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DNA Methylation and Cancer
Shen-Chih Chang, Ph.D Epi 243 May 14, 2009
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Presentation Outline Epigenetics and DNA methylation
DNA methylation and Cancer Techniques of measuring DNA methylation Methylation-Specific PCR (MSP) Selected results on lung and head and neck cancer MethyLight Taqman real-time Methylation Assay Selected results on bladder cancer Selected results on liver cancer
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Epigenetics The study of heritable changes of DNA, not involving changes in DNA sequence, that regulate gene expression. Classic genetics alone cannot explain the diversity of phenotypes within a population. Identical twins or cloned animals have different phenotypes and susceptibilities to diseases. Epigenetics provides additional instructions on how, where, and when the genetic information should be used. Epigenetics controls gene expression in two main ways: Chemically alteration of DNA: DNA methylation Modification of histones: chromatin structure modulation
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Epigenetic Mechanisms
Qiu J, 2006
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Mapping chromosomal regions with differential DNA methylation in Monozygous twins by using comparative genomic hybridization for methylated DNA Mapping chromosomal regions with differential DNA methylation in MZ twins by using comparative genomic hybridization for methylated DNA. Competitive hybridization onto normal metaphase chromosomes of the AIMS products generated from 3- and 50-year-old twin pairs. Examples of the hybridization of chromosomes 1, 3, 12, and 17 are displayed. The 50-year-old twin pair shows abundant changes in the pattern of DNA methylation observed by the presence of green and red signals that indicate hypermethylation and hypomethylation events, whereas the 3-year-old twins have a very similar distribution of DNA methylation indicated by the presence of the yellow color obtained by equal amounts of the green and red dyes. Significant DNA methylation changes are indicated as thick red and green blocks in the ideograms. Fraga M. F. et.al. PNAS 2005;102: ©2005 by National Academy of Sciences
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DNA Methylation Chemical modification of DNA
Addition of a methyl group to the number 5 carbon of the cytosine, to convert cytosine to 5-methylcytosine. In humans, DNA methylation occurs in a cytosine which is immediately followed by a guanine (dinucleotide CpGs). (The CpG notation is used to distinguish a cytosine followed by guanine from a cytosine base paired to a guanine).
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CpG Sites and CpG islands
CpG sites are not randomly distributed in the genome - the frequency of CpG sites in human genomes is 1%, which is less than the expected (~4-6%). Around 60-90% of CpGs are methylated in mammals. DNA methylation frequently occurs in repeated sequences, and may help to suppress junk DNA and prevent chromosomal instability. Unmethylated CpGs are grouped in clusters called “CpG islands” which tend to be located in the promoter regions of many genes.
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Function of DNA Methylation
In humans, DNA is methylated by three enzymes, DNA methyltransferase 1, 3a, and 3b (DNMT1, DNMT3a, DNMT3b). DNMT3a and 3b are the de novo methyltransferases that set up DNA methylation patterns early in development. DNMT1 is the maintenance methyltransferase that is responsible for copying DNA methylation patterns to the daughter strands during DNA replication. DNA methylation is important in: Transcriptional gene silencing Maintain genome stability Embryonic development Genomic imprinting X chromosome inactivation
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DNA Methylation and Cancer
Hypomethylation – decreased methylation levels A lower level of DNA methylation in tumors as compared to their normal-tissue counterparts was one of the first epigenetic alterations to be found in human cancer. (Feinberg AP, et al., 1983). Global hypomethylation of DNA sequences that are normally heavily methylated may result in Chromosomal instability Increased transcription from transposable elements An elevated mutation rate due to mitotic recombination Promoter hypomethylation of proto-oncogenes will activate the repressed gene expression
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DNA Methylation and Cancer
Hypermethylation – increased methylation levels Promoter hypermethylation can suppress gene expression in two ways: Methylated DNA may itself impede the binding of transcriptional proteins to the gene Methylated DNA may be bound by proteins which can modify histones to form compact, inactive chromatin. Promoter hypermethylation of tumor-suppressor genes is a major event in the origin of many cancers. The profiles of hypermethylation of the CpG islands are specific to the cancer type.
