DNA methylation and hepatocellular carcinoma

Epigenetic alterations caused by aflatoxin b1: a public health risk in the induction of hepatocellular carcinoma

Aflatoxin B1 (AFB1) is currently the most commonly studied mycotoxin due to its great toxicity, its distribution in a wide variety of foods such as grains and cereals and its involvement in the development of + (hepatocellular carcinoma; HCC). HCC is one of the main types of liver cancer, and has become a serious public health problem, due to its high incidence mainly in Southeast Asia and Africa. Studies show that AFB1 acts in synergy with other risk factors such as hepatitis B and C virus leading to the development of HCC through genetic and epigenetic modifications. The genetic modifications begin in the liver through the biomorphic AFB1, the AFB1-exo-8.9-Epoxy active, which interacts with DNA to form adducts of AFB1-DNA. These adducts induce mutation in codon 249, mediated by a transversion of G-T in the p53 tumor suppressor gene, causing HCC. Thus, this review provides an overview of the evidence for AFB1-induced epigenetic alterations and the potential mechanisms involved in the development of HCC, focusing on a critical analysis of the importance of severe legislation in the detection of aflatoxins.

The status of global DNA methylation in the spermatozoa of smokers and non-smokers

RESEARCH QUESTION

Does regular smoking affect semen quality and the levels of DNA methylation in mature human spermatozoa?

DESIGN

Spermatozoa from 109 men were evaluated (55 smokers and 54 non-smokers). DNA was extracted from purified spermatozoa, and DNA methylation was quantified by enzyme-linked immunosorbent assay (ELISA).

RESULTS

Global DNA methylation of non-smokers is significantly lower (P < 0.001) than that of smokers (4.85 ± 2.72 and 7.08 ± 1.77 ng/μl, respectively). Moreover, the mean global DNA methylation levels were significantly correlated (r = 0.22;P = 0.02) with non-condensed chromatin in the spermatozoa. Levels of non-condensed chromatin were significantly higher (P < 0.001) in smokers (29.75 ± 9.38%) compared with non-smokers (20.96 ± 11.31%). Furthermore, global sperm DNA methylation was negatively correlated with high significance (P < 0.010) with sperm: count (r = -0.27), motility (r = -0.30) and vitality (r = -0.26).

CONCLUSION

Smoking interferes with DNA methylation. Also, DNA methylation is significantly correlated with sperm parameters and sperm non-condensed chromatin. These data emphasize another detrimental effect of smoking on male fertility. DNA methylation may, therefore, be considered as a fertility marker in men.

MiR-545-3p/MT1M axis regulates cell proliferation, invasion and migration in hepatocellular carcinoma

Studies have shown that metallothionein 1 M (MT1M) is a tumor suppressor gene which is frequently down-regulated in human hepatocellular carcinoma (HCC). The methylation of MT1M promoter region is one of the important transcriptional regulation mechanisms that contribute to the loss of its expression. In our study, we found that there are still half of the 55 HCC tumor tissues in our cohort do not share the promoter methylation of MT1M. So, we speculated there maybe another mechanism participating in the downregulation of MT1M in HCC. Then, we provided evidences that miR-545-3p, which served as a tumor promoter, post-transcriptionally regulate MT1M in HCC through binding to its untranslated region (3'UTR). Taking together, we investigated the role of miR-545-3p in the process of HCC through regulating MT1M.

Delta-like 3 is silenced by HBx via histone acetylation in HBV-associated HCCs

Hepatocellular carcinoma (HCC) is a common malignant tumor with poor prognosis. We previously showed that expression of Delta-like 3 (DLL3), a member of the family of Delta/Serrate/Lag2 ligands for the Notch receptor, is silenced by aberrant DNA methylation and that overexpression of DLL3 in an HCC cell line induces cellular apoptosis. However, how DLL3 expression is regulated during hepatocarcinogenesis is still unclear. Here, we show that silencing of DLL3 during hepatocarcinogenesis is closely related to viral infection, especially hepatitis B virus (HBV) infection (p = 0.005). HepG2.2.15 cells, which are stably transformed with the HBV genome, showed lower DLL3 expression than the parent cell line, HepG2 cells. Treatment with Hepatitis B virus X protein (HBx) small interfering RNA upregulated DLL3 expression in HepG2.2.15 cells, and overexpression of HBx in HepG2 cells downregulated DLL3 expression. Treatment of cells with a histone deacetylase inhibitor induced DLL3 expression in HepG2.2.15 cells. These data suggest that DLL3 expression is silenced during hepatocarcinogenesis in association with HBV infection via an epigenetic mechanism.

