Hypomethylation of glycine dehydrogenase promoter in peripheral blood mononuclear cells is a new diagnostic marker of hepatitis B virus-associated hepatocellular carcinoma

Background: Glycine dehydrogenase(GLDC) plays an important role in the initiation and proliferation of several human cancers. In this study, we aimed to detect the methylation status of GLDC promoter and its diagnostic value for hepatitis B virus-associated hepatocellular carcinoma(HBV-HCC). Methods: We enrolled 197 patients, 111 with HBV-HCC, 51 with chronic hepatitis B(CHB), and 35 healthy controls(HCs). The methylation status of GLDC promoter in peripheral mononuclear cells(PBMCs) was identified by methylation specific polymerase chain reaction(MSP). The mRNA expression was examined using real-time quantitative polymerase chain reaction(q PCR). Results: The methylation frequency of the GLDC promoter was significantly lower in HBV-HCC patients(27.0%) compared to that in CHB patients(68.6%) and HCs(74.3%)( P < 0.001). The methylated group had lower alanine aminotransferase level( P = 0.035) and lower rates of tumor node metastasis(TNM) Ⅲ/Ⅳ( P = 0.043) and T3/T4( P = 0.026). TNM stage was identified to be an independent factor for GLDC promoter methylation. GLDC mRNA levels in CHB patients and HCs were significantly lower than those in HBV-HCC patients( P = 0.022 and P < 0.001, respectively). GLDC mRNA levels were significantly higher in HBV-HCC patients with unmethylated GLDC promoters than those with methylated GLDC promoters( P = 0.003). The diagnostic accuracy of alpha-fetoprotein(AFP) combined with GLDC promoter methylation for HBV-HCC was improved compared with that of AFP alone(AUC: 0.782 vs. 0.630, P < 0.001). In addition, GLDC promoter methylation was an independent predictor for overall survival of HBV-HCC patients( P = 0.038). Conclusions: The methylation frequency of GLDC promoter was lower in PBMCs from HBV-HCC patients than that from patients with CHB and HCs. The combination of AFP and GLDC promoter hypomethylation significantly improved the diagnostic accuracy of HBV-HCC.

Methylation of Dickkopf-3 as a prognostic factor in cirrhosis-related hepatocellular carcinoma

AIM:To investigate the prevalence and time of Dickkopf(DKK) family methylation and its clinical significance in hepatocarcinogenesis. METHODS:Methylation of DKK family genes was quantitatively analyzed in 115 liver tissue samples,including 50 pairs of primary hepatocellular carcinoma(HCC) and matched noncancerous cirrhotic tissue samples,as well as 15 liver cirrhosis biopsy samples. RESULTS:The methylation level of DKK3 was significantly higher in HCC tissue samples than in matched noncancerous cirrhotic tissue samples(P<0.0001) orin liver cirrhosis biopsy samples(P=0.0139) .Receiver operator characteristic curve analysis confirmed that the percent of methylated reference(PMR) values of DKK3 could effectively discriminate HCC tissue samples from noncancerous tissue samples(AUC=0.8146) or liver cirrhosis biopsy samples(AUC=0.7093) .Kaplan-Meier survival curves revealed that the progression-free survival time of patients with a higher DKK3 methylation level(PMR >1%) was significantly shorter than that of those with a lower DKK3 methylation level(PMR≤1%)(P=0.0255) . Multivariate Cox analysis indicated that methylated DKK3 was significantly and independently related with a shorter survival time(relative risk=2.527,95%CI:1.063-6.008,P=0.036) of HCC patients. CONCLUSION:Methylation of DKK3 is an important event in early malignant transformation and HCC progression,and therefore might be a prognostic indicator for risk assessment of HCC.

Blood DNA methylation markers in prospectively identifiedhepatocellular carcinoma cases and controls from Taiwan