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Baylin et al. 2001; Jones et al. 2002
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Laird PW, 1997
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Das PM 2004
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Das PM 2004
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Factors associated with DNA Methylation
Aging Nutrient intake Genetic polymorphisms Metal exposure Tobacco Smoking Alcohol Drinking
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Application of DNA Methylation Measurement
Early diagnosis – Detection of CpG-island hypermethylation in biological fluids (serum/plasma) Prognosis – Hypemethylation of specific genes Whole DNA methylation profiles Prediction – CpG island hypermethylation as a marker of response to chemotherapy Prevention – Developing DNMTs inhibitors as chemopreventive drugs to reactive silenced genes
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Techniques of Measuring Gene-Specific Hypermethylation
Methylation Specific PCR (MSP) MethyLight Taqman Real-Time Methylation Assay
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Methylation Specific PCR (MSP)
DNA Modification C U CM C Two set of primers Methylated Unmethylated Positive control (Universal Methylated DNA) Negative control (H2O)
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Results from the MSP p16 GSTP1 MGMT
These are the results from the MSP. “+” is the positive control; they should show a band with “M” primer but not with “U” primer. “-” is the negative control; they should not show anything either with “M” nor with “U” primer to make sure that both primers are not containment. As a results, sample 486 is defined to be “Yes” in the p16 hypermethylation whereas sample 487 is defined to be “No”.
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Selected Results on Lung and Head and Neck Cancer
Shu-Chun Chuang, Ph.D Aim: To evaluate the associations between lung and head and neck cancer and promoter-region methylation of selected genes, including P16INK4a, MGMT , and GSTP1 genes in buccal cell DNA in a population-based case-control study in Los Angeles county.
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Materials and Methods Study design: population-based case-control study Subject selection criteria: Cases were newly diagnosed and pathologically confirmed. Controls were matched to cases on age, gender, and neighborhood. Eligibility: Current resident of Los Angeles County 18-65 during the observation period, either speak English or Spanish or have translators available have no other primary cancers (cases) have no history of lung or head and neck cancers (controls) Biological samples: buccal cell samples were collected during the interview This is a population-based case-control study. Cases were newly diagnosed and pathologically confirmed from a Cancer Surveillance Program for the Los Angeles County. Controls were matched to cases on age (within 10 years old), sex, and neighborhood. Cases were current resident of Los Angeles County, years old during the observation period: , either speak English or Spanish or translator available, and no history of lung and head and neck cancers. All participants were interviewed by trained interviewers; ml cell samples were collected after the interview.
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Response Rate The response rate was 68% for control, but it is a little bit lower for cases. In lung cancer cases, the reasons for non-participation were die before we contacted them (25%), unwilling to participate (16%), and incorrect address (14%). In head and neck cancer cases, they are unwilling to participate (21%), incorrect address (18%), die or too ill to participate (14%). The buccal cell response rates are good. Except for oral and pharyngeal cancer cases, the response rates are almost 90%.
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Main Effect of p16 Hypermethylation
Controls N (%) Lung Head and Neck Crude OR (95% CI) Adjusted OR1 Adjusted OR2 No 769 (84) 433 (81) 1.00 293 (84) Yes 146 (16) 100 (19) 1.22 ( ) 1.31 ( ) 57 (16) 1.03 ( ) 1.03 ( ) Adjusted for age, sex, race, and pack-years of smoking. Adjusted for age, sex, race, pack-years of smoking, and drink-years of alcohol consumption
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Main Effect of GSTP1 Hypermethylation
Controls N (%) Lung Head and Neck Crude OR (95% CI) Adjusted OR1 Adjusted OR2 No 675 (88) 354 (85) 1.00 254 (86) Yes 96 (12) 61 (15) 1.21 ( ) 1.17 ( ) 40 (14) 1.11 ( ) 1.04 ( ) Adjusted for age, sex, race, and pack-years of smoking. Adjusted for age, sex, race, pack-years of smoking, and drink-years of alcohol consumption
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Main Effect of MGMT Hypermethylation
