Methylation In Normal Tissues Research Articles

Methylation of PCDH17 and NEFH as prognostic biomarker for nonmetastatic RCC: A cohort study.

DNA methylation makes up a main part of the molecular mechanism of cancer evolution and has shown promising results in the prognosis of renal cell cancer (RCC). In this study, we investigated the possible association of promoter methylation of PCDH17, NEFH, RASSF1A, and FHIT, genes with the prognosis of nonmetastatic RCC patients. Cancerous and normal adjacent tissues from surgical specimens of 41 patients with long follow-up were treated for DNA isolation and bisulfite conversion. The gene promoter methylation was determined with quantitative methylation-specific PCR (qMSP). Wilcoxon signed-rank test was used for paired methylation comparisons, while univariate linear regression and Mann-Whitney test were applied for associating methylation status with clinical and disease characteristics. Cox regression proportional hazards models and Kaplan-Meier plots were used for survival analyses in reference to methylation status. Paired comparisons showed tissue-specific hypermethylation for PCDH17 (P < .001), NEFH (P < .001), RASSF1A (P = .032), while a positive association of methylation in normal tissues with age was demonstrated for PCDH17 (P < .001), RASSF1A (P < .001), FHIT (P < .001). PCDH17 was more methylated in cases with clear cell RCC (P = .015) and high-grade tumor (P = .013), while NEFH methylation was higher in locally advanced cases (P = .032). PCDH17 hypermethylation in cancerous and normal tissues was linked to shorter disease-specific survival (DSS, P = .026, P = .004), disease-free survival (DFS, P = .004, P = .019) while NEFH hypermethylation in cancerous tissues was related to shorter DSS (P = .032). Increased methylation difference of NEFH was also associated with shorter DSS (P = .041) and DFS (P = .020), while the corresponding parameter for PCDH17 was associated with poor DFS (P = .014). Kaplan-Meier curves for hypermethylation in cancer tissues demonstrated different clinical courses for PCDH17 (P = .017), NEFH (P = .023) regarding DSS, and PCDH17 (P = .001) regarding DFS. Our study not only highlights the prognostic value of promoter methylation of PCDH17 and NEFH in cancer tissues but also is the first report of the prognostic value of methylation alterations in normal tissues. Our findings are the first report of the prognostic value of methylation alterations in normal tissues, which can contribute to improved assessment of recurrence risk.

Disentangling tumorigenesis-associated DNA methylation changes in colorectal tissues from those associated with ageing

ABSTRACT Physiological ageing and tumorigenesis are both associated with epigenomic alterations in human tissue cells, the most extensively investigated of which entails de novo cytosine methylation (i.e., hypermethylation) within the CpG dinucleotides of CpG islands. Genomic regions that become hypermethylated during tumorigenesis are generally believed to overlap regions that acquire methylation in normal tissues as an effect of ageing. To define the extension of this overlap, we analysed the DNA methylomes of 48 large-bowel tissue samples taken from women of different ages during screening colonoscopy: 18 paired samples of normal and lesional tissues from donors harbouring a precancerous lesion and 12 samples of normal mucosa from tumour-free donors. Each sample was subjected to targeted, genome-wide bisulphite sequencing of ~2.5% of the genome, including all CpG islands. In terms of both its magnitude and extension along the chromatin, tumour-associated DNA hypermethylation in these regions was much more conspicuous than that observed in the normal mucosal samples from older (vs. younger) tumour-free donors. 83% of the ageing-associated hypermethylated regions (n = 2501) coincided with hypermethylated regions observed in tumour samples. However, 86% of the regions displaying hypermethylation in precancerous lesions (n = 16,772) showed no methylation changes in the ageing normal mucosa. The tumour-specificity of this latter hypermethylation was validated using published sets of data on DNA methylation in normal and neoplastic colon tissues. This extensive set of genomic regions displaying tumour-specific hypermethylation represents a rich vein of putative biomarkers for the early, non-invasive detection of colorectal tumours in women of all ages.

