Hypermethylation Events Research Articles

Analysis of CpG Island DNA Methylation of p15INK4b and RIL in Bone Marrow Samples of Patients with Monoclonal Gammopathies

Introduction: Adding a methyl group on the cytosine residues of CpG dinucleotides (CpGs) is a basic phenomenon in DNA methylation. This modification belongs to a group of epigenetic changes that are thought to play one of the key roles in tumor development and progression. DNA hypermethylation occurs mainly in CpG islands of the promoter region in tumor-supressor (TS) genes, which leads to gene silencing. On the other hand, global DNA hypomethylation leads to a genomic instability. Many specific genes are epigenetically changed in individual malignant diseases and these genes are intensively studied by the scientific community. According to the recent research in plasma cell neoplasms, the global genic hypomethylation is predominant in contrast to hypermethylation events. Epigenetic changes of TS genes may worsen prognosis, drug response and microenvironment interaction in multiple myeloma patients. Our aim was to assess the methylation level of the RIL and p15INK4b gene. RIL protein acts as suppressor of cell proliferation and it sensitizes tumor cells to apoptosis, on the other hand, the p15INK4bplays an important role in inhibiting the cell cycle progression in G1 phase.Methods: Our updated study includes 72 bone marrow aspirate-samples from 68 patients with multiple myeloma (MM) or monoclonal gammopathy of undetermined significance (MGUS). 68 samples were acquired at the time of the diagnosis and four patients with MM were assessed also in remission after chemotherapy. Extracted DNA after bisulfite modification was examined by pyrosequencing method (Pyromark Q96, Qiagen, Germany) and the selected gene regions – RIL promotor, p15INK4b promotor and p15INK4b exon were analysed. Nine CpGs in the RIL promoter, thirteen CpGs in the p15INK4b promoter and sixteen CpGs in the p15INK4bexon were studied. Average methylation level (MtL) was generated and samples were sorted according to the mean MtL (%) into four groups for the RIL gene (less than 10% MtL, 11-19% MtL, 21-50% and more than 50%). We used commercially available unmethylated DNA and methylated DNA control. Statistical analysis was performed using Pyromark Software and Wilcoxon rank sum test.Results: Out of the four groups for the methylation level of the RIL gene promoter, the groups with 11-19% MtL and 21-50% MtL, detected significant and highly significant differences respectively at both p-values - p-value ≤0.05 and p-value ≤0.01. There were only 2 samples with MtL level over 50% in patients with active MM, precluding valid statistical analysis. In both regions of the p15INK4b gene, i.e. the promoter and the exon, we did not find any significant differences between the methylation levels - mean MtL ranged from 3% to 6% in p15INK4b promotor and from 3% to 12% in p15INK4b exon. The time-dependend analysis of the DNA methylation level changes in four patients assessed at the time of diagnosis and in remission of the disease after chemotherapy course revealed a significant decrease of CpGs methylation in all MM patients reaching therapeutic response.Conclusions: Updated data on the epigenetic analysis in patients with monoclonal gammopathies confirmed an important role of the RIL gene in the epigenetic network acting in pathogenesis of MM. The presented results suggest possible prognostic value and therapeutic target in patients with MM. In contrast, the p15INK4b gene known as a frequent focus of epigenetic modifications in many tumors, did not show statistically significant differences in our study. Our results indicate that for DNA methylation analyses of MM or MGUS patients, the RIL gene could be more useful marker than the p15INK4b gene. Moreover, the decrease of the methylation level in patients undergoing systemic chemotherapy might be associated with treatment response, suggesting its potential prognostic value.The paper was supported by the grant IGA MZ CR NT14393. DisclosuresNo relevant conflicts of interest to declare.

Abstract 2305: Acute depletion reveals novel co-regulation of DNA methylation at conserved loci by DNMT1 and DNMT3B

Abstract DNA methyltransferases (DNMTs) are responsible for establishing (DNMT3A, 3B, 3L) and maintaining (DNMT1) DNA methylation genome-wide. Aberrant DNA methylation is frequently observed in cancer; however, little is known about how regulation of this modification goes awry. In this study, we aim to understand how DNA methylation is regulated by the DNMTs throughout the genome by identifying specific and broad changes in methylation patterning upon depletion of the DNMTs. We utilize siRNA technology to acutely deplete NCCIT embryonal carcinoma cells of DNMT mRNA (individually and in combination), and then assay the impact on genome-wide DNA methylation patterns using the HumanMethylation450 Bead Chip (450K array). Depletion of DNMT1 (individual/combination) resulted in widespread hypomethylation, most notably in gene bodies, 3′UTRs, and intergenic sequences. DNMT3 knockdown resulted in more specific changes in DNA methylation, but surprisingly, more hypermethylation (predominately in gene bodies) than hypomethylation events occurred. These specific hypermethylation events, particularly in samples with DNMT3B KD, significantly overlapped with sites hypomethylated in DNMT1 KD conditions, indicating a potential cross-regulatory role for DNMT1 and DNMT3B in regulating DNA methylation across gene bodies. To gain a more comprehensive genome-wide view of DNA methylation in the absence of DNMT3B, we performed Methyl-CpG-Binding-Domain(MBD)-seq on DNMT3B KD cells. MBD-seq revealed dynamic changes in methylation with minor hypermethylation in promoters and subtle hypomethylation across gene bodies; however, analysis of only the most significant methylation changes (> 4-fold) revealed that more hypermethylation events occur in intronic sequences, consistent with results obtained using the 450K array. To further investigate the overlap between DNMT1 hypomethylated and DNMT3B hypermethylated sites, we examined DNA methylation in HCT116 colorectal carcinoma cells lacking (KO) or over-expressing (KI) DNMT1/DNMT3B. Interestingly, a marked number of CpG sites that gained methylation in the DNMT3B KO overlapped significantly with sites that became hypermethylated in DNMT1 and DNMT3B KI, and hypomethylated in DNMT1 KO. Additionally, these HCT116 hypermethylated CpG sites gained methylation in NCCIT DNMT3B KD (individual/combination) and lost methylation in DNMT1 KD. Taken together, these results suggest that DNMT1 and DNMT3B co-regulate DNA methylation at conserved loci across cell types in an opposing fashion, providing novel insight into a potential regulatory mechanism for DNA methylation patterning. Further elucidation of this DNMT1 and DNMT3B co-regulation holds the potential to yield novel therapeutic strategies for correcting aberrant methylation events in cancer. Citation Format: Rochelle Tiedemann, Jeong-Hyeon Choi, Keith Robertson. Acute depletion reveals novel co-regulation of DNA methylation at conserved loci by DNMT1 and DNMT3B. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2305. doi:10.1158/1538-7445.AM2014-2305