Molecular mechanism of hepatitis B virus (HBV) on suppression of raf kinase inhibitor protein (RKIP) expression

Raf kinase inhibitor protein (RKIP) has been shown to be a suppressor of the mitogen-activated protein kinase pathway and is reported to be involved in human malignancy. However, the molecular mechanism of hepatitis B virus (HBV) in regulating RKIP expression is not yet clarified. In this study, we compared RKIP expression in 107 pairs of matched liver cancer and adjacent non-cancerous liver tissues. Among seven HBV-encoded proteins, we found HBV X (HBX) protein could significantly inhibit the expression level of RKIP, indicating that HBV could suppress RKIP expression through regulating HBX. To further elucidate the mechanism, analyses on transcriptional regulation and promoter methylation inhibition were conducted in Huh7 cells. Our results showed that HBX can interact with AP1 protein to inhibit the RKIP transcription. Moreover, we observed that the promoter methylation level of RKIP could be enhanced by HBV. In conclusion, our study revealed that RKIP could act as a molecular marker for HBV-infected liver cancer, but had no tumor-suppressing effect.

New Insights into the Epigenetics of Hepatocellular Carcinoma

Hepatocellular Carcinoma (HCC) is one of the most predominant malignancies with high fatality rate. This deadly cancer is rising at an alarming rate because it is quite resistant to radio- and chemotherapy. Different epigenetic mechanisms such as histone modifications, DNA methylation, chromatin remodeling, and expression of noncoding RNAs drive the cell proliferation, invasion, metastasis, initiation, progression, and development of HCC. These epigenetic alterations because of potential reversibility open way towards the development of biomarkers and therapeutics. The contribution of these epigenetic changes to HCC development has not been thoroughly explored yet. Further research on HCC epigenetics is necessary to better understand novel molecular-targeted HCC treatment and prevention. This review highlights latest research progress and current updates regarding epigenetics of HCC, biomarker discovery, and future preventive and therapeutic strategies to combat the increasing risk of HCC.

Hepatitis B virus inhibits the expression of CD82 through hypermethylation of its promoter in hepatoma cells

The tumor suppressor gene CD82, also known as KAI1, may act as a general suppressor of metastasis in numerous types of cancer. It is hypothesized that downregulation of CD82 gene expression may be an important factor in the induction of hepatocellular carcinoma (HCC), however the mechanism for this requires further study. In the present study, the relative mRNA and protein expression levels of the CD82 gene were determined in HCC and adjacent non‑tumor tissues. The association between the CD82 gene and the hepatitis B virus (HBV) was also investigated, by quantitative polymerase chain reaction, western blotting, luciferase reporter assays and mass spectrometry with matrix‑assisted laser desorption/ionization time‑of‑flight mass array. CD82 expression was shown to be suppressed in response to HCC promoter methylation. Relative CD82 mRNA and protein expression levels were downregulated in HCC tissues (P<0.05). HBx protein inhibited CD82 promoter activity and subsequently the mRNA and protein expression levels. Furthermore, it was demonstrated that HBV could inhibit the expression of CD82 at the transcriptional level, and repress the activity of the CD82 promoter through hypermethylation. In addition, the methyl enzyme inhibitor 5‑aza‑CdR could induce the CD82 promoter activity and the relative expression level of CD82 mRNA, as observed by an increase in luciferase activity driven by the CD82 promoter. The observations of the present study suggest that hypermethylation of the CD82 promoter may be an event leading to the development of HCC. Low expression of CD82 is likely to be involved in tumor progression. HBV may inhibit the expression of CD82 through hypermethylation of the promoter in hepatoma cells.