Age-, tumor-, and metastatic tissue-associated DNA hypermethylation of a T-box brain 1 locus in human kidney tissue

BackgroundWhile a considerable number of tumor-specific hypermethylated loci have been identified in renal cell cancer (RCC), DNA methylation of loci showing successive increases in normal, tumoral, and metastatic tissues could point to genes with high relevance both for the process of tumor development and progression. Here, we report that DNA methylation of a locus in a genomic region corresponding to the 3′UTR of the transcription factor T-box brain 1 (TBR1) mRNA accumulates in normal renal tissues with age and possibly increased body mass index. Moreover, a further tissue-specific increase of methylation was observed for tumor and metastatic tissue samples.ResultsBiometric analyses of the TCGA KIRC methylation data revealed candidate loci for age-dependent and tumor-specific DNA methylation within the last exon and in a genomic region corresponding to the 3′UTR TBR1 mRNA. To evaluate whether methylation of TBR1 shows association with RCC carcinogenesis, we measured 15 tumor cell lines and 907 renal tissue samples including 355 normal tissues, 175 tissue pairs of normal tumor adjacent and corresponding tumor tissue as well 202 metastatic tissues samples of lung, bone, and brain metastases by the use of pyrosequencing. Statistical evaluation demonstrated age-dependent methylation in normal tissue (R = 0.72, p < 2 × 10−16), association with adiposity (P = 0.019) and tumor-specific hypermethylation (P = 6.1 × 10−19) for RCC tissues. Comparison of tumor and metastatic tissues revealed higher methylation in renal cancer metastases (P = 2.65 × 10−6).ConclusionsOur analyses provide statistical evidence of association between methylation of TBR1 and RCC development and disease progression.

Highly variant DNA methylation in normal tissues identifies a distinct subclass of cancer patients.

The "CpG Island Methylator Phenotype" (CIMP) has been found to be a useful concept in stratifying several types of human cancer into molecularly and clinically distinguishable subgroups. We have identified an additional epigenetic stratification category, the "Outlier Methylation Phenotype" (OMP). Whereas CIMP is defined on the basis of hyper-methylation in tumor genomes, OMP is defined on the basis of highly variant (either or both hyper- and hypo-methylation) methylation at many sites in normal tissues. OMP was identified and defined, originally, as being more common among low birth weight individuals conceived in vitro but we have also identified OMP individuals among colon cancer patients profiled by us, as well as multiple types of cancer patients in the TCGA database. The cause(s) of OMP are unknown, as is whether these individuals identify a clinically useful subgroup of patients, but both the causes of, and potential consequences to, this epigenetically distinct group are of great interest.

Abstract 484: Epigenetic regulation of hsa-miR-3663 in colon cancer

Abstract Colon Cancer is the third most common cancer in the world and a major cause of morbidity and mortality. Molecular mechanisms of colon carcinoma have been deeply studied and current evidences indicate that microRNAs play a pivotal role in its tumorigenesis and progression. MicroRNAs (miRNAs) are small 19 to 22 nucleotides of RNA classified as non-coding RNAs that negatively regulate gene expression at the post-translational level controlling numerous biological processes including development, cell proliferation, apoptosis, differentiation and cell migration. Aberrant expression of miRNAs due to epigenetic alterations has been associated with carcinogenesis. Aimed to identify epigenetically regulated miRNAs involved in colon cancer, we analyzed DNA methylation profiles available in The Cancer Genome Atlas. One of the main hits identified was hsa-miR-3663, hypermethylated in 26% of colon cancer patients (n=286, p&amp;lt; 0.001) in comparison with complete lack of methylation in normal tissues (n=38), suggesting its potential function as a putative tumor suppressor. In order to study the role of DNA methylation controlling hsa-miR-3663, HumanMethylation450K methylation profiles were generated for a panel of colon cancer cell lines (n=10), including the HCT116-DNA methyltransferase knock-out model (DKO, double knockout of DNMT1 and DNMT3B). We found a significant correlation between methylation status of hsa-miR-3663 and expression in colon cancer cell lines. Furthermore, epigenetic regulation of hsa-miR-3663 was confirmed in HCT116 methylated cell line by restored expression upon treatment with DNA demethylating agent 5-aza-2′-deoxycytidine and in the HCT116-DKO model. In order to elucidate the function of hsa-miR-3663, we stably expressed hsa-miR-3663 in a panel of five methylated colorectal cancer cell lines (HCT116, RKO, DLD1, SW48 and SW480). Our initial functional assays revealed that hsa-miR-3663 is not involved in cell proliferation or migration. We are now performing additional assays to further study hsa-miR-3663 and its potential role in colon cancer. Note: This abstract was not presented at the meeting. Citation Format: Laia Pique, Humberto Jorge Ferrerira, Manel Esteller. Epigenetic regulation of hsa-miR-3663 in colon cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 484. doi:10.1158/1538-7445.AM2017-484

Platinum-Based Chemotherapy Induces Methylation Changes in Blood DNA Associated with Overall Survival in Patients with Ovarian Cancer.