Effects of lanthanum on POD expression and DNA methylation of purple pepper under salt stress

Pepper seedlings were hydroponically cultivated in 0–20 mg/L extraneous lanthanum chloride (La3+) for different numbers of days to investigate its regulating effects under salt stress. The results showed that, depending on the salt stress of 0.75 g/L, a lower concentration of La3+ (1.0 mg/L) might result in the lowest death rate, increase POD activity and change the band type of the stem and root on the 8th day. Furthermore, a methylation analysis by the methylation-sensitive amplified polymorphism (MSAP) technique indicated that a lower concentration of La3+ (1.0 mg/L) triggered the lowest methylation level of 26.1%, of which the hypermethylation events were the primary type of methylation. In addition, the sequencing of 14 differentially expressed polymorphic fragments and the subsequent blast search revealed that La3+ could induce methylation events in salt-tolerance sequences.

DNA methylation alterations in grade II- and anaplastic pleomorphic xanthoastrocytoma

BackgroundPleomorphic xanthoastrocytoma (PXA) is a rare WHO grade II tumor accounting for less than 1% of all astrocytomas. Malignant transformation into PXA with anaplastic features, is unusual and correlates with poorer outcome of the patients.MethodsUsing a DNA methylation custom array, we have quantified the DNA methylation level on the promoter sequence of 807 cancer-related genes of WHO grade II (n = 11) and III PXA (n = 2) and compared to normal brain tissue (n = 10) and glioblastoma (n = 87) samples. DNA methylation levels were further confirmed on independent samples by pyrosequencing of the promoter sequences.ResultsIncreasing DNA promoter hypermethylation events were observed in anaplastic PXA as compared with grade II samples. We further validated differential hypermethylation of CD81, HCK, HOXA5, ASCL2 and TES on anaplastic PXA and grade II tumors. Moreover, these epigenetic alterations overlap those described in glioblastoma patients, suggesting common mechanisms of tumorigenesis.ConclusionsEven taking into consideration the small size of our patient populations, our data strongly suggest that epigenome-wide profiling of PXA is a valuable tool to identify methylated genes, which may play a role in the malignant progression of PXA. These methylation alterations may provide useful biomarkers for decision-making in those patients with low-grade PXA displaying a high risk of malignant transformation.

DNA methylation profiling of well-differentiated thyroid cancer uncovers markers of recurrence free survival

Thyroid cancer is a heterogeneous disease with several subtypes characterized by cytological, histological and genetic alterations, but the involvement of epigenetics is not well understood. Here, we investigated the role of aberrant DNA methylation in the development of well-differentiated thyroid tumors. We performed genome-wide DNA methylation profiling in the largest well-differentiated thyroid tumor series reported to date, comprising 83 primary tumors as well as 8 samples of adjacent normal tissue. The epigenetic profiles were closely related to not only tumor histology but also the underlying driver mutation; we found that follicular tumors had higher levels of methylation, which seemed to accumulate in a progressive manner along the tumorigenic process from adenomas to carcinomas. Furthermore, tumors harboring a BRAF or RAS mutation had a larger number of hypo- or hypermethylation events, respectively. The aberrant methylation of several candidate genes potentially related to thyroid carcinogenesis was validated in an independent series of 52 samples. Furthermore, through the integration of methylation and transcriptional expression data, we identified genes whose expression is associated with the methylation status of their promoters. Finally, by integrating clinical follow-up information with methylation levels we propose etoposide-induced 2.4 and Wilms tumor 1 as novel prognostic markers related to recurrence-free survival. This comprehensive study provides insights into the role of DNA methylation in well-differentiated thyroid cancer development and identifies novel markers associated with recurrence-free survival.

