to enable the early detection of cancer for these patients is clearly imperative.One promising approach is the identification of lung cancer-specific biomarkers at an early stage. The de novo methylation of CpG islands within the promoters of tumor suppressor genes is one of the most frequently acquired epigenetic changes during the pathogenesis of lung cancer and usually associated with transcriptional downregulation of a gene. The analysis of DNA methylation patterns in sputum, bronchial fluid, plasma, or serum could become a powerful tool for the accurate and early diagnosis of lung cancer with unparalleled specificity and sensitivity.

Differences among brain tumor stem cell types and fetal neural stem cells in focal regions of histone modifications and DNA methylation, broad regions of modifications, and bivalent promoters

Background

Aberrational epigenetic marks are believed to play a major role in establishing the abnormal features of cancer cells. Rational use and development of drugs aimed at epigenetic processes requires an understanding of the range, extent, and roles of epigenetic reprogramming in cancer cells. Using ChIP-chip and MeDIP-chip approaches, we localized well-established and prevalent epigenetic marks (H3K27me3, H3K4me3, H3K9me3, DNA methylation) on a genome scale in several lines of putative glioma stem cells (brain tumor stem cells, BTSCs) and, for comparison, normal human fetal neural stem cells (fNSCs).

Results

We determined a substantial “core” set of promoters possessing each mark in every surveyed BTSC cell type, which largely overlapped the corresponding fNSC sets. However, there was substantial diversity among cell types in mark localization. We observed large differences among cell types in total number of H3K9me3+ positive promoters and peaks and in broad modifications (defined as >50 kb peak length) for H3K27me3 and, to a lesser extent, H3K9me3. We verified that a change in a broad modification affected gene expression of CACNG7. We detected large numbers of bivalent promoters, but most bivalent promoters did not display direct overlap of contrasting epigenetic marks, but rather occupied nearby regions of the proximal promoter. There were significant differences in the sets of promoters bearing bivalent marks in the different cell types and few consistent differences between fNSCs and BTSCs.

Conclusions

Overall, our “core set” data establishes sets of potential therapeutic targets, but the diversity in sets of sites and broad modifications among cell types underscores the need to carefully consider BTSC subtype variation in epigenetic therapy. Our results point toward substantial differences among cell types in the activity of the production/maintenance systems for H3K9me3 and for broad regions of modification (H3K27me3 or H3K9me3). Finally, the unexpected diversity in bivalent promoter sets among these multipotent cells indicates that bivalent promoters may play complex roles in the overall biology of these cells. These results provide key information for forming the basis for future rational drug therapy aimed at epigenetic processes in these cells.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-724) contains supplementary material, which is available to authorized users.

Distribution of estrogen and progesterone receptors isoforms in endometrial cancer

Background

70–80% of sporadic endometrial carcinomas are defined as endometrioid carcinoma (EC). Early-stage, well differentiated endometrial carcinomas usually retain expression of estrogen and progesterone receptors (ER and PR, respectively), as advanced stage, poorly differentiated tumors often lack one or both of these receptors. Well-described EC prognosis includes tumor characteristics, such as depth of myometrial invasion. Therefore, in the current study, we evaluated the expression profile of ER and PR isoforms, including ER-α, PR-A and PR–B, in correlation to EC tumor histological depth.

Methods

Using immunohistochemistry and image analysis software, the expression of ER-α, PR-A, PR–B and Ki67 was assessed in endometrial stroma and epithelial glands of superficial, deep and extra-tumoral sections of 15 paraffin embedded EC specimens, and compared to 5 biopsies of non-malignant endometrium.

Results

Expression of PR-A and ER-α was found to be lower in EC compared to nonmalignant tissue, as the stromal expression was dramatically reduced compared to epithelial cells. Expression ratios of both receptors were significantly high in superficial and deep portions of EC; in non-tumoral portion of EC were close to the ratios of nonmalignant endometrium. PR-B expression was low in epithelial glands of EC superficial and deep portions, and high in the extra-tumoral region. Elevated PR-B expression was found in stroma of EC, as well.

Conclusions

The ratio of ER-α and PR-A expression in the epithelial glands and the stroma of EC biopsies may serve as an additional parameter in the histological evaluation of EC tumor.

Virtual slides

The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/1155060506119016

CDKN2A promoter hypermethylation in astrocytomas is associated with age and sex

CDKN2A promoter hypermethylation has been widely related to many cancers. In astrocytomas, although CDKN2A (p16(INK4A) protein) is often inactivated, there are still some controversial issues regarding the mechanism by which this alteration occurs. Thus, we analyzed a series of astrocytomas to assess the association between CDKN2A expression and methylation of grade I-IV tumors (WHO) and clinicopathological parameters. DNA extracted from formalin-fixed paraffin-embedded material of 93 astrocytic tumors was available for CDKN2A promoter methylation analysis and p16(INK4A) expression by methylation-specific PCR and immunohistochemistry, respectively. A strong negative correlation between nuclear and cytoplasmic immunostaining and CDKN2A promoter methylation was found. Additionally, a significant negative correlation between CDKN2A promoter methylation and age was observed; also, female patients had statistically more CDKN2A methylated promoters (p = 0.036) than men. In conclusion, CDKN2A inactivation by promoter methylation is a frequent event in astrocytomas and it is related to the age and sex of patients.