Purpose: DNA damage repair can lead to epigenetic changes. DNA mismatch repair proteins bind to platinum DNA adducts and at sites of DNA damage can recruit the DNA methylating enzyme DNMT1, resulting in aberrant methylation. We hypothesised that DNA damage repair during platinum-based chemotherapy may cause aberrant DNA methylation in normal tissues of patients such as blood.Experimental Design: We used Illumina 450k methylation arrays and bisulphite pyrosequencing to investigate methylation at presentation and relapse in blood DNA from patients with ovarian cancer enrolled in the SCOTROC1 trial (n = 247) and in a cohort of ovarian tumor DNA samples collected at first relapse (n = 46). We used an ovarian cancer cell line model to investigate the role of the DNA mismatch repair gene MLH1 in platinum-induced methylation changes.Results: Specific CpG methylation changes in blood at relapse are observed following platinum-based chemotherapy and are associated with patient survival, independent of other clinical factors [hazard ratio, 3.7; 95% confidence interval, 1.8-7.6, P = 2.8 × 10-4]. Similar changes occur in ovarian tumors at relapse, also associated with patient survival (hazard ratio, 2.6; 95% confidence interval, 1.0-6.8, P = 0.048). Using an ovarian cancer cell line model, we demonstrate that functional mismatch repair increases the frequency of platinum-induced methylation.Conclusions: DNA methylation in blood at relapse following chemotherapy, and not at presentation, is informative regarding survival of patients with ovarian cancer. Functional DNA mismatch repair increases the frequency of DNA methylation changes induced by platinum. DNA methylation in blood following chemotherapy could provide a noninvasive means of monitoring patients' epigenetic responses to treatment without requiring a tumor biopsy. Clin Cancer Res; 23(9); 2213-22. ©2016 AACR.

Promoter methylation of RNF180 is associated with H.pylori infection and serves as a marker for gastric cancer and atrophic gastritis.

Promoter methylation (PM) of RING-finger protein (RNF) 180 affects gastric cancer (GC) prognosis, but its association with risk of GC or atrophic gastritis (AG) is unclear. We investigated relationships between RNF180 PM and GC or AG, and the effects of Helicobactor pylori (H.pylori) infection on RNF180 PM. This study included 513 subjects (159 with GC, 186 with AG, and 168 healthy controls [CON]) for RNF180 PM analysis, and another 55 GC patients for RNF180 gene expression analysis. Methylation was quantified using average methylation rates (AMR), methylated CpG site counts (MSC) and hypermethylated CpG site counts (HSC). RNF180 promoter AMR and MSC increased with disease severity. Optimal cut-offs were GC + AG: AMR > 0.153, MSC > 4 or HSC > 1; GC: AMR > 0.316, MSC > 15 and HSC > 6. Hypermethylation at 5 CpG sites differed significantly between GC/AG and CON groups, and was more common in GC patients than AG and CON groups for 2 other CpG sites. The expression of RNF180 mRNA levels in tumor were significantly lower than those in non-tumor, with the same as in hypermethylation than hypomethylation group. H.pylori infection increased methylation in normal tissue or mild gastritis, and increased hypermethylation risk at 3 CpG sites in AG. In conclusion, higher AMR, MSC and HSC levels could identify AG + GC or GC. Some RNF180 promoter CpG sites could identify precancerous or early-stage GC. H.pylori affects RNF180 PM in normal tissue or mild gastritis, and increases hypermethylation in 3 CpG sites in AG.

Tissue-independent and tissue-specific patterns of DNA methylation alteration in cancer.

Background There is growing evidence that DNA methylation alterations contribute to carcinogenesis. While cancer tissue exhibits widespread DNA methylation changes, the proportion of tissue-specific versus tissue-independent DNA methylation alterations in cancer is unclear. In addition, it is unknown which factors determine the patterns of aberrant DNA methylation in cancer.ResultsUsing HumanMethylation450 BeadChips (450k), we here analyze genome-wide DNA methylation patterns of ten types of fetal tissue, in addition to matched normal-cancer data for corresponding tissue types, encompassing over 3000 samples. We demonstrate that the level of aberrant cancer DNA methylation in gene promoters and gene bodies is highly correlated between cancer types. We estimate that up to 60 % of the DNA methylation variation in a cancer genome of a given tissue type is explained by the corresponding variation in a cancer genome of another type, implying that much of the cancer DNA methylation landscape is tissue independent. We further show that histone marks in normal cells are better predictors of aberrant cancer DNA methylation than the corresponding signals in human embryonic stem cells. We build predictors of cancer DNA methylation patterns and show that although inclusion of three histone marks (H3K4me3, H3K27me3 and H3K36me3) improves model accuracy, the bivalent marks are the most predictive. Finally, we show that chromatin accessibility of gene promoters in normal tissue dictates the promoter’s propensity to acquire aberrant DNA methylation in cancer in so far as it determines its level of DNA methylation in normal tissue.ConclusionsOur data show that a considerable fraction of the aberrant cancer DNA methylation landscape results from a mechanism that is largely tissue specific. Histone marks as specified in the normal cell of origin provide highly predictive models of aberrant cancer DNA methylation and outperform those derived from the same marks in hESCs.Electronic supplementary materialThe online version of this article (doi:10.1186/s13072-016-0058-4) contains supplementary material, which is available to authorized users.