Evaluation of INK4A promoter methylation using pyrosequencing and circulating cell-free DNA from patients with hepatocellular carcinoma

Hyper-methylation of CpG dinucleotides in the promoter region of inhibitor of cyclin-dependent kinase 4A (INK4A) has been reported in 60%-80% of hepatocellular carcinoma (HCC). As INK4A promoter hypermethylation event occurs early in HCC progression, the quantification of INK4A promoter methylation in blood sample may represent a useful biomarker for non-invasive diagnosis and prediction of response to therapy. We examined INK4A promoter methylation using circulating cell-free DNA (ccfDNA) in a total of 109 serum specimens, including 66 HCC and 43 benign chronic liver diseases. Methylation of the individual seven CpG sites was examined using pyrosequencing. Our results showed that there were significantly higher levels of methylated INK4A in HCC specimens than controls and that the seven CpG sites had different levels of methylation and might exist in different PCR amplicons. The area under receiver operating characteristic (ROC) curve was 0.82, with 65.3% sensitivity and 87.2% specificity at 5% (LOD), 39.0% sensitivity and 96.5% specificity at 7% LOD, and 20.3% sensitivity and 98.8% specificity at 10% LOD, respectively. Our results support additional studies incorporating INK4A methylation testing of ccfDNA to further validate the diagnostic, predictive, and prognostic characteristics of this biomarker in HCC patients. The knowledge of the existence of epi-alleles should help improve assay design to maximize detection.

Aberrant Methylation of Hypermethylated-in-Cancer-1 and Exocyclic DNA Adducts in Tobacco Smokers

Tobacco smoke has been shown to produce both DNA damage and epigenetic alterations. However, the potential role of DNA damage in generating epigenetic changes is largely underinvestigated in human studies. We examined the effects of smoking on the levels of DNA methylation in genes for tumor protein p53, cyclin-dependent kinase inhibitor2A, hypermethylated-in-cancer-1 (HIC1), interleukin-6, Long Interspersed Nuclear Element type1, and Alu retrotransposons in blood of 177 residents in Thailand using bisulfite-PCR andpyrosequencing. Then, we analyzed the relationship of this methylation with the oxidative DNA adduct, M₁dG (a malondialdehyde adduct), measured by ³²P-postlabeling. Multivariate statistical analyses showed that HIC1 methylation levels were significantly increased in smokers compared with nonsmokers (p ≤ .05). A dose response was observed, with the highest HIC1 methylation levels in smokers of ≥ 10 cigarettes/day relative to nonsmokers and intermediate values in smokers of 1-9 cigarettes/day (p for trend ≤ .001). No additional relationships were observed. We also evaluated correlations between M₁dG and the methylation changes at each HIC1 CpG site individually. The levels of this adduct in smokers showed a significant linear correlation with methylation at one of the 3 CpGs evaluated in HIC1: hypermethylation at position 1904864340 was significantly correlated with the adduct M₁dG (covariate-adjusted regression coefficient (β) = .224 ± .101 [SE], p ≤ .05). No other correlations were detected. Our study extends prior work by others associating hypermethylation of HIC1 with smoking; shows that a very specific hypermethylation event can arise from smoking; and encourages future studies that explore a possible role for M₁dG in connecting smoking to this latter hypermethylation.

Coordinate H3K9 and DNA methylation silencing of ZNFs in toxicant-induced malignant transformation

Genome-wide disruption of the epigenetic code is a hallmark of malignancy that encompasses many distinct, highly interactive modifications. Delineating the aberrant epigenome produced during toxicant-mediated malignant transformation will help identify the underlying epigenetic drivers of environmental toxicant-induced carcinogenesis. Gene promoter DNA methylation and gene expression profiling of arsenite-transformed prostate epithelial cells showed a negative correlation between gene expression changes and DNA methylation changes; however, less than 10% of the genes with increased promoter methylation were downregulated. Studies described herein confirm that a majority of the DNA hypermethylation events occur at H3K27me3 marked genes that were already transcriptionally repressed. In contrast to aberrant DNA methylation targeting H3K27me3 pre-marked silent genes, we found that actively expressed C2H2 zinc finger genes (ZNFs) marked with H3K9me3 on their 3′ ends, were the favored targets of DNA methylation linked gene silencing. DNA methylation coupled, H3K9me3 mediated gene silencing of ZNF genes was widespread, occurring at individual ZNF genes on multiple chromosomes and across ZNF gene family clusters. At ZNF gene promoters, H3K9me3 and DNA hypermethylation replaced H3K4me3, resulting in a widespread downregulation of ZNF gene expression, which accounted for 8% of all the downregulated genes in the arsenical-transformed cells. In summary, these studies associate toxicant exposure with widespread silencing of ZNF genes by DNA hypermethylation-linked H3K9me3 spreading, further implicating epigenetic dysfunction as a driver of toxicant associated carcinogenesis.

Dysregulation of the epigenome in triple-negative breast cancers: Basal-like and claudin-low breast cancers express aberrant DNA hypermethylation

A subset of human breast cancer cell lines exhibits aberrant DNA hypermethylation that is characterized by hyperactivity of the DNA methyltransferase enzymes, overexpression of DNMT3b, and concurrent methylation-dependent silencing of numerous epigenetic biomarker genes. The objective of this study was to determine if this aberrant DNA hypermethylation (i) is found in primary breast cancers, (ii) is associated with specific breast cancer molecular subtypes, and (iii) influences patient outcomes. Analysis of epigenetic biomarker genes (CDH1, CEACAM6, CST6, ESR1, GNA11, MUC1, MYB, SCNN1A, and TFF3) identified a gene expression signature characterized by reduced expression levels or loss of expression among a cohort of primary breast cancers. The breast cancers that express this gene expression signature are enriched for triple-negative subtypes — basal-like and claudin-low breast cancers. Methylation analysis of primary breast cancers showed extensive promoter hypermethylation of epigenetic biomarker genes among triple-negative breast cancers, compared to other breast cancer subclasses where promoter hypermethylation events were less frequent. Furthermore, triple-negative breast cancers either did not express or expressed significantly reduced levels of protein corresponding to methylation-sensitive biomarker gene products. Together, these findings suggest strongly that loss of epigenetic biomarker gene expression is frequently associated with gene promoter hypermethylation events. We propose that aberrant DNA hypermethylation is a common characteristic of triple-negative breast cancers and may represent a fundamental biological property of basal-like and claudin-low breast cancers. Kaplan–Meier analysis of relapse-free survival revealed a survival disadvantage for patients with breast cancers that exhibit aberrant DNA hypermethylation. Identification of this distinguishing trait among triple-negative breast cancers forms the basis for development of new rational therapies that target the epigenome in patients with basal-like and claudin-low breast cancers.

