The CpG island methylator phenotype in breast cancer is associated with the lobular subtype

Identification of Novel Molecular and Clinical Biomarkers of Survival in Glioblastoma Multiforme Patients: A Study Based on The Cancer Genome Atlas Data

Glioblastoma multiforme (GBM) is the most prevalent type of brain tumour; although advancements in treatment have been made, the median survival time for GBM patients has persisted at 15 months. This study is aimed at investigating the genetic alterations and clinical features of GBM patients to find predictors of survival. GBM patients' methylation and gene expression data along with clinical information from TCGA were retrieved. The most overrepresented pathways were identified independently for each omics dataset. From the genes found in at least 30% of these pathways, one gene that was identified in both sets was further examined using the Kaplan-Meier method for survival analysis. Additionally, three groups of patients who started radio and chemotherapy at different times were identified, and the influence of these variations in treatment modality on patient survival was evaluated. Four pathways that seemed to negatively impact survival and two with the opposite effect were identified. The methylation status of PRKCB was highlighted as a potential novel biomarker for patient survival. The study also found that treatment with chemotherapy prior to radiotherapy can have a significant impact on patient survival, which could lead to improvements in clinical management and therapeutic approaches for GBM patients.

Recent advances in understanding DNA methylation of prostate cancer

Epigenetic modifications, such as DNA methylation, is widely studied in cancer. DNA methylation patterns have been shown to distinguish between benign and malignant tumors in various cancers, including prostate cancer. It may also contribute to oncogenesis, as it is frequently associated with downregulation of tumor suppressor genes. Aberrant patterns of DNA methylation, in particular the CpG island hypermethylator phenotype (CIMP), have shown associative evidence with distinct clinical features and outcomes, such as aggressive subtypes, higher Gleason score, prostate-specific antigen (PSA), and overall tumor stage, overall worse prognosis, as well as reduced survival. In prostate cancer, hypermethylation of specific genes is significantly different between tumor and normal tissues. Methylation patterns could distinguish between aggressive subtypes of prostate cancer, including neuroendocrine prostate cancer (NEPC) and castration resistant prostate adenocarcinoma. Further, DNA methylation is detectable in cell-free DNA (cfDNA) and is reflective of clinical outcome, making it a potential biomarker for prostate cancer. This review summarizes recent advances in understanding DNA methylation alterations in cancers with the focus on prostate cancer. We discuss the advanced methodology used for evaluating DNA methylation changes and the molecular regulators behind these changes. We also explore the clinical potential of DNA methylation as prostate cancer biomarkers and its potential for developing targeted treatment of CIMP subtype of prostate cancer.

The Clonal Relationship Between the Ductal and Lobular Components of Mixed Ductal-Lobular Carcinomas Suggested a Ductal Origin in Most Tumors

The relationship between the ductal and lobular components of invasive ductolobular carcinomas (IDLC) has not been fully elucidated. In this study, the molecular alterations of both components were analyzed in a series of 20 IDLC that were selected, not only by morphologic criteria, but also by the loss of E-cadherin expression in the lobular component. We found that 80% of tumors shared alterations of driver genes in both components, being PIK3CA the most common alteration. In addition, 45% of IDLC carried CDH1 mutations in their lobular component that were absent in the ductal component. Fluorescent in situ hybridization analysis of the CDH1 gene excluded homozygous CDH1 loss as a frequent cause of E-cadherin loss in tumors without CDH1 mutations. In addition, no pathogenic mutations of catenin genes were detected in this series of tumors. In 25% of tumors, actionable mutations in PIK3CA , AKT1 , and ERBB2 were found in only 1 component. Altogether, our results confirm that most IDLC derive from invasive carcinoma of no special type, in which a population of cells lose E-cadherin and acquire a lobular phenotype. The frequency of CDH1 mutations in IDLC appears to be lower than in conventional invasive lobular carcinomas, suggesting the implication of alternative mechanisms of E-cadherin loss. Moreover, molecular heterogeneity between ductal and lobular areas suggests the need for molecular characterization of both components to guide targeted therapies.