Digital transcriptome profiling of normal and glioblastoma-derived neural stem cells identifies genes associated with patient survival

Background

Glioblastoma multiforme, the most common type of primary brain tumor in adults, is driven by cells with neural stem (NS) cell characteristics. Using derivation methods developed for NS cells, it is possible to expand tumorigenic stem cells continuously in vitro. Although these glioblastoma-derived neural stem (GNS) cells are highly similar to normal NS cells, they harbor mutations typical of gliomas and initiate authentic tumors following orthotopic xenotransplantation. Here, we analyzed GNS and NS cell transcriptomes to identify gene expression alterations underlying the disease phenotype.

Methods

Sensitive measurements of gene expression were obtained by high-throughput sequencing of transcript tags (Tag-seq) on adherent GNS cell lines from three glioblastoma cases and two normal NS cell lines. Validation by quantitative real-time PCR was performed on 82 differentially expressed genes across a panel of 16 GNS and 6 NS cell lines. The molecular basis and prognostic relevance of expression differences were investigated by genetic characterization of GNS cells and comparison with public data for 867 glioma biopsies.

Results

Transcriptome analysis revealed major differences correlated with glioma histological grade, and identified misregulated genes of known significance in glioblastoma as well as novel candidates, including genes associated with other malignancies or glioma-related pathways. This analysis further detected several long non-coding RNAs with expression profiles similar to neighboring genes implicated in cancer. Quantitative PCR validation showed excellent agreement with Tag-seq data (median Pearson r = 0.91) and discerned a gene set robustly distinguishing GNS from NS cells across the 22 lines. These expression alterations include oncogene and tumor suppressor changes not detected by microarray profiling of tumor tissue samples, and facilitated the identification of a GNS expression signature strongly associated with patient survival (P = 1e-6, Cox model).

Conclusions

These results support the utility of GNS cell cultures as a model system for studying the molecular processes driving glioblastoma and the use of NS cells as reference controls. The association between a GNS expression signature and survival is consistent with the hypothesis that a cancer stem cell component drives tumor growth. We anticipate that analysis of normal and malignant stem cells will be an important complement to large-scale profiling of primary tumors.

Promoter Methylation of RASSF1A Associates to Adult Secondary Glioblastomas and Pediatric Glioblastomas

While allelic losses and mutations of tumor suppressor genes implicated in the etiology of astrocytoma have been widely assessed, the role of epigenetics is still a matter of study. We analyzed the frequency of promoter hypermethylation by methylation-specific PCR (MSP) in five tumor suppressor genes (PTEN, MGMT, RASSF1A, p14^ARF, and p16^INK4A), in astrocytoma samples and cell lines. RASSF1A was the most frequently hypermethylated gene in all grades of astrocytoma samples, in cell lines, and in adult secondary GBM. It was followed by MGMT. PTEN showed a slight methylation signal in only one GBM and one pilocytic astrocytoma, and in two cell lines; while p14^ARF and p16^INK4A did not show any evidence of methylation in primary tumors or cell lines. In pediatric GBM, RASSF1A was again the most frequently altered gene, followed by MGMT; PTEN, p14 and p16 showed no alterations. Lack or reduced expression of RASSF1A in cell lines was correlated with the presence of methylation. RASSF1A promoter hypermethylation might be used as a diagnostic marker for secondary GBM and pediatric GBM. Promoter hypermethylation might not be an important inactivation mechanism in other genes like PTEN, p14^ARF and p16^INK4A, in which other alterations (mutations, homozygous deletions) are prevalent.

The epigenetics of brain tumors

Glioblastoma, medulloblastoma, and ependymoma represent molecularly and clinically diverse forms of adult and pediatric brain tumors. While each tumor displays genetic, transcriptional, and cytogenetic heterogeneity, the epigenome of these tumors has only recently emerged as a major field of interest. Here, we describe advances in our understanding of the epigenetics of brain tumors, focusing on DNA methylation, histone modifications, and microRNA deregulation which contribute to the pathogenesis of these diseases.

The CpG island methylator phenotype in colorectal cancer: progress and problems

In recent years, attention has focused on the biology and potential clinical importance of the CpG island methylator phenotype (CIMP) in colorectal cancer (CRC). While it is generally well accepted that etiologically and clinically distinct subgroups exist in this disease, a precise definition of CIMP remains to be established. Here, we summarize existing literature that documents the prevalence of CIMP in CRC, with particular attention to the various methods and definitions used to classify a tumor as CIMP positive. Through a systematic review on both case-series and population based studies, we examined only original research articles reporting on sporadic CRC and/or adenomas in unselected cases. Forty-eight papers published between January 1999 and August 2011 met the inclusion criteria. We describe the use of multiple gene panels, marker threshold values, and laboratory techniques which results in a wide range in the prevalence of CIMP. Because there is no universal standard or consensus on quantifying the phenotype, establishing its true prevalence is a challenge. This bottleneck is becoming increasingly evident as molecular pathological epidemiology continues to offer possibilities for clear answers regarding environmental risk factors and disease trends. For the first time, large, unselected series of cases are available for analysis, but comparing populations and pooling data will remain a challenge unless a universal definition of CIMP and a consensus on analysis can be reached, and the primary cause of CIMP identified.