AIM: To determine if gene-specific DNA methylation in prospectively collected blood samples is associated with later development of hepatocellular carcinoma(HCC).METHODS: Comparing genome-wide DNA methylation profiles using Illumina Human methylation 450 K arrays, we previously identified a list of loci that were differentially methylated between tumor and adjacent nontumor tissues. To examine if dysregulation of DNAmethylation patterns observed in tumor tissues can be detected in white blood cell(WBC) DNA, we conducted a prospective case-control study nested within a community-based cancer screening cohort in Taiwan with 16 years of follow up. We measured methylation levels in ninety-six loci that were aberrant in DNA methylation in HCC tumor tissues compared to adjacent tissues. Baseline WBC DNA from 159 HCC cases and 312 matched controls were bisulfite treated and assayed by Illumina Bead Array. We used the χ2 test for categorical variables and student's t-test for continuous variables to assess the difference in selected characteristics between cases and controls. To estimate associations with HCC risk, we used conditional logistic regression models stratified on the matching factors to calculate odds ratios(OR) and 95%CI. RESULTS: We found that high methylation level in cg10272601 in WNK2 was associated with increased risk of HCC, with an OR of 1.91(95%CI: 1.27-2.86). High methylation levels in both cg12680131 in TPO and cg22511877 in MYT1 L, however, were associated with decreased risk. The ORs(95%CI) were 0.59(0.39-0.87) and 0.50(0.33-0.77), respectively, for those with methylation levels of cg12680131 and cg22511877 above the median compared with those with levels below the median. These associations were still statistically significant in multivariable conditional logistic regression models after adjusting for hepatitis B virus infection and alcohol consumption. CONCLUSION: These findings support the measurement of methylation markers in WBC DNA as biomarkers of HCC susceptibility but should be replicated in additional prospective studies.

Association between Ras association domain family 1A promoter methylation and hepatocellular carcinoma: A meta-analysis

AIM:To assess diagnostic accuracy of Ras association domain family 1A(RASSF1A)promoter methylation in body fluids(serum,plasma and whole blood)for hepatocellular carcinoma(HCC).METHODS:Relative information about study characteristics and incidence of RASSF1A methylation was collected.Quality of all included studies was evaluated by Quality Assessment of Diagnostic Accuracy Studies-2.Sensitivity and specificity were pooled using a randomeffect model,and a summary receiver operating characteristic curve was used to demonstrate the overall diagnostic performance.Positive likelihood ratio(PLR),negative likelihood ratio(NLR),and diagnostic odds ratio(DOR)with 95%CI were also calculated.Meta-regression was applied to analyze observed heterogeneity,and Deeks’test was performed to detect publication bias.RESULTS:After a systematic literature review,seven studies with a total of 302 cases of HCC and 250 cases of chronic liver diseases were included in the analysis.The pooled sensitivity and specificity were 0.70(95%CI:0.49-0.85)and 0.72(95%CI:0.54-0.85),respectively.The PLR was 2.51(95%CI:1.64-3.86),NLR was 0.41(95%CI:0.25-0.68),and DOR was 6.13(95%CI:3.17-11.84).Theχ2values of sensitivity,specificity,PLR,NLR and DOR were 59.41(P<0.001),50.50(P<0.001),17.40(P=0.010),31.24(P<0.001)and80.51(P<0.001),respectively.The area under the curve was 0.77(95%CI:0.73-0.81).Three factors were analyzed by univariate meta-regression and none was significant to interpret the observed heterogeneity(P>0.05).No significant publication bias was detected by Deeks’test(P=0.346).CONCLUSION:We showed the potential diagnostic value of RASSF1A methylation in body fluids in HCC patients and it may improve diagnostic accuracy combined with theα-fetoprotein test.

Promoter methylation and mRNA expression of DKK-3 and WIF-1 in hepatocellular carcinoma

AIM:To investigate the promoter methylation status and mRNA expression of DKK-3 and WIF-1 gene in hepatocellular carcinoma(HCC).METHODS:DKK-3 and WIF-1 acted as Wnt-antagonists and tumor suppressors,but hypermethylation of the gene promoter and low mRNA expression activated Wnt signaling aberrantly and induced the development of HCC.Methylation status of the DKK-3 and WIF-1 gene promoter was investigated using methylation specific polymerase chain reaction(PCR) in tumor and adjacent non-cancerous tissues from 33 HCC patients and 20 normal liver tissues served as control.The expression of DKK-3 and WIF-1 mRNA was also determined by real-time quantitative reverse transcriptase PCR.The relationship between methylation,mRNA expression,and clinical data,as well as methylation and mRNA expression of the two genes were analyzed.RESULTS:The methylation of DKK-3 and WIF-1 genes in HCC increased significantly compared with adjacent non-cancerous tissues and normal control tissues(χ2 =7.79,P < 0.05;χ2 = 4.89,P < 0.05),and no significant difference in methylation between adjacent non-cancerous tissues and normal control tissues was observed.In HCC tissues,significant differences in the DKK-3 promoter methylation were observed in age and cirrhosis,and significant differences of the WIF-1 promoter methylation were observed in HBsAg and cirrhosis.The average expression of DKK-3 mRNA in HCC and adjacent non-cancerous tissues was increased significantly compared with normal control tissues.The average expression of WIF-1 mRNA showed no significant difference among the three tissues.The mRNA expression of DKK-3 gene in HCC was decreased as the pathological grade increased.CONCLUSION:The aberrant promoter methylation and decreased expression of DKK-3 and WIF-1 may be an important mechanism in HCC,and may be a far-reaching significance in early diagnosis and therapy of HCC.