Abstract 2954: Low level methylation (1-20%) or methylation seeds is a distinct epigenetic regulator of gene expression and is a strong predictor of methylation gains in AML and MDS patients

Abstract DNA methylation is an important epigenetic regulator of tumour suppressor genes in several cancers and is an established target for therapy. Genome wide studies indicate distinct set of genes hypermethylated among different types of cancer. Identifying why only certain genes are predisposed to hypermethylation in a cancer type will help us develop better epigenetic therapies. To understand this important aspect, we studied methylation in tissues from healthy individuals and cancer patients. Study of methylation in normal tissues identified a distinct methylation category that strongly regulates gene expression and predisposes to hypermethylation in cancer patients. We studied methylation at SmaI (CCCGGG) sites using Digital Restriction Enzyme Analysis of Methylation (DREAM) and validated our results using ENCODE Reduced Representation Bisulphite Sequencing (RRBS) data. Study of methylation using DREAM in normal tissues identified methylation seeds or low (but non zero) methylation (1-20%) at a subset of promoter CpG islands. These seeded promoters were distinct from unmethylated (0-1%) promoters and covered around 448, 702 and 1103 genes in testis, liver and WBC, respectively. Seeded genes were enriched in developmental and differentiation pathways unrelated to that tissue, while unmethylated genes were enriched for housekeeping functions. It is well known that hypermethylation of promoter CpG islands inhibit gene expression but effects of very low levels of methylation have not been studied genome wide. Hence we analyzed ENCODE RNA-seq data for above 3 tissues. Surprisingly, correlation studies between methylation and gene expression identified that both seeded (1-20%) and methylated (20-100%) genes correlated with significantly reduced gene expression compared to unmethylated genes (0-1%). This data suggested that even very low methylation significantly decreases gene expression. To directly test this, we cloned different mammalian promoters into luciferase expression vectors, methylated them in vitro (to 10-20%) and then transfected them into 293T cells. As expected, all the seeded (10-20%) promoter constructs showed significantly reduced luciferase activity establishing that methylation seeds directly decrease gene expression. Importantly, comparison of methylation in WBC using DREAM between normal controls (N = 13), AML (N = 108) or MDS (N = 26) patients identified that seeded CpG sites in normal were 17 fold more frequently hypermethylated (&amp;gt;40% difference) in AML patients than unmethylated CpG sites. (MDS = 80 fold more frequently). This indicates that having low methylation in normal tissues predisposes to gain methylation in cancer. To our knowledge, this is the first genome wide study identifying that very low levels of methylation can affect gene expression and is an important contributor of hypermethylation in leukemias. Citation Format: Priyanka Madireddi, Jaroslav Jelinek, Justin Lee, Matteo Cesaroni, Rodrigo Rodrigues, Yan Zhang, Jean-Pierre Issa. Low level methylation (1-20%) or methylation seeds is a distinct epigenetic regulator of gene expression and is a strong predictor of methylation gains in AML and MDS patients. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2954. doi:10.1158/1538-7445.AM2015-2954

Age-related DNA methylation in normal breast tissue and its relationship with invasive breast tumor methylation