Insulation of tumor suppressor genes by the nuclear factor CTCF

One of the most outstanding nuclear factors, which has chromatin insulator and transcriptional properties and also contribute to genomic organization, is the zinc-finger protein CCCTC-binding factor (CTCF). Among its multiple functions, a growing amount of evidence implicates CTCF in the epigenetic regulation of genes responsible for the control of the cell cycle, and its mis-regulation can lead to aberrant epigenetic silencing of genes involved in cancer development. Detailed studies are now revealing that CTCF can serve as a barrier against the spread of DNA methylation and histone repressive marks over promoter regions of tumor suppressor genes. Moreover, new evidences points out to the capacity of CTCF to be covalently modified, in particular, through poly(ADP-ribosyl)ation with regulatory consequences. An unexplored aspect of CTCF is its intergenic and intragenic distribution in certain loci. Such distribution seems to facilitate the formation of an optimal chromatin structure and the recruitment of chromatin remodelers with the possible incorporation of RNA polymerase II. Therefore, in the context of tumor suppressor genes and cancer development, CTCF appears to play a relevant role by incorporating a combination of mechanisms involved in the protection against epigenetic silencing components and the maintenance of optimal higher-order organization of the corresponding loci.

Epigenetic Alteration by DNA Promoter Hypermethylation of Genes Related to Transforming Growth Factor-β (TGF-β) Signaling in Cancer

Epigenetic alterations in cancer, especially DNA methylation and histone modification, exert a significant effect on the deregulated expression of cancer-related genes and lay an epigenetic pathway to carcinogenesis and tumor progression. Global hypomethylation and local hypermethylation of CpG islands in the promoter region, which result in silencing tumor suppressor genes, constitute general and major epigenetic modification, the hallmark of the neoplastic epigenome. Additionally, methylation-induced gene silencing commonly affects a number of genes and increases with cancer progression. Indeed, cancers with a high degree of methylation (CpG island methylator phenotype/CIMP) do exist and represent a distinct subset of certain cancers including colorectal, bladder and kidney. On the other hand, signals from the microenvironment, especially those from transforming growth factor-β (TGF-β), induce targeted de novo epigenetic alterations of cancer-related genes. While TGF-β signaling has been implicated in two opposite roles in cancer, namely tumor suppression and tumor promotion, its deregulation is also partly induced by epigenetic alteration itself. Although the epigenetic pathway to carcinogenesis and cancer progression has such reciprocal complexity, the important issue is to identify genes or signaling pathways that are commonly silenced in various cancers in order to find early diagnostic and therapeutic targets. In this review, we focus on the epigenetic alteration by DNA methylation and its role in molecular modulations of the TGF-β signaling pathway that cause or underlie altered cancer-related gene expression in both phases of early carcinogenesis and late cancer progression.

Aberrant DNA methylation of some tumor suppressor genes in lung cancers from workers with chromate exposure

Our previous studies revealed a variety of genetic changes in lung cancers from chromate-exposed workers (chromate lung cancer). In the present study, we examined epigenetic changes in chromate lung cancers. Nested-methylation-specific PCR was employed in studying the methylation of CpG islands in the APC, MGMT, hMLH1 genes in 36 chromate lung cancers and 25 nonchromate lung cancers. Methylation in chromate lung cancers was detected at 86% for APC, 20% for MGMT, and 28% for hMLH1. Whereas, it occurred at lower frequencies in nonchromate lung cancers, particularly in APC (44%) and hMLH1 (0%) genes. Our previous study showed that methylation of p16 gene in chromate lung cancer and nonchromate lung cancer was 33% and 26%, respectively. The mean methylation index (MI), a reflection of the overall methylation status, was significantly higher in chromate lung cancers than nonchromate lung cancers (0.41 vs. 0.21, P=0.001). Methylation of multiple genes (particularly hMLH1, p16, and APC genes) had experienced more than 15 yr of chromate exposure in chromate lung cancer (MI: <15 yr; 0.19, ≥ 15 yr, 0.42). There is a significant correlation of p16 and hMLH1 methylation with the expressional decrease or loss of the corresponding gene products (P=0.037 and 0.024) respectively, and an inverse correlation between APC and MGMT methylation (P = 0.014). This study provides a novel evidence for the chromium carcinogenesis that chromate lung cancer is linked to the progressive methylation of some tumor suppressor genes, which may be related to genomic instability.

Molecular identification of ancient and modern mammalian magnesium transporters

A large number of mammalian Mg2+ transporters have been hypothesized on the basis of physiological data, but few have been investigated at the molecular level. The recent identification of a number of novel proteins that mediate Mg2+ transport has enhanced our understanding of how Mg2+ is translocated across mammalian membranes. Some of these transporters have some similarity to those found in prokaryocytes and yeast cells. Human Mrs2, a mitochondrial Mg2+ channel, shares many of the properties of the bacterial CorA and yeast Alr1 proteins. The SLC41 family of mammalian Mg2+ transporters has a similarity with some regions of the bacterial MgtE transporters. The mammalian ancient conserved domain protein (ACDP) Mg2+ transporters are found in prokaryotes, suggesting an ancient origin. However, other newly identified mammalian transporters, including TRPM6/7, MagT, NIPA, MMgT, and HIP14 families, are not represented in prokaryotic genomes, suggesting more recent development. MagT, NIPA, MMgT, and HIP14 transporters were identified by differential gene expression using microarray analysis. These proteins, which are found in many different tissues and subcellular organelles, demonstrate a diversity of structural properties and biophysical functions. The mammalian Mg2+ transporters have no obvious amino acid similarities, indicating that there are many ways to transport Mg2+ across membranes. Most of these proteins transport a number of divalent cations across membranes. Only MagT1 and NIPA2 are selective for Mg2+. Many of the identified mammalian Mg2+ transporters are associated with a number of congenital disorders encompassing a wide range of tissues, including intestine, kidney, brain, nervous system, and skin. It is anticipated that future research will identify other novel Mg2+ transporters and reveal other diseases.