DNA methylation,microRNAs,and their crosstalk as potential biomarkers in hepatocellular carcinoma

Epigenetic alterations have been identified as a major characteristic in human cancers.Advances in the field of epigenetics have contributed significantly in refining our knowledge of molecular mechanisms underlying malignant transformation.DNA methylation and microRNA expression are epigenetic mechanisms that are widely altered in human cancers including hepatocellular carcinoma(HCC),the third leading cause of cancer related mortality worldwide.Both DNA methylation and microRNA expression patterns are regulated in developmental stage specific-,cell type specific-and tissue-specific manner.The aberrations are inferred in the maintenance of cancer stem cells and in clonal cell evolution during carcinogenesis.The availability of genome-wide technologies for DNA methylation and microRNA profiling has revolutionized the field of epigenetics and led to the discovery of a number of epigenetically silenced microRNAs in cancerous cells and primary tissues.Dysregulation of these microRNAs affects several key signalling pathways in hepatocarcinogenesis suggesting that modulation of DNA methylation and/or microRNA expression can serve as new therapeutic targets for HCC.Accumulative evidence shows that aberrant DNA methylation of certain microRNA genes is an event specifically found in HCC which correlates with unfavorable outcomes.Therefore,it can potentially serve as a biomarker for detection as well as for prognosis,monitoring and predicting therapeutic responses in HCC.

DNA methylation in hepatocellular carcinoma

As for many other tumors,development of hepatocellular carcinoma(HCC)must be understood as a multistep process with accumulation of genetic and epigenetic alterations in regulatory genes,leading to activation of oncogenes and inactivation or loss of tumor suppressor genes(TSG).In the last decades,in addition to genetic alterations,epigenetic inactivation of(tumor suppressor) genes by promoter hypermet hylation has been recognized as an important and alternative mechanism in tumorigenesis.In HCC,aberrant methylation of promoter sequences occurs not only in advanced tumors, it has been also observed in premalignant conditions just as chronic viral hepatitis B or C and cirrhotic liver. This review discusses the epigenetic alterations in hepatocellular carcinoma focusing DNA methylation.

MT1M and MT1G promoter methylation as biomarkers for hepatocellular carcinoma

AIM:To investigate the potential of promoter methylation of two tumor suppressor genes(TSGs)as biomarkers for hepatocellular carcinoma(HCC).METHODS:A total of 189 subjects were included in this retrospective cohort,which contained 121 HCC patients without any history of curative treatment,37 patients with chronic hepatitis B(CHB),and 31 normal controls(NCs).DNA samples were extracted from 400μL of serum of each subject and then modified using bisulfite treatment.Methylation of the promoters of the TSGs(metallothionein1M,MT1M;and metallothionein 1G,MT1G)was determined using methylation-specific polymerase chain reaction.The diagnostic value of combined MT1M and MT1G promoter methylation was evaluated using the area under the receiver operating characteristic curves.RESULTS:Our results indicated that the methylation status of serum MT1M(48.8%,59/121)and MT1G(70.2%,85/121)promoters in the HCC group was significantly higher than that in the CHB group(MT1M 5.4%,2/37,P<0.001;MT1G 16.2%,6/37,P<0.001)and NC group(MT1M 6.5%,2/31,P<0.001;MT1G 12.9%,4/27,P<0.001).Aberrant serum MT1M promoter methylation gave higher specificity to discriminate HCC from CHB(94.6%)and NCs(93.5%),whereas combined methylation of serum MT1M and MT1G promoters showed higher diagnostic sensitivity(90.9%),suggesting that they are potential markers for noninvasive detection of HCC.Furthermore,MT1M promoter methylation was positively correlated with tumor size(rs=0.321,P<0.001),and HCC patients with both MT1M and MT1G promoter methylation tended to show a higher incidence of vascular invasion or metastasis(P=0.018).CONCLUSION:MT1M and MT1G promoter methylation may be used as serum biomarkers for noninvasive detection of HCC.

