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1.  Global hypomethylation in hepatocellular carcinoma and its relationship to aflatoxin B1 exposure 
World Journal of Hepatology  2012;4(5):169-175.
AIM: To determine global DNA methylation in paired hepatocellular carcinoma (HCC) samples using several different assays and explore the correlations between hypomethylation and clinical parameters and biomarkers, including that of aflatoxin B1 exposure.
METHODS: Using the radio labeled methyl acceptance assay as a measure of global hypomethylation, as well as two repetitive elements, including satellite 2 (Sat2) by MethyLight and long interspersed nucleotide elements (LINE1), by pyrosequencing.
RESULTS: By all three assays, mean methylation levels in tumor tissues were significantly lower than that in adjacent tissues. Methyl acceptance assay log (mean ± SD) disintegrations/min/ng DNA are 70.0 ± 54.8 and 32.4 ± 15.6, respectively, P = 0.040; percent methylation of Sat2 42.2 ± 55.1 and 117.9 ± 88.8, respectively, P < 0.0001 and percent methylation LINE1 48.6 ± 14.8 and 71.7 ± 1.4, respectively, P < 0.0001. Aflatoxin B1-albumin (AFB1-Alb) adducts, a measure of exposure to this dietary carcinogen, were inversely correlated with LINE1 methylation (r = -0.36, P = 0.034).
CONCLUSION: Consistent hypomethylation in tumor compared to adjacent tissue was found by the three different methods. AFB1 exposure is associated with DNA global hypomethylation, suggesting that chemical carcinogens may influence epigenetic changes in humans.
doi:10.4254/wjh.v4.i5.169.
PMCID: PMC3365436  PMID: 22666524
Hepatocellular carcinoma; Epigenetics; Hypomethylation; [3H]-methyl acceptance assay; Satellite 2; Long interspersed nucleotide element-1; Aflatoxin B1
2.  Oxidative Stress Biomarkers in Sporadic ALS 
Objective
To investigate oxidative stress biomarkers in a cross-sectional pilot study of 50 participants with sporadic ALS (sALS) compared to 46 control subjects.
Methods
We measured urinary 8-oxodeoxyguanosine (8-oxodG), urinary 15-F2t-isoprostane (IsoP), and plasma protein carbonyl by ELISA methods. We also determined if ELISA measurement of 8-oxodG could be validated against measures from high pressure liquid chromatography coupled with electrochemical detection, the current standard method.
Results
8-oxodG and IsoP levels adjusted for creatinine were significantly elevated in sALS participants. These differences persisted after age and gender were controlled in regression analyses. These markers are highly and positively correlated with each other. 8-oxodG measured by the two techniques from the same urine sample were positively correlated (P < .0001). Protein carbonyl was not different between sALS participants and controls.
Conclusion
Using ELISA we confirmed that certain oxidative stress biomarkers were elevated in sALS participants. ELISA may be reliable and thus useful in epidemiology studies requiring large numbers of samples to determine the significance of increased oxidative stress markers in sALS. Further studies are required.
doi:10.1080/17482960801933942
PMCID: PMC4332387  PMID: 18574762
epidemiology; amyotrophic lateral sclerosis (ALS); biomarkers; oxidative stress; neurodegeneration
3.  DNA double-strand break repair genotype and phenotype and breast cancer risk within sisters from the New York site of the Breast Cancer Family Registry (BCFR) 
Cancer causes & control : CCC  2013;24(12):2157-2168.
Purpose
We previously observed that poor DNA repair phenotype is associated with increased breast cancer (BC) risk within families. Here, we examined whether genetic variation in double strand break repair (DSBR) genes is associated with BC risk and if genotypes are related to phenotype in unaffected women.
Methods
Using data from the New York site of the Breast Cancer Family Registry, we investigated 25 SNPs involved in DSBR using biospecimens from 337 BC cases and 410 unaffected sister controls.
Results
Genotypes in XRCC4 were associated with BC risk, with ORs of 1.67 (95% CI = 1.01–2.76) for the combined GA/AA of rs1805377 and 1.69 (95%CI=1.03–2.77) for rs1056503 TG/GG; these associations were no longer statistically significant in multivariable conditional logistic regression models. When examining the association of SNPs with phenotype, we found that genotypes of XRCC5 rs3834 and rs1051685, which were highly correlated with each other, were associated with end joining (EJ) capacity; women with the XRCC5 rs3834 GA genotype had better DNA repair as measured by higher levels of EJ capacity (37.8±14.1% for GA versus 27.9±11.8% for GG carriers (p=0.0006). Women with the AA genotype of BRCA1 rs799917 also had higher EJ capacity (35.1±9.2%) than those with GG (26.4±10.1%, p=0.02).
Conclusions
Overall we found that selected DSBR genotypes were associated with phenotype, although they were not associated with BC risk itself, suggesting that phenotypic measures are influenced by endogenous and exogenous factors across the lifecourse and may be better markers than genotypic measures for ascertaining BC risk.
doi:10.1007/s10552-013-0292-z
PMCID: PMC3947831  PMID: 24062231
breast cancer; double-strand break; end-joining capacity; polymorphism
4.  Arabidopsis thaliana Nfu2 accommodates [2Fe-2S] or [4Fe-4S] clusters and is competent for in vitro maturation of chloroplast [2Fe-2S] and [4Fe-4S] cluster-containing proteins† 
Biochemistry  2013;52(38):10.1021/bi4007622.