Introduction to epigenomics and epigenome-wide analysis

Epigenetics is the study of heritable change other than those encoded in DNA sequence. Cytosine methylation of DNA at CpG dinucleotides is the most well-studied epigenetic phenomenon, although epigenetic changes also encompass non-DNA methylation mechanisms, such as covalent histone modifications, micro-RNA interactions, and chromatin remodeling complexes. Methylation changes, both global and gene specific, have been observed to be associated with disease, particularly in cancer.This chapter begins with a general overview of epigenomics, and then focuses on understanding and analyzing genome-wide cytosine methylation data. There are many microarray-based techniques available to measure cytosine methylation across the genome, as well as gold-standard techniques based on sequencing bisulfite converted DNA, which is used to measure methylation in a smaller, more targeted set of loci. We have provided an overview of many of the current technologies - their advantages, limitations, and recent improvements. Regardless of which technology is used, the goal is to produce a set of methylation measurements that are highly consistent with true methylation levels of the corresponding set of CpG dinucleotides.Identifying all loci with aberrant methylation or hypomethylation in disease, or in natural processes such as aging, requires the comparison of methylation levels across many samples. In such studies, the development of methylation-based diagnostic tools may be of interest, potentially to be used as early disease detection strategies based on a set of sentinel loci. In addition, the identification of loci with potentially reversible methylation events may result in new therapeutic options. Given the vast number of measurable sites, prioritization of candidate loci is an important and complex issue and rests on a foundation of appropriate statistical testing and summarization. Coupled with statistical estimates of importance, the genomic context of each locus measured may offer important information about the mechanisms by which epigenetic changes impact disease and allows us further refinement of candidate loci. We will conclude this chapter by identifying issues in building methylation-based models for prediction and potential directions of further statistical research in epigenetics.

Predicting relapse in favorable histology Wilms tumor using gene expression analysis: a report from the Renal Tumor Committee of the Children's Oncology Group

PURPOSE

The past two decades has seen significant improvement in the overall survival of patients with favorable histology Wilms tumor (FHWT); however, this progress has reached a plateau. Further improvements may rely on the ability to better stratify patients by risk of relapse. This study determines the feasibility and potential clinical utility of classifiers of relapse based on global gene expression analysis.

EXPERIMENTAL DESIGN

Two hundred fifty FHWT of all stages enriched for relapses treated on National Wilms Tumor Study-5 passed quality variables and were suitable for analysis using oligonucleotide arrays. Relapse risk stratification used support vector machine; 2- and 10-fold cross-validations were applied.

RESULTS

The number of genes associated with relapse was less than that predicted by chance alone for 106 patients (32 relapses) with stages I and II FHWT treated with chemotherapy, and no further analyses were done. This number was greater than expected by chance for 76 local stage III patients. Cross-validation including an additional 68 local stage III patients (total 144 patients, 53 relapses) showed that classifiers for relapse composed of 50 genes were associated with a median sensitivity of 47% and specificity of 70%.

CONCLUSIONS

This study shows the feasibility and modest accuracy of stratifying local stage III FHWT using a classifier of <50 genes. Validation using an independent patient population is needed. Analysis of genes differentially expressed in relapse patients revealed apoptosis, Wnt signaling, insulin-like growth factor pathway, and epigenetic modification to be mechanisms important in relapse. Potential therapeutic targets include FRAP/MTOR and CD40.

Gene regulation by methylation

Epigenetic gene regulation of specific genes strongly affects clinical outcome of malignant glioma. MGMT is the best studied gene for the connection of promoter methylation and clinical course in glioblastoma. While MGMT promoter methylation analysis currently does not alter treatment of glioblastoma patients, mainly because of a lack of convincing therapy to radiotherapy and concomitant administration of alkylating drugs, there is increasing interest on the part of patients and physicians in having this molecular parameter assessed. This chapter gives a short overview of the physiological characteristics of the epigenome in normal cells and tissues and the changes in epigenetic gene regulation following malignant transformation. It discusses the technical aspects, advantages, and shortcomings of currently used approaches for single-gene and genome-wide methylation analyses. Finally, an outlook is given on potential therapeutic avenues and targets to overcome tumor-suppressor gene silencing by aberrant promoter methylation in gliomas.

Epigenetic markers in human gliomas: prospects for therapeutic intervention

Gliomas represent the most common CNS cancers in adults. Prognosis for patients harboring malignant gliomas is particularly dismal and, despite current treatment strategies comprising surgery, radiotherapy and chemotherapy, the median survival time after diagnosis is still in the range of just 12 months. In recent years, there has been an increased effort to identify tumor biomarkers that can be used as diagnostic tools, or markers for predicting therapeutic response and prognosis. Investigation of genetic changes has identified several such markers that have shown some success in predicting the most effective therapy. In recent years, however, it has become apparent that the biology of many cancers of the CNS is determined not only by their genetic profile but also their epigenetic profile. Epigenetic biomarkers show great potential in effectively predicting patient prognosis and response to therapy. The eventual application of epigenetic profiling of tumors may help to indicate the most effective tailored therapy for individual patients.