Abstract B34: Acute depletion reveals novel divisions of labor among human DNA methyltransferases in cancer

Abstract DNA methyltransferases (DNMTs) are responsible for establishing (DNMT3A, DNMT3B, DNMT3L) and maintaining (DNMT1) DNA methylation genome-wide. Hypomethylation of repetitive sequences and transposable elements coupled with gene-specific promoter hypermethylation events contribute to the genomic instability and loss of tumor suppressor gene transcription observed in cancer. Regulation of aberrant methylation in cancer remains poorly understood. The aim of our study was to identify unique and overlapping target sites for each of the DNMTs to better understand regulation of normal and aberrant DNA methylation. We hypothesized that acute depletion of the DNMTs (individual and combination) mediated by siRNA technology in NCCIT human embryonic carcinoma cells would result in both distinct and broad changes in DNA methylation patterning. Genome-wide methylation was assayed using the HumanMethylation450 Bead Chip (450K array) allowing for specific CpG site methylation status determination. Select target sites were verified by bisulfite genomic sequencing. DNMT1 knockdown samples (individual/combination) revealed genome-wide hypomethylation, with the strongest demethylation occurring in gene bodies, 3′UTR, and intergenic sequences. Interestingly, only the DNMT1 individual knockdown showed significant hypermethylation in gene promoters. DNMT3 knockdowns showed more specific changes in DNA methylation, but surprisingly, more hypermethylation events occurred than hypomethylation at CpG dinucleotides. Hypermethylation observed in DNMT3 knockdown occurred primarily in gene bodies and 3′UTR, and overlapped significantly with those genes that become hypomethylated in DNMT1 knockdown, indicating a potential cross-regulatory role for the DNMTs to maintain proper regulation of DNA methylation at specific gene termini. Conversely, gene promoters were targeted for hypomethylation in DNMT3 knockdown, and did not significantly overlap with genes that become hypermethylated in DNMT1 knockdown. Of particular interest was that DNMT3B knockdown resulted in widespread non-CpG hypomethylation. In contrast, DNMT3L knockdown showed non-CpG hypermethylation, indicating a potential mechanism for regulation of non-CpG methylation where DNMT3B is responsible for non-CpG methylation, and DNMT3L acts to restrict DNMT3B's activity at non-CpG dinucleotides. Our results reveal a complex view of DNA methylation regulation, in which DNMTs not only target specific sites for methylation, but also cooperate to establish and maintain proper levels of DNA methylation at CpG and non-CpG dinucleotides. Moving forward, we believe our results will provide the framework needed to define the regulatory mechanisms by which DNA methylation is conferred and ultimately develop therapeutic strategies to correct aberrant methylation events that occur in cancer. Citation Format: Rochelle L. Tiedemann, Jeong-Hyeon Choi, Keith D. Robertson. Acute depletion reveals novel divisions of labor among human DNA methyltransferases in cancer. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Jun 19-22, 2013; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2013;73(13 Suppl):Abstract nr B34.

Abstract 2970: Acute depletion of DNA methyltransferases reveals unique and overlapping target sites in cancer.

Abstract DNA methyltransferases (DNMTs) are responsible for establishing (DNMT3A, DNMT3B, DNMT3L) and maintaining (DNMT1) DNA methylation to regulate gene transcription and promote overall genome stability. Global changes in DNA methylation, such as hypomethylation of repetitive sequences and hypermethylation of tumor supressor gene promoters, are commonly observed in various types of cancer; however, the DNMTs’ contribution to this aberrant methylation remains largely unknown. In this study, we aim to identify unique and overlapping target sites for each of the DNMTs in order to better understand aberrant DNA methylation in cancer that will ultimately permit development of new therapeutic strategies. We utilize siRNA-mediated knockdown technology to acutely deplete the mRNA for each of the DNMTs in both individual and combinatorial fashion in NCCIT embryonal carcinoma cells. Subsequently, DNA methylation is observed genome-wide in each DNA sample using two different methodologies: (1) Methyl-CpG Binding Domain (MBD)-seq, which identifies regions of the genome that are enriched for DNA methylation, and (2) Illumina Infinium HumanMethylation450 BeadChip (450K array) allowing for specific CpG site methylation status determination. Aligned MBD-seq sequences for individual DNMT knockdowns are analyzed by read coverage nomalization within 100Kbp windows and using various peak-calling algorithms (e.g. MACS, BALM). For the 450K array, DNA samples for both individual and combination knockdowns undergo bisulfite conversion and array processing; β-values for each CpG site are derived from the array signal intensities using GenomeStudio and R/Bioconductor (minfi). Genome-wide DNA methylation analysis reveals that DNMT1 depletion, both individual and in combination with knockdown of other DNMTs, results in global demethylation among all genomic features. Interestingly, a small population of genes exhibit hypermethylation in gene-promoter CpG islands for DNMT1 (individual only) depletion. In contrast, de novo methyltransferase depletion (individual and combination) shows more specific demethylation effects. In particular, hypomethylation events resulting from DNMT3B depletion (individual and combination (not 3B+3L)) occur within gene bodies and largely outside of CpG islands and flanking regions (shores, shelves). Additionally, a number of hypermethylation events occurring within the 3’UTR region of genes are observed in de novo methyltransferase depleted samples. We anticipate further analysis will reveal unique and overlapping target sites for each of the DNMTs that will lay the ground-work necessary to characterize and understand DNMT recruitment both in normal and cancerous tissues. Citation Format: Rochelle L. Tiedemann, Jeong-Hyeon Choi, Keith D. Robertson. Acute depletion of DNA methyltransferases reveals unique and overlapping target sites in cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2970. doi:10.1158/1538-7445.AM2013-2970