Nfu-type proteins are essential in the biogenesis of iron-sulfur (Fe-S) clusters in numerous organisms. A number of phenotypes including low levels of Fe-S cluster incorporation are associated with deletion of the gene encoding a chloroplast-specific Nfu-type protein, Nfu2 from Arabidopsis thaliana (AtNfu2). Here we report that recombinant AtNfu2 is able to assemble both [2Fe-2S] and [4Fe-4S] clusters. Analytical data and gel filtration studies support cluster/protein stoichiometries of one [2Fe-2S] cluster/homotetramer and one [4Fe-4S] cluster/homodimer. The combination of UV-visible absorption and circular dichroism, resonance Raman and Mössbauer spectroscopies has been employed to investigate the nature, properties and transfer of the clusters assembled on Nfu2. The results are consistent with subunit-bridging [2Fe-2S]2+ and [4Fe-4S]2+ clusters coordinated by the cysteines in the conserved CXXC motif. The results also provided insight into the specificity of Nfu2 for maturation of chloroplastic Fe-S proteins via intact, rapid and quantitative cluster transfer. [2Fe-2S] cluster-bound Nfu2 is shown to be an effective [2Fe-2S]2+ cluster donor for glutaredoxin S16, but not glutaredoxin S14. Moreover, [4Fe-4S] cluster-bound Nfu2 is shown to be a very rapid and efficient [4Fe-4S]2+ cluster donor for adenosine 5′-phosphosulfate reductase (APR1) and yeast two-hybrid studies indicate that APR1 forms a complex with Nfu2, but not with Nfu1 and Nfu3, the two other chloroplastic Nfu proteins. This cluster transfer is likely to be physiologically relevant and is particularly significant for plant metabolism as APR1 catalyzes the second step in reductive sulfur assimilation which ultimately results in the biosynthesis of cysteine, methionine, glutathione, and Fe-S clusters.
doi:10.1021/bi4007622
PMCID: PMC3819817  PMID: 24032747
5.  Global DNA methylation in a population with aflatoxin B1 exposure 
Epigenetics  2013;8(9):962-969.
We previously reported that global DNA hypomethylation, measured as Sat2 methylation in white blood cells (WBC), and aflatoxin B1 (AFB1) exposure were associated with increased hepatocellular carcinoma risk. In this study, we assessed the association between AFB1 exposure and global DNA methylation. We measured LINE-1 and Sat2 methylation in WBC DNA samples from 1140 cancer free participants of the Cancer Screening Program (CSP) cohort. Blood and urine samples were used to determine the level of AFB1-albumin (AFB1-Alb) adducts and urinary AFB1 metabolites. In continuous models, we found reverse associations of urinary AFB1 with LINE-1 and Sat2 methylation. The odds ratio (OR) per 1 unit decrease were 1.12 (95%CI = 1.03–1.22) for LINE-1 and 1.48 (95%CI = 1.10–2.00) for Sat2 methylation. When compared with subjects in the highest quartile of LINE-1, we found that individuals in the 2nd and 3rd quartiles were less likely to have detectable AFB1-Alb adducts, with ORs (95%CI) of 0.61 (0.40–0.93), 0.61 (0.40-.94), and 1.09 (0.69–1.72), respectively. The OR for detectable AFB1-Alb was 1.81 (95%CI = 1.15–2.85) for subjects in the lowest quartile of Sat2 methylation. The OR for detection of urinary AFB1 for those with LINE-1 methylation in the lowest quartile compared with those in the highest quartile was 1.87 (95%CI = 1.15–3.04). The corresponding OR was 1.75 (95%CI = 1.08–2.82) for subjects in the lowest quartile of Sat2 methylation. The association between AFB1 exposure and global DNA methylation may have implications for the epigenetic effect of AFB1 on hepatocellular carcinoma development and also suggests that changes in DNA methylation may represent an epigenetic biomarker of dietary AFB1 exposure.
doi:10.4161/epi.25696
PMCID: PMC3883773  PMID: 23867725
DNA methylation; Hepatitis B virus; LINE-1; Sat2; aflatoxin B1; global DNA methylation; white blood cell
6.  Genomic Methylation Changes Over Time in Peripheral Blood Mononuclear Cell DNA: Differences by Assay Type and Baseline Values 
Background
Lower levels of genomic DNA methylation in blood DNA has been associated with risk of different cancers and several cancer risk factors. To understand the use of genomic methylation measures as biomarkers of cancer risk, data are needed on within-individual changes over time.
Methods
Using information from 77 subjects with blood collected at 2 visits on average 8 years apart, we examined whether levels of DNA methylation change with time and if so, whether selected cancer risk factors predict these changes. We measured DNA methylation levels in peripheral blood mononuclear cells (PBMC) using three assays that have been used in epidemiologic studies: (i) luminometric methylation assay (LUMA)(ii) LINE-1 by pyrosequencing, and (iii) Sat2 by MethyLight.
Results
Close to a third of all individuals had large changes over time (≥10%) in LUMA with 19.5% increasing and 13.0% decreasing. For Sat2, two-thirds of individuals had large changes with 40% increasing and 26% decreasing over time. In contrast, only 3.9% of individuals had large changes in LINE-1 over time. The degree of change in PBMC DNA methylation was statistically significantly inversely associated with methylation levels at baseline; greater decreases were observed in individuals with higher baseline values for each assay.