CDH1 (E-cadherin) Gene Methylation in Human Breast Cancer: Critical Appraisal of a Long and Twisted Story

Simple Summary

Genes can be inactivated by specific modifications of DNA bases, most often by adding a methyl group to the DNA base cytosine if it is followed by guanosine (CG methylation). This modification prevents gene expression and has been reported for many different genes in nearly all types of cancer. A prominent example is the gene CDH1, which encodes the cell-adhesion molecule E-cadherin. This is an important player in the spreading of tumor cells within the body (metastasis). Particularly in human breast cancer, many different research groups have studied the inactivation of the CDH1 gene via DNA methylation using various methods. Over the last 20 years, different, in part, even contradicting results have been published for the CDH1 gene in breast cancer. This review summarizes the most important publications and explains the bewildering heterogeneity of results through careful analysis of the methods which have been used.

Abstract

Epigenetic inactivation of a tumor suppressor gene by aberrant DNA methylation is a well-established defect in human tumor cells, complementing genetic inactivation by mutation (germline or somatic). In human breast cancer, aberrant gene methylation has diagnostic, prognostic, and predictive potential. A prominent example is the hypermethylation of the CDH1 gene, encoding the adhesion protein E-Cadherin (“epithelial cadherin”). In numerous publications, it is reported as frequently affected by gene methylation in human breast cancer. However, over more than two decades of research, contradictory results concerning CDH1 gene methylation in human breast cancer accumulated. Therefore, we review the available evidence for and against the role of DNA methylation of the CDH1 gene in human breast cancer and discuss in detail the methodological reasons for conflicting results, which are of general importance for the analysis of aberrant DNA methylation in human cancer specimens. Since the loss of E-cadherin protein expression is a hallmark of invasive lobular breast cancer (ILBC), special attention is paid to CDH1 gene methylation as a potential mechanism for loss of expression in this special subtype of human breast cancer. Proper understanding of the methodological basis is of utmost importance for the correct interpretation of results supposed to demonstrate the presence and clinical relevance of aberrant DNA methylation in cancer specimens.

Acute lymphoblastic leukemia displays a distinct highly methylated genome

DNA methylation is tightly regulated during development and is stably maintained in healthy cells. In contrast, cancer cells are commonly characterized by a global loss of DNA methylation co-occurring with CpG island hypermethylation. In acute lymphoblastic leukemia (ALL), the commonest childhood cancer, perturbations of CpG methylation have been reported to be associated with genetic disease subtype and outcome, but data from large cohorts at a genome-wide scale are lacking. Here, we performed whole-genome bisulfite sequencing across ALL subtypes, leukemia cell lines and healthy hematopoietic cells, and show that unlike most cancers, ALL samples exhibit CpG island hypermethylation but minimal global loss of methylation. This was most pronounced in T cell ALL and accompanied by an exceptionally broad range of hypermethylation of CpG islands between patients, which is influenced by TET2 and DNMT3B. These findings demonstrate that ALL is characterized by an unusually highly methylated genome and provide further insights into the non-canonical regulation of methylation in cancer.

O6-Methylguanine-DNA Methyltransferase and ATP-Binding Cassette Membrane Transporter G2 Promotor Methylation: Can Predict the Response to Chemotherapy in Advanced Breast Cancer?

Background

ATP-binding cassette membrane transporter G2 (ABCG2) gene is one of transporter family and well characterized for their association with chemoresistance. Promoter methylation is a mechanism for regulation of gene expression. O6-Methyl guanine DNA methyl transferase (MGMT) gene plays a fundamental role in DNA repair. MGMT has the ability to remove alkyl adducts from DNA at the O6 position of guanine. Alkylating agents exert their function through adding these alkyls adducts to DNA leading to cell death unless it is repaired by MGMT. MGMT promoter was found to be methylated in several malignancies. The aim of the present work is to study the relation of MGMT and ABCG2 promoter methylation status in advanced breast cancer patients to response to cyclophosphamide-doxorubicin (AC) based therapeutic regime.