Methylation patterns of estrogen receptor α promoter correlate with estrogen receptor α expression and clinicopathological factors in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is the seventh most common type of cancer; notably, the incidence of HCC is four to eight times higher in men than women. Previous studies reported that the estrogen receptor (ER) signaling pathway is involved in the pathogenesis of HCC, although the extent of its involvement is unclear due to several conflicting reports. In the present study, tumor and paired adjacent non-cancerous tissues from 157 HCC patients were collected. Transcriptome sequencing and real-time quantitative polymerase chain reaction were used to quantify the ER α (ESR1) expression levels, and the Sequenom EpiTYPER assay was used to delineate the methylation patterns in the ESR1 promoter. We found that ESR1 expression was significantly reduced in tumor tissues (P < 0.001) compared to adjacent non-cancerous tissues. The CpG sites around the transcription start site were significantly hypermethylated in the tumor (P < 0.0001). This methylation pattern also correlated with the gene expression (P < 0.0001). Additionally, we found that the hypermethylation of ESR1 was associated with the presence of fibrous capsules (P = 1.2 × 10^-4), the absence of microvascular invasions (P = 8.0 × 10^-4), thin trabecular pattern (P = 0.025), and lower histologic gradings (P = 5.2 × 10^-3). Thus, ESR1 expression is a candidate tumor suppressor gene in HCC. Further, promoter hypermethylation may be a mechanism by which expression of ESR1 is repressed, and the extent of hypermethylation of ESR1 may be a marker for HCC status and progression.

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 400 μL of serum of each subject and then modified using bisulfite treatment. Methylation of the promoters of the TSGs (metallothionein 1M, 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.

Breast cancer and the importance of early life nutrition

Epigenetic processes play a central role in regulating the tissue-specific expression of genes. Alterations in these processes can lead to profound changes in phenotype and have been implicated in the pathogenesis of many human diseases including human cancer. There is growing evidence that the environment, particularly variations in diet, during specific developmental periods can induce changes in the epigenome, which are then stably maintained throughout life influencing susceptibility to cancer in later life. This chapter will review the evidence that alterations in early life nutritional exposure can affect breast cancer risk through the altered epigenetic regulation of genes and discuss how detection of such altered epigenetic marks in early life may provide biomarkers to detect individuals at increased risk of disease.

Tackling hepatitis B virus-associated hepatocellular carcinoma--the future is now

Hepatocellular carcinoma (HCC) is one of the most lethal and prevalent cancers in many developing countries including India. Among the various etiological factors being implicated in the cause of HCC, the most important cause, however, is hepatitis B virus (HBV) infection. Among all HBV genes, HBx is the most critical carcinogenic component, the molecular mechanisms of which have not been completely elucidated. Despite its clinical significance, there exists a very elemental understanding of the molecular, cellular, and environmental mechanisms that drive disease pathogenesis in HCC infected with HBV. Furthermore, there are only limited therapeutic options, the clinical benefits of which are insignificant. Therefore, the quest for novel and effective therapeutic regimen against HBV-related HCC is of paramount importance. This review attempts to epitomize the current state of knowledge of this most common and dreaded liver neoplasm, highlighting the putative treatment avenues and therapeutic research strategies that need to be implemented with immediate effect for tackling HBV-related HCC that has plagued the medical and scientific fraternity for decades. Additionally, this review proposes a novel "five-point" management algorithm for HBV-related HCC apart from portraying the unmet needs, principal challenges, and scientific perspectives that are relevant to controlling this accelerating global health crisis.

Methylation and liver cancer

Cancer evolution at all stages (including initiation, progression and invasion) is driven by both epigenetic abnormalities and genetic alterations. Epigenetics refer to any structural modification of genomic regions, which lead to modification in gene expression without alterations in DNA sequence. Progressive deregulation of epigenetic process is being increasingly recognized in liver carcinogenesis. This review will provide an overview of DNA methylation, one of the most commonly epigenetic events, which profoundly contributes to liver cancer initiation and progression. Furthermore, the recent advancements in the knowledge of epigenetic reprogramming underlying hepatic cancer stem cells will be highlighted.

Analysis of age-related global DNA methylation in chicken

DNA methylation is an epigenetic modification that plays an important role in the normal development and function of organisms. The level of DNA methylation is species-, tissue-, and organelle-specific, and the methylation pattern is determined during embryogenesis. DNA methylation has also been correlated with age. The aim of this study was to determine the global DNA methylation levels and their correlation with age in the chicken, using a Polish autosexing chicken breed, Polbar. A quantitative technique based on an immunoenzymatic assay was used for global DNA methylation analysis. The results show increased global DNA methylation levels with older Polbar embryos. Global DNA methylation levels decrease with the age of hens in the postembryonic stage. This study expands the current knowledge of the Polbar epigenome and the general knowledge of the function of epigenetic mechanisms in birds.

