Distinct functional patterns of gene promoter hypomethylation and hypermethylation in cancer genomes

Background

Aberrant DNA methylation plays important roles in carcinogenesis. However, the functional significance of genome-wide hypermethylation and hypomethylation of gene promoters in carcinogenesis currently remain unclear.

Principal Findings

Based on genome-wide methylation data for five cancer types, we showed that genes with promoter hypermethylation were highly consistent in function across different cancer types, and so were genes with promoter hypomethylation. Functions related to “developmental processes” and “regulation of biology processes” were significantly enriched with hypermethylated genes but were depleted of hypomethylated genes. In contrast, functions related to “cell killing” and “response to stimulus”, including immune and inflammatory response, were associated with an enrichment of hypomethylated genes and depletion of hypermethylated genes. We also observed that some families of cytokines secreted by immune cells, such as IL10 family cytokines and chemokines, tended to be hypomethylated in various cancer types. These results provide new hints for understanding the distinct functional roles of genome-wide hypermethylation and hypomethylation of gene promoters in carcinogenesis.

Conclusions

Genes with promoter hypermethylation and hypomethylation are highly consistent in function across different cancer types, respectively, but these two groups of genes tend to be enriched in different functions associated with cancer. Especially, we speculate that hypomethylation of gene promoters may play roles in inducing immunity and inflammation disorders in precancerous conditions, which may provide hints for improving epigenetic therapy and immunotherapy of cancer.     

Overexpression of the MUC2 gene through promoter hypomethylation in mucinous cell carcinomas and signet ring cell carcinomas of gastric cancer

Gastric carcinoma (GC) remains an important cause of mortality and morbidity in East Asia and the histological classification is still controversial, despite considerable understanding of the molecular nature of this disease and its precursor lesions. Mucins play important roles in carcinogenesis or tumor invasion and their aberrant expression are also associated with pathophysiological conditions and clinical outcomes. To investigate if differences with MUC2 expression in GC are associated through changes in promoter methylation and to evaluate the relationship with the histological features of GCs, the expression and methylation status of MUC2 gene was examined in samples from 40 gastric mucosa of GC by immunohistochemistry (IHC) and by methylation-specific PCR (MSP). MUC2 was minimally and focally expressed in welldifferentiated (WD) and moderately-differentiated (MD) GC, while mucinous cell carcinomas (MCC) and signet ring cell carcinomas (SRC) displayed a uniform and strong staining intensity with a diffused cytoplasmic pattern. In addition, the MUC2 hypomethylation were found in 33% of the WD, 0% of the MD, 77% of the MCC, 75% of the MCC/SRC, and 80% of the SRC. Moreover, IHC and MSP analyses showed that MUC2 hypomethylation correlated with its overexpression. Collectively, these results suggest that MUC2 overexpression event in MCC and SRC types of GCs. However, further studies with large numbers of patients will be needed to confirm these findings.     

Beta-adrenergic regulation of c-fos gene expression in an epithelial cell line

Stimulation of beta-adrenoreceptors in the RSMT-A5 epithelial cell line is accompanied by an early and transient increase in the expression of the proto-oncogene c-fos. Maximal induction was at 30 min, returning to basal levels after 2 h. Similar results were obtained when cells were incubated with 8-bromo-cAMP. The induction of c-fos is specific since the expression of p53, a transformation-related gene, is not modulated by isoproterenol or 8-bromo-cAMP. The increase in c-fos gene expression is not associated with proliferative activity in these epithelial cells.     

Curcumin activates AMPK and suppresses gluconeogenic gene expression in hepatoma cells