Methods

This retrospective study included Forty-two female patients with advanced breast cancer assessed before receiving chemotherapy and after the completion of regimens. They were grouped into responders and non-responders according to RECIST criteria. Methylation analysis of MGMT and ABCG2 genes were performed on breast cancer tissues.

Results

MGMT promoter was methylated in 40.5% of the cases. ABCG2 promoter was methylated in 14.3% of cases. There was no statistically significant association between MGMT and ABCG2 promoter methylation status and clinicopathological parameters. There was statistically significant association between methylation status of both promoters and response to AC when followed by Taxane.

Conclusion

Methylation of MGMT and ABCG2 promoters combined could be a potential predictive factor for response to cyclophosphamide-doxorubicin based therapeutic regime.

Inter-observer agreement for the histological diagnosis of invasive lobular breast carcinoma

Invasive lobular breast carcinoma (ILC) is the second most common breast carcinoma (BC) subtype and is mainly driven by loss of E‐cadherin expression. Correct classification of BC as ILC is important for patient treatment. This study assessed the degree of agreement among pathologists for the diagnosis of ILC. Two sets of hormone receptor (HR)‐positive/HER2‐negative BCs were independently reviewed by participating pathologists. In set A (61 cases), participants were provided with hematoxylin/eosin (HE)‐stained sections. In set B (62 cases), participants were provided with HE‐stained sections and E‐cadherin immunohistochemistry (IHC). Tumor characteristics were balanced. Participants classified specimens as non‐lobular BC versus mixed BC versus ILC. Pairwise inter‐observer agreement and agreement with a pre‐defined reference diagnosis were determined with Cohen's kappa statistics. Subtype calls were correlated with molecular features, including CDH1/E‐cadherin mutation status. Thirty‐five pathologists completed both sets, providing 4,305 subtype calls. Pairwise inter‐observer agreement was moderate in set A (median κ = 0.58, interquartile range [IQR]: 0.48–0.66) and substantial in set B (median κ = 0.75, IQR: 0.56–0.86, p < 0.001). Agreement with the reference diagnosis was substantial in set A (median κ = 0.67, IQR: 0.57–0.75) and almost perfect in set B (median κ = 0.86, IQR: 0.73–0.93, p < 0.001). The median frequency of CDH1/E‐cadherin mutations in specimens classified as ILC was 65% in set A (IQR: 56–72%) and 73% in set B (IQR: 65–75%, p < 0.001). Cases with variable subtype calls included E‐cadherin‐positive ILCs harboring CDH1 missense mutations, and E‐cadherin‐negative ILCs with tubular elements and focal P‐cadherin expression. ILCs with trabecular growth pattern were often misclassified as non‐lobular BC in set A but not in set B. In conclusion, subtyping of BC as ILC achieves almost perfect agreement with a pre‐defined reference standard, if assessment is supported by E‐cadherin IHC. CDH1 missense mutations associated with preserved E‐cadherin protein expression, E‐ to P‐cadherin switching in ILC with tubular elements, and trabecular ILC were identified as potential sources of discordant classification.

Methylated biomarkers for breast cancer identified through public database analysis and plasma target capture sequencing

Background

Aberrant methylation is common during the early stage of cancer development. This study was designed to investigate DNA methylation as biomarker for breast cancer.

Methods

Public database analysis and methylation-specific whole-gene sequencing were conducted to identify methylated biomarkers that would enable early non-invasive diagnosis of breast cancer. Firstly, the data was obtained from the TCGA Database and the Blueprint Epigenome Database. Secondly, methylation-specific whole-gene sequencing was conducted in 10 female patients with early-stage breast cancer and 10 healthy female volunteers from Nanfang Hospital of Southern Medical University between March 2018 and July 2018. Thirdly, the R language was used for data analysis, and KEGG and DAVID online tool was used for annotations.