Controls N (%) Lung Head and Neck Crude OR (95% CI) Adjusted OR1 Adjusted OR2 No 721 (82) 380 (77) 1.00 250 (76) Yes 157 (18) 112 (23) 1.35 ( ) 1.19 ( ) 78 (24) 1.43 ( ) 1.34 ( ) Adjusted for age, sex, race, and pack-years of smoking. Adjusted for age, sex, race, pack-years of smoking, and drink-years of alcohol consumption Stratified by Site CDH1 is expressed in all epithelial cells acting as an adhesion molecule. Inactivation of CDH1 induces the impairment of cell adhesiveness and proliferation and results in tumor progression. MGMT protects cells from DNA damage cause by mutagenic agents leading to alkylation at O6-guanine. MGMT Hypermethylation Controls N (%) Pharynx Crude OR (95% CI) Adjusted OR No 721 (82) 38 (68) 1.00 Yes 157 (18) 18 (32) 2.18 ( ) 2.00 ( ) Adjusted for age, sex, race, pack-years of smoking, and drink-years of alcohol consumption
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MethyLight Taqman Methylation Assay
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Real-Time PCR Real-time PCR is a PCR-based method using fluorescent molecules to directly measure the reaction while amplification is taking place. Data are collected throughout the PCR process rather than the end of the process. It measures the point in time when amplification of a target is first detected during cycling rather than by the amount of target accumulated at the end of PCR. Can be used to achieve both qualitative and quantitative measurements.
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Traditional Standard PCR
5’ 3’ 5’ 3’ 5’ 3’ 5’ 3’ Denaturation Primer Annealing Elongation Taq 5’ 3’ 5’ 5’ 5’ 3’ Taq Repeat In theory, product accumulation is proportional to 2n, where n is the number of amplification cycle repeats
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However, in reality...
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Limitation in standard PCR
Amplification is exponential, but the exponential increase is limited: Theoretical A linear increase follows exponential Eventually plateaus plateau Real Life linear Log Target DNA Geometric Cycle #
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Standard PCR as endpoint
Identical reactions will have very different final amounts of fluorescence at endpoint
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Real-Time PCR The point at which the fluorescence rises appreciably above threshold is called CT Identical reactions will have identical CT values Threshold CT
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How to measure DNA concentration?
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How to measure DNA concentration?
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Setup for MethyLight MSP
Modified DNA as templates Methylation sequence specific forward and backward primers Taqman Probes: 5’-FAM TEMRA-3’ Taqman Universal PCR Master Mix Negative control contains PCR reagents but without DNA – ddH2O Replicate wells -- using two or more replicate reactions per sample to ensure statistical significance.
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Setup for MethyLight MSP
A calibrator -- The sample used as the basis for comparative results. A universal methylated positive control was used in this study as a calibrator. An endogenous control gene -- A gene present at a consistent expression level in all experimental samples. An endogenous gene is used as an internal control of the difference amount of input DNA. ACTB gene without CpG dinucleotides was used as endogenous control gene in this study.
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Setup for MethyLight MSP
Endogenous control gene; others are all target genes Calibrator Negative control
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Analyzing Relative Quantification Data
∆∆CT Method ∆CT (sample) = CT (marker)- CT (ACTB) ∆CT (calibrator) = CT (marker)- CT (ACTB) ∆∆CT = ∆CT (sample) - ∆CT (calibrator) Relative quantification of methylated 5’-cytosine = E(-∆∆CT) E: efficiency of amplification Assumption: E = 2 for both marker and endogenous gene
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Analyzing Relative Quantification Data -- Amplification Plot (linear plot of reporter signal vs cycle number) -- negative control ACTB gene
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Analyzing Relative Quantification Data -- Amplification plot of positive control--
linear plot of reporter signal vs cycle number logarithmic plot of baseline-corrected reporter signal vs. cycle number
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Analyzing Relative Quantification Data -- Amplification plot of p16 gene hypermethylation--
After adjusting baseline and threshold, software automatically calculates relative quantity (RQ) of the sample compared to the calibrator logarithmic plot of baseline-corrected reporter signal vs. cycle number
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Selected Results on Bladder Cancer
Yu-Ching Kelly Yang, Ph.D Aim: To evaluate the associations between promoter hypermethylation status of genes involved in bladder tumorigenesis (including P16INK4a, P14ARF, APC, CDH1, RASSF1A, MGMT, and GSTP1) in WBC, NBC, CIS, and, cancer tissues from 73 bladder cancer patients.