Aberrantly Methylated DNA as a Biomarker in Breast Cancer

Aberrant DNA hypermethylation at gene promoters is a frequent event in human breast cancer. Recent genome-wide studies have identified hundreds of genes that exhibit differential methylation between breast cancer cells and normal breast tissue. Due to the tumor-specific nature of DNA hypermethylation events, their use as tumor biomarkers is usually not hampered by analytical signals from normal cells, which is a general problem for existing protein tumor markers used for clinical assessment of breast cancer. There is accumulating evidence that DNA-methylation changes in breast cancer patients occur early during tumorigenesis. This may open up for effective screening, and analysis of blood or nipple aspirate may later help in diagnosing breast cancer. As a more detailed molecular characterization of different types of breast cancer becomes available, the ability to divide patients into subgroups based on DNA biomarkers may improve prognosis. Serial monitoring of DNA-methylation markers in blood during treatment may be useful, particularly when the cancer burden is below the detection level for standard imaging techniques. Overall, aberrant DNA methylation has a great potential as a versatile biomarker tool for screening, diagnosis, prognosis and monitoring of breast cancer. Standardization of methods and biomarker panels will be required to fully exploit this clinical potential.

Tumor-suppressor Gene Promoter Hypermethylation in Saliva of Head and Neck Cancer Patients

Head and neck squamous cell carcinoma (HNSCC) accounts for a bulk of the oral and laryngeal cancers, the majority (70%) of which are associated with smoking and excessive drinking, major known risk factors for the development of HNSCC. In contrast to reports that suggest an inverse relationship between smoking and global DNA CpG methylation, hypermethylation of promoters of a number of genes was detected in saliva collected from patients with HNSCC. Using a sensitive methylation-specific polymerase chain reaction (MSP) assay to determine specific methylation events in the promoters of RASSF1A, DAPK1, and p16 genes, we demonstrate that we can detect tumor presence with an overall accuracy of 81% in the DNA isolated from saliva of patients with HNSCC (n = 143) when compared with the DNA isolated from the saliva of healthy nonsmoker controls (n = 31). The specificity for this MSP panel was 87% and the sensitivity was 80% (with a Fisher exact test P < .0001). In addition, the test panel performed extremely well in the detection of the early stages of HNSCCs, with a sensitivity of 94% and a specificity of 87%, and a high κ concordance value of 0.8, indicating an excellent overall agreement between the presence of HNSCC and a positive MSP panel result. In conclusion, we demonstrate that the promoter methylation of RASSF1A, DAPK1, and p16 MSP panel is useful in detecting hypermethylation events in a noninvasive manner in patients with HNSCC.

Abstract 5448: Common targets of epigenetic dysfunction in distinct target tissues of arsenic and cadmium induced malignant transformation

Abstract Arsenic and cadmium are known human carcinogens and rank as number one and seven respectively on the Agency for Toxic Substances and Disease Registry (ATSDR) substance priority list. Accumulating evidence suggests that long-term exposure to arsenic or cadmium induces epigenetic dysfunction and this effect may be an important aspect of their carcinogenic activity. To this end we analyzed the epigenetic dysfunction associated with arsenic or cadmium induced malignant transformation of immortalized urothelial and prostate epithelial cells. Using methyl-DNA immunoprecipitations coupled to human promoter microarrays as well as Sequenom MassArray, we found that arsenic and cadmium mediated malignant transformation of immortalized urothelial and prostate epithelial cells produced thousands of DNA methylation changes. Many of the DNA hypermethylation events appear to be localized to individual genes whereas others cluster into groups that are within large genomic regions on the order of 100kb. Significant aggregates of DNA hypermethylation events occur within the protocadherin and HOX gene clusters. Intersecting the arsenic induced hypermethylation events from the two distinct models results in an overlap of 113kb of DNA which represents roughly 100 genes. This overlap is significantly more than expected by chance, suggesting these genes are targeted for aberrant DNA methylation in both models of arsenic induced malignant transformation. A similar result is seen in the cell lines transformed by cadmium, and the cadmium induced DNA hypermethylation events are highly concordant with the hypermethylation profiles induced by arsenic. Most of the DNA hypermethylated regions found in the arsenic or cadmium transformed cells are also targets of aberrant DNA hypermethylation in human bladder tumors. Comparing the hypermethylated regions from our models to publicly available H3K27me3 ChIP-seq data from embryonic stem cells revealed that the targets of DNA hypermethylation fall disproportionately within H3K27me3 domains of human stem cells. H3K27me3 chromatin immunoprecipitations coupled to real-time PCR confirmed that the promoters of candidate genes NPR3 and LTK are marked with H3K27me3 in normal and immortalized cells before becoming DNA hypermethylated in the arsenic transformed cells. This H3K27me3 data supports the previously discovered association between H3K27me3 marked regions of normal cells and DNA hypermethylation in malignant cells. All together, these observations suggest commonality in the mechanisms of epigenetic change induced by carcinogenic metals. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5448. doi:1538-7445.AM2012-5448