Curcumin, the bioactive component of curry spice turmeric, and its related structures possess potent anti-oxidant and anti-inflammatory properties. Several lines of evidence suggest that curcumin may play a beneficial role in animal models of diabetes, both by lowering blood glucose levels and by ameliorating the long-term complications of diabetes. However, current understanding of the mechanism of curcumin action is rudimentary and is limited to its anti-oxidant and anti-inflammatory effects. In this study we examine potential anti-diabetic mechanisms of curcumin, curcumin C3 complex^®, and tetrahydrocurcuminoids (THC). Curcuminoids did not exert a direct effect on receptor tyrosine kinase activity, 2-deoxy glucose uptake in L6-GLUT4myc cells, or intestinal glucose metabolism measured by DPP4/α-glucosidase inhibitory activity. We demonstrate that curcuminoids effectively suppressed dexamethasone-induced phosphoenol pyruvate carboxy kinase (PEPCK) and glucose6-phosphatase (G6Pase) in H4IIE rat hepatoma and Hep3B human hepatoma cells. Furthermore, curcuminoids increased the phosphorylation of AMP-activated protein kinase (AMPK) and its downstream target acetyl-CoA carboxylase (ACC) in H4IIE and Hep3B cells with 400 times (curcumin) to 100,000 times (THC) the potency of metformin. These results suggest that AMPK mediated suppression of hepatic gluconeogenesis may be a potential mechanism mediating glucose-lowering effects of curcuminoids.     

Ectopic expression of the coxsackievirus and adenovirus receptor increases susceptibility to adenoviral infection in the human cervical cancer cell line, SiHa.

The expression level of the coxsackievirus and adenovirus receptor (CAR) gene in human cervical cancer cell lines (Hela, Caski, HT-3, and SiHa) appears to be correlated with their susceptibility to adenoviral vector-based gene transfer. Hela, Caski, and HT-3 cells, which express the CAR molecule on the cell surface, showed a higher susceptibility to infection of AdCMVGFP than SiHa cells with no detectable level of CAR expression. Transient expression of the CAR gene in SiHa cells dramatically enhanced the susceptibility to adenoviral infection. Furthermore, SiHa-CAR, a stable transfectant which expresses the CAR gene showed a highly increased susceptibility to adenoviral infection in contrast to SiHa. These results demonstrate that the low susceptibility of SiHa to adenoviral infection is closely related to its loss of the CAR gene expression. In addition, the low infection efficacy can be overcome by the ectopic expression of the CAR gene. These results also give insight into a possible application of the CAR gene to adenovirus-mediated gene delivery.     

Global hypomethylation and promoter methylation in small intestinal neuroendocrine tumors

Aberrant DNA methylation is a feature of human cancer affecting gene expression and tumor phenotype. Here, we quantified promoter methylation of candidate genes and global methylation in 44 small intestinal-neuroendocrine tumors (SI-NETs) from 33 patients by pyrosequencing. Findings were compared with gene expression, patient outcome and known tumor copy number alterations. Promoter methylation was observed for WIF1, RASSF1A, CTNNB1, CXCL14, NKX2–3, P16, LAMA1, and CDH1. By contrast APC, CDH3, HIC1, P14, SMAD2, and SMAD4 only had low levels of methylation. WIF1 methylation was significantly increased (P = 0.001) and WIF1 expression was reduced in SI-NETs vs. normal references (P = 0.003). WIF1, NKX2–3, and CXCL14 expression was reduced in metastases vs. primary tumors (P < 0.02). Low expression of RASSF1A and P16 were associated with poor overall survival (P = 0.045 and P = 0.011, respectively). Global methylation determined by pyrosequencing of LINE1 repeats was reduced in tumors vs. normal references, and was associated with loss in chromosome 18. The tumors fell into three clusters with enrichment of WIF1 methylation and LINE1 hypomethylation in Cluster I and RASSF1A and CTNNB1 methylation and loss in 16q in Cluster II. In Cluster III, these alterations were low-abundant and NKX2-3 methylation was low. Similar analyses in the SI-NET cell lines HC45 and CNDT2 showed methylation for CDH1 and WIF1 and/or P16, CXCL14, NKX2-3, LAMA1, and CTNNB1. Treatment with the demethylating agent 5-azacytidine reduced DNA methylation and increased expression of these genes in vitro. In conclusion, promoter methylation of tumor suppressor genes is associated with suppressed gene expression and DNA copy number alterations in SI-NETs, and may be restored in vitro.     

Characterization of promoter elements required for cell-specific expression of the neurotensin/neuromedin N gene in a human endocrine cell line.