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Materials and Methods Hospital-based case-only study
Memorial Sloan-Kettering Cancer Center Recruitment period: Oct 1993 to June 1997 Cases selection criteria: Newly diagnosed and pathologically confirmed bladder cancer cases In stable medical condition Have lived in the US for at least one year Fresh bladder tissues were obtained from radical cystectomy This is a population-based case-control study. Cases were newly diagnosed and pathologically confirmed from a Cancer Surveillance Program for the Los Angeles County. Controls were matched to cases on age (within 10 years old), sex, and neighborhood. Cases were current resident of Los Angeles County, years old during the observation period: , either speak English or Spanish or translator available, and no history of lung and head and neck cancers. All participants were interviewed by trained interviewers; ml cell samples were collected after the interview.
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Study Population Patients with tissue blocks N = 152
Only have cancerous tissues N = 33 Did not conform to pathological criteria N = 46 Patients with cancerous tissue and non-cancerous tissue (NBC) N = 73
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Proportion of methylation detected in seven tumor-related genes in white blood cells (WBC), in situ (CIS), non-cancerous (NBC), and cancerous tissue specimens of the bladder cancer patients. WBC CIS NBC Cancer Gene analyzed Methylation detected P16 0/11 0.00 0/6 0/73 21/73 0.29 APC 3/6 0.5 42/73 0.58 MGMT 3/73 0.04 RASSF1A 1/11 0.09 2/6 0.33 10/73 0.14 28/73 0.38 CDH1 2/11 0.18 4/6 0.67 22/73 0.30 45/73 0.62 GSTP1 1/73 0.01 2/73 0.03 ARF WBC:white blood cell; CIS: carcinoma in situ; NBC: epithelium showing no remarkable histological change No DNA methylation of the P14ARF gene was detected in any specimen sample analyzed. Although the CDH1 and RASSF1A genes were methylated even in WBC, methylation of other genes was never detected in WBC samples. All genes except the P14ARF gene were methylated in bladder cancer tissues. The prevalence of DNA methylation of the APC, CDH1, and RASSF1A increased progressively from WBC through NBC to cancer tissues, whereas DNA methylation of the P16INK4A and MGMT were prominent only in cancer tissues and never in NBC.
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The mean and standard deviation of average number of methylated genes in white blood cells (WBC), carcinoma in situ (CIS), epithelium showing no remarkable histological change (NBC) and cancer tissues of bladder cancer patients The average number of methylated genes was higher in NBC, CIS, and cancer tissue than that in WBC (p=0.05, 0.03, and <0.01, respectively). Compared with NBC, the number of methylated genes was higher in cancer tissue (p<0.01). However, there was no obvious difference in the average number of methylated genes between CIS and cancer tissues.
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The association between hypermethylation in promoter-region of tumor-related genes and environmental exposures, including cigarette smoking and alcohol drinking we found a marginal reverse association between cigarette smoking and hypermethylation in the P16INK4A gene
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The association between hypermethylation in promoter-region of six tumor-related gene and clinicopathological factors The prevalence of DNA methylation of at least one gene and the number of methylated genes increased significantly in tumors with vascular invasion than tumors without vascular invasion (p=0.008 and 0.01, respectively). We also found a strong association between vascular invasion and hypermethylation in the CDH1 gene (p=0.032).
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The association between hypermethylation in six tumor-related genes and survival time
No obvious association was found between the favorable patient’s prognoses and the MI
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Selected Results on Liver Cancer
Shen-Chih Chang, Ph.D Aim: To evaluate the associations between HCC and promoter-region methylation of selected genes, including APC, CDH1, P16INK4a, and MGMT genes in peripheral blood DNA in a Chinese population. Also, to examine the associations of hypermethylation with age, gender, tobacco smoking, and alcohol consumption.