SOCS-1 promoter methylation and treatment response in chronic hepatitis C patients receiving pegylated-interferon/ribavirin

PURPOSE

Suppressor of cytokine signaling-1 (SOCS-1) is a negative regulator of the Janus kinase/signal transducer and activation of transcription pathway. The purpose of this study was to investigate the relationship between methylation of SOCS-1 and sustained virologic response (SVR) in chronic hepatitis C (CHC) patients treated with pegylated interferon (PEG-IFN)-alpha and ribavirin (RBV).

METHODS

In total, 106 CHC patients treated with PEG-IFN-alpha and RBV were included. Serum samples were obtained at baseline (P), end of treatment (EOT), and 6 months post treatment (F6). Methylation status of the promoter region of SOCS-1 was examined by quantitative methylation specific PCR (qMSP).

RESULTS

Median baseline methylation level of SOCS-1 was -0.95 log10 copies/mL, which increased to 0.57 log10 copies/mL at EOT and then returned to -0.57 log10 copies/mL at F6 (baseline vs EOT, P < 0.001; EOT vs F6, P < 0.001). The overall SVR was 75.5%. Univariate analysis indicated that SVR was significantly associated with genotype, baseline HCV RNA, body mass index (BMI) and higher EOT SOCS-1 methylation. Multivariate analysis confirmed that the SVR was significantly associated with genotype (OR: 13.40, 95% CI: 1.73-103.58, P = 0.013), baseline HCV RNA (OR: 0.19, 95% CI: 0.06-0.59, P = 0.004), BMI (OR: 0.73, 95% CI: 0.56-0.96, P = 0.022), and EOT SOCS-1 methylation (OR: 1.71, 95% CI: 1.11-2.62, P = 0.014).

CONCLUSION

CHC patients with significantly higher SOCS-1 methylation at the end of treatment had better SVRs. The role of SOCS-1 methylation in affecting treatment response deserves further investigation.

Delta-like 3 is silenced by methylation and induces apoptosis in human hepatocellular carcinoma

The genetic and epigenetic events of hepatocarcinogenesis are relatively poorly understood. By analyzing genes from human hepatocellular carcinoma (HCC) with restriction landmark genomic scanning, several aberrantly methylated genes, including Delta-like 3 (DLL3), have been isolated. In this study, we investigated the function of DLL3 in hepatocarcinogenesis. Methylation of the DLL3 gene in HCC cell lines was investigated with methylation-specific PCR and expression of DLL3 mRNA in HCC cells was examined by RT-PCR. Reactivation of DLL3 expression by treatment with a demethylating agent was examined in methylation-silenced HuH2 cells. Human DLL3 cDNA was cloned and DLL3 function was examined by restoring DLL3 expression in HuH2 cells. The effects of DLL3 on cell growth were evaluated by colony formation assay. Induction of cell death by overexpression of DLL3 was examined by flow cytometric assay using Annexin V and PI. Apoptotic cells were detected by TUNEL staining and the amount of single-stranded DNA was measured by ELISA. As a result, the promoter region of the DLL3 gene was methylated in four of ten HCC cell lines. This aberrant methylation correlated well with the suppression of RNA expression and a demethylating agent reactivated DLL3 expression in methylation-silenced HCC cells. Interestingly, the restoration of DLL3 in the methylation-silenced HuH2 cells led to growth suppression on colony formation assay. Flow cytometric assay with Annexin V and PI showed that this growth suppression by DLL3 expression is associated with the induction of apoptosis. Furthermore, these apoptotic effects were confirmed by TUNEL staining and measurement of single-stranded DNA. These results suggest that DLL3 was silenced by methylation in human HCC and that it negatively regulates the growth of HCC cells.

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, SMMC7721, 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 real-time 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 μmol 5-aza-2-deoxycytidine, a demethylating agent. Promoter CpG island methylation levels decreased 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.