Hypomethylation of Thyroid Peroxidase as a Biomarker for Hepatocellular Carcinoma with Tumor Thrombosis

Objective Thyroid hormones(THs)regulate multiple physiological activities in the liver,including cellular metabolism,differentiation,and cell growth,and play important roles in the pathogenesis of hepatocellular carcinoma(HCC).Thyroid peroxidase(TPO)is a key molecule involved in the THs synthesis and signaling pathway.As an epigenetic modification,DNA methylation has a critical role in tumorigenesis with diagnostic potential.However,the connection between THs and DNA methylation has been rarely investigated.Methods The methylation of key TH-related genes was analyzed by in-house epigenome-wide scanning,and we further analyzed the methylation levels of the TPO promotor in 164 sample pairs of HCC and adjacent non-cancerous tissues by Sequenom EpiTYPER assays,and evaluated their clinical implications.Results We identified that the methylation of the TPO promoter was downregulated in the HCC tissues(P<0.0001)with a mean difference ranging from 18.5%to 22.3%.This methylation pattern correlated with several clinical factors,including a multi-satellite tumor,fibrous capsule,and the presence of tumor thrombus.The receiver operator characteristic(ROC)curve analysis further confirmed that the percent methylated reference(PMR)values for TPO were predictive of the tumor[the area under the curve(AUC)ranged from 0.755 to 0.818]and the thrombosis in the HCC patients(the AUC ranged from 0.706 to 0.777).Conclusion These findings demonstrated that epigenetic alterations of TPO,as indicated by the PMR values,were a potential biomarker for HCC patients with tumor thrombosis.

Aberrant methylation of SPARC in human hepatocellular carcinoma and its clinical implication

AIM:To investigate the methylation status of secreted protein acidic and rich in cysteine(SPARC) in human hepatocellular carcinoma(HCC) and evaluate its clinical implication.METHODS:The methylation status of SPARC was analyzed in one HCC cell line(SMMC-7721) and 60 pairs of HCC and corresponding nontumorous tissues by methylation-specific polymerase chain reaction and bisulfite sequencing.The expression of SPARC mRNA and protein were examined by reverse transcription polymerase chain reaction and immunohistochemistry,respectively.The correlations between the methylation status and the gene expression,the clinicopathological parameters,as well as the prognosis after surgery were analyzed.RESULTS:In the SMMC-7721 cell line,the loss of SPARC expression was correlated with the aberrant methylation and could be reactivated by the demethylating agent 5-aza-2'-deoxycytidine.Methylation frequency of SPARC in HCC was significantly higher than that in the corresponding nontumorous tissues(45/60 vs 7/60,P < 0.001),and it was correlated with the pathological classification(P = 0.019).The downregulation of the SPARC mRNA expression in HCC was correlated with the SPARC methylation(P = 0.040).The patients with methylated SPARC had a poorer overall survival than those without methylated SPARC(28.0 mo vs 41.0 mo,P = 0.043).CONCLUSION:Aberrant methylation is an important mechanism for SPARC inactivation in HCC and SPARC methylation may be a promising biomarker for the diagnosis and prognosis of HCC.

Diagnosis of Hepatocellular Carcinoma by Using Methylation Specific-PCR

To find a more sensitive and earlier diagnostic marker for hepatocellular carcinoma, methylation-profils of CpG islands in the promoter of eleven genes in hepatocellular carcinoma（HCC） carcinoma and pericarcinoma tissues from ten patients were examined by using methylation-specific PCR （MSP） method. MSP was used to detect the methylation of p16, p53, Secreted frizzled-related protein 1 （SFRP 1） and SFRP2 promoters. Meanwhile, plasma alpha-fetoprotein （AFP） levels in 53 patients were also determined. The results showed that HCC was closely correlated to methylation in promoter of tumor-suppressing gene p16, p53, SFRP1 and SFRP2. The results suggest that methylation of SFRP2 promoter is possible a better marker for diagnosis of HCC than plasma Alpha-fetoprotein （AFP） levels. The false negative of SFRP1 and SFRP2 are perfectly complementary. If SFRP1 and SFRP2 were both considered as a complementary positive marker at the same time, the accurate rate for diagnosis of HCC is 100%.