Results

We found that methylation levels at 13 cytosine-phosphate-guanine (CpG) sites (cg04066177, cg04281344, cg05995576, cg06221609, cg08642731, cg11388802, cg12665414, cg14557216, cg19404723, cg19457909, cg24570211, cg25818763, and cg26215982) in the malignant tissue DNA were highly comparable to those of circulating cell-free DNA (cfDNA) of breast cancer patients, but were significantly different from those of normal tissue DNA, cfDNA of healthy women, and leukocyte DNA. In addition, three CpG sites (cg04281344, cg24570211, and cg26215982) were confirmed in clinical research, which showed that the sensitivity and specificity of these CpGs as biomarkers for breast cancer were 69.4–83.7% and 85.7–88.6%, respectively.

Conclusions

New biomarkers were identified and confirmed for breast cancer by comparing the methylation of tumour tissues, leukocytes, and non-plasma DNA.

Epigenetics in Breast Cancer Therapy-New Strategies and Future Nanomedicine Perspectives

Epigenetic dysregulation has been recognized as a critical factor contributing to the development of resistance against standard chemotherapy and to breast cancer progression via epithelial-to-mesenchymal transition. Although the efficacy of the first-generation epigenetic drugs (epi-drugs) in solid tumor management has been disappointing, there is an increasing body of evidence showing that epigenome modulation, in synergy with other therapeutic approaches, could play an important role in cancer treatment, reversing acquired therapy resistance. However, the epigenetic therapy of solid malignancies is not straightforward. The emergence of nanotechnologies applied to medicine has brought new opportunities to advance the targeted delivery of epi-drugs while improving their stability and solubility, and minimizing off-target effects. Furthermore, the omics technologies, as powerful molecular epidemiology screening tools, enable new diagnostic and prognostic epigenetic biomarker identification, allowing for patient stratification and tailored management. In combination with new-generation epi-drugs, nanomedicine can help to overcome low therapeutic efficacy in treatment-resistant tumors. This review provides an overview of ongoing clinical trials focusing on combination therapies employing epi-drugs for breast cancer treatment and summarizes the latest nano-based targeted delivery approaches for epi-drugs. Moreover, it highlights the current limitations and obstacles associated with applying these experimental strategies in the clinics.

Transcriptome analysis of MAPK signaling pathway and associated genes to angiogenesis in chicken erythrocytes on response to thiram-induced tibial lesions

This study was planned to investigate TD (Tibial dyschondroplasia) on the potential MAPK signaling pathway and angiogenesis related genes. Forty-eight broilers were allotted into control (C) and treatment (T) groups of 2, 6 and 15 days as C1, C2, C3, T1, T2 and T3. The histopathology results revealed that tibiotarsus bone of chickens had more lesions on day 6 (T2 group). The chondrocytes were disordered, and the size, shape and proliferation were affected. Transcriptome results revealed that differentially expressed genes (DEGs) identified were 63, 1026, 623, 130, 141 and 146 in C1 (2 days control vs 6 days control); C2 (2 days control vs 15 days control); C3 (6 days control vs 15 days control); T1 (2 days treatment vs 6 days treatment); T2 (2 days treatment vs 15 days treatment) and T3 (6 days treatment vs 15 days treatment) groups respectively. Whereas, 10 angiogenesis related-genes RHOC, MEIS2, BAIAP2, TGFBI, KLF2, CYR61, PTPN11, PLXNC1, HSPH1 and NRP2 were downregulated on day 6 in the treatment group. The pathway which was found enriched in the control and treatment groups was MAPK signaling pathway. Therefore selected 10 MAPK signaling pathway-related genes RAC2, MAP3K1, PRKCB, FLNB, IL1R1, PTPN7, RPS6KA, MAP3K6, GNA12 and HSPA8 which were found significantly downregulated in the treatment group on day 6. It is concluded that angiogenesis and MAPK signaling pathway related genes has an essential role in TD, as those top screened genes found downregulated in the thiram fed chickens when TD observed severed on day 6.