Epigenetic changes in gliomas

Epigenetics are defined, in broad-terms, as alterations in gene expression without changes in DNA sequence. While histone modifications and DNA methylation are two classical means to regulate gene expression, miRNA has also recently been documented to govern gene expression in normal as well as cancer cells. In this review, we will first describe briefly histone modifications, DNA methylation and miRNAs and the functions of these epigenetic marks during different cellular processes involving DNA metabolism. We will then highlight some epigenetic changes in glioblastomas, a malignant form of brain tumor, and potential application of epigenetic means for diagnosis, prognosis, and treatment of gliomas. We expect that novel therapies will be developed to counter epigenetic changes in this deadly disease.

RUNX3 methylation reveals that bladder tumors are older in patients with a history of smoking

Exposure to tobacco smoke is associated with increased DNA methylation at certain genes in both lung and bladder tumors. We sought to identify interactions in bladder cancer between DNA methylation and a history of smoking, along with any possible effect of aging. We measured DNA methylation in 342 transitional cell carcinoma tumors at BCL2, PTGS2 (COX2), DAPK, CDH1 (ECAD), EDNRB, RASSF1A, RUNX3, TERT, and TIMP3. The prevalence of methylation at RUNX3, a polycomb target gene, increased as a function of age at diagnosis (P = 0.031) and a history of smoking (P = 0.015). RUNX3 methylation also preceded methylation at the other eight genes (P < 0.001). It has been proposed that DNA methylation patterns constitute a "molecular clock" and can be used to determine the "age" of normal tissues (i.e., the number of times the cells have divided). Because RUNX3 methylation increases with age, is not present in normal urothelium, and occurs early in tumorigenesis, it can be used for the first time as a molecular clock to determine the age of a bladder tumor. Doing so reveals that tumors from smokers are "older" than tumors from nonsmokers (P = 0.009) due to tumors in smokers either initiating earlier or undergoing more rapid cell divisions. Because RUNX3 methylation is acquired early on in tumorigenesis, then its detection in biopsy or urine specimens could provide a marker to screen cigarette smokers long before any symptoms of bladder cancer are present.

Potential link between estrogen receptor-alpha gene hypomethylation and uterine fibroid formation

Uterine leiomyomas are the most common uterine tumors in women. Estrogen receptor-alpha (ER-alpha) is more highly expressed in uterine leiomyomas than in normal myometrium, suggesting a link between uterine leiomyomas and ER-alpha expression. DNA methylation is an epigenetic mechanism of gene regulation and plays important roles in normal embryonic development and in disease progression including cancers. Here, we investigated the DNA methylation status of the ER-alpha promoter region (-1188 to +229 bp) in myometrium and leiomyoma. By sodium bisulfite sequencing, 49 CpG sites in the proximal promoter region of ER-alpha gene were shown to be unmethylated in both leiomyoma and normal myometrium. At seven CpG sites in the distal promoter region of the ER-alpha gene, there was a variation in DNA methylation status in myometrium and leiomyoma. Further analysis of the DNA methylation status by bisulfite restriction mapping among 11 paired samples of myometrium and leiomyoma indicated that CpG sites in the distal region of ER-alpha promoter are hypomethylated in leiomyomas of nine patients. In those patients, ER-alpha mRNA levels tended to be higher in the leiomyoma than in the myometrium. In conclusion, there was an aberrant DNA methylation status in the promoter region of ER-alpha gene in uterine leiomyoma, which may be associated with high ER-alpha mRNA expression.

Examination of a CpG island methylator phenotype and implications of methylation profiles in solid tumors

The CpG island methylator phenotype (CIMP), thoroughly described in colorectal cancer and to a lesser extent in other solid tumors, is important in understanding epigenetics in carcinogenesis and may be clinically useful for classification of neoplastic disease. Therefore, we investigated whether this putative phenotype exists in exposure-related solid tumors, where somatic gene alterations and enhanced clonal growth are selected for by carcinogens, and examined the ability of methylation profiles to classify malignant disease. We studied promoter hypermethylation of 16 tumor suppressor genes and 3 MINT loci (acknowledged classifiers of CIMP) in 344 bladder cancers, 346 head and neck squamous cell carcinomas (HNSCC), 146 non-small-cell lung cancer (NSCLC), and 71 malignant pleural mesotheliomas (MPM). We employed rigorous statistical methods to examine the distribution of promoter methylation and the usefulness of these profiles for disease classification. In bladder cancer, HNSCC, and NSCLC, there was a significant correlation (P < 0.0001) between methylation of the three MINT loci and methylation index, although the distribution of methylated loci varied significantly across these disease. Although there was a significant (P < 0.001) association between gene methylation profile and disease, rates of misclassification of each disease by their methylation profile ranged from 28% to 32%, depending on the classification scheme used. These data suggest that a form of CIMP exists in these solid tumors, although its etiology remains elusive. Whereas the gene profiles of hypermethylation among examined loci could not unequivocally distinguish disease type, the existence of CIMP and the relative preponderance of hypermethylation in these cancers suggest that methylation analysis may be clinically useful as a targeted screening tool.