Prognostic potential of the small GTPase Ran and its methylation in hepatocellular carcinoma

Background: Hepatocellular carcinoma(HCC) is a common malignant tumor with high mortality. The prognostic significance of Ran, a member of Ras superfamily, remains unclear in HCC patients. Methods: Based on The Cancer Genome Atlas(TCGA) database and Tumor Immune Estimation Resource(TIMER), we analyzed the correlations among Ran expression, promoter methylation and immune cell infiltration. We also investigated the Ran expression levels in HCC tissues and normal tissues by using quantitative real-time PCR. Results: Ran m RNA expression was significantly increased in HCC tissues compared with the normal tissues( P < 0.001). Time-dependent receiver operating characteristic(ROC) curves showed that Ran expression had predictive value of the 1-, 3-and 5-year overall survival for HCC patients, and the areas under the curves(AUC) were 0.747, 0.634 and 0.704, respectively. Cox regression analysis showed that Ran expression was an independent prognostic factor for HCC patients(HR = 1.492, 95% CI: 1.129-1.971, P = 0.005). We also found a negative relationship between Ran m RNA expression and its promoter methylation( r =-0.36, P < 0.001). High Ran expression and promoter hypomethylation predicted worse overall survival and progression-free survival( P < 0.05) and were involved in the progression of HCC. Ran expression exhibited significant correlations with immune infiltrates and prognostic immune-related genes. Conclusions: The present study provides further insight into the prognosis of HCC, and Ran could serve as a biomarker for predicting the survival of HCC patients.

Global hypomethylation in hepatocellular carcinoma and its relationship to aflatoxin B_1 exposure

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 B 1 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 B 1 albumin(AFB 1-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.AFB 1 exposure is associated with DNA global hypomethylation,suggesting that chemical carcinogens may influence epigenetic changes in humans.

Aberrant methylation and downregulation of sall3 in human hepatocellular carcinoma

AIM: To investigated whether sall3 transcription was regulated by promoter CpG island hypermethylation in hepatocellular carcinoma (HCC). METHODS: The cell lines Huh7, HepG2, SK-HEP1, SM-MC7721, Bel7402, QGY7703 and a cohort of 38 HCC tissue specimens and corresponding nontumorous tissues were subjected to analysis for sall3 promoter CpG island methylation and mRNA transcription. sall3 promoter CpG island methylation levels were determined using the MassARRAY platform and mRNA transcription levels of the gene were detected by quantitative realtime polymerase chain reaction.RESULTS: The levels of sall3 mRNA were decreased by more than twofold in 33 of 38 tumor tissues compared to adjacent noncancerous tissues. Among these 33 tumor tissues with lower levels of sall3 mRNA, 24 showed higher levels of methylation. Based on these results, we hypothesized that the decrease in sall3 mRNA transcription level was likely due to promoter CpG island hypermethylation. Changes in sall3 mRNA transcription and promoter CpG island methylation were determined in the above six cell lines after treatment with 0, 0.1, 0.5 and 2.5 mmol 5-aza-2-deoxycytidine, a demethylating agent. Promoter CpG island methylation levels de- creased in a dose-dependent manner in all six cell lines, while the mRNA transcription level increased dose-dependently in Huh7, HepG2, SK-HEP1 and SMMC7721 cells and irregularly in Bel7402 and QGY7703 cells. CONCLUSION: These results indicated that promoter CpG island hypermethylation contributes to the downregulation of sall3 mRNA transcription in HCC.

Integrating transcriptomes and somatic mutations to identify RNA methylation regulators as a prognostic marker in hepatocellular carcinoma

Background:RNA methylation modifying plays an important role in the occurrence and progression of a range of human cancers including hepatocellular carcinoma(HCC),which is characterized by a mass of genetic and epigenetic alterations.However,the treatment targeting these alterations is limited.Methods:We used comprehensive bioinformatics analysis to analyze the correlation between cancerassociated RNA methylation regulators and HCC malignant features in network datasets.Results:We identified two HCC subgroups(cluster 1 and 2),which had clearly distinct clinicopathological,biofunctional and prognostic characteristics,by consensus clustering.The cluster 2 subgroup correlated with malignancy of the primary tumor,higher tumor stage,higher histopathological grade and higher frequency of TP53 mutation,as well as with shorter survival when compared with cluster 1.Gene enrichment indicated that the cluster 2 correlated to the tumor malignancy signaling and biological processes.Based on these findings,an 11-gene risk signature was built,which not only was an independent prognostic marker but also had an excellent power to predict the tumor features.Conclusions:Our study indicated that RNA methylation regulators are vital for HCC malignant progression and provide an important evidence for RNA methylation,methylation regulators are actionable targets for anticancer drug discovery.