Conclusions
These data, if replicated, suggest that changes in DNA methylation over time are highly associated with baseline values of the assay and vary by assay type.
Impact
These findings suggest that assays that change more over time may warrant consideration for studies that measure later life exposures.
doi:10.1158/1055-9965.EPI-12-0300
PMCID: PMC4032622  PMID: 22665578
7.  Exploring genome-wide DNA methylation profiles altered in hepatocellular carcinoma using Infinium HumanMethylation 450 BeadChips 
Epigenetics  2013;8(1):34-43.
Hepatocellular carcinoma (HCC) incidence has increased in the US and also has one of the fastest growing death rates of any cancer. The purpose of the current study was to discover novel genome-wide aberrant DNA methylation patterns in HCC tumors that are predominantly HCV-related. Infinium HumanMethylation 450K BeadChip arrays were used to examine genome-wide DNA methylation profiles in 66 pairs of HCC tumor and adjacent non-tumor tissues. After Bonferroni adjustment, a total of 130,512 CpG sites significantly differed in methylation level in tumor compared with non-tumor tissues, with 28,017 CpG sites hypermethylated and 102,495 hypomethylated in tumor tissues. Absolute tumor/non-tumor methylation differences ≥ 20% were found in 24.9% of the hypermethylated and 43.1% of the hypomethylated CpG sites; almost 10,000 CpG sites have ≥ 30% DNA methylation differences. Most (60.1%) significantly hypermethylated CpG sites are located in CpG islands, with 21.6% in CpG shores and 3.6% in shelves. In contrast, only a small proportion (8.2%) of significantly hypomethylated CpG sites are situated in islands, while most are found in open sea (60.2%), shore (17.3%) or shelf (14.3%) regions. A total of 2,568 significant CpG sites (2,441 hypermethylated and 127 hypomethylated) covering 589 genes are located within 684 differentially methylated regions defined as regions with at least two significant CpG sites displaying > 20% methylation differences in the same direction within 250-bp. The top 500 significant CpG sites can significantly distinguish HCC tumor from adjacent tissues with one misclassification. Within adjacent non-tumor tissues, we also identified 75 CpG sites significantly associated with gender, 228 with HCV infection, 17,207 with cirrhosis, and 56 with both HCV infection and cirrhosis after multiple comparisons adjustment. Aberrant DNA methylation profiles across the genome were identified in tumor tissues from US HCC cases that are predominantly related to HCV infection. These results demonstrate the significance of aberrant DNA methylation in HCC tumorigenesis.
doi:10.4161/epi.23062
PMCID: PMC3549879  PMID: 23208076
genome-wide; DNA methylation; alterations; hepatocellular carcinoma; 450K BeadChips
8.  Differences in DNA methylation by extent of breast cancer family history in unaffected women 
Epigenetics  2013;9(2):243-248.
Breast cancer clusters within families but genetic factors identified to date explain only a portion of this clustering. Lower global DNA methylation in white blood cells (WBC) has been associated with increased breast cancer risk. We examined whether WBC DNA methylation varies by extent of breast cancer family history in unaffected women from high-risk breast cancer families. We evaluated DNA methylation levels in LINE-1, Alu and Sat2 in 333 cancer-free female family members of the New York site of the Breast Cancer Family Registry, the minority of which were known BRCA1 or BRCA2 mutation carriers. We used generalized estimated equation models to test for differences in DNA methylation levels by extent of their breast cancer family history after adjusting for age. All unaffected women had at least one sister affected with breast cancer. LINE-1 and Sat2 DNA methylation levels were lower in individuals with 3 or more (3+) first-degree relatives with breast cancer relative to women with only one first-degree relative. For LINE-1, Alu, and Sat2, having 3+ affected first-degree relatives was associated with a decrease of 23.4% (95%CI = −46.8%, 0.1%), 17.9% (95%CI = −39.5%, 3.7%) and 11.4% (95% CI = −20.3%, −2.5%), respectively, relative to individuals with only one affected first-degree relative, but the results were only statistically significant for Sat2. Individuals having an affected mother had 17.9% lower LINE-1 DNA methylation levels (95% CI = −28.8%, −7.1%) when compared with those not having an affected mother. No associations were observed for Alu or Sat2 by maternal breast cancer status. If replicated, these results indicate that lower global WBC DNA methylation levels in families with extensive cancer histories may be one explanation for the clustering of cancers in these families. Family clustering of disease may reflect epigenetic as well as genetic and shared environmental factors.
doi:10.4161/epi.26880
PMCID: PMC3962534  PMID: 24172832
breast cancer; family history; LINE-1; Sat2; DNA methylation; white blood cells
9.  Repetitive element DNA methylation levels in white blood cell DNA from sisters discordant for breast cancer from the New York site of the Breast Cancer Family Registry 
Carcinogenesis  2012;33(10):1946-1952.