Downregulation of RUNX3 and TES by hypermethylation in glioblastoma

Glioblastoma, the most aggressive and least treatable form of malignant glioma, is the most common human brain tumor. Although many regions of allelic loss occur in glioblastomas, relatively few tumor suppressor genes have been found mutated at such loci. To address the possibility that epigenetic alterations are an alternative means of glioblastoma gene inactivation, we coupled pharmacological manipulation of methylation with gene profiling to identify potential methylation-regulated, tumor-related genes. Duplicates of three short-term cultured glioblastomas were exposed to 5 microM 5-aza-dC for 96 h followed by cRNA hybridization to an oligonucleotide microarray (Affymetrix U133A). We based candidate gene selection on bioinformatics, reverse transcription-polymerase chain reaction (RT-PCR), bisulfite sequencing, methylation-specific PCR and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Two genes identified in this manner, RUNX3 and Testin (TES), were subsequently shown to harbor frequent tumor-specific epigenetic alterations in primary glioblastomas. This overall approach therefore provides a powerful means to identify candidate tumor-suppressor genes for subsequent evaluation and may lead to the identification of genes whose epigenetic dysregulation is integral to glioblastoma tumorigenesis.

Methylated tumor-specific DNA as a plasma biomarker in patients with glioma

OBJECTIVE

Patients with systemic malignancies have substantial quantities of tumor-specific DNA in their plasma which may serve as a potential biomarker for tumor burden. This approach has not been studied in gliomas.

METHODS

Methylation specific polymerase chain reaction (MSP) was used to determine the methylation status the promoters for p16/(INK4a), MGMT, p73, and RARbeta within glioma tissue and plasma. Blood was collected prior to craniotomy in 10 patients with glioma. DNA was extracted from tumor and plasma samples and assayed with MSP. Total plasma DNA also was quantified. Tumor-specific plasma DNA was defined as identification of the same methylated promoter (MP) in both tumor and plasma.

RESULTS

Total plasma DNA concentration was markedly elevated (mean 6,503 ng/ml, SEM 1,400 ng/ml). Glioma tissue contained methylation of at least one promoter in 9 out of 10 (90 percent) of patients studied. Of these patients, 6 out of 9 (67 percent) demonstrated methylation of at least one of the same promoters in plasma. Five of these had one MP identified in the plasma and one had 2 MP. Overall, glioma-specific plasma DNA was present in plasma of 6 out of 10 (60 percent) of patients. Each MP DNA marker found in the plasma also was present in the intracranial tumor.

CONCLUSIONS

Patients with high grade gliomas have large amounts of DNA in the plasma. Of these primary brain tumors, 90 percent contained methylated gene promoters, and in over 60 percent of these patients the same methylated promoters present in the tumor also were found in the plasma. This represents the first step to developing a quantitative plasma biomarker that could be used to monitor glioma status.

Prediction of colorectal neoplasia by quantitative methylation analysis of estrogen receptor gene in nonneoplastic epithelium from patients with ulcerative colitis

PURPOSE

The incidence of colorectal neoplasia has increased among patients with longstanding and extensive ulcerative colitis (UC). Therefore, surveillance colonoscopy has been widely recommended. However, there is controversy about the impact of cancer surveillance, and ways to improve its effectiveness are being sought. The estrogen receptor (ER) gene shows age-related methylation in the colorectal epithelium and is frequently methylated in colorectal neoplasia, suggesting that ER methylation occurs early in the process of colorectal tumorigenesis.

EXPERIMENTAL DESIGN

To clarify whether methylation analysis of the ER gene in nonneoplastic epithelium can help predict an increased risk for UC-associated neoplasia, a total of 105 nonneoplastic colorectal epithelia from 18 patients with longstanding and extensive UC, including 8 patients with neoplasia and 10 patients without neoplasia, were analyzed. In all patients, multiple samples were taken from six regions of the colorectum. The combined bisulfite restriction analysis method was used to determine the methylation status of the ER gene.

RESULTS

The mean methylation level of the ER gene was 25.4% in the nonneoplastic epithelia from UC patients with neoplasia, whereas it was only 4.0% in those without neoplasia (P<0.001). The methylation level of the ER gene in UC patients with neoplasia was significantly higher than in UC patients without neoplasia throughout the colorectum except for the cecum. In UC patients with neoplasia, the mean ER methylation level in the distal colon (36.1%) was significantly higher than in the proximal colon (14.6%; P<0.001).

CONCLUSIONS

These results suggest that the analysis of ER gene methylation in nonneoplastic colorectal epithelium could have the potential to be a useful adjunct for identifying individuals with longstanding and extensive UC who are at increased risk of neoplasia and contribute to more effective cancer surveillance.

CpG island methylator phenotype in cancer

DNA hypermethylation in CpG-rich promoters is now recognized as a common feature of human neoplasia. However, the pathophysiology of hyper-methylation (why, when, where) remains obscure. Cancers can be classified according to their degree of methylation, and those cancers with high degrees of methylation (the CpG island methylator phenotype, or CIMP) represent a clinically and aetiologically distinct group that is characterized by 'epigenetic instability'. Furthermore, CIMP-associated cancers seem to have a distinct epidemiology, a distinct histology, distinct precursor lesions and distinct molecular features.

p16INK4A Hypermethylation Is Associated with Hepatitis Virus Infection, Age, and Gender in Hepatocellular Carcinoma

Purpose: The tumor suppressor gene p16INK4A is mainly inactivated by an epigenetic change involving promoter hypermethylation in hepatocarcinogenesis. The possible clinical impact of p16INK4A methylation and the potential risk factors for this epigenetic alteration have not been thoroughly investigated.