RASSF1A methylation as a biomarker for detection of colorectal cancer and hepatocellular carcinoma

BACKGROUND Studies have validated the potential of methylated cell-free DNA as a biomarker in various tumors,and methylated DNA in plasma may be a potential biomarker for cancer.AIM To evaluate the diagnostic value of RASSF1A methylation in plasma for colorectal cancer(CRC)and hepatocellular carcinoma(HCC).METHODS A total of 92 CRC patients,67 colorectal polyp(CRP)patients,63 HCC patients,and 66 liver cirrhosis(LC)patients were enrolled.The plasma DNA was subjected to DNA extraction,double-strand DNA concentration determination,bisulfite conversion,purification,single-strand DNA concentration determination,and digital polymerase chain reaction(PCR)detection.The methylation rate was calculated.The diagnostic value was evaluated by the area under the curve(AUC).RESULTS The age and sex in the CRC and CRP groups and the HCC and LC groups were also matched.The DNA methylation rate of RASSF1A in plasma in the CRC group was 2.87±1.80,and that in the CRP group was 1.50±0.64.DNA methylation of RASSF1A in plasma showed a significant difference between the CRC and CRP groups.The AUC of RASSF1A methylation for discriminating the CRC and CRP groups was 0.82(0.76-0.88).The AUCs of T1,T2,T3 and T4 CRC and CRP were 0.83(0.72-0.95),0.87(0.78-0.95),0.86(0.77-0.95),and 0.75(0.64-0.85),respectively.The DNA methylation rate of RASSF1A in plasma in the HCC group was 4.45±2.93,and that in the LC group was 2.46±2.07.DNA methylation of RASSF1A in plasma for the HCC and LC groups showed a significant difference.The AUC of RASSF1A methylation for discriminating the HCC and LC groups was 0.70(0.60-0.79).The AUCs of T1,T2,T3 and T4 HCC and LC were 0.80(0.61,1.00),0.74(0.59-0.88),0.60(0.42-0.79),and 0.68(0.53-0.82),respectively.CONCLUSION RASSF1A methylation in plasma detected by digital PCR may be a potential biomarker for CRC and HCC.

Study on MXR7 methylation in hepatocellular carcinoma

Objective:To obtain information at the molecular level on the possible mechanism of MXR7 gene overexpressed in hepatocellular carcinoma (HCC) and also to provide a clue for further study. Methods:Genomic DNA was isolated from 20 samples of hepatoma and paired non-HCC liver tissues, 2 cases of blood tumor and two types of cells (HepG2, MCF-7) and digested with two kinds of endonucleases (EcoR Ⅰ and EagⅠwhich is methylation sensitive endonuclease). And the condition of MXR7 gene methylation was examined and analyzed by Southern blot. Results: MXR7 was unmethylated neither in tested tumorous liver samples nor in paired non-HCC liver tissues. In addition, the same result was found in 2 blood tumor samples and HepG2. Only two paired samples had different methylation outcome, one was unmethylated and the other was partly methylated. Conclusion: MXR7 is unmethylated in HHC, suggesting methylation of MXR7 may have no relation with its expression and regulation.

Bioinformatics analysis of aberrantly methylated-differentially expressed genes and pathways in hepatocellular carcinoma

AIM To discover methylated-differentially expressed genes(MDEGs) in hepatocellular carcinoma(HCC) and to explore relevant hub genes and potential pathways. METHODS The data of expression profiling GSE25097 and methylation profiling GSE57956 were gained from GEO Datasets. We analyzed the differentially methylated genes and differentially expressed genes online using GEO2 R. Functional and enrichment analyses of MDEGs were conducted using the DAVID database. A protein-protein interaction(PPI) network was performed by STRING and then visualized in Cytoscape. Hub genes were ranked by cytoH ubba, and a module analysis of the PPI network was conducted by MCODE in Cytoscape software. RESULTS In total, we categorized 266 genes as hypermethylated, lowly expressed genes(Hyper-LGs) referring to endogenous and hormone stimulus, cell surface receptor linked signal transduction and behavior. In addition, 161 genes were labelled as hypomethylated, highly expressed genes(Hypo-HGs) referring to DNA replication and metabolic process, cell cycle and division. Pathway analysis illustrated that Hyper-LGs were enriched in cancer, Wnt, and chemokine signalling pathways, while Hypo-HGs were related to cell cycle and steroid hormone biosynthesis pathways. Based on PPI networks, PTGS2, PIK3 CD, CXCL1, ESR1, and MMP2 were identified as hub genes for Hyper-LGs, and CDC45, DTL, AURKB, CDKN3, MCM2, and MCM10 were hub genes for Hypo-HGs by combining six ranked methods of cytoH ubba. CONCLUSION In the study, we disclose numerous novel genetic and epigenetic regulations and offer a vital molecular groundwork to understand the pathogenesis of HCC. Hub genes, including PTGS2, PIK3 CD, CXCL1, ESR1, MMP2, CDC45, DTL, AURKB, CDKN3, MCM2, and MCM10, can be used as biomarkers based on aberrant methylation for the accurate diagnosis and treatment of HCC.

