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Role of the cytosine DNA-methyltransferase and p16INK4a genes in the development of mouse lung tumors.

CpG island methylation is an epigenetic modification of DNA associated with the silencing of gene transcription. The p16INK4a (p16) tumor suppressor gene is inactivated in human non-small cell lung cancers (NSCLCs) by either homozygous deletion or aberrant methylation. Inactivation of tumor suppressor genes by methylation has been linked in part to altered activity of the cytosine DNA-methyltransferase (DNA-MTase), the enzyme that catalyzes DNA methylation at CpG sites. The purpose of these studies was to define the role of DNA-MTase and p16 in the development of murine lung cancer. DNA-MTase activity was determined in alveolar type II and Clara cells from A/J and C3H mice that exhibit high and low susceptibility, respectively, for lung tumor formation. Increased DNA-MTase activity leading to an increase in overall DNA methylation was found only in alveolar type II cells, the target for murine adenocarcinomas. Both DNA-MTase and DNA methylation changes were detected 7 days after carcinogen exposure and, thus, were early events in neoplastic evolution. In addition, enzyme activity increased incrementally during lung cancer progression. Expression of p16 was detected in all primary lung tumors from A/J mice; however, levels of expression differed by up to 15-fold between tumors. The apparent low levels of expression seen in approximately half of the tumors was not attributed to methylation of the p16 gene. In contrast to the detection of p16 expression in primary tumors, this gene was deleted in four tumor-derived cell lines induced in the A/J mouse by NNK. The results from these studies indicate that the modulation of DNA-MTase activity was cell specific, segregated with susceptibility, and occurred early in neoplastic evolution. Thus, the marked increase in enzyme activity detected in alveolar type II cells after carcinogen treatment could be a major factor contributing to the high susceptibility for chemical-induced neoplasia associated with the A/J mouse strain. The inactivation of the p16 gene in murine cancers induced by NNK most likely arises as a late event via homozygous deletion.

Adenocarcinoma↗

Loss of reiterated DNA sequences during serial passage of human diploid fibroblasts.

A specific family of tandemly repeated DNA sequences was found to diminish in the human genome after serial passage of three strains of diploid fibroblasts. Eco RI restriction fragments of 340 and 680 bp were significantly reduced in quantity at late passage as determined by autoradiography of 14C-DNA and also by ethidium bromide fluorescence. The reduction in these closely related DNA sequences was confirmed by saturation hybridization to excess 14H-RNA transcribed from a homogeneous restriction fragment recleaved from the 340 bp DNA. The maximal fraction of DNA hybridizing to the 3H-RNA probe declined by 33-50% over 21-41 population doublings. Divergence and/or methylation of such sequences could not account for these results since the thermal stability of cRNA:DNA duplexes actually increased by 0.3 degrees C at late passage. Total highly repetitive sequences assayed by reassociation kinetics were also substantially reduced at late passage, implying that depletion may be common to many repeat families in DNA. The denaturation temperature for such rapidly reassociated duplexes again increased slightly at late passage, possibly reflecting the minor decreases in DNA methylation which were detected in two of the cell strains. Karyotype analyses demonstrated that over 95% euploidy was maintained, with no specific chromosome loss and no visible deletions at late passage. The depletion of reiterated sequences during repeated cell division is thus attributed to numerous small DNA deletions, which may arise from unequal recombination coupled with selection or from a nonreciprocal mechanism such as excision.

Cell Division↗

Persistent infection of hepatitis B virus is involved in high rate of p16 methylation in hepatocellular carcinoma.

High rate of chronic hepatitis B virus (HBV) infection and p16 promoter methylation were found in the majority of hepatocellular carcinoma (HCC). To investigate the potential linkage between high rate of p16 methylation and HBV infection, p16 methylation was detected with methylation-specific polymerase chain reaction (PCR), and HBV markers were examined with real-time PCR and immunologic method. p16 methylation was detected in 5.5% of patients with hepatitis B, 9.1% of noncancerous liver, 36.6% of cirrhotic liver tissue, and 70.5% of cancerous tissue of HCC, primarily in cirrhotic (46.7%) and cancerous tissue (90.6%) with HBV infection. In noncancerous tissue, p16 methylation could only be detected in samples with HBV infection, although no significant difference, the frequency of p16 methylation in noncancerous tissue with HBV infection was higher than those without it. The results showed that, in cancerous, cirrhotic, or noncancerous tissues, the frequency of p16 methylation in samples with HBV infection was higher than those without it, suggesting possible association between HBV infection and p16 methylation. The result of HBV-DNA analysis showed that 96.1% (49/51) samples with p16 methylation also showed detectable HBV-DNA; it signifies that replication and/or integration of HBV may contribute to high rate of p16 methylation in hepatocarcinogenesis. Generally, these results indicate that persistent HBV infection may be associated with high rate of p16 methylation, and involved in development of HCC through this way.