Partially methylated domains are hypervariable in breast cancer and fuel widespread CpG island hypermethylation

Global loss of DNA methylation and CpG island (CGI) hypermethylation are key epigenomic aberrations in cancer. Global loss manifests itself in partially methylated domains (PMDs) which extend up to megabases. However, the distribution of PMDs within and between tumor types, and their effects on key functional genomic elements including CGIs are poorly defined. We comprehensively show that loss of methylation in PMDs occurs in a large fraction of the genome and represents the prime source of DNA methylation variation. PMDs are hypervariable in methylation level, size and distribution, and display elevated mutation rates. They impose intermediate DNA methylation levels incognizant of functional genomic elements including CGIs, underpinning a CGI methylator phenotype (CIMP). Repression effects on tumor suppressor genes are negligible as they are generally excluded from PMDs. The genomic distribution of PMDs reports tissue-of-origin and may represent tissue-specific silent regions which tolerate instability at the epigenetic, transcriptomic and genetic level.

Gene-specific methylation profiles in BRCA-mutation positive and BRCA-mutation negative male breast cancers

Male breast cancer (MBC) is a rare disease. Due to its rarity, MBC research and clinical approach are mostly based upon data derived from female breast cancer (FBC). Increasing evidence indicate that on molecular level MBC may be an heterogeneous disease different from FBC. In order to investigate whether epigenetic signatures could define molecular subgroups of MBCs, we performed promoter methylation analysis of genes involved in signal transduction and hormone signalling in BRCA1/2 mutation-positive and -negative MBCs. We examined 69 MBCs, paired blood samples, and 15 normal tissues for promoter methylation of hTERT, ESR1, RASSF1, AR, MYC and WNT1 genes. MBCs showed higher gene promoter methylation levels compared to paired blood and normal breast samples. Significantly higher RASSF1 methylation levels were observed in association with BRCA1/2 mutations, HER2 expression and high tumor grade. Significantly higher AR methylation levels were observed in BRCA1/2 wild-type cases and higher WNT1 methylation levels in PR negative cases. Overall, our results indicate that alterations in gene methylation profiles are common in MBC and that methylation pattern of tumor-associated genes may allow for the identification of MBC molecular subgroups, that could have implications in clinical management of MBC patients.

A 63 signature genes prediction system is effective for glioblastoma prognosis

The present study aimed to explore possible prognostic marker genes in glioblastoma (GBM). Differentially expressed genes (DEGs) were screened by comparing microarray data of tumor and normal tissue samples from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) dataset GSE22866. Subsequently, the prognosis-associated DEGs were screened via Cox regression analysis, followed by construction of gene/protein/pathway interaction networks of these DEGs by calculating the correlation coefficient between the DEGs. Next, a prognostic prediction system was constructed using Bayes discriminant analysis, which was validated by the microarray data of samples from patients with good and bad prognosis from the TCGA and Chinese Glioma Genome Atlas (CGGA), as well as the GEO dataset. Finally, a co-expression network of the signature genes in the prediction system was constructed in combination with the significant pathways. A total of 288 overlapping DEGs (false discovery rate <0.5 and |log2 of fold change|>1) were screened, 123 of which were identified to be associated with the prognosis of GBM patients. The co-expression network of these prognosis-associated DEGs included 1405 interactions and 112 DEGs, and 6 functional modules were identified in the network. The prognostic prediction system was comprised of 63 signature genes with a specificity value of 0.929 and a sensitivity value of 0.948. GBM samples with good and bad prognosis in the TCGA, CGGA and GEO datasets were distinguishable by these signature genes (P=1.33×10⁻⁶, 1.63×10⁻⁴ and 0.00534, respectively). The co-expression network of signature genes with significant pathways was comprised of 56 genes and 361 interactions. Protein kinase Cγ (PRKCG), protein kinase Cβ (PRKCB) and calcium/calmodulin-dependent protein kinase IIα (CAMK2A) were important genes in the network, and based on the expression of these genes, it was possible to distinguish between samples with significantly different survival risks. In the present study, an effective prognostic prediction system for GBM patients was constructed and validated. PRKCG, PRKCB and CAMK2A may be potential prognostic factors for GBM.