Expression of the gene encoding neurotensin/neuromedin N (NT/N) is mostly limited to the brain and specialized enteroendocrine cells (N cells) of the distal small intestine. We have analyzed the NT/N DNA sequences upstream of the RNA start site that direct cell-specific expression using a novel human endocrine cell line, BON, that resembles intestinal N cells in several important aspects, including NT/N precursor protein processing, ratios of different NT/N mRNA forms, and high levels of constitutive expression of the NT/N gene. Transient transfection assays with plasmids with progressive 5' deletions of the rat NT/N promoter identified the proximal 216 bp of 5' flanking sequences as essential for high-level constitutive NT/N expression in BON cells. In addition, a detailed mutational analysis defined multiple regions within the proximal 216 bp that contribute to cell-specific NT/N expression. These elements include a proximal cyclic AMP response element (CRE)/AP-1-like motif (TGACATCA) that binds c-Jun, JunD, CRE-binding (CREB), and ATF proteins, a near-consensus glucocorticoid response element, and a distal consensus AP-1 site that binds c-Fos, Fra-1, and JunD. In addition, elements contained within two 21-bp imperfect direct repeats play an important role in NT/N expression in BON cells and may bind novel factors that act as positive regulators of NT/N expression. DNase I footprinting and gel shift analyses demonstrate that the sites identified by mutational analysis, and at least one additional site, specifically bind BON cell nuclear proteins in vitro. We speculate that a complex pattern of regulation requiring interaction between a proximal CRE/AP-1-like motif and other upstream control elements play an important role in the high-level constitutive expression of NT/N in the human endocrine cell line BON. In addition, the BON cell line provides a unique model to further characterize the factors regulating cell-specific NT/N expression and to better understand the mechanisms responsible for the terminal differentiation of the N-cell lineage in the gut.     

Proliferation of peripheral blood mononuclear cells causes increased expression of the sodium-dependent multivitamin transporter gene and increased uptake of pantothenic acidopen star

Antigenic or mitogenic stimulation of peripheral blood mononuclear cells (PBMC) causes rapid cell proliferation. PBMC proliferation is associated with increased activities of pantothenic acid-dependent metabolic pathways, suggesting increased demand for pantothenic acid. We sought to determine whether PBMC respond to proliferation by increased cellular uptake of pantothenic acid and, if so, by what mechanism(s) the increased uptake is mediated. Uptake of pantothenic acid into PBMC was mediated by the sodium-dependent multivitamin transporter, SMVT, as judged by sodium dependency of uptake, substrate affinity and specificity, and RT-PCR of PBMC RNA. Proliferating PBMC accumulated two times more [3H]pantothenic acid than quiescent PBMC. Rates of [3H]pantothenic acid uptake paralleled rates of PBMC proliferation, as judged by uptake of [3H]thymidine. The increased uptake of [3H]pantothenic acid into proliferating PBMC was mediated by increased expression of SMVT (as judged by RT-PCR using total RNA from PBMC), leading to an increased number of transporters on the cell surface (as judged by maximal transport rates for pantothenic acid). We conclude that proliferating PBMC increase expression of the gene encoding SMVT to increase uptake of pantothenic acid.     

Synthetic promoter libraries--tuning of gene expression

The study of gene function often requires changing the expression of a gene and evaluating the consequences. In principle, the expression of any given gene can be modulated in a quasi-continuum of discrete expression levels but the traditional approaches are usually limited to two extremes: gene knockout and strong overexpression. However, applications such as metabolic optimization and control analysis necessitate a continuous set of expression levels with only slight increments in strength to cover a specific window around the wild-type expression level of the studied gene; this requirement can be met by using promoter libraries. This approach generally consists of inserting a library of promoters in front of the gene to be studied, whereby the individual promoters might deviate either in their spacer sequences or bear slight deviations from the consensus sequence of a vegetative promoter. Here, we describe the two different methods for obtaining promoter libraries and compare their applicability.     

羟基脲对人红白血病细胞株中球蛋白基因表达和细胞分化的影响

人红白血病细胞株（ＨＥＬ细胞）中珠蛋白基因表达具有自己的特点。即只表达胚胎型的γ－珠蛋白基因而不表达成人型的β－珠蛋白基因。羟基脲是一种抑制ＤＮＡ的小分子有机化合物。它在临床上被用来治疗地中海盆血和镰刀型贫血。我们的实验结果表明：胡羟基脲浓度增加ＨＥＬ细胞增殖速度减慢。用常规ＲＴ－ＰＣＲ方法和定量ＰＣＲ分析证明,用羟基脲诱导ＨＥＬ细胞后,β－珠蛋白基因表达增加,α－珠蛋白基因表达减少,而γ－珠蛋白