Carcinoma, Hepatocellular↗

In vivo alkylation studies with dichlorvos at practical use concentrations.

Twenty male CFE rats were exposed to atmospheres containing 0.064 microgram/l of [Me-14C] dichlorvos (113 Ci/mol) for 12 h. Analysis of the DNA and RNA from the total soft tissues of these rats revealed no methylation of the N7 atom of guanine moieties. The limits of detection of methylation were one methyl group per 6.0 X 10(11) and per 2 X 10(9) nucleotide units for DNA and RNA, respectively. Only 0.000001% of the administered dose would have needed to react with DNA in order to produce detectable methylation of this macromolecule. The exposure period employed in this study (12 h) constituted a significant fraction of the half-life of 7-methylguanine moieties in DNA (3 days). On the basis of this information and the extremely rapid metabolism of dichlorvos in a wide range of mammalian tissues and species it was concluded that dichlorvos does not methylate the nucleic acids of mammalian tissues when it is inhaled continuously at practical use concentrations.

Alkylating Agents↗

The isolation of monoclonal antibodies selected for the detection of imidazole ring-opened N7-ethylguanine in purified DNA and in cells in situ. Crossreaction with methyl, 2-hydroxyethyl and sulphur mustard adducts.

Monoclonal antibodies have been obtained against imidazole ring-opened N7-ethylguanine (RON7-EtGua) in DNA. The antibodies were selected for good performance in the ELISA with either DNA or nucleated blood cells as immobilized antigen. Antibodies thus selected were studied for their suitability for the in situ detection of RON7-EtGua in the nuclei of cells by means of immunofluorescence microscopy (IFM). Two antibodies have been characterized in detail with respect to specificity and sensitivity. Competitive ELISA demonstrated that the antibodies recognize not only RON7-EtGua but also the corresponding methyl and 2-hydroxyethyl components, with efficiencies that vary with the chemical environment (base, nucleoside or DNA), the nature of the alkyl group and the antibody. They have a clear specificity for the ring-opened alkyl adducts and show an at least 100-fold stronger preference for such structures in DNA when compared to the free nucleoside adducts. Furthermore, they hardly bind to non-alkylated DNA, and do not bind to guanosine or N1- or O6-ethylguanosine. Analysis by DNA-ELISA showed that the binding preference of antibody N7E-026 for ring-opened alkyl adducts is methyl approximately ethyl greater than 2-hydroxyethyl much greater than sulphur mustard, while that of N7E-102 is 2-hydroxyethyl greater than ethyl greater than methyl approximately sulphur mustard. Analysis of RON7-EtGua in DNA with competitive ELISA, DNA-ELISA and IFM showed that in all cases the lowest detection limit can be reached with antibody N7E-026. Competitive ELISA was the most sensitive method, followed by DNA-ELISA and IFM, with detection limits of 2.2, 16 and 23 RON7-EtGua/10(6) nucleotides respectively. In the DNA-ELISA, 12 methyl adducts/10(6) nucleotides can be detected with N7E-026 and 11 2-hydroxyethyl adducts/10(6) nucleotides with N7E-102.

Animals↗

Detection of aberrant p16 methylation in the plasma and serum of liver cancer patients.

We have studied the feasibility of detecting tumor-associated aberrant p16 methylation in the circulation of patients with hepatocellular carcinoma (HCC). We extracted DNA from the tumor tissues and peripheral blood plasma or serum of 22 HCC patients. p16 methylation was found in 73% (16 of 22) of HCC tissues using methylation-specific PCR. Among the 16 cases with aberrant methylation in the tumor tissues, similar changes were also detected in the plasma/serum samples of 81% (13 of 16) of the cases. No methylated p16 sequences were detected in the peripheral plasma/serum of the six HCC cases without these changes in the tumor, in 38 patients with chronic hepatitis/cirrhosis, or in 10 healthy control subjects. These results suggest that circulating liver tumor DNA may be detected using tumor-associated DNA methylation changes. Because methylation abnormalities have been found in many other genes and tumor types, this approach may have implications for the noninvasive detection of a wide variety of cancers.