Aberrant CpG island hypermethylation and down-regulation of Oct-6 mRNA expression in human hepatocellular carcinoma

BACKGROUND

Aberrant CpG island hypermethylation is a major epigenetic mechanism that can inactivate the transcription of cancer-related genes.

PURPOSE

This study aimed to investigate whether Oct-6 transcription was regulated by CpG island methylation in hepatocellular carcinoma (HCC).

METHODS

Quantitative real-time PCR and the MassARRAY platform (Sequenom) were employed in 38 HCC tissues samples and four cell lines.

RESULTS

The levels of Oct-6 mRNA were decreased by more than twofold in 31 of 38 tumor tissues compared to that of adjacent non-cancerous tissues. Among the 31 tumor tissues with lower levels of Oct-6 mRNA, 17 tumor tissues also had higher methylation levels in Oct-6 CpG island. Based on these results, we hypothesized that CpG island hypermethylation may down-regulate Oct-6 mRNA expression in HCC. To confirm this hypothesis, we also analyzed the changes in Oct-6 mRNA expression and CpG island methylation in four HCC cell lines (Huh7, Bel-7402, HepG2 and SMMC-7721) after treatment with 0.1, 0.5 and 2.5 μM 5-Aza-2-deoxycytidine (5-Aza-CdR), a demethylating agent. The results demonstrated that the CpG island methylation levels decreased and Oct-6 mRNA levels increased in a dose-dependent manner in both Huh7 and Bel7402 cells, but there were only slight changes in HepG2 cell. Interestingly, there were no significant alterations of Oct-6 mRNA levels observed in SMMC7721 cell; although lower levels of CpG island methylation were detected after treatment with 5-Aza-CdR.

CONCLUSIONS

Our study shows that CpG island hypermethylation contributes to down-regulation of Oct-6 mRNA expression in HCC.

The CpG island methylation regulated expression of endothelial proangiogenic genes in response to β-carotene and arachidonic acid

β-carotene (BC) and arachidonic acid (AA) were demonstrated to modulate carcinogenesis by influencing angiogenesis. DNA methylation is an epigenetic mechanism regulating gene expression. The aim of this study was to investigate whether BC and AA change DNA methylation and expression of the proangiogenic genes, which might help explain their impact on carcinogenesis. Human umbilical vein endothelial cells (HUVECs) and endothelial progenitors (EPCs) were incubated with BC or AA for 24 h. Based on microarray results, we selected 18 genes for DNA methylation analysis. CpG island methylation was quantified using the combined bisulphite restriction analysis method and methylation sensitive restriction enzymes. Relative gene expression was quantified using a quantitative real-time PCR (qRT-PCR) method. Incubation with AA significantly decreased methylation of the promoters of both KDR (P = 0.048) and Notch4 (P = 0.027) genes in HUVECs. In EPCs, BC increased methylation of the connexin 43 gene (P = 0.036). qRT-PCR showed that AA (P = 0.059) and BC (P = 0.044) upregulated the KDR gene expression in HUVECs. Connexin 43 gene expression was induced in the presence of 1 μM (P = 0.039) and 3 μM (P = 0.043) BC in EPCs. No significant changes in the Notch4 gene expression were found. The impact of BC and AA on carcinogenesis may be due, at least in part, to changes in expression of angiogenic genes and these transcriptional effects may be mediated by changes in methylation of CpG islands in the gene promoters. However more research is necessary to confirm this hypothesis.

[New possibilities of targeted therapy in the treatment of hepatocellular carcinoma with the help of molecular biology]

Hepatocellular carcinoma (HCC) has a poor prognosis. Approximately 85% of patients are not candidates for curative treatments at the time of diagnosis; hence palliative modalities (transcatheter arterial chemoembolisation, radiofrequency ablation, systemic chemotherapy) are used. Systemic chemotherapies have disappointing results. The increasing knowledge in the molecular biology of HCC will increase the possibilities of targeted therapy. The multi-tyrosine kinase inhibitor sorafenib is the only drug which has approved. The VEGF-inhibitors (bevacizumab, sunitinib), EGFR-blocker agents (erlotinib), as well as the inhibition of mTOR (rapamycin) are promising. Combination of sorafenib or other anti-angiogenic agents with local ablative procedure (transcatheter arterial chemoembolisation, radiofrequency ablation), or with curative hepatectomy also can be favorable. Alteration of Wnt pathway, retinoid compounds, inhibition of the cell cycle as well as the proteosome, and epigenetic therapy can be other potential promising targets in HCC.