Abstract A38: Whole methylome explorations of paired lung tumor and non-tumor clinical samples

Abstract Background: Hypermethylation in specific candidate gene promoters has been found during progressive lung carcinogenesis. To explore common methylation events on a genome-wide scale in lung cancer, we analyzed the methylation profiles of paired NSCLC tumor and far adjacent non-tumor samples using the HELP-microarray assay, which yields information on 1.2 million fragments throughout the genome. Methods: The HELP (HpaII tiny fragment Enriched by Ligation mediated PCR) assay is based on the generation of restriction enzyme libraries generated by methylation sensitive (HpaII) and methylation insensitive (MspI) isoschizomers, in its second generation as a microarray platform. The assay lends itself to low starting amounts of DNA (3 ug) and robust assessment of methylation status by comparing ratios of HpaII- generated-fragments to MspI- generated fragments co-hybridized to a Nimbelgen custom high-density microarrays. The CCGG sites were weighted if neighboring CCGGs were methylated in same direction. Here, 24 pairs of tumor and adjacent non-tumor samples were analyzed using the HELP assay. Summary of results: At p = 5E-6, we identified 26,138 differentially methylated fragments (corresponding to 2 CpG sites each) in tumor versus non-tumor. The overall trend was consistent with genome-wide hypomethylation and locus specific hypermethylation (localized to CG-island containing promoters). We could identify both known and novel regions of the genome as well as specific gene-promoters that are hypermethylated in tumor versus non-tumor. Region # loci # signif loci T Hypomethyl T Hypermethyl Promoter 151,568 576 69% 31% Gene Body 551,628 9,817 62% 38% Intergenic 540,473 15,745 97% 3% Conclusion: An interrogation of methylation status of 1.2 million loci throughout the genome in paired lung tumor/non-tumor specimens reveals many more differential methylation events in gene bodies and intergenic regions than in promoters. That said, many previously unreported differentially-methylated gene promoters were identified. We are able to discover individual methylation events common across different clinical specimens. Based on a set of priors, we have narrowed down promoter-specific hypermethylation events for further validation using tagged Bisulfite Genomic Sequencing. We are also working on the integration of methylome date with other genome-wide epigenetic and expression data from the same clinical samples. [Funding source: NCI 1RC1 CA145422-01; 1K24-CA139054-01]

Cancer Drivers Affected by Aberrant DNA Methylation in MDS and AML

Abstract 1716Cytosine methylation is an epigenetic mark affecting accessibility of DNA to transcription. Cancer is associated with hypermethylation in CpG islands (dense clusters of CpG sites frequently present around gene transcription starts) and hypomethylation of sparse CpG sites outside CpG islands. Complex changes of DNA methylation in leukemia permanently disturb epigenetic regulation and participate in leukemogenesis. To characterize epigenetic aberrations in myeloid neoplasms, we analyzed DNA methylation in 16 patients with myelodysplastic syndrome (MDS), 7 patients with acute myeloid leukemia (AML) and 5 healthy controls. Using Digital Restriction Enzyme Analysis of Methylation, we quantified DNA methylation at CpG dinucleotides within approximately 40,000 CCCGGG restriction sites across the genome. We analyzed methylation differences between healthy controls and patients with MDS and AML. CpG sites within CpG islands (CGI sites) are typically not methylated in normal tissues. We found 18,738 CGI sites with methylation <5% in normal controls. MDS and AML patients showed heterogeneous hypermethylation >20% in these sites, ranging from 5 to 2720 (median 186) hypermethylated sites in individual patients. The median number of hypermethylated CGI sites was 146 in MDS and 1234 in AML patients. Altogether, we found 5069 CGI sites corresponding to 2183 genes differentially hypermethylated in MDS or AML. GpG sites outside CpG islands (NCGI sites) are generally methylated. We found only 3262 NCGI sites unmethylated (<5% methylation) in normal controls. Hypermethylation pattern of these NCGI sites in individual MDS and AML patients was similar to that of CGI (r=0.85), with 5–388 (median 38) sites hypermethylated over 20%. Altogether, we found 848 NCGI sites corresponding to 629 genes hypermethylated. Hypermethylation affecting both CGI and NCGI sites was found in 273 genes. In order to identify potential drivers in the plethora of methylation changes, we compared the hypermethylated genes with the Sanger Institute “Cancer Consensus” listing 457 genes. The list of 2539 hypermethylated genes contained 74 genes (3%) from the cancer list (51 in CGI, 10 in NCGI and 13 in both CGI and NCGI). Next we analyzed hypomethylation events in MDS and AML. We found 10,509 CpG sites (1210 CGI, 9299 NCGI) with methylation level >80% in normal controls. Methylation levels <30% in MDS and AML patients were observed at 1–439 (median 23) sites. Hypomethylation affected mostly NCGI sites and the numbers of sites hypomethylated in individual patients positively correlated with hypermethylation at CGI sites (r=0.39). The total of 1153 hypomethylated sites corresponded to 777 genes. Twenty-two genes (3%) were present on the cancer list. Six genes (CBFA2T3, FGFR3, FLI1, MLLT1, PHOX2B and PRDM16) showed both hyper and hypomethylation in different parts of the gene when compared to normal controls. Interestingly, translocations involving 5 of these genes have been reported in blood malignancies. The number of ‘cancer' genes affected by epigenetic events in individual patients was 1–29 (median 8) in MDS and 2–44 (median 20) in AML. In summary, we have detected tens to thousands of CpG sites with aberrant methylation in MDS and AML patients. Our data suggest that approximately 3% of DNA hypermethylation and hypomethylation events are potential drivers in the leukemogenic process in MDS and AML. DNA methylation changes were detected in 90 genes (13%) of the 457 cancer gene list. Our findings thus support the importance of epigenetics in leukemia. Disclosures:Neumann:Sanofi-Aventis: Employment. Issa:GSK: Consultancy; SYNDAX: Consultancy; Merck: Research Funding; Eisai: Research Funding; Celgene: Research Funding; Celgene: Honoraria; Novartis: Honoraria; J&J: Honoraria.