Global decreases in DNA methylation, particularly in repetitive elements, have been associated with genomic instability and human cancer. Emerging, though limited, data suggest that in white blood cell (WBC) DNA levels of methylation, overall or in repetitive elements, may be associated with cancer risk. We measured methylation levels of three repetitive elements [Satellite 2 (Sat2)], long interspersed nuclear element-1 (LINE-1) and Alu) by MethyLight, and LINE-1 by pyrosequencing in a total of 282 breast cancer cases and 347 unaffected sisters from the New York site of the Breast Cancer Family Registry (BCFR) using DNA from both granulocytes and total WBC. We found that methylation levels in all markers were correlated between sisters (Spearman correlation coefficients ranged from 0.17 to 0.55). Sat2 methylation was statistically significantly associated with increased breast cancer risk [odds ratio (OR) = 2.09, 95% confidence interval (CI) = 1.09–4.03; for each unit decrease in the natural log of the methylation level, OR = 2.12, 95% CI = 0.88–5.11 for the lowest quartile compared with the highest quartile]. These associations were only observed in total WBC but not granulocyte DNA. There was no association between breast cancer and LINE-1 and Alu methylation. If replicated in larger prospective studies, these findings support that selected markers of epigenetic changes measured in WBC, such as Sat2, may be potential biomarkers of breast cancer risk.
doi:10.1093/carcin/bgs201
PMCID: PMC3499042  PMID: 22678115
10.  Global DNA methylation levels in white blood cell DNA from sisters discordant for breast cancer from the New York site of the Breast Cancer Family Registry 
Epigenetics  2012;7(8):868-874.
Lower global DNA methylation is associated with genomic instability and it is one of the epigenetic mechanisms relevant to carcinogenesis. Emerging evidence for several cancers suggests that lower overall levels of global DNA methylation in blood are associated with different cancer types, although less is known about breast cancer. We examined global DNA methylation levels using a sibling design in 273 sisters affected with breast cancer and 335 unaffected sisters from the New York site of the Breast Cancer Family Registry. We measured global DNA methylation in total white blood cell (WBC) and granulocyte DNA by two different methods, the [3H]-methyl acceptance assay and the luminometric methylation assay (LUMA). Global methylation levels were only modestly correlated between sisters discordant for breast cancer (Spearman correlation coefficients ranged from -0.08 to 0.24 depending on assay and DNA source). Using conditional logistic regression models, women in the quartile with the lowest DNA methylation levels (as measured by the [3H]-methyl acceptance assay) had a 1.8-fold (95% CI = 1.0–3.3) higher relative association with breast cancer than women in the quartile with the highest DNA methylation levels. When we examined the association on a continuous scale, we also observed a positive association (odds ratio, OR = 1.3, 95% CI = 1.0–1.7, for a one unit change in the natural logarithm of the DPM/μg of DNA). We observed no association between measures by the LUMA assay and breast cancer risk. If replicated in prospective studies, this study suggests that global DNA methylation levels measured in WBC may be a potential biomarker of breast cancer risk even within families at higher risk of cancer.
doi:10.4161/epi.20830
PMCID: PMC3427282  PMID: 22705975
blood; breast cancer; epigenetics; global DNA methylation; global methylation; LUMA; luminometric methylation assay; methyl acceptance assay; white blood cell; [3H]-methyl acceptance assay
11.  Global DNA methylation levels in white blood cells as a biomarker for hepatocellular carcinoma risk: a nested case–control study 
Carcinogenesis  2012;33(7):1340-1345.
Global DNA hypomethylation is associated with genomic instability and human cancer and blood DNAs collected at the time of cancer diagnosis have been used to examine the relationship between global methylation and cancer risk. To test the hypothesis that global hypomethylation is associated with increased risk of hepatocellular carcinoma (HCC), we conducted a prospective case–control study nested within a community-based cohort with 16 years of follow-up. We measured methylation levels in Satellite 2 (Sat2) by MethyLight and LINE-1 by pyrosequencing using baseline white blood cell DNA from 305 HCC cases and 1254 matched controls. We found that Sat2 hypomethylation was associated with HCC risk [odds ratio (OR) per unit decrease in natural log Sat2 methylation = 1.77, 95% confidence interval (CI) = 1.06–2.95]. The association was significant among individuals diagnosed with HCC before age 62 (OR per unit decrease in natural log Sat2 methylation = 2.47, 95% CI = 1.06–5.73) but not after (OR = 1.67, 95% CI = 0.84–3.32). We did not observe an association of LINE-1 with HCC overall risk by age at diagnosis. Among carriers of hepatitis B virus surface antigen (HBsAg), with each 1U decrease in natural log Sat2 methylation level, the OR for HCC increased by 2.19 (95% CI = 1.00–4.89). LINE-1 hypomethylation was associated with about a 2-fold increased risk of HCC, with ORs (95% CI) of 2.39 (1.06–5.39), 2.09 (0.91–4.77) and 2.28 (0.95–5.51, P trend = 0.14) for HBsAg carriers in the third, second and lowest quartile of LINE-1 methylation, respectively compared with carriers in the fourth. These results suggest that global hypomethylation may be a useful biomarker of HCC susceptibility.
doi:10.1093/carcin/bgs160
PMCID: PMC3499052  PMID: 22581841
12.  Genome-wide DNA Methylation Profiles in Hepatocellular Carcinoma 
Hepatology (Baltimore, Md.)  2012;55(6):1799-1808.