Hepatocellular carcinoma displays distinct DNA methylation signatures with potential as clinical predictors

BACKGROUND

Hepatocellular carcinoma (HCC) is characterized by late detection and fast progression, and it is believed that epigenetic disruption may be the cause of its molecular and clinicopathological heterogeneity. A better understanding of the global deregulation of methylation states and how they correlate with disease progression will aid in the design of strategies for earlier detection and better therapeutic decisions.

METHODS AND FINDINGS

We characterized the changes in promoter methylation in a series of 30 HCC tumors and their respective surrounding tissue and identified methylation signatures associated with major risk factors and clinical correlates. A wide panel of cancer-related gene promoters was analyzed using Illumina bead array technology, and CpG sites were then selected according to their ability to classify clinicopathological parameters. An independent series of HCC tumors and matched surrounding tissue was used for validation of the signatures. We were able to develop and validate a signature of methylation in HCC. This signature distinguished HCC from surrounding tissue and from other tumor types, and was independent of risk factors. However, aberrant methylation of an independent subset of promoters was associated with tumor progression and etiological risk factors (HBV or HCV infection and alcohol consumption). Interestingly, distinct methylation of an independent panel of gene promoters was strongly correlated with survival after cancer therapy.

CONCLUSION

Our study shows that HCC tumors exhibit specific DNA methylation signatures associated with major risk factors and tumor progression stage, with potential clinical applications in diagnosis and prognosis.

The possible evolutionary role of tumors in the origin of new cell types

The ability of tumor cells to differentiate in combination with their ability to express genes that are not expressed in normal tissues, may result in the emergence of new cell types in evolution. Tumors may play an evolutionary role by providing conditions (space and resources) for the expression of newly evolving genes. Genetically or epigenetically predetermined tumors at the early stages of progression, benign tumors, and some tumor-like processes in invertebrates and plants, all of which are modes of excess cell growth which provide evolving multicellular organisms with extra cell masses, are considered as potentially evolutionarily meaningful. Malignant tumors at the late stages of progression, however, are not. The preexisting cell types of multicellular organisms had restricted potential for the expression of newly evolving genes. Because of regulation and gene competition, some of the newly evolving genes may stay silent. Multicellular organisms would need excess cell masses for the expression of newly evolving genes. The preexisting cell types cannot provide such excess cell masses because of limitations imposed on the number of possible cell divisions. Tumors could provide the evolving multicellular organisms with the excess cell masses for the expression of newly evolving genes. We suggest that tumors could be a sort of proving ground (or reservoir) for the expression of newly evolving genes that originate in the course of genome evolution in the DNA of germ cells (i.e., not in tumor cells themselves). The case in which the expression of a newly evolving gene in tumors results in the origin of a new function would be associated with the origin of new feedback and regulatory circuits, as in root nodules in legumes and macromelanophores in Xiphophorus fishes. Tumor cells would differentiate, resulting in a new cell type for the given multicellular species. This cell type would be inherited because of epigenomic mechanisms similar to those in preexisting cell types. Populations of tumor-bearing organisms with genetically or epigenetically programmed tumors could represent the transition between established species of organisms at different stages of progressive evolution. Experimental confirmation of the prediction of the hypothesis of evolution by tumor cells differentiation concerning the expression of evolutionarily new genes and/or silent (neutrally evolving) sequences in tumor cells is presented.

Individuality and epigenetics in obesity

Excessive weight gain arises from the interactions among environmental factors, genetic predisposition and the individual behavior. However, it is becoming evident that interindividual differences in obesity susceptibility depend also on epigenetic factors. Epigenetics studies the heritable changes in gene expression that do not involve changes to the underlying DNA sequence. These processes include DNA methylation, covalent histone modifications, chromatin folding and, more recently described, the regulatory action of miRNAs and polycomb group complexes. In this review, we focus on experimental evidences concerning dietary factors influencing obesity development by epigenetic mechanisms, reporting treatment doses and durations. Moreover, we present a bioinformatic analysis of promoter regions for the search of future epigenetic biomarkers of obesity, including methylation pattern analyses of several obesity-related genes (epiobesigenes), such as FGF2, PTEN, CDKN1A and ESR1, implicated in adipogenesis, SOCS1/SOCS3, in inflammation, and COX7A1 LPL, CAV1, and IGFBP3, in intermediate metabolism and insulin signalling. The identification of those individuals that at an early age could present changes in the methylation profiles of specific genes could help to predict their susceptibility to later develop obesity, which may allow to prevent and follow-up its progress, as well as to research and develop newer therapeutic approaches.

