Breast Cancer DNA Methylation Profiles Are Associated with Tumor Size and Alcohol and Folate Intake

Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, United States of America.
PLoS Genetics (Impact Factor: 7.53). 07/2010; 6(7):e1001043. DOI: 10.1371/journal.pgen.1001043
Source: PubMed


Although tumor size and lymph node involvement are the current cornerstones of breast cancer prognosis, they have not been extensively explored in relation to tumor methylation attributes in conjunction with other tumor and patient dietary and hormonal characteristics. Using primary breast tumors from 162 (AJCC stage I-IV) women from the Kaiser Division of Research Pathways Study and the Illumina GoldenGate methylation bead-array platform, we measured 1,413 autosomal CpG loci associated with 773 cancer-related genes and validated select CpG loci with Sequenom EpiTYPER. Tumor grade, size, estrogen and progesterone receptor status, and triple negative status were significantly (Q-values <0.05) associated with altered methylation of 209, 74, 183, 69, and 130 loci, respectively. Unsupervised clustering, using a recursively partitioned mixture model (RPMM), of all autosomal CpG loci revealed eight distinct methylation classes. Methylation class membership was significantly associated with patient race (P<0.02) and tumor size (P<0.001) in univariate tests. Using multinomial logistic regression to adjust for potential confounders, patient age and tumor size, as well as known disease risk factors of alcohol intake and total dietary folate, were all significantly (P<0.0001) associated with methylation class membership. Breast cancer prognostic characteristics and risk-related exposures appear to be associated with gene-specific tumor methylation, as well as overall methylation patterns.

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    • "Methylation differences were evaluated using unsupervised hierarchical clustering with the Manhattan metric and average linkage as previously described [22]. We used recursively partitioned mixture modeling (RPMM) to test associations between methylation status and tumor (histology and location) and demographic (age at diagnosis and sex) characteristics as described [23] and implemented [22,24]. Briefly, samples are assigned to a methylation class using a model-based form of unsupervised clustering. "
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    ABSTRACT: Aberrant DNA methylation is a prominent feature of many cancers, and may be especially relevant in germ cell tumors (GCTs) due to the extensive epigenetic reprogramming that occurs in the germ line during normal development. We used the Illumina GoldenGate Cancer Methylation Panel to compare DNA methylation in the three main histologic subtypes of pediatric GCTs (germinoma, teratoma and yolk sac tumor (YST); N = 51) and used recursively partitioned mixture models (RPMM) to test associations between methylation pattern and tumor and demographic characteristics. We identified genes and pathways that were differentially methylated using generalized linear models and Ingenuity Pathway Analysis. We also measured global DNA methylation at LINE1 elements and evaluated methylation at selected imprinted loci using pyrosequencing. Methylation patterns differed by tumor histology, with 18/19 YSTs forming a distinct methylation class. Four pathways showed significant enrichment for YSTs, including a human embryonic stem cell pluripotency pathway. We identified 190 CpG loci with significant methylation differences in mature and immature teratomas (q < 0.05), including a number of CpGs in stem cell and pluripotency-related pathways. Both YST and germinoma showed significantly lower methylation at LINE1 elements compared with normal adjacent tissue while there was no difference between teratoma (mature and immature) and normal tissue. DNA methylation at imprinted loci differed significantly by tumor histology and location. Understanding methylation patterns may identify the developmental stage at which the GCT arose and the at-risk period when environmental exposures could be most harmful. Further, identification of relevant genetic pathways could lead to the development of new targets for therapy.
    Full-text · Article · Jun 2013 · BMC Cancer
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    • "The role of epigenetic mechanisms in alcohol-related breast cancer also has been investigated. In a recent study of the methylation profiles of 1,413 CpG sites, Christensen and colleagues (2010) showed a strong trend toward decreased DNA methylation with increasing alcohol intake, and a trend toward increased methylation with increasing dietary folate. Other studies have shown altered methylation patterns for several genes associated with alcohol consumption, including hyper-methylation of the ER-a (Zhu et al. 2003) and E-cadherin genes (Tao et al. 2011) and hypomethylation of p16 (Tao et al. 2011). "
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    ABSTRACT: Cancer is one of the most significant diseases associated with chronic alcohol consumption, and chronic drinking is a strong risk factor for cancer, particularly of the upper aerodigestive tract, liver, colorectum, and breast. Several factors contribute to alcohol-induced cancer development (i.e., carcinogenesis), including the actions of acetaldehyde, the first and primary metabolite of ethanol, and oxidative stress. However, increasing evidence suggests that aberrant patterns of DNA methylation, an important epigenetic mechanism of transcriptional control, also could be part of the pathogenetic mechanisms that lead to alcohol-induced cancer development. The effects of alcohol on global and local DNA methylation patterns likely are mediated by its ability to interfere with the availability of the principal biological methyl donor, S-adenosylmethionine (SAMe), as well as pathways related to it. Several mechanisms may mediate the effects of alcohol on DNA methylation, including reduced folate levels and inhibition of key enzymes in one-carbon metabolism that ultimately lead to lower SAMe levels, as well as inhibition of activity and expression of enzymes involved in DNA methylation (i.e., DNA methyltransferases). Finally, variations (i.e., polymorphisms) of several genes involved in one-carbon metabolism also modulate the risk of alcohol-associated carcinogenesis.
    Full-text · Article · Mar 2013 · Alcohol research : current reviews
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    • "In multiple meta-analyses of prospective and case–control studies of breast cancer, a 10% excess risk for each alcoholic drink per day has been reported (Hamajima et al., 2002; Key et al., 2006). A study of breast tumor DNA methylation profiles demonstrated a significant, independent association (controlling for age, dietary folate, and other variables) between alcohol intake and tumor DNA methylation profile (based on 1413 CpG loci; Christensen et al., 2010). In addition to DNA methylation, ethanol exposure has been shown to selectively acetylate histone H3 at lysine 9 (H3K9) in primary culture of rat hepatocytes (Park et al., 2003) and in rats in vivo (Kim and Shukla, 2006), though studies in humans are necessary . "
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    ABSTRACT: This review considers the emerging relationships between environmental factors and epigenetic alterations and the application of genome-wide assessments to better define these relationships. First we will briefly cover epigenetic programming in development, one-carbon metabolism, and exposures that may disrupt normal developmental programming of epigenetic states. In addition, because a large portion of epigenetic research has focused on cancer, we discuss exposures associated with carcinogenesis including asbestos, alcohol, radiation, arsenic, and air pollution. Research on other exposures that may affect epigenetic states such as endocrine disruptors is also described, and we also review the evidence for epigenetic alterations associated with aging that may reflect cumulative effects of exposures. From this evidence, we posit potential mechanisms by which exposures modify epigenetic states, noting that understanding the true effect of environmental exposures on the human epigenome will require additional research with appropriate epidemiologic studies and application of novel technologies. With a more comprehensive understanding of the affects of exposures on the epigenome, including consideration of genetic background, the prediction of the toxic potential of new compounds may be more readily achieved, and may lead to the development of more personalized disease prevention and treatment strategies.
    Preview · Article · Nov 2011 · Frontiers in Genetics
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