Alterations in DNA methylation frequently occur in hepatocellular cancer (HCC). We have previously demonstrated that hypermethylation in candidate genes can be detected in plasma DNA prior to HCC diagnosis. To identify with a genome-wide approach additional genes hypermethylated in HCC that could be used for more accurate analysis of plasma DNA for early diagnosis, we analyzed tumor and adjacent non-tumor tissues from 62 Taiwanese HCC cases using Illumina methylation arrays that screen 26,486 autosomal CpG sites. After Bonferroni adjustment, a total of 2,324 CpG sites significantly differed in methylation level, with 684 CpG sites significantly hypermethylated and 1,640 hypomethylated in tumor compared to non-tumor tissues. Array data were validated with pyrosequencing in a subset of 5 of these genes; correlation coefficients ranged from 0.92 to 0.97. Analysis of plasma DNA from 38 cases demonstrated that 37% to 63% of cases had detectable hypermethylated DNA (≥5% methylation) for these 5 genes individually. At least one of these genes was hypermethylated in 87% of cases, suggesting that measurement of DNA methylation in plasma samples is feasible. The panel of methylated genes indentified in the current study will be further tested in large cohort of prospectively collected samples to determine their utility as early biomarkers of hepatocellular carcinoma.
doi:10.1002/hep.25569
PMCID: PMC3330167  PMID: 22234943
Genome-wide; DNA mehtylation; Hepatocellular Carcinoma
13.  Topical Application of Green Tea Polyphenol (−)-Epigallocatechin-3-gallate (EGCG) for Prevention of Recurrent Oral Neoplastic Lesions 
Journal of orofacial sciences  2012;4(10):43-50.
Objective
A preliminary study was conducted to investigate feasibility of using an oral cancer chemopreventive agent (−)-epigallocatechin-3-gallate (EGCG), the most biologically active component in the green tea extract, in a form of ‘swish-and-spit’ mouthwash. Such application of EGCG is beneficial as it maximizes exposure of the oral mucosa to the agent but minimizes systemic side effect.
Study design
The study was conducted on individuals suspected to have oral field cancerization who are at a high risk for developing recurrent oral precancerous and carcinomatous lesions. EGCG was used as a daily mouthwash for 7 days. EGCG’s ability to modulate target molecules implicated in oral carcinogenesis was assessed by measuring the change in expression level of biomarkers.
Results
Immunohistochemical expression of phosphoactivated epidermal growth factor receptor (pEGFR), cyclooxygenase-2 (cox-2) and ki-67 were evaluated at baseline and at the endpoint (day 8). Although not statistically significant, overall decrease in expression levels of pEGFR (27.5%), cox-2 (15.9%) and ki-67 positive cells (51.8%) were observed following EGCG treatment. Moreover, a detectable level of EGCG was found in saliva but not in plasma after the one-week treatment regime, demonstrating local availability of EGCG in oral mucosa without significant systemic absorption.
Conclusion
To best of our knowledge this is the first study to explore use of oral cancer chemopreventive agent in a form of mouthwash in patients with oral field cancerization. Although a definitive conclusion was not reached due to limited sample size, if proven effective, EGCG therapy may offer a non-invasive preventive modality for oral field cancerization.
PMCID: PMC3630371  PMID: 23606799
(−)-epigallocatechin-3-gallate; oral field cancerization; topical chemopreventive agent; feasibility trial
14.  Oscillation regulation of Ca2+/calmodulin and heat-stress related genes in response to heat stress in rice (Oryza sativa L.) 
Plant Signaling & Behavior  2012;7(9):1056-1057.
The Ca2+/calmodulin (CaM) signaling pathway mediates the heat stress (HS) response and acquisition of thermotolerance in plants. We showed that the rice CaM1-1 isoform can interpret a Ca2+ signature difference in amplitude, frequency, and temporal–spatial properties in regulating transcription of nucleoplasmic small heat-shock protein gene (sHSPC/N) during HS. Ca2+ and A23187 treatments under HS generated an intense and sustained increase in [Ca2+]cyt and accelerated the expression of CaM1-1 and sHSPC/N genes, which suggests that HS-induced apoplastic Ca2+ influx was responsible for the [Ca2+]cyt transient and downstream HS signaling. Here, we discuss an emerging paradigm in the oscillation regulation of CaM1-1 expression during HS and highlight the areas that need further investigation.
doi:10.4161/psb.21124
PMCID: PMC3489625  PMID: 22899079
Ca2+; calmodulin; heat shock signaling; temporal–spatial regulation; thermotolerance
15.  Expression of Activated Checkpoint Kinase 2 and Histone 2AX in Exfoliative Oral Cells after Exposure to Ionizing Radiation 
Radiation research  2009;171(6):771-775.
γ-H2AX (activated histone 2AX) and pChk2 (activated checkpoint kinase 2), which are DNA damage response molecules, are produced in irradiated cells and may be signature molecules of radiation exposure. We investigated their use as potential biomarkers to identify individuals exposed to ionizing radiation. We collected exfoliated oral epithelial cell samples from 100 healthy individuals undergoing routine dental radiographic examination (2.34 cGy) both before and after the radiograph using a non-invasive technique. The expression levels of pChk2 and γ-H2AX in oral cells were assessed by immunohistochemical assay. Both biomarkers showed statistically significant increases in levels of expression after the radiation exposure (P < 0.001). This suggests that pChk2 and γ-H2AX may serve as sensitive indicators of low-dose radiation exposure.
doi:10.1667/RR1560.1
PMCID: PMC3575577  PMID: 19580484
16.  Aberrant Promoter Hypermethylation and Genomic Hypomethylation in Tumor, Adjacent Normal Tissues and Blood from Breast Cancer Patients 
Anticancer research  2010;30(7):2489-2496.