Age is a key risk factor for breast cancer and epigenetic alterations may contribute to age-related increases in breast cancer risk, though the relation of age-related methylation in normal breast tissues with altered methylation in breast tumors is unclear. We investigated the relation of age with DNA methylation in normal breast tissues genome-wide using two data sets from the Gene Expression Omnibus (GEO) database (GSE32393 and GSE31979). We validated our observations in an independent set of normal breast tissues, examined age-related methylation in normal breast for enrichment of genomic features, and compared age-related methylation in normal tissue with methylation alterations in breast tumors. Between the two array-based methylation data sets, there were 204 CpG loci with significant (P < 0.05) and consistent age-related methylation, 97% of which were increases in methylation. Our validation sets confirmed the direction of age-related DNA methylation changes in all measured regions. Among the 204 age-related CpG loci, we observed a significant enrichment for CpG islands (P = 8.7E-6) and polycomb group protein target genes (P = 0.03). In addition, 24 of the 204 CpGs with age-related methylation in normal breast were significantly differentially methylated between normal and breast tumor tissues. We identified consistent age-related methylation changes in normal breast tissue that are further altered in breast tumors and may represent early events contributing to breast carcinogenesis. This work identifies age-related methylation in normal breast tissue and begins to deconstruct the contribution of aging to epigenetic alterations present in breast tumors.

Analysis of APC and IGFBP7 promoter gene methylation in Swedish and Vietnamese colorectal cancer patients

The tumour suppressor gene adenomatous polyposis coli (APC) is a key component that drives colorectal carcinogenesis. The reported DNA methylation in the promoter of APC varies greatly among studies of colorectal cancer (CRC) in different populations. Insulin-like growth factor binding protein 7 (IGFBP7), also known as IGFBP-related protein 1 (IGFBP-rP1), is expressed in various tissue types, including the lung, brain, prostate and gastrointestinal tract, and has been suggested to play a tumour suppressor role against colorectal carcinogenesis. Studies have indicated that IGFBP7 is inactivated by DNA methylation in human colon, lung and breast cancer. In the present study, we used the methylation-specific polymerase chain reaction to study the methylation status of the APC and IGFBP7 gene promoters in cancerous and paired normal tissue to evaluate its impact on clinical factors and association with ethnicity, represented by Swedish and Vietnamese CRC patients. We also investigated the distribution of CpG islands and the CpG dinucleotide density of each CpG island in the regions which were the subject of our investigation. Overall, normal tissue from Swedish patients exhibited a significantly higher frequency of IGFBP7 gene methylation in comparison with that of Vietnamese patients. Moreover, a significantly higher number of cancer tissues from Vietnamese individuals showed higher levels of methylation versus the paired normal tissue compared with that of Swedish patients. When we studied the methylation in cancer compared with the matched normal tissue in individuals, we found that a significantly higher number of Vietnamese patients had a higher degree of IGFBP7 gene methylation in cancer versus matched normal tissue in comparison with Swedish patients. Taken together, our results suggest that the methylation of the APC and IGFBP7 gene promoter region in cancerous tissue, in combination with the predominance of methylation in normal tissue, may serve as a prognostic factor in CRC patients.

Abstract 4517: Syndecan-2 methylation is an early detection biomarker for colorectal cancer with high sensitivity and specificity in small serum sample volumes

Abstract BACKGROUND: Colorectal cancer (CRC) is a major cause of morbidity and mortality in the world. Epigenetics has been a useful tool in the development of sensitive and specific screening tests for CRC. Targeting genes highly methylated in CRC has allowed us to develop an accurate method to select novel candidate genes and validate their sensitivity and selectivity through testing in clinical samples. METHODS: We performed CpG microarray analysis using methylation enriched DNA from tumors and matched normal appearing tissues to identify genes methylated in CRC. We then applied a step-wise filtering method to narrow our field of candidate genes. Six genes were verified for high methylation-positivity in CRC cell lines and underwent negative selection in healthy normal samples using bisulfate-pyrosequencing. Genes SORCS3, SIM1, SDC2 were selected for low levels of methylation in normal tissue followed by verification with MSP-pyrosequencing. RESULTS: SDC2 was then selected because of high methylation levels in tumor and very low levels in normal tissue. SDC2 methylation levels were measured in 133 tumors and were found to be significantly methylated at all stages. Next, 500αl sera samples from 42 CRC patients were tested using qMSP which demonstrated sensitivity at 71.4% and specificity 92.9%. CONCLUSIONS: This study utilized refined technologies to identify and validate a novel candidate SCD2 for CRC screening in serum with high sensitivity and selectivity using only 500αl. These findings demonstrate a new level of candidate selection, verification and application that we feel will meet the need for a new minimally-invasive screening test. 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 4517. doi:1538-7445.AM2012-4517

An integrative analysis of DNA methylation and RNA-Seq data for human heart, kidney and liver