Adult↗

Increased cytosine DNA-methyltransferase activity is target-cell-specific and an early event in lung cancer.

The association between increased DNA-methyltransferase (DNA-MTase) activity and tumor development suggest a fundamental role for this enzyme in the initiation and progression of cancer. A true functional role for DNA-MTase in the neoplastic process would be further substantiated if the target cells affected by the initiating carcinogen exhibit changes in enzyme activity. This hypothesis was addressed by examining DNA-MTase activity in alveolar type II (target) and Clara (nontarget) cells from A/J and C3H mice that exhibit high and low susceptibility, respectively, for lung tumor formation. Increased DNA-MTase activity was found only in the target alveolar type II cells of the susceptible A/J mouse and caused a marked increase in overall DNA methylation in these cells. Both DNA-MTase and DNA methylation changes were detected 7 days after carcinogen exposure and, thus, were early events in neoplastic evolution. Increased gene expression was also detected by RNA in situ hybridization in hypertrophic alveolar type II cells of carcinogen-treated A/J mice, indicating that elevated levels of expression may be a biomarker for premalignancy. Enzyme activity increased incrementally during lung cancer progression and coincided with increased expression of the DNA-MTase activity are strongly associated with neoplastic development and constitute a key step in carcinogenesis. The detection of premalignant lung disease through increased DNA-MTase expression and the possibility of blocking the deleterious effects of this change with specific inhibitors will offer new intervention strategies for lung cancer.

Animals↗

Natural and conditional ageing of mouse fibroblasts: genetic vs. epigenetic control.

Mouse embryonic fibroblasts were fused with a spontaneously immortalized mouse fibroblast cell line and a large number of heterogeneous hybrid populations were obtained. These showed variations with respect to their chromosomal number as well as in vitro life span but none acquired immortal phenotype. Apart from demonstrating the dominant nature of senescence over immortalization in mouse system, we also provide the first report on the analysis of genomic DNA methylation during in vitro passaging of parental and hybrid cell populations representing the normal and conditional ageing, respectively. Since no random decline in DNA methylation could be detected in any of the cases, our results suggest that it is unlikely that mortality of cells in culture is the outcome of random loss of epigenetic control imposed by 5-methyldeoxycytidine at CpG sites in the genome.

Animals↗

Molecular diagnosis of the Prader-Willi and Angelman syndromes by detection of parent-of-origin specific DNA methylation in 15q11-13.

The Prader-Willi syndrome (PWS) and the Angelman syndrome (AS) are distinct genetic disorders that are caused by a deletion of chromosome region 15q11-13 or by uniparental disomy for chromosome 15. Whereas PWS results from the absence of a paternal copy of 15q11-13, the absence of a maternal copy of 15q11-13 leads to AS. We have found that an MspI/HpaII restriction site at the D15S63 locus in 15q11-13 is methylated on the maternally derived chromosome, but unmethylated on the paternally derived chromosome. Based on this difference, we have devised a rapid diagnostic test for patients suspected of having PWS and AS.

Adult↗

Methylation of human T-cell leukemia virus proviral DNA and viral RNA expression in short- and long-term cultures of infected cells.

Leukemic peripheral blood lymphocytes from individuals infected with the human T-cell leukemia/lymphoma virus (HTLV) were found to express little or no viral RNA before being put into tissue culture. Within 24-48 hr, viral RNA expression increased at least four- to eightfold. Established HTLV-infected cell lines constitutively express viral RNA. Southern blots of DNA from HTLV-infected cells digested with the methylation-sensitive restriction enzyme HpaII showed that the proviral DNA was methylated in all of the uncultured peripheral blood cells tested. In contrast, no proviral methylation was detected in any of the cell lines examined, suggesting a functional correlation between methylation and viral RNA expression. However, DNA from HTLV-infected lymphocytes cultured for 48 hr (by which time increases in viral RNA expression are evident) did not differ detectably with respect to proviral DNA methylation from uncultured cells, suggesting that the increase in viral RNA expression after short-term culture is mediated by mechanisms independent of changes in DNA methylation.