Background
Promoter hypermethylation and global hypomethylation in the human genome are hallmarks of most cancers. Detection of aberrant methylation in white blood cells (WBC) has been suggested as a marker for cancer development, but has not been extensively investigated. This study was carried out to determine whether aberrant methylation in WBC DNA can be used as a surrogate biomarker for breast cancer risk.
Patients and Methods
Promoter hypermethylation of 8 tumor suppressor genes (RASSF1A, APC, HIN1, BRCA1, cyclinD1, RARβ, CDH1 and TWIST1) and DNA methylation for three repetitive elements (LINE1, Sat2M1 and AluM2) were analyzed in invasive ductal carcinoma of the breast, paired adjacent normal tissue and WBC from 40 breast cancer patients by the MethyLight assay. Methylation in WBC from 40 controls was also analyzed.
Results
Tumor and adjacent tissues showed frequent hypermethylation for all genes tested, while WBC DNA was rarely hypermethylated. For HIN1, RASSF1A, APC and TWIST1 there was agreement between hypermethylation in tumor and adjacent tissues (P=0.04, P=0.02, P=0.005 and P<0.0001, respectively). DNA methylation for the three repetitive elements was lower in tumor compared to adjacent tissue and WBC DNA. Significant correlations in the methylation of Sat2M1 between tumor and adjacent tissues and WBC DNA were found (P<0.0001 and P=0.046, respectively). There was also a significant difference in methylation of Sat2M1 between cases and controls (P=0.01).
Conclusion
These results suggest that further studies of WBC methylation, including prospective studies, may provide biomarkers of breast cancer risk.
PMCID: PMC3568974  PMID: 20682973
Breast cancer; promoter hypermethylation; genomic methylation; tumor suppressor genes; repetitive elements; WBC DNA
17.  Aflatoxin B1 Exposure, Hepatitis B Virus Infection and Hepatocellular Carcinoma in Taiwan 
To evaluate the role of aflatoxin B1 (AFB1) exposure on risk of hepatocellular carcinoma (HCC), a case-control study nested within a community-based cohort was conducted. Baseline blood and urine samples were used to determine the level of AFB1-albumin adducts and urinary AFB1 metabolites. Conditional logistic regression analysis was used to calculate odds ratios (ORs) and 95% confidence intervals (CIs) to assess the effect of AFB1 exposure on risk of HCC. The adjusted-ORs (95%CIs) were 1.54 (1.01–2.36) and 1.76 (1.18–2.58), respectively, for those with AFB1-albumin adducts and urinary AFB1 metabolites levels above the mean compared to those with levels below the mean. When compared to subjects in the lowest quartile of urinary AFB1 metabolites, there was an increase in risk of HCC, with adjusted ORs (95% CIs) of 0.57 (0.14–2.43), 1.43 (0.32–6.42) and 4.91 (1.18–20.48; Ptrend=0.02), respectively, among noncarriers of hepatitis B virus (HBV) infection. The adjusted OR (95%CI) was 7.49 (5.13–10.93) for carriers of HBsAg compared to noncarriers, regardless of AFB1 status. The ORs (95%CI) were 10.38 (5.73–18.82) and 15.13 (7.83–29.25), for carriers of HBsAg with levels of AFB1-albumin adducts and urinary AFB1 metabolites above the mean, respectively. The combined effect of aflatoxin exposure and HBV infection did not differ by duration of follow-up. Consistent with our previous study with fewer subjects, these data demonstrate that AFB1 exposure is a risk factor for HCC risk. However, in this larger study, the effect of combined AFB1 exposure and HBV infection is more consistent with an additive than a multiplicative model.
doi:10.1158/1055-9965.EPI-08-0697
PMCID: PMC3535829  PMID: 19273485
Aflatoxins; AFB1-albumin adducts; Hepatitis B virus; Hepatocellular carcinoma; Urinary aflatoxin metabolites
18.  Early life socioeconomic factors and genomic DNA methylation in mid-life 
Epigenetics  2013;8(1):23-27.
Epigenetic modifications may be one mechanism linking early life factors, including parental socioeconomic status (SES), to adult onset disease risk. However, SES influences on DNA methylation patterns remain largely unknown. In a US birth cohort of women, we examined whether indicators of early life and adult SES were associated with white blood cell methylation of repetitive elements (Sat2, Alu and LINE-1) in adulthood. Low family income at birth was associated with higher Sat2 methylation (β = 19.7, 95% CI: 0.4, 39.0 for lowest vs. highest income quartile) and single parent family was associated with higher Alu methylation (β = 23.5, 95% CI: 2.6, 44.4), after adjusting for other early life factors. Lower adult education was associated with lower Sat2 methylation (β = -16.7, 95% CI: -29.0, -4.5). There were no associations between early life SES and LINE-1 methylation. Overall, our preliminary results suggest possible influences of SES across the life-course on genomic DNA methylation in adult women. However, these preliminary associations need to be replicated in larger prospective studies.
doi:10.4161/epi.22989
PMCID: PMC3549876  PMID: 23196856
birth cohort; early life; socioeconomic status; adult genomic DNA methylation; lifecourse
19.  Silencing of Hint1, a novel tumor suppressor gene, by promoter hypermethylation in hepatocellular carcinoma 
Cancer letters  2008;275(2):277-284.