Novel candidate colorectal cancer biomarkers identified by methylation microarray-based scanning

DNA hypermethylation is a common epigenetic abnormality in colorectal cancers (CRCs) and a promising class of CRC screening biomarkers. We conducted a genome-wide search for novel neoplasia-specific hypermethylation events in the colon. We applied methylation microarray analysis to identify loci hypermethylated in 17 primary CRCs relative to eight non-neoplastic colonic mucosae (NCs) from neoplasia-free subjects. These CRC-associated hypermethylation events were then individually evaluated for their ability to discriminate neoplastic from non-neoplastic cases, based on real-time quantitative methylation-specific PCR (qMSP) assays in 113 colonic tissues: 51 CRCs, nine adenomas, 19 NCs from CRC patients (CRC-NCs), and 34 NCs from neoplasia-free subjects (control NCs). A strict microarray data filtering identified 169 candidate CRC-associated hypermethylation events. Fourteen of these 169 loci were evaluated using qMSP assays. Ten of these 14 methylation events significantly distinguished CRCs from age-matched control NCs (P<0.05 by receiver operator characteristic curve analysis); methylation of visual system homeobox 2 (VSX2) achieved the highest discriminative accuracy (83.3% sensitivity and 92.3% specificity, P<1×10(-6)), followed by BEN domain containing 4 (BEND4), neuronal pentraxin I (NPTX1), ALX homeobox 3 (ALX3), miR-34b, glucagon-like peptide 1 receptor (GLP1R), BTG4, homer homolog 2 (HOMER2), zinc finger protein 583 (ZNF583), and gap junction protein, gamma 1 (GJC1). Adenomas were significantly discriminated from control NCs by hypermethylation of VSX2, BEND4, NPTX1, miR-34b, GLP1R, and HOMER2 (P<0.05). CRC-NCs were significantly distinguished from control NCs by methylation of ALX3 (P<1×10(-4)). In conclusion, systematic methylome-wide analysis has identified ten novel methylation events in neoplastic and non-neoplastic colonic mucosae from CRC patients. These potential biomarkers significantly discriminate CRC patients from controls. Thus, they merit further evaluation in stool- and circulating DNA-based CRC detection studies.

MicroRNAs as Novel Targets for NSAID Chemoprevention of Colon Carcinogenesis

Background & Objective: In the United States, colorectal cancer (CRC) is the third most prevalent and deadly malignancy. Development of novel CRC-specific abnormal DNA biomarkers may advance non-invasive, cost-efficient population-based CRC screening and ultimately reduces CRC death. DNA hypermethylation is a common epigenetic abnormality in CRCs and represents a promising class of cancer biomarkers. The objective of the current study was to develop optimal DNA hypermethylation-based biomarkers for use in fecesor serum-based average-risk CRC screening. Design: We first applied DNAmethylationmicroarray analysis in order to identify novel loci demonstrating neoplasia-specific methylation in the colon. This array analysis allowed us to investigate 55% of CpG islands within the genome and was applied to 17 primary CRCs relative to 8 non-neoplastic colonic tissues (NCs) from neoplasia-free subjects. The detected CRC-associated hypermethylation events were then individually measured in 113 colonic tissues comprising 51 CRCs, 9 adenomas, 19 NCs from CRC patients (CRC-NCs), and 34 NCs from neoplasia-free subjects (control NCs) using highly sensitive and quantitative real-time quantitative methylation-specific PCR (qMSP) assays. Receiver-operator characteristics (ROC) curve analysis was applied to the qMSP data in order to assess each individual event as well as combination of events for their ability to discriminate neoplastic from non-neoplastic cases. Results: Microarray-based global methylation profiles discriminated CRCs from NCs. A bioinformatic filtering of the microarray data identified 169 candidate CRC-associated hypermethylation events, including one previously validated hypermethylation marker for fecal DNA-based CRC detection, SFRP2. Fourteen of these 169 loci were evaluated using qMSP assays. Ten of these 14 methylation events significantly distinguished CRCs from control NCs (p<.01). Of these ten events, methylation of VSX2 achieved the highest discriminative accuracy (83.3% sensitivity and 92.3% specificity; Area under ROC curve, or AUC, 0.93, p<1E-6). Similarly, CRC-NCs were significantly discriminated from control NCs by methylation of ALX3 (AUC 0.78, p<1E-4). The discrimination of CRC-NCs from control NCs was improved by a multi-locus methylation panel (AUC 0.83, p<1E-6) relative to ALX3. Although the sample numbers were small, two methylation events significantly distinguished adenomas from control NCs (p<.01). Conclusions: Systematic methylome analysis has identified 11 novel methylation events in neoplastic and non-neoplastic colonic mucosa from CRC patients that accurately discriminate CRC patients from controls. These markers merit further evaluation as candidate biomarkers for stool and circulating DNA-based CRC detection.