Experimental Design: We studied the methylation status and mRNA and protein expression of p16INK4A in 50 hepatocellular carcinomas and corresponding nonneoplastic liver lesions using methylation-specific PCR, reverse transcription-PCR, and immunohistochemical techniques.

Results: p16INK4A hypermethylation was observed in 58% (29 of 50) of the hepatocellular carcinomas and 16% (6 of 38) of the corresponding chronic hepatitis and cirrhosis tissue samples. p16INK4A methylation was significantly associated with mRNA and protein expression (P &lt; 0.001 and P = 0.003, respectively). All of the p16INK4A-methylated tumors were positive for hepatitis B virus or hepatitis C virus markers, but none of the virus-negative tumors exhibited p16INK4A methylation (P = 0.006). The frequency of p16INK4A hypermethylation tended to be higher in hepatitis C virus-related tumors (23 of 32, 72%) than in hepatitis B virus-related tumors (6 of 13, 46%; P = 0.1). Aberrant methylation of p16INK4A was also related significantly to increasing age, female gender, and normal levels of serum PIVKA-II (P = 0.02, 0.04, and 0.04, respectively). No statistically significant difference in survival was observed between patients with p16INK4A hypermethylation and those without.

Conclusions: Our observations suggest that p16INK4A hypermethylation may contribute to hepatocarcinogenesis from an early stage and that multiple risk factors, such as viral infections, age, and gender, may be associated with p16INK4A hypermethylation in hepatocarcinogenesis.

Distinction of acute lymphoblastic leukemia from acute myeloid leukemia through microarray-based DNA methylation analysis

Patterns of DNA methylation are substantially altered in malignancies compared to normal tissue, with both genome-wide hypomethylation and regional increase of cytosine methylation at dinucleotides of cytosine and guanine, i.e., CpG dinucleotides. While genome-wide hypomethylation renders chromosomes instable, hypermethylation of CpGs in promoter regions is generally associated with transcriptional silencing, e.g., of tumor suppressor genes. To investigate whether disease-specific methylation profiles exist for different entities of acute leukemia, a microarray-based DNA methylation analysis simultaneously assessing 249 CpG dinucleotides originating from 57 genes was employed. Hereby, samples from precursor B-cell acute lymphoblastic leukemia (ALL) could be distinguished from cases of acute myeloid leukemia by virtue of N33, EGR4, CDC2, CCND2, or MOS hypermethylation in ALL.

CpG island methylation in gastroenterologic neoplasia: a maturing field

Fifteen years after the first demonstration of epigenetic tumor-suppressor gene inactivation associated with promoter methylation, the field has reached a level of understanding that threatens a re-writing of established biologic concepts. In gastrointestinal malignancies, epigenetic analysis has led to novel hypotheses regarding the etiology of age-associated cancer susceptibility and the interactions between environmental exposures and neoplasia. Methylation profiling has uncovered a distinct pathway to colorectal neoplasia that may arise from a hitherto underestimated precursor lesion, the proximal hyperplastic polyp-serrated adenoma pathway. Epigenetic information has shown promise in clarifying susceptibility to cancer and defining poor prognosis groups in gastrointestinal cancers. Finally, the field has engendered renewed interest in therapeutic targeting of epigenetic regulatory molecules, and several such drugs are currently in clinical trials. It is likely that epigenetic pathways will be integrated in the routine management of gastrointestinal malignancies over the next decade.

Tumor-Specific Methylation in Bronchial Lavage for the Early Detection of Non-Small-Cell Lung Cancer

Purpose

The aim of this study was to identify tumor-specific methylation in bronchial lavage for the early detection of non-small-cell lung cancer (NSCLC) by differentiating the age-related methylation from the tumor-specific methylation in NSCLC.

Patients and Methods

Eighty-five NSCLC patients and 127 cancer-free subjects participated in this study. Aberrant methylation at the promoters of the p16, Ras association domain family 1A (RASSF1A), fragile histidine triad (FHIT), H-cadherin, and retinoic acid receptor β (RARβ) genes were evaluated in the resected tumor tissues and bronchial lavage samples of NSCLC patients and in the bronchial lavage samples of cancer-free subjects by methylation-specific polymerase chain reaction.

Results

Of the 127 cancer-free samples, methylation was detected in 6% for p16, 13% for RARβ, 3% for H-cadherin, 4% for RASSF1A, and 28% for FHIT. Hypermethylation of the p16, RARβ, H-cadherin, and RASSF1A genes was not associated with patient age and smoking, whereas hypermethylation of the FHIT promoter occurred more frequently in older patients (P = .02) and was associated with exposure to tobacco smoke (P = .001). A strong correlation between age and smoking was found in patients with hypermethylation of the FHIT gene (r = 0.36; P = .03). A total of 68% of the bronchial lavage samples from the 85 NSCLC patients showed methylation of at least one of p16, RARβ, H-cadherin, and RASSF1A genes.