The Hint1 protein, a member of the histidine triad (HIT) family, is highly conserved in diverse species and ubiquitously expressed in mammalian tissues. Previous studies in mice provided evidence that Hint1 may be haplosufficient with respect to its function as a tumor suppressor. In the present study, we investigated the aberrant methylation of Hint1 and explored possible relationships between aberrant methylation and clinicopathological features in hepatocellular carcinoma (HCC). Hypermethylation of Hint1 was evaluated by the methylation specific PCR (MSP) method in 40 patients with HCC (tumor and paired adjacent non-tumor tissues) from Taiwan, 22 cases of normal liver tissue (14 from Taiwan and 8 from the U.S.). HINT1 expression in tissues was detected by immunohistochemistry. The frequencies of hypermethylation of Hint1 in tumor, paired adjacent non-tumor and normal liver tissue were 55.0%, 37.5% and 9.1%, respectively. A statistically significant inverse association was found between Hint1 methylation status and expression of the HINT1 protein in tumor tissues (p<0.003). The relationship between Hint1 methylation status and clinical features and other, previously measured biomarkers was also analyzed. p16 hypermethylation was statistically significantly associated with Hint1 methylation status (p=0.035). There were no correlations between Hint1 methylation and HBV or HCV infection status or AFB1- and PAH-DNA adduct levels. These results suggest that promoter hypermethylation of Hint1 may play a role in hepatocarcinogenesis.
doi:10.1016/j.canlet.2008.10.042
PMCID: PMC3522093  PMID: 19081673
Hint1; HCC; epigenetic changes; promoter hypermethylation; p16; environmental carcinogens
20.  The Role of Aflatoxins in Hepatocellular Carcinoma 
Hepatitis Monthly  2012;12(10 HCC):e7238.
Context
Hepatocellular carcinoma (HCC) is one of the most common cancers in the world but with a striking geographical variation in incidence; most of the burden is in developing countries. This geographic variation in HCC incidence might be due to geographic differences in the prevalence of various etiological factors.
Evidence Acquisition
Here, we review the epidemiological evidence linking dietary exposure to aflatoxin B1 (AFB1) and risk of HCC, possible interactions between AFB1 and hepatitis B virus (HBV) or polymorphisms of genes involved in AFB1-related metabolism as well as DNA repair.
Results
Ecological, case-control and cohort studies that used various measures of aflatoxin exposure including dietary questionnaires, food surveys and biomarkers are summarized.
Conclusions
Taken together, the data suggest that dietary exposure to aflatoxins is an important contributor to the high incidence of HCC in Asia and sub-Saharan Africa, where almost 82% of the cases occur.
doi:10.5812/hepatmon.7238
PMCID: PMC3496858  PMID: 23162603
Aflatoxins; Aflatoxin-albumin Adducts; Hepatitis B Virus; Hepatocellular Carcinoma
21.  Global DNA methylation levels in girls with and without a family history of breast cancer 
Epigenetics  2011;6(1):29-33.
Lower levels of global DNA methylation in white blood cell (WBC) DNA have been associated with adult cancers. It is unknown whether individuals with a family history of cancer also have lower levels of global DNA methylation early in life. We examined global DNA methylation in WBC (measured in three repetitive elements, LINE1, Sat2 and Alu, by MethyLight and in LINE1 by pyrosequencing) in 51 girls aged 6–17 years. Compared to girls without a family history of breast cancer, methylation levels were lower for all assays in girls with a family history of breast cancer and statistically significantly lower for Alu and LINE1 pyrosequencing. After adjusting for age, body mass index (BMI) and Tanner stage, only methylation in Alu was associated with family history of breast cancer. If these findings are replicated in larger studies, they suggest that lower levels of global WBC DNA methylation observed later in life in adults with cancer may also be present early in life in children with a family history of cancer.
doi:10.4161/epi.6.1.13393
PMCID: PMC3052913  PMID: 20930546
Alu; DNA global methylation; early life exposure; epigenetics; LINE1; methylight; pyrosequencing; Sat2
22.  Global methylation profiles in DNA from different blood cell types 
Epigenetics  2011;6(1):76-85.
DNA methylation measured in white blood cell DNA is increasingly being used in studies of cancer susceptibility. However, little is known about the correlation between different assays to measure global methylation and whether the source of DNA matters when examining methylation profiles in different blood cell types. Using information from 620 women, 217 and 403 women with DNA available from granulocytes (Gran) and total white blood cells (WBC), respectively, and 48 women with DNA available from four different sources [WBC, Gran, mononuclear (MN) and lymphoblastoid cell lines (LCL)], we compared DNA methylation for three repetitive elements (LINE1, Sat2, Alu) by MethyLight, luminometric methylation assay (LUMA) and [3H]-methyl acceptance assay. For four of the five assays, DNA methylation levels measured in Gran were not correlated with methylation in LCL, MN or WBC; the exception was Sat2. DNA methylation in LCL was correlated with methylation in MN and WBC for the [3H]-methyl acceptance, LINE1 and Alu assays. Methylation in MN was correlated with methylation in WBC for the [3H]-methyl acceptance and LUMA assays. When we compared the five assays to each other by source of DNA, we observed statistically significant correlations ranging from 0.3–0.7 for each cell type with one exception (Sat2 and Alu in MN). Among the 620 women stratified by DNA source, correlations among assays were highest for the three repetitive elements (range 0.39–0.64). Results from the LUMA assay were modestly correlated with LINE1 (0.18–0.20). These results suggest that both assay and source of DNA are critical components in the interpretation of global DNA methylation patterns from WBC.
doi:10.4161/epi.6.1.13391
PMCID: PMC3052916  PMID: 20890131
[3H]-methyl acceptance assay; Alu; DNA demethylation; epigenetics; LINE1; LUMA; methylight; Sat2
23.  DNA methylation in white blood cells 
Epigenetics  2011;6(7):828-837.
