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Studies of vitamin D-pathway genetic variants in relation to cancer risk have been inconsistent. We examined the associations between vitamin D-related genetic polymorphisms, plasma 25-hydroxyvitamin D [25(OH)D], and breast cancer risk. In a population-based case–control study of 967 incident breast cancer cases and 993 controls, we genotyped 25 polymorphisms encoding the vitamin D receptor (VDR) gene, 1α-hydroxylase (CYP27B1), 24-hydroxylase (CYP24A1), and vitamin D-binding protein (GC) and measured plasma 25(OH)D. We used multivariable logistic regression to estimate adjusted odds ratios (ORs) and 95 % confidence intervals (CIs). Among CYP24A1 polymorphisms, rs6068816 was associated with a 72 % reduction in breast cancer risk (TT vs. CC, OR 0.28, 95 % CI 0.10–0.76; p trend = 0.01), but for rs13038432, the 46 % decrease included the null value (GG vs. AA, OR 0.54, 95 % CI 0.17–1.67; p trend = 0.03). Increased risk that included the null value was noted for CYP24A1 rs3787557 (CC vs. TT, OR 1.34, 95 % CI 0.92–1.89). The VDR polymorphism, TaqI (rs731236), was associated with a 26 % risk reduction (TT vs. CC, OR 0.74, 95 % CI 0.56–0.98; p trend = 0.01). For other polymorphisms, ORs were weak and included the null value. The inverse association for plasma 25(OH)D with breast cancer was more pronounced (OR 0.43, 95 % CI 0.27–0.68) among women with the common allele for CYP24A1, rs927650 (p for interaction on a multiplicative scale = 0.01). Breast cancer risk may be associated with specific vitamin D-related polymorphisms, particularly CYP24A1. Genetic variation in the vitamin D pathway should be considered when designing potential intervention strategies with vitamin D supplementation.

Background: Among Hispanic breast cancer survivors, we examined the long-term effects of a short-term culturally based dietary intervention on increasing fruits/vegetables (F/V), decreasing fat, and changing biomarkers associated with breast cancer recurrence risk. Methods: Spanish-speaking women (n = 70) with a history of stage 0–III breast cancer who completed treatment were randomized to ¡Cocinar Para Su Salud! (n = 34), a culturally based 9-session program (24 hours over 12 weeks, including nutrition education, cooking classes, and food-shopping field trips), or a control group (n = 36, written dietary recommendations for breast cancer survivors). Diet recalls, fasting blood, and anthropometric measures were collected at baseline, 6, and 12 months. We report changes between groups at 12 months in dietary intake and biomarkers using 2-sample Wilcoxon t tests and generalized estimating equation (GEE) models. Results: At 12 months, the intervention group compared with the control group reported higher increases in mean daily F/V servings (total: +2.0 vs. −0.4; P < 0.01), and nonsignificant decreases in the percentage of calories from fat (−2.2% vs. −1.1%; P = 0.69) and weight (−2.6 kg vs. −1.5 kg; P = 0.56). Compared with controls, participants in the intervention group had higher increases in plasma lutein (+20.4% vs. −11.5%; P < 0.01), and borderline significant increases in global DNA methylation (+0.8% vs. −0.5%; P = 0.06). Conclusions: The short-term ¡Cocinar Para Su Salud! program was effective at increasing long-term F/V intake in Hispanic breast cancer survivors and changed biomarkers associated with breast cancer recurrence risk. Impact: It is possible for short-term behavioral interventions to have long-term effects on behaviors and biomarkers in minority cancer patient populations. Results can inform future study designs. Cancer Epidemiol Biomarkers Prev; 25(11); 1491–502. ©2016 AACR.

Background Epigenome-wide studies in hepatocellular carcinoma (HCC) have identified numerous genes with aberrant DNA methylation. However, methods for triaging functional candidate genes as useful biomarkers for epidemiological study have not yet been developed. Methods We conducted targeted next-generation bisulfite sequencing (bis-seq) to investigate associations of DNA methylation and mRNA expression in HCC. Integrative analyses of epigenetic profiles with DNA copy number analysis were used to pinpoint functional genes regulated mainly by altered DNA methylation. Results Significant differences between HCC tumor and adjacent non-tumor tissue were observed for 28 bis-seq amplicons, with methylation differences varying from 12% to 43%. Available mRNA expression data in Oncomine were evaluated. Two candidate genes (GRASP and TSPYL5) were significantly under-expressed in HCC tumors in comparison with precursor and normal liver tissues. The expression levels in tumor tissues were, respectively, 1.828 and − 0.148, significantly lower than those in both precursor and normal liver tissue. Validations in an additional 42 paired tissues showed consistent under-expression in tumor tissue for GRASP (−7.49) and TSPYL5 (−9.71). A highly consistent DNA hypermethylation and mRNA repression pattern was obtained for both GRASP (69%) and TSPYL5 (73%), suggesting that their biological function is regulated by DNA methylation. Another two genes (RGS17 and NR2E1) at Chr6q showed significantly decreased DNA methylation in tumors with loss of DNA copy number compared to those without, suggesting alternative roles of DNA copy number losses and hypermethylation in the regulation of RGS17 and NR2E1. Conclusions These results suggest that integrative analyses of epigenomic and genomic data provide an efficient way to filter functional biomarkers for future epidemiological studies in human cancers. Electronic supplementary material The online version of this article (doi:10.1186/s12920-015-0105-1) contains supplementary material, which is available to authorized users.