Nutrition in early life, and risk of cancer and metabolic disease: alternative endings in an epigenetic tale?

There is substantial evidence which shows that constraints in the early life environment are an important determinant of risk of metabolic disease and CVD. There is emerging evidence that higher birth weight, which reflects a more abundant prenatal environment, is associated with increased risk of cancer, in particular breast cancer and childhood leukaemia. Using specific examples from epidemiology and experimental studies, this review discusses the hypothesis that increased susceptibility to CVD, metabolic disease and cancer have a common origin in developmental changes induced in the developing fetus by aspects of the intra-uterine environment including nutrition which involve stable changes to the epigenetic regulation of specific genes. However, the induction of specific disease risk is dependent upon the nature of the environmental challenge and interactions between the susceptibility set by the altered epigenome and the environment throughout the life course.

[Epidemiology, risk factors and molecular pathogenesis of primary liver cancer]

Primary liver cancer is the fifth most common cancer worldwide. Hepatocellular carcinoma accounts for 85-90% of primary liver cancers. Distribution of hepatocellular carcinoma shows variations among geographic regions and ethnic groups. Males have higher liver cancer rates than females. Hepatocellular carcinoma occurs within an established background of chronic liver disease and cirrhosis (70-90%). Major causes (80%) of hepatocellular carcinoma are hepatitis B, C virus infection, and aflatoxin exposition. Its development is a multistep process. We have a growing understanding on the molecular pathogenesis. Genetic and epigenetic changes activate oncogenes, inhibit tumorsuppressor genes, which result in autonomous cell proliferation. The chromosomal instability caused by telomere dysfunction, the growth-retrained environment and the alterations of the micro- and macroenvironment help the expansion of the malignant cells. Understanding the molecular mechanisms could improve the screening of patients with chronic liver disease, or cirrhosis, and the prevention as well as treatment of hepatocellular carcinoma.

Practical applications for epigenetic biomarkers in cancer diagnostics

Cancer represents a major global health problem and improvement of cancer treatment requires the development of new and useful molecular diagnostic tests that enable the detection of occult tumors, direction of personalized treatments, monitoring of patients during therapeutic intervention and prediction of long-term clinical outcomes. The ideal molecular diagnostic for cancer testing will be based upon non-invasive sources of DNA and will employ biomarkers that have excellent sensitivity, specificity and overall predictive value. Numerous genes are known to be hypermethylated during cancer development and progression. These methylation-sensitive genes represent potentially valuable epigenetic biomarkers for development of practical cancer molecular diagnostics. In fact, many epigenetic biomarkers have proven to possess excellent predictive value in assays designed to detect occult (or developing) neoplasms and/or forecast clinical course/outcome. The progress to date in this emerging area of cancer diagnostics suggests that we are not far away from a time when testing for epigenetic biomarkers will represent an integral part of cancer screening protocols that can be effectively applied to the general population and/or to groups of people with defined risk factors for specific cancer types.

Use of DNA Methylation for Cancer Detection and Molecular Classification

Conjugation of the methyl group at the fifth carbon of cytosines within the palindromic dinucleotide 5'-CpG-3' sequence (DNA methylation) is the best studied epigenetic mechanism, which acts together with other epigenetic entities: histone modification, chromatin remodeling and microRNAs to shape the chromatin structure of DNA according to its functional state. The cancer genome is frequently characterized by hypermethylation of specific genes concurrently with an overall decrease in the level of 5-methyl cytosine, the pathological implication of which to the cancerous state has been well established. While the latest genome-wide technologies have been applied to classify and interpret the epigenetic layer of gene regulation in the physiological and disease states, the epigenetic testing has also been seriously explored in clinical practice for early detection, refining tumor staging and predicting disease recurrence. This critique reviews the latest research findings on the use of DNA methylation in cancer diagnosis, prognosis and staging/classification.