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Materials and Methods Population-based case-control study
Taixing, China Recruitment period: Jan 1, 2000 to Jun 30, 2000 Cases selection criteria: Newly diagnosed liver cancer cases Age 25-70 Have no history of any previous diagnosis of cancer Have lived in Taixing for at least 10 years A group of healthy population controls were frequency-matched (on age and gender) to cases with a control-to-case ratio of 2:3 from the general population in Taixing (one common control group to three case groups) Epidemiology data collection Face-to-face interview Blood samples collected during interview This is a population-based case-control study. Cases were newly diagnosed and pathologically confirmed from a Cancer Surveillance Program for the Los Angeles County. Controls were matched to cases on age (within 10 years old), sex, and neighborhood. Cases were current resident of Los Angeles County, years old during the observation period: , either speak English or Spanish or translator available, and no history of lung and head and neck cancers. All participants were interviewed by trained interviewers; ml cell samples were collected after the interview.
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Study Population 358 incident liver cancer cases were diagnosed
204 (57%) recruited 199 blood samples 194 DNA extracted 464 potential controls were identified 415 (90%) recruited 410 blood samples 393 DNA extracted
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Associations between promoter hypermethylation of APC, CDH1, MGMT, and P16 gene and HCC
Case (%) Control (%) Crude OR (95% CI) Adjusted OR1 Adjusted OR2 APC - 181 (95.6) 332 (94.1) 1.00 + 8 (4.2) 21 (6.0) 0.70 (0.30, 1.61) 0.52 (0.19, 1.41) 0.70 (0.24, 2.08) p-value 0.3998 0.1981 0.5233 CDH1 100 (52.9) 173 (49.4) 89 (47.1) 177 (50.6) 0.87 (0.61, 1.24) 0.93 (0.61, 1.42) 1.05 (0.65, 1.68) 0.4406 0.7287 0.8548 MGMT 190 (100.0) 351 (100.0) 0 (0.0) P16 348 (99.4) 2 (0.6) No. of methylated genes None 99 (52.4) 171 (48.9) 1 83 (43.9) 160 (45.7) 0.90 (0.62, 1.29) 0.98 (0.63, 1.51) 1.04 (0.64, 1.69) 2 7 (3.7) 19 (5.4) 0.64 (0.26, 1.57) 0.50 (0.17, 1.47) 0.78 (0.24, 2.59) 1: Adjusted on age, gender, BMI, education, smoking pack-years, alcohol drinking, HBsAg, and plasma AFB1-albumin adducts 2: Further adjusted on plasma levels of folate, vitamin B12, and homocysteine
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Associations between promoter hypermethylation of APC and CDH1 gene and HCC, stratified on plasma folate levels ≦12.76 nM >12.76 nM Case/ Control Crude OR (95% CI) Adjusted OR* APC - 93/169 1.00 84/159 + 2/10 0.36 (0.08, 1.69) 0.20 (0.04, 1.06) 6/11 1.03 (0.37, 2.89) 1.01 (0.26, 3.86) p-value 0.1974 0.0583 0.9513 0.9920 CDH1 48/82 49/89 47/96 0.84 (0.51, 1.38) 0.98 (0.54, 1.77) 41/79 0.94 (0.56, 1.58) 0.82 (0.43, 1.59) 0.4825 0.9412 0.8218 0.5653 APC+CDH1 (continuous) 0.78 (0.50, 1.22) 0.81 (0.48, 1.34) 0.96 (0.63, 1.47) 0.87 (0.50, 1.51) 0.2727 0.4084 0.8646 0.6294 *Adjusted on age, gender, BMI, education, smoking pack-years, alcohol drinking, HBsAg, and plasma AFB1-albumin adducts