Relation among p130Cas,E-cadherin and β-catenin expression,clinicopathologic significance and prognosis in human hepatocellular carcinoma

BACKGROUND:p130Cas(p130Crk-associated substance) is a junction protein that is important to the adhesion between cytoskeleton and extracellular matrix.Also the adhesion molecules E-cadherin andβ-catenin play important roles in the invasiveness of carcinoma.This study was undertaken to investigate the effects of p130Cas E-cadherin andβ-catenin on the invasion,metastasis and prognosis of hepatocellular carcinoma(HCC). METHODS:Immunohistochemistry was used to evaluate the expression of p130Cas,E-cadherin,andβ-catenin in 40 patients with HCC.All patients were followed up postoperatively,and the relationship between expression and clinicopathological prognostic parameters was analyzed RESULTS:The positive expression rates of p130Cas and E-cadherin in HCC tissue(n=40)were 62.50%and 55.00% but in normal liver tissue 10%,and 100%,respectively (P<0.05).The abnormal expression rate ofβ-catenin in HCC tissue was 70%,while in normal liver tissue it was 13.33%(P<0.05).The positive rate of p130Cas was correlated with lymph node invasion,pathological stage TNM stage,and a worse prognosis,but not with gender age,HBV infection,hepatic cirrhosis,alpha-fetoprotein (AFP)level before operation,and tumor diameter Similarly,the expression of E-cadherin andβ-catenin was correlated with lymph node invasion,pathological stage,TNM stage,and worse prognosis,but not with gender,age,HBV infection,hepatic cirrhosis,AFP level before operation,and tumor size.Correlations were found between p130Cas and abnormal E-cadherin/β-catenin expression(P<0.001 and<0.05,respectively).CONCLUSIONS:In HCC,there is a negative correlation between the positive expression of p130Cas and the normal expression of the adhesion molecules E-cadherin/β-catenin, and p130Cas plays important roles in the invasion, metastasis and prognosis of HCC.p130Cas may be involved in alterating the structure and function of E-cadherin/ β-catenin,by regulating tyrosine phosphorylation via the p130Cas-Src signal pathway.

No association exists between E-cadherin gene polymorphism and tumor recurrence in patients with hepatocellular carcinoma after transplantation

BACKGROUND: E-cadherin is an epithelial cell adhesion molecule, and decreased E-cadherin expression in liver cancer is associated with poor prognosis. A -160 C -> A polymorphism in the promoter region of E-cadherin has been reported to decrease gene transcription. This allelic variation may be a potential genetic marker for identifying those individuals at higher risk for invasive/metastatic disease. METHODS: The effect of E-cadherin gene polymorphism on risk of tumor recurrence was studied in 93 patients with hepatocellular carcinoma (HCC) after liver transplantation, and determined whether this polymorphism is a biomarker for the risk of tumor recurrence. RESULTS: The genotype frequencies in the patients with recurrence were C/C: 0.667, C/A: 0.311, and A/A: 0.022, and in-the patients without recurrence C/C: 0.604, C/A: 0.271 and A/A: 0.125. No significant difference was found between the two groups (P = 0.171). Between -160 C -> A polymorphism and the clinicopathological data, there were no statistically significant differences in the distribution of the parameters as to age, gender, portal vein tumor thrombi, preoperative alpha-fetoprotein level, tumor size, or histopathological grading (P > 0.05). CONCLUSION: The results of this study show no association exists between the E-cadherin genotype and the risk of tumor recurrence in Chinese patients with HCC.