How Sensitive Is Genetic Data?

The rising demand to use genetic data for research goes hand in hand with an increased awareness of privacy issues related to its use. Using human genetic data in a legally compliant way requires an examination of the legal basis as well as an assessment of potential disclosure risks. Focusing on the relevant legal framework in the European Union, we discuss open questions and uncertainties around the handling of genetic data in research, which can result in the introduction of unnecessary hurdles for data sharing. First, we discuss defining features and relative disclosure risks of some DNA-related biomarkers, distinguishing between the risk for disclosure of (1) the identity of an individual, (2) information about an individual's health and behavior, including previously unknown phenotypes, and (3) information about an individual's blood relatives. Second, we discuss the European legal framework applicable to the use of DNA-related biomarkers in research, the implications of including both inherited and acquired traits in the legal definition, as well as the issue of “genetic exceptionalism”—the notion that genetic information has inherent characteristics that require different considerations than other health and medical information. Finally, by mapping the legal to specific technical definitions, we draw some initial conclusions concerning how sensitive different types of “genetic data” may actually be. We argue that whole genome sequences may justifiably be considered “exceptional” and require special protection, whereas other genetic data that do not fulfill the same criteria should be treated in a similar manner to other clinical data. This kind of differentiation should be reflected by the law and/or other governance frameworks as well as agreed Codes of Conduct when using the term “genetic data.”

Survival differences of CIMP subtypes integrated with CNA information in human breast cancer

CpG island methylator phenotype of breast cancer is associated with widespread aberrant methylation at specified CpG islands and distinct patient outcomes. However, the influence of copy number contributing to the prognosis of tumors with different CpG island methylator phenotypes is still unclear. We analyzed both genetic (copy number) and epigenetic alterations in 765 breast cancers from The Cancer Genome Atlas data portal and got a panel of 15 biomarkers for copy number and methylation status evaluation. The gene panel identified two groups corresponding to distinct copy number profiles. In status of mere-loss copy number, patients were faced with a greater risk if they presented a higher CpG islands methylation pattern in biomarker panels. But for samples presenting merely-gained copy number, higher methylation level of CpG islands was associated with improved viability. In all, the integration of copy number alteration and methylation information enhanced the classification power on prognosis. Moreover, we found the molecular subtypes of breast cancer presented different distributions in two CpG island methylation phenotypes. Generated by the same set of human methylation 450K data, additional copy number information could provide insights into survival prediction of cancers with less heterogeneity and might help to determine the biomarkers for diagnosis and treatment for breast cancer patients in a more personalized approach.

Das Tumorepigenom – von der Genregulation über die Tumorklassifikation zum Therapietarget

Epigenetische Regulationsmechanismen sind essenziell für den koordinierten Ablauf zahlreicher zellulärer Prozesse wie die Differenzierung und Entwicklung oder auch die Anpassung der Genaktivität an die herrschenden Umweltbedingungen. Insbesondere Tumorerkrankungen gehen mit oftmals umfangreichen Alterationen im Epigenom einher. Diese Veränderungen sind dabei vielfach charakteristisch entweder für die Tumorentität, das Stadium der Erkrankung oder aber das klinische Ansprechen des Tumors auf eine Therapie und damit die individuelle Prognose des Patienten. Nach einer kurzen Darstellung epigenetischer Marker und ihrer Bedeutung bei malignen Erkrankungen werden in diesem Artikel Alterationen im Tumorepigenom und ihre Nutzbarkeit im Rahmen einer individualisierten Medizin exemplarisch vorgestellt.