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Associations between promoter hypermethylation of APC and CDH1 gene and HCC, stratified on plasma vitamin B12 levels ≦ pM > pM Case/ Control Crude OR (95% CI) Adjusted OR* APC - 33/160 1.00 145/166 + 1/15 0.32 (0.04, 2.53) 0.24 (0.03, 2.04) 7/6 1.34 (0.44, 4.07) 1.62 (0.39, 6.69) p-value 0.2824 0.1922 0.6096 0.5060 CDH1 19/79 80/92 15/94 0.66 (0.32, 1.39) 0.78 (0.33, 1.82) 72/79 1.05 (0.68, 1.62) 1.05 (0.59, 1.85) 0.2773 0.5628 0.8334 0.8726 APC+CDH1 (continuous) 0.64 (0.34, 1.21) 0.68 (0.34, 1.36) 1.07 (0.73, 1.58) 1.10 (0.67, 1.83) 0.1728 0.2781 0.7185 0.7060 *Adjusted on age, gender, BMI, education, smoking pack-years, alcohol drinking, HBsAg, and plasma AFB1-albumin adducts
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Associations between promoter hypermethylation of APC and CDH1 gene and HCC, stratified on plasma homocysteine levels ≦9.50 µM >9.50 µM Case/ Control Crude OR (95% CI) Adjusted OR* APC - 79/168 1.00 100/161 + 4/10 0.85 (0.26, 2.80) 0.95 (0.24, 3.81) 4/11 0.59 (0.18, 1.89) 0.26 (0.05, 1.23) p-value 0.7899 0.9468 0.3706 0.0890 CDH1 44/92 55/79 39/84 0.97 (0.58, 1.64) 1.00 (0.52, 1.92) 49/92 0.77 (0.47, 1.25) 0.75 (0.41, 1.39) 0.9115 0.9938 0.2825 0.3625 APC+CDH1 (continuous) 0.96 (0.61, 1.49) 1.00 (0.58, 1.70) 0.76 (0.50, 1.16) 0.67 (0.39, 1.15) 0.8393 0.9842 0.2020 0.1427 *Adjusted on age, gender, BMI, education, smoking pack-years, alcohol drinking, HBsAg, and plasma AFB1-albumin adducts
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Associations between promoter hypermethylation of APC and CDH1 gene and age, gender, smoking, and alcohol drinking habits in the control group Hypermethylation APC CDH1 No. of methylated genes No (N, %) Yes P* 1 2 Age < 55 124 (37.4) 8 (38.1) 0.95 70 (40.5) 60 (33.9) 0.20 69 (40.4) 54 (33.8) 7 (36.8) 0.46 ≥ 55 208 (62.7) 13 (61.9) 103 (59.5) 117 (66.1) 102 (59.7) 106 (66.3) 12 (63.2) Gender Female 104 (31.3) 6 (28.6) 0.79 54 (31.2) 54 (30.5) 0.89 53 (31.0) 50 (31.3) 5 (26.3) 0.91 Male 228 (68.7) 15 (71.4) 119 (68.8) 123 (69.5) 118 (69.0) 110 (68.8) 14 (73.7) Smoking Never 173 (52.3) 12 (57.1) 0.66 99 (57.6) 84 (47.5) 0.06 97 (57.1) 76 (47.5) 10 (52.6) 0.22 Ever 158 (47.7) 9 (42.9) 73 (42.4) 93 (52.5) 73 (42.9) 84 (52.5) 9 (47.4) Alcohol Drinking 168 (51.1) 0.47 90 (52.6) 85 (48.0) 0.39 88 (52.1) 80 (50.0) 0.45 161 (48.9) 81 (47.4) 92 (52.0) 81 (47.9) *P-value from χ2 tests or Fisher’s exact test
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Compare MSP and MethyLight
Methylation Specific PCR MethyLight Methylation assay Advantage Inexpensive Easy to perform Less prone to human error Faster, more efficient than MSP More specific by adding Taqman probe Disadvantage Prone to human error Easily get contaminated Labor-intensive Higher expenses for equipment maintenance
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Other Techniques Gene-Specific DNA Methylation Global DNA Methylation
Sequencing Microarray High-resolution Melting Method (Roche) BeadChip Technology (Illumina) Global DNA Methylation Liquid Chromatography-Mass Spectrometry ELISA-based global methylation analysis assay (Sigma Aldrich)
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References http://www.appliedbiosystems.com
Eads CA., et al. MethyLight: a high-throughput assay to measure DNA methylation. Nucleic Acids Res., 28: e32, 2000. Esteller M. Epigenetics in cancer. New England Journal of Medicine, 358: , 2008 Qiu J. Epigenetics: unfinished symphony. Nature, 441: , 2006. Zeschniqk M., et al. A novel real-time PCR assay for quantitative analysis of methylated alleles (QAMA): analysis of the retinoblastoma locus. Nucleic Acids Res., 7: 3125, 2004.
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