Conclusion

Our study suggests that tumor-specific methylation of the p16, RASSF1A, H-cadherin, and RARβ genes may be a valuable biomarker for the early detection of NSCLC in bronchial lavage, and that the age-related methylation of FHIT gene in the normal bronchial epithelium is related to the exposure to tobacco smoke.

Distinct methylation profiles of glioma subtypes

Gliomas are tumors of the central nervous system with a wide spectrum of different tumor types. They range from pilocytic astrocytoma, with a generally good prognosis, to the extremely aggressive malignant glioblastoma. In addition to these 2 types of contrasting neoplasms, several other subtypes can be distinguished, each characterized by specific phenotypic, as well as genotypic features. Recently, the epigenotype, as evident from differentially methylated DNA loci, has been proposed to be useful as a further criterion to distinguish between tumor types. In our study, we screened 139 tissue samples, including 33 pilocytic astrocytomas, 46 astrocytomas of different grades, 7 oligoastrocytomas, 10 oligodendrogliomas, 10 glioblastoma multiforme samples and 33 control tissues, for methylation at CpG islands of 15 different gene loci. We used the semiquantitative high throughput method MethyLight to analyze a gene panel comprising ARF, CDKN2B, RB1, APC, CDH1, ESR1, GSTP1, TGFBR2, THBS1, TIMP3, PTGS2, CTNNB1, CALCA, MYOD1 and HIC1. Seven of these loci showed tumor specific methylation changes. We found tissue as well as grade specific methylation profiles. Interestingly, pilocytic astrocytomas showed no evidence of CpG island hypermethylation, but were significantly hypomethylated, relative to control tissues, at MYOD1. Our results show that glioma subtypes have characteristic methylation profiles and, with the exception of pilocytic astrocytomas, show both locus specific hyper- as well as hypomethylation.

Global and gene-specific methylation patterns in cancer: aspects of tumor biology and clinical potential

Heritable alterations of DNA that do not affect the base pair sequence itself but nevertheless regulate the predetermined activity of genes are referred to as epigenetic. Epigenetic mechanisms comprise diverse phenomena including stable feedback loops, nuclear compartmentalization, differential replication timing, heritable chromatin structures, and, foremost, DNA cytosine methylation (1-3). DNA cytosine methylation has recently gained major attention in the field of basic molecular biology as well as in studies of human diseases including cancer. Changes in DNA methylation patterns in human malignancies have been shown to contribute to carcinogenesis in multiple ways. Both hypo- and hypermethylation events have been described in various neoplasias leading to chromosomal instability and transcriptional gene silencing. DNA methylation research has entered the clinical arena and methylation patterns have become a major focus of clinicians seeking novel prognostic factors and therapeutic targets. The following minireview covers aspects of the basic molecular biology of DNA methylation and summarizes its importance in human cancers.

DNA methylation of nuclear receptor genes--possible role in malignancy

The members of the nuclear receptor superfamily are known to mediate a wide array of basic biological processes, such as regulation of cell growth and differentiation, and induction of apoptosis. In several human malignancies, this central control function of nuclear receptors is disturbed, which seems to play an important role in tumor development and progression. Many nuclear receptor genes have been reported to be downregulated in malignancies; however, only a few mutations, gene arrangements, deletions or similar genetic changes have been shown to occur in these tumors. During the last decade, increasing attention has been directed towards epigenetic mechanisms of gene regulation such as DNA methylation. Many nuclear receptor genes can be silenced through aberrant methylation in tumors; epigenetic silencing, therefore, represents an additional mechanism that modifies expression of key genes during carcinogenesis. This review will give insights into the role of DNA methylation in the silencing of nuclear receptor genes and its involvement in human malignancies.

Expression of the Hypermethylated in Cancer gene (HIC-1) is associated with good outcome in human breast cancer

A new cancer gene, HIC-1 (Hypermethylated in Cancer) telomeric to p53 on chromosome 17p may be of clinical importance in sporadic breast cancer. Regional DNA hypermethylation of 17p13.3 resulting in suppression of gene expression has been shown to precede 17p structural changes in human carcinogenesis. In addition, loss of heterozygosity studies have suggested clinically significant involvement of a gene on 17p13.3 associated with poor prognosis in breast cancer. Using RT-PCR analysis, we demonstrate that the MCF7 (wild type p53) cell line expressed HIC-1 transcripts but the MDAMB231 (mutant p53) cell line did not, suggesting loss of HIC-1 expression and p53 malfunction may be synergistic events in sporadic breast cancer. HIC-1 expression was examined using RT-PCR on RNA extracted from 50 primary untreated, human breast cancers and was detected in only 7/50 (14%) cancers. All seven patients with HIC-1 expression were alive without disease recurrence after 8 years follow-up and 5/7 had detectable p53 wild type mRNA expression. This suggests that retained HIC-1 expression may offer a survival advantage. However the seven cancers had 17p13.3 loss of heterozygosity (LOH; four patients), a feature previously associated with poor prognosis, or were homozygous (three patients) suggesting there may be two genes at 17p13.3 involved in breast carcinogenesis. Using a demethylating drug 5-aza-2'-deoxycytidine (DeoxyC), HIC-1 expression was restored in the MDAMB231 cells, also suggesting restoration of HIC-1 function by reversing HIC-1 hypermethylation may offer a therapeutic avenue in breast cancer.