BackgroundMany groups, including our own, have proposed the use of DNA methylation profiles as biomarkers for various disease states. While much research has been done identifying DNA methylation signatures in cancer vs. normal etc., we still lack sufficient knowledge of the role that differential methylation plays during normal cellular differentiation and tissue specification. We also need thorough, genome level studies to determine the meaning of methylation of individual CpG dinucleotides in terms of gene expression.ResultsIn this study, we have used (insert statistical method here) to compile unique DNA methylation signatures from normal human heart, lung, and kidney using the Illumina Infinium 27 K methylation arraysand compared those to gene expression by RNA sequencing. We have identified unique signatures of global DNA methylation for human heart, kidney and liver, and showed that DNA methylation data can be used to correctly classify various tissues. It indicates that DNA methylation reflects tissue specificity and may play an important role in tissue differentiation. The integrative analysis of methylation and RNA-Seq data showed that gene methylation and its transcriptional levels were comprehensively correlated. The location of methylation markers in terms of distance to transcription start site and CpG island showed no effects on the regulation of gene expression by DNA methylation in normal tissues.ConclusionsThis study showed that an integrative analysis of methylation array and RNA-Seq data can be utilized to discover the global regulation of gene expression by DNA methylation and suggests that DNA methylation plays an important role in normal tissue differentiation via modulation of gene expression.

Effect of WBC BRCA1 promoter methylation on ovarian cancer risk.

5029 Background: Recently, some studies have reported BRCA1 WBC hypermethylation to be associated with increased risk of breast cancer. We assessed WBC BRCA1 promoter methylations in ovarian (OC) and breast cancer (BC) patients and healthy controls. In an OC subgroup harboring WBC BRCA1 methylation, we confirmed promoter methylation status in normal tissue. Methods: WBC DNA from 899 OC patients, 425 BC patients and 719 healthy controls were analyzed for BRCA1 promoter methylation by methylation specific PCR. In addition, we analyzed WBC DNA from 256 OC and 393 BC patients in blood samples drawn prior to diagnosis in a population-based study. We also analyzed 24 BC patients with a family history (BRCAPRO scores > 80%; Manchester score >40) without BRCA1/2 mutations. Paraffin-embedded normal tissue from 5 OC patients harboring WBC BRCA1 methylation was analyzed for BRCA1 methylation status. Finally, to determine potential risk factors in cis, we investigated BRCA1 haplotype status in a sub-cohort of 10 individuals with WBC methylated BRCA1and 13 controls. Results: We detected WBC BRCA1 promoter hypermethylation in 2.4% of healthy controls and 3.1% of BC patients (all BC individuals). No difference in BRCA1 methylation incidence was recorded between BC patients with blood samples drawn before (4.1%) or after (2.1%) diagnosis. In contrast, we detected WBC BRCA1 methylation in 10.3% of OC patients having blood samples drawn at diagnosis. Among OC patients with blood sampling 0-13 years (median 4.6 y) prior to diagnosis, BRCA1 promoter methylation was detected in 6.6%. BRCA1 promoter methylation was associated with a non-significant elevated risk of BC (HR 1.302; 95% CI 0.697-2.431) but a significantly increased risk of OC in the cohort of patients with blood samples drawn at time of (OR 4.765; CI 2.814-8.069) or prior to (OR 2.937; CI 1.476-5.845) diagnosis. We confirmed BRCA1 promoter methylation in normal tissue from all 5 individuals analyzed, excluding WBC promoter methylation being due to circulating DNA contamination. No association between BRCA1methylation and promoter haplotype was found. Conclusions: WBC BRCA1 promoter methylation is associated with increased risk of ovarian cancer.This finding has clinical as well as biological implications..

Abstract 4883: Differences in epigenetic patterns of HOX genes in normal lung and Non-small cell lung cancer