Emergence of the Noncoding Cancer Genome: A Target of Genetic and Epigenetic Alterations

The emergence of whole-genome annotation approaches is paving the way for the comprehensive annotation of the human genome across diverse cell and tissue types exposed to various environmental conditions. This has already unmasked the positions of thousands of functional cis-regulatory elements integral to transcriptional regulation, such as enhancers, promoters, and anchors of chromatin interactions that populate the noncoding genome. Recent studies have shown that cis-regulatory elements are commonly the targets of genetic and epigenetic alterations associated with aberrant gene expression in cancer. Here, we review these findings to showcase the contribution of the noncoding genome and its alteration in the development and progression of cancer. We also highlight the opportunities to translate the biological characterization of genetic and epigenetic alterations in the noncoding cancer genome into novel approaches to treat or monitor disease.

SIGNIFICANCE

The majority of genetic and epigenetic alterations accumulate in the noncoding genome throughout oncogenesis. Discriminating driver from passenger events is a challenge that holds great promise to improve our understanding of the etiology of different cancer types. Advancing our understanding of the noncoding cancer genome may thus identify new therapeutic opportunities and accelerate our capacity to find improved biomarkers to monitor various stages of cancer development. Cancer Discov; 6(11); 1215-29. ©2016 AACR.

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.

DNA methylation assessment as a prognostic factor in invasive breast cancer using methylation-specific multiplex ligation dependent probe amplification

DNA methylation of promoter regions is a common molecular mechanism for inactivation of tumor suppressor genes that participates in carcinogenesis. Determining the methylation status of genes in cancer and their association with clinical features play an essential role in early diagnosis, prognosis and determine appropriate treatment for patients. The purpose of the present study was to evaluate the methylation of tumor suppressor genes in patients with invasive ductal carcinoma (IDC). Furthermore, we evaluated the association between clinical parameters and DNA methylation as a biomarker in diagnostic IDC patients. The methylation-specific multiplex ligation dependent probe amplification (MS-MLPA) assay was used to analyze the methylation profile of 24 genes in formalin-fixed paraffin embedded (FFPE) tissue samples from 75 patients with IDC. Each of the patients showed a distinctive methylation profile. We observed higher methylation in the RASSF1 (48 %), CDH13 (44 %) and GSTP1 (36 %) genes. Some of the methylated genes were associated with clinical features. Methylation of GSTP1 (P=0.028) and RASSF1 (P=0.012) were related with lymph node metastasis. Methylation of GSTP1 (P=0.005) was associated with high histological grade. Moreover, concurrent methylation of GSTP1 and CDH13 was observed in IDC patients (p<0.001). Hierarchical cluster analysis based on the methylation profile revealed two main clusters of patients, the highly methylated cluster being significantly associated with high histological grade and lymph node metastasis. The results of this study indicate that the methylation status of RASSF1 and CDH13 and GSTP1 can be a prognostic marker to better management of IDC patients.

Type 2 diabetes and leucocyte DNA methylation: an epigenome-wide association study in over 1,500 older adults

AIMS/HYPOTHESIS

Development of type 2 diabetes depends on environmental and genetic factors. We investigated the epigenome-wide association of prevalent diabetes with DNA methylation (DNAm) in peripheral blood.

METHODS

DNAm was measured in whole blood with the Illumina Infinium HumanMethylation450 BeadChip in two subsamples of participants from the ESTHER cohort study. Cohort 1 included 988 participants, who were consecutively recruited between July and October 2000 and cohort 2 included 527 randomly selected participants. The association of DNAm with prevalent type 2 diabetes at recruitment was estimated using median regression analysis adjusting for sex, age, BMI, smoking behaviour, cell composition and batch at 361,922 CpG sites.