Alterations in DNA methylation patterns, both at specific loci and overall in the genome, have been associated with many different health outcomes. In cancer and other diseases, most of these changes have been observed at the tissue level. Data on whether DNA methylation changes in white blood cells (WBC) can serve as a useful biomarker for different health outcomes are much more limited, but rapidly emerging. Epidemiologic studies have reported associations between global WBC methylation and several different cancers including cancers of the colon, bladder, stomach, breast, and head and neck, as well as schizophrenia and myelodysplastic syndrome. Evidence for WBC methylation at specific loci and disease risk is more limited, but increasing. Differences in WBC DNA methylation by selected risk factors including demographic (age, gender, race), environmental exposures (benzene, persistent organic pollutants, lead, arsenic and air pollution), and other risk factors (cigarette smoke, alcohol drinking, body size, physical activity and diet) have been observed in epidemiologic studies though the patterns are far from consistent. Challenges in inferences from the existing data are primarily due to the cross-sectional fashion and small size of most studies performed to date, as well as to the differences in results across assay type and source of DNA. Large, prospective studies will be needed to understand whether changes in risk factors are associated with changes in DNA methylation patterns, and if changes in DNA methylation patterns are associated with changes in disease endpoints.
doi:10.4161/epi.6.7.16500
PMCID: PMC3154425  PMID: 21636973
white blood cells; DNA methylation; global; gene-specific; risk factors; epidemiology
24.  Heat shock-triggered Ca2+ mobilization accompanied by pectin methylesterase activity and cytosolic Ca2+ oscillation are crucial for plant thermotolerance 
Plant Signaling & Behavior  2010;5(10):1252-1256.
Apoplastic Ca2+ concentration controls membrane permeability, cell wall stabilization and cell integrity; however, little is known about its role in thermotolerance in plants. Here, we report that the acquired thermotolerance of etiolated rice seedlings (Oryza sativa) was abolished by an exogenously supplied Ca2+ chelator, EGTA, related to increased cellular content leakage during heat shock (HS) treatment. Thermotolerance was restored by the addition of Ca2+ during EGTA incubation. Pectin methylesterase (EC 3.1.1.11), a cell-wall remodeling enzyme, was activated in response to HS and its elevated activity was related to the recovery of the HS-released Ca2+ concentration. EGTA interfered with the capability of HS to increase oscillation of [Ca2+]cyt content. We assume that heat-activated PME activity is involved in cell-wall localized Ca2+. The removal of apoplastic Ca2+ might participate in HS signaling to induce HS protein expression and cell-wall remodeling to retain plasma membrane integrity, prevent cellular content leakage and confer thermoprotection.
doi:10.4161/psb.5.10.12607
PMCID: PMC3115360  PMID: 20948293
Ca2+; cell wall; EGTA; HSP; HSR; pectin methylesterase; thermotolerance
25.  Multiple genetic variants in telomere pathway genes and breast cancer risk 
Purpose
To explore the etiologic role of genetic variants in telomere pathway genes and breast cancer risk.
Methods
A population-based case-control study — the Long Island Breast Cancer Study Project (LIBCSP) was conducted, and 1,067 cases and 1,110 controls were included in the present study. Fifty-two genetic variants of nine telomere related genes were genotyped.
Results
There were a total of seven single nucleotide polymorphisms (SNPs) showing significant case-control differences at the level p<0.05. The top three statistically significant SNPs under a dominant model were TERT-07 (rs2736109), TERT-54 (rs3816659) and POT1-03 (rs33964002). The ORs were 1.56 (95%CI: 1.22-1.99) for TERT-07 G-allele, 1.27 (95%CI: 1.05-1.52) for TERT-54 T-allele and 0.79 (95%CI: 0.67-0.95) for POT1-03 A-allele. TERT-67 (rs2853669) was statistically significant under a recessive model; the OR of the CC genotype was 0.69 (95%CI: 0.69-0.93) compared with the T-allele. However, none of the SNPs retained significance after Bonferroni adjustment for multiple testing at the level of p<0.001 (0.05/52) except for TERT-07. When restricted to Caucasians (94% of the study subjects), a stronger association for the TERT-07 G-allele was observed with an OR of 1.60 (95%CI: 1.24-2.05, p=0.0002). No effect modifications were found for variant alleles and menopausal status, telomere length, cigarette smoking, BMI status and family history on breast cancer risk.
Conclusions
Four SNPs in TERT and POT1 genes were significantly related with overall breast cancer risk. This initial analysis provides valuable clues for further exploration of the biological role of telomere pathway genes in breast cancer.
doi:10.1158/1055-9965.EPI-09-0771
PMCID: PMC2805470  PMID: 20056641
Genetic variants; telomere; breast cancer

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