DNA Methylation Microarray Identifies Novel Methylation Biomarkers for Colorectal Cancer Detection

Background & Objective: In the United States, colorectal cancer (CRC) is the third most prevalent and deadly malignancy. Development of novel CRC-specific abnormal DNA biomarkers may advance non-invasive, cost-efficient population-based CRC screening and ultimately reduces CRC death. DNA hypermethylation is a common epigenetic abnormality in CRCs and represents a promising class of cancer biomarkers. The objective of the current study was to develop optimal DNA hypermethylation-based biomarkers for use in fecesor serum-based average-risk CRC screening. Design: We first applied DNAmethylationmicroarray analysis in order to identify novel loci demonstrating neoplasia-specific methylation in the colon. This array analysis allowed us to investigate 55% of CpG islands within the genome and was applied to 17 primary CRCs relative to 8 non-neoplastic colonic tissues (NCs) from neoplasia-free subjects. The detected CRC-associated hypermethylation events were then individually measured in 113 colonic tissues comprising 51 CRCs, 9 adenomas, 19 NCs from CRC patients (CRC-NCs), and 34 NCs from neoplasia-free subjects (control NCs) using highly sensitive and quantitative real-time quantitative methylation-specific PCR (qMSP) assays. Receiver-operator characteristics (ROC) curve analysis was applied to the qMSP data in order to assess each individual event as well as combination of events for their ability to discriminate neoplastic from non-neoplastic cases. Results: Microarray-based global methylation profiles discriminated CRCs from NCs. A bioinformatic filtering of the microarray data identified 169 candidate CRC-associated hypermethylation events, including one previously validated hypermethylation marker for fecal DNA-based CRC detection, SFRP2. Fourteen of these 169 loci were evaluated using qMSP assays. Ten of these 14 methylation events significantly distinguished CRCs from control NCs (p<.01). Of these ten events, methylation of VSX2 achieved the highest discriminative accuracy (83.3% sensitivity and 92.3% specificity; Area under ROC curve, or AUC, 0.93, p<1E-6). Similarly, CRC-NCs were significantly discriminated from control NCs by methylation of ALX3 (AUC 0.78, p<1E-4). The discrimination of CRC-NCs from control NCs was improved by a multi-locus methylation panel (AUC 0.83, p<1E-6) relative to ALX3. Although the sample numbers were small, two methylation events significantly distinguished adenomas from control NCs (p<.01). Conclusions: Systematic methylome analysis has identified 11 novel methylation events in neoplastic and non-neoplastic colonic mucosa from CRC patients that accurately discriminate CRC patients from controls. These markers merit further evaluation as candidate biomarkers for stool and circulating DNA-based CRC detection.

Abstract 4794: Monoamine oxidase A expression correlates with cholangiocarcinoma tumor grade and survival and is suppressed via IL-6-driven hypermethylation of the promoter

Abstract The metabolism of dopamine and serotonin is dysregulated in cholangiocarcinoma (CCA), which has subsequent growth promoting effects. Monoamine oxidase A (MAOA), the enzyme responsible for the degradation of serotonin and dopamine, is switched off in CCA although the mechanism by which this occurs is unknown. MAOA transcriptional activity can be suppressed by hypermethylation. IL-6 is known to be overproduced in CCA and can control hypermethylation events. The aims of this study were to 1) Correlate MAOA expression with pathophysiological parameters of CCA; 2) determine if IL-6 drivenhypermethylation of the MAOA promoter is involved in the suppression of expression. Methods: MAOA expression was assessed in biopsy samples from 84 patients with hilar CCA, or non-malignant controls by immunohistochemistry and realtime PCR and Kaplan-Meier survival analysis and Log Rank test performed. Hypermethylation of the MAOA promoter was assessed in four CCA cell lines previously shown to have suppressed MAOA expression, in two non-malignant cholangiocyte lines (H69 and HIBEC), and in human tumor samples using bisulfite modification followed by pyrosequencing analysis. Mz-ChA-1 and H69 cells were treated with a DNA methyltransferase inhibitor (5-aza; 10μM) for 4 days to inhibit the hypermethylation followed by qPCR assessment of MAOA expression. In parallel, Mz-ChA-1 cells were treated with a neutralizing IL-6 antibody (1μg/mL) for 4 days, or IL-6 expression was knocked down by stable transfection of IL-6 shRNA plasmids and MAOA expression was assessed by qPCR. Results: MAOA expression has a negative correlation with tumor differentiation (correlation coefficient: -2.68; P=0.014&amp;lt;0.05(2-tailed)). Furthermore there was a distinct correlation between MAOA expression and total survival (10.8 ± 0.9 months for low MAOA expression vs 27.2 ± 4.3 months for moderate or strong expression group, P&amp;lt;0.01). The MAOA promoter region was hypermethylated in CCA cells, but not H69 or HIBEC and treatment with 5-aza increased MAOA expression in Mz-ChA-1 cells, but not H69 cholangiocytes. Suppression of IL-6 expression either by neutralizing antibodies or by specific knock down of expression (to 3% of the parental cell line) reversed the hypermethylation and increased the subsequent MAOA expression. Conclusions: MAOA expression correlates with both differentiation grade and overall survival of CCA patients. Aberrant IL-6 expression seen in CCA cells may drive the suppression of MAOA expression by regulating promoter methylation and subsequent MAOA gene expression. Agents that may restore MAOA expression may have therapeutic value in the treatment of CCA. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4794. doi:10.1158/1538-7445.AM2011-4794