Background.Previous studies, including ours, have examined the regulation of microRNAs (miRNAs) by DNA methylation, but whether this regulation occurs at a genome-wide level in hepatocellular carcinoma (HCC) is unclear.Subjects/Methods.Using a two-phase study design, we conducted genome-wide screening for DNA methylation and miRNA expression to explore the potential role of methylation alterations in miRNAs regulation.Results.We found that expressions of 25 miRNAs were statistically significantly different between tumor and nontumor tissues and perfectly differentiated HCC tumor from nontumor. Six miRNAs were overexpressed, and 19 were repressed in tumors. Among 133 miRNAs with inverse correlations between methylation and expression, 8 miRNAs (6%) showed statistically significant differences in expression between tumor and nontumor tissues. Six miRNAs were validated in 56 additional paired HCC tissues, and significant inverse correlations were observed for miR-125b and miR-199a, which is consistent with the inactive chromatin pattern found in HepG2 cells.Conclusion.These data suggest that the expressions of miR-125b and miR-199a are dramatically regulated by DNA hypermethylation that plays a key role in hepatocarcinogenesis.

Previous studies, including ours have examined aberrant expression of microRNAs (miRNAs) and altered DNA methylation, and several miRNAs have been identified as regulated by DNA methylation. However, whether this mechanism occurs at a genome-wide level and is related to the profiles of dysregulated miRNA commonly observed in hepatocellular carcinoma (HCC) patients is largely unknown. Using a two-phase study design, we conducted a genome-wide screening for miRNA expression and DNA methylation profiles in the tumor and adjacent non-tumor tissues from US HCC cases. The discovery and validation sets included, respectively, 10 and 56 paired tumor/non-tumor tissues. TaqMan Low Density Arrays (TLDA) covering 733 miRNAs were used to measure expression profiles, and quantitative RT-PCR was used to validate candidate miRNA signatures. Infinium HumanMethylation 450K BeadChip arrays covering 3,439 CpG sites for 727 miRNAs were used to determine DNA methylation patterns. Comparing expression profiles in HCC tumor and adjacent non-tumor tissues, we found that 25 miRNAs were statistically significantly different with over 2-fold expression changes after adjusting for false discovery rate (FDR); a perfect classification of HCC tissues was observed. Six of the aberrant miRNAs were over-expressed in HCC tumor tissue (range from 2.7 to 18-fold), while 19 miRNAs were downregulated in tumor tissue (range from -2.5 to -7.5-fold). Several miRNAs (miR-139, miR-196b, miR-381, miR-486 and miR-1180) were identified for the first time as having a role in hepatocarcinogenesis. After Bonferroni adjustment, a total of 1,256 CpG sites covering 412 miRNAs showed significant differences in DNA methylation levels between tumor and adjacent non-tumor tissues, including 185 hypermethylated and 1,071 hypomethylated CpG sites in tumor tissues. We further conducted integrative analyses of the correlations between miRNAs expression and DNA methylation patterns for 222 miRNAs detected in over 80% of the tissue samples. As expected, inverse correlations were observed for 91.7% (55/60) of up-regulated miRNAs with a DNA hypomethylation change, and for 48.1% (78/162) of down-regulated miRNAs with a DNA hypermethylation change. However, for only 8 miRNAs’ (3.6%) did expression levels achieve statistically significant differences between tumor and non-tumor tissues in accord with DNA methylation alterations. A validation study of six of the candidates in an additional 56 paired HCC tissues confirmed the aberrant miRNAs expression patterns observed in tumor tissue. The inverse correlations between miRNAs’ expression and DNA methylation were concordant for all 27 CpG sites in the 4 miRNAs (miR-18a, miR-125b-1, miR-182 and miR-199a-1). These data suggest that a small proportion of DNA methylation changes can lead to significant dysregulation of miRNAs in HCC tumor tissue. Citation Format: Jing Shen, Shuang Wang, Abby B. Siegel, Helen Remotti, Qiao Wang, Iryna Sirosh, Regina M. Santella. Integrative analyses of genome-wide expression of miRNAs and DNA methylation patterns in hepatocellular carcinoma to improve functional biomarker identification. [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 285. doi:10.1158/1538-7445.AM2014-285