RESULTS

Type 2 diabetes was prevalent in 16% of the participants, and diabetes was poorly controlled in 45% of the diabetic patients. In cohort 1 (discovery) DNAm at 39 CpGs was significantly associated with prevalent diabetes after correction for multiple testing. In cohort 2 (replication) at one of these CpGs, DNAm was still significantly associated. Decreasing methylation levels at cg19693031 with increasing fasting glucose and HbA1c concentrations were observed using restricted cubic spline analysis. In diabetic patients with poorly controlled diabetes, the decrease in estimated DNAm levels was approximately 5% in comparison with participants free of diagnosed diabetes.

CONCLUSIONS/INTERPRETATION

Cg19693031, which is located within the 3'-untranslated region of TXNIP, might play a role in the pathophysiology of type 2 diabetes. This result appears biologically plausible given that thioredoxin-interacting protein is overexpressed in diabetic animals and humans and 3'-untranslated regions are known to play a regulatory role in gene expression.

Promoter Hypermethylation Profiling Identifies Subtypes of Head and Neck Cancer with Distinct Viral, Environmental, Genetic and Survival Characteristics

BACKGROUND

Epigenetic and genetic alteration plays a major role to the development of head and neck squamous cell carcinoma (HNSCC). Consumption of tobacco (smoking/chewing) and human papilloma virus (HPV) are also associated with an increase the risk of HNSCC. Promoter hypermethylation of the tumor suppression genes is related with transcriptional inactivation and loss of gene expression. We investigated epigenetic alteration (promoter methylation of tumor-related genes/loci) in tumor tissues in the context of genetic alteration, viral infection, and tobacco exposure and survival status.

METHODOLOGY

The study included 116 tissue samples (71 tumor and 45 normal tissues) from the Northeast Indian population. Methylation specific polymerase chain reaction (MSP) was used to determine the methylation status of 10 tumor-related genes/loci (p16, DAPK, RASSF1, BRAC1, GSTP1, ECAD, MLH1, MINT1, MINT2 and MINT31). Polymorphisms of CYP1A1, GST (M1 & T1), XRCC1and XRCC2 genes were studied by using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and multiplex-PCR respectively.

PRINCIPAL FINDINGS

Unsupervised hierarchical clustering analysis based on methylation pattern had identified two tumor clusters, which significantly differ by CpG island methylator phenotype (CIMP), tobacco, GSTM1, CYP1A1, HPV and survival status. Analyzing methylation of genes/loci individually, we have found significant higher methylation of DAPK, RASSF1, p16 and MINT31 genes (P = 0.031, 0.013, 0.031 and 0.015 respectively) in HPV (+) cases compared to HPV (-). Furthermore, a CIMP-high and Cluster-1 characteristic was also associated with poor survival.

CONCLUSIONS

Promoter methylation profiles reflecting a correlation with tobacco, HPV, survival status and genetic alteration and may act as a marker to determine subtypes and patient outcome in HNSCC.

Emerging technologies for studying DNA methylation for the molecular diagnosis of cancer

DNA methylation is an epigenetic mechanism that plays a key role in regulating gene expression and other functions. Although this modification is seen in different sequence contexts, the most frequently detected DNA methylation in mammals involves cytosine-guanine dinucleotides. Pathological alterations in DNA methylation patterns are described in a variety of human diseases, including cancer. Unlike genetic changes, DNA methylation is heavily influenced by subtle modifications in the cellular microenvironment. In all cancers, aberrant DNA methylation is involved in the alteration of a large number of oncological pathways with relevant theranostic utility. Several technologies for DNA methylation mapping have been developed recently and successfully applied in cancer studies. The scope of these technologies varies from assessing a single cytosine-guanine locus to genome-wide distribution of DNA methylation. Here, we review the strengths and weaknesses of these approaches in the context of clinical utility for the molecular diagnosis of human cancers.