Abstract HOX genes have determinative roles in cell fate during embryogenesis and adult cellular differentiation. Their dysregulation has been implicated in many human cancers. Loss of or de novo expression of the genes by methylation abnormality are also reported in non-small cell lung cancer (NSCLC). In this study, we screened the expression profiles of the HOX D genes in normal lung tissues, a bronchial epithelial cell line, 9 NSCLC cell lines and 10 normal-tumor pairs of NSCLC tissues and compared epigenetic patterns of the genes by Quantitative Real-Time PCR, Dual-Specific Bisulfite PCR (DSBP) and ChIP-on-chip assay. We showed frequent cancer specific de novo expression of HOX D9, D11, and D13 genes in NSCLC tissues and cells in contrast to normal lung tissues. In methylation assay, unexpectedly, the genes are frequently hypermethylated in cancerous samples but show low level of methylation in normal tissues. In ChIP-on-chip assay, we observed that normal tissues show repressive or bivalent histone modification pattern characterized by high level of H3K27me3 and low level of H4K20me3 and H4K16ac at the up-stream region of the genes. In contrast, cancer tissues showed permissive or active histone modification patterns at the region characterized by low level of H3K27me3 and high level of H4K20me3 and H4K16ac. The results suggest that normal epigenetic state of the genes in lung tissue could be defined as bivalent histone modification pattern, no DNA methylation and no gene expression. In lung cancer, epigenetic state of the genes are dysregulated to permissive histone modification pattern, DNA hypermethylation and de novo expression of the genes. (This study was supported by a grant of the Korea Healthcare technology R&amp;D Project, Ministry for Health, Welfare &amp; Family Affairs, Republic of Korea. (A084921), This study was supported by a grant of the Korea Health 21 R&amp;D Project, Ministry of Health &amp; Welfare, Republic of Korea. (A062254)) Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 4883.

Variable DNA methylation patterns associated with progression of disease in hepatocellular carcinomas

Hepatocellular carcinoma (HCC) most commonly arises from chronic inflammation due to viral infection, as a result of genetic and epigenetic abnormalities. A global picture of epigenetic changes in HCC is lacking. We used methylated CpG island amplification microarrays (MCAMs) to study 6458 CpG islands in HCC and adjacent preneoplastic tissues [chronic hepatitis (CH) or liver cirrhosis (LC)] in comparison with normal liver tissues where neither viral infection nor hepatitis has existed. MCAM identified 719 (11%) prominent genes of hypermethylation in HCCs. HCCs arising from LC had significantly more methylation than those arising from CH (1249 genes or 19% versus 444 genes or 7%, P < 0.05). There were four patterns of aberrant methylation: Type I (4%, e.g. matrix metalloproteinase 14) shows a substantially high methylation level in adjacent tissue and does not increase further in cancer. Type II (55%, e.g. RASSF1A) shows progressively increasing methylation from adjacent tissue to HCC. Type III (4%, e.g. GNA14) shows decreased methylation in adjacent tissue but either similar or increased methylation in HCC. Type IV (37%, e.g. CDKN2A) shows low levels of methylation in normal tissue and adjacent tissue but high levels in HCC. These DNA methylation changes were confirmed by quantitative pyrosequencing methylation analysis in representative 24 genes and were analyzed for correlation with clinicopathological parameters in 38 patients. Intriguingly, methylation in the Type IV genes is characteristic of moderately/poorly differentiated cancer. Our global epigenome analysis reveals distinct patterns of methylation that are probably to represent different pathophysiologic processes in HCCs.

Clustering of Lynch syndrome malignancies with no evidence for a role of DNA mismatch repair

Objectives We ascertained a large kindred with an excess of Lynch syndrome-associated cancers. Our objective was to determine if a defect in one of the DNA mismatch repair (DMMR) genes was the probable cause of cancer susceptibility as microsatellite instability (MSI) and immunohistochemical (IHC) analysis of the probands' tumors did not provide a clear indication. Methods A detailed history and review of medical records was undertaken to construct a four-generation pedigree. Blood samples were obtained for analysis of germline DNA. Polymorphic repeats from the MLH1, MSH2, MSH6, and PMS2 loci were genotyped and the co-segregation of markers and disease was assessed. DMMR gene expression for all available tumors was evaluated by IHC. Combined bisulfite restriction analysis (COBRA) of MLH1 was utilized to test for germline epimutation. Results Four gynecologic carcinomas, 3 colon carcinomas, and 13 cases of adenomatous polyps were identified. The family met Amsterdam II criteria. The mean age of cancer diagnosis in the kindred was 63 years (range 44–82 years). DNA marker analyses excluded linkage to MLH1, MSH2, MSH6, and PMS2. Furthermore, MSI and IHC analysis of tumors did not suggest a role for DMMR. Methylation of the MLH1 promoter was identified in the peripheral blood leukocytes (PBLs) of a family member with an early onset colon cancer. Conclusions We identified a large family with multiple Lynch malignancies and no evidence for an inherited defect in DMMR. This family represents an important but poorly understood form of autosomal dominant inherited cancer susceptibility. Aberrant MLH1 promoter methylation in normal tissues may be a marker for cancer susceptibility in families such as this.

Genome-Wide Profiling of DNA Methylation Reveals a Class of Normally Methylated CpG Island Promoters

The role of CpG island methylation in normal development and cell differentiation is of keen interest, but remains poorly understood. We performed comprehensive DNA methylation profiling of promoter regions in normal peripheral blood by methylated CpG island amplification in combination with microarrays. This technique allowed us to simultaneously determine the methylation status of 6,177 genes, 92% of which include dense CpG islands. Among these 5,549 autosomal genes with dense CpG island promoters, we have identified 4.0% genes that are nearly completely methylated in normal blood, providing another exception to the general rule that CpG island methylation in normal tissue is limited to X inactivation and imprinted genes. We examined seven genes in detail, including ANKRD30A, FLJ40201, INSL6, SOHLH2, FTMT, C12orf12, and DPPA5. Dense promoter CpG island methylation and gene silencing were found in normal tissues studied except testis and sperm. In both tissues, bisulfite cloning and sequencing identified cells carrying unmethylated alleles. Interestingly, hypomethylation of several genes was associated with gene activation in cancer. Furthermore, reactivation of silenced genes could be induced after treatment with a DNA demethylating agent or in a cell line lacking DNMT1 and/or DNMT3b. Sequence analysis identified five motifs significantly enriched in this class of genes, suggesting that cis-regulatory elements may facilitate preferential methylation at these promoter CpG islands. We have identified a group of non-X–linked bona fide promoter CpG islands that are densely methylated in normal somatic tissues, escape methylation in germline cells, and for which DNA methylation is a primary mechanism of tissue-specific gene silencing.

Prognostic Value of Apoptosis-Associated Speck-like Protein Containing a CARD Gene Promoter Methylation in Resectable Non-Small-Cell Lung Cancer

BackgroundThe apoptosis-associated speck-like protein containing a CARD (ASC) is a newly identified tumor suppressor gene that is frequently inactivated by de novo promoter methylation in non-small-cell lung cancer (NSCLC). Patients and MethodsWe studied 79 patients with NSCLC who had undergone surgery with curative intent. The ASC promoter methylation status was determined by methylation-specific polymerase chain reaction. Statistical analyses (all 2-sided) were performed to determine the prognostic effect of hypermethylation on various clinical parameters. ResultsASC promoter hypermethylation was detectable by methylation-specific polymerase chain reaction in 9 of 70 (12.9%) normal lungs and in 33 of 70 (47.1%) matching tumor samples of patients with NSCLC. The mean ASC methylation level was significantly higher in tumor than in matching normal tissue (P < 0.001). ASC methylation in normal tissue was always accompanied with ASC methylation in matching tumor tissue. Patients without ASC promoter hypermethylation showed a significantly better survival than patients with ASC promoter hypermethylation (P = 0.007). Multivariate analysis revealed ASC promoter methylation as an independent unfavorable prognostic factor (P = 0.009). ConclusionOur results indicate that ASC promoter hypermethylation is a common event in patients with primary NSCLC, and this epigenetic alteration is associated with inferior survival, suggesting that ASC promoter hypermethylation might be an important biomarker for a biologic, aggressive disease in NSCLC.

Progressive accumulation of DNA methylation with malignant progression in breast tissue

Abstract Introduction: The detection of methylated tumor suppressor genes (TSGs) in ductal aspirates/lavages from breast cancer (BC) patients suggests a role for DNA methylation in molecular screening. We measured DNA methylation in normal tissue from non-cancer patients (Nl), normal tissue from BC patients (Nl-CA), and malignant tissue from patients with in situ (DCIS) or invasive (CA) BC to determine whether methylation changes can distinguish between normal and cancer. Methods: DNA was extracted and bisulfite converted from fresh frozen tissue (reduction mammoplasty (Nl, 7), matched Nl-CA and CA (48)) or microdissected paraffinized tissue (Nl from benign biopsy (3), or DCIS (7)). Methylation of APC, ESR1, HPP1, and p16 was assayed using the MethyLight assay. Results: All Nl specimens were unmethylated. Methylation of the 4 TSGs was observed in tissues from cancer patients (Table). The mean number of methylated genes (NMG) increased from Nl (0) to Nl-CA (0.5), to cancer (DCIS 1.1, CA 1.2) (p Conclusions: The increased NMG from Nl to cancer suggests a progressive accumulation of methylation with malignant progression. Nl-CA tissue displays elevated levels of TSG methylation, suggesting a methylation field effect. When assessing several genes simultaneously, methylation can distinguish between normal and cancer tissue. The discriminatory power will likely increase with the number of genes assayed. These findings support the evaluation of DNA methylation as a biomarker for molecular screening.