Cells, Cultured↗

Promoter methylation and expression of DNA repair genes hMLH1 and MGMT in acute myeloid leukemia.

Gene silencing of DNA repair genes hMLH1 and MGMT caused by aberrant promoter methylation has been detected in various solid tumors. However, in acute myeloid leukemia (AML) the frequency of hMLH1 and MGMT promoter methylation is not yet fully elucidated. To determine the methylation status and expression of hMLH1 and MGMT, we investigated 22 AML cases by methylation-specific polymerase chain reaction (MS-PCR) and reverse transcription PCR (RT-PCR). To exclude unspecific PCR amplifications DNA sequencing was performed. hMLH1 promoter methylation was detectable in 4 of 20 AML cases. However, DNA sequencing could only confirm a methylated hMLH1 promoter in one case. mRNA expression was absent in one case and reduced in another. However, these cases did not display aberrant promoter methylation. In contrast, MGMT promoter methylation was not detectable in the investigated AML patient samples. Accordingly, MGMT mRNA expression was found to be normal in all but one case. Aberrant promoter methylation of hMLH1 was detectable only in a small number of AML cases. Additionally, in two cases the promoter methylation detected by MS-PCR could not be confirmed by sequencing, clearly indicating the importance of controlling MS-PCR results by the more specific sequence analysis. Surprisingly, hMLH1 promoter methylation was not associated with gene silencing, suggesting monoallelic methylation or promoter methylation only in a small subpopulation of malignant cells. The reduced mRNA expression in additional samples may indicate an involvement of hMLH1 in the malignant transformation in a small subset of cases. In contrast, MGMT does not seem to be involved in the pathogenesis of AML.

Adaptor Proteins, Signal Transducing↗

Development and preliminary validation of plasma cell-free DNA methylation-based diagnostic prediction model for colorectal cancer detection.

BACKGROUND: Colorectal cancer (CRC) is a common malignancy associated with genetic and epigenetic alterations. Several methylation biomarkers have been investigated for non-invasive CRC detection; however, their reported performance varies across clinical settings, and the detection of early-stage or precancerous disease and discrimination from non-malignant colorectal conditions remain challenging. This exploratory study aimed to identify reproducible CRC-associated plasma cell-free DNA (cfDNA) methylation regions and to develop and preliminarily evaluate diagnostic prediction model for distinguishing CRC from healthy controls and benign samples. METHODS: Public CRC tissue methylation datasets from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) were analyzed to identify reproducible CRC-associated methylation alterations. Plasma cfDNA methylation was profiled using methyl-CpG-binding-domain enrichment followed by paired-end sequencing in patients with CRC, patients with colorectal polyps, and healthy controls. After quality-control filtering, 30 CRC and healthy-control samples were randomly allocated at the participant level in a 7:3 ratio to a development set comprising 10 patients with CRC and 11 healthy controls and a held-out test set comprising 4 patients with CRC and 5 healthy controls. Hypermethylated regions were selected using least absolute shrinkage and selection operator (LASSO) logistic regression. The 12-region model was evaluated in the held-out test set and subsequently applied to 10 colorectal polyp samples without refitting or recalibration. RESULTS: Tissue methylation analysis identified reproducible CRC-associated alterations across independent datasets. In the plasma development set, 707 differentially methylated regions (DMRs) were identified between CRC and healthy-control samples, including 324 hypermethylated and 383 hypomethylated regions. LASSO regression selected a 12-region hypermethylation signature. In the held-out test set, the model achieved an area under the curve (AUC) of 0.85 [95% confidence interval (CI): 0.579-1.000]. At the development-set-derived threshold, sensitivity was 75.0% (3/4), specificity was 60.0% (3/5), and accuracy was 66.7% (6/9). When the original model was applied to colorectal polyp samples, model scores were significantly higher in both CRC and polyp samples than in healthy controls, while CRC samples showed a tendency toward higher scores than polyp samples. CONCLUSIONS: This exploratory study identified a 12-region plasma cfDNA hypermethylation signature associated with CRC and developed a LASSO-based diagnostic prediction model that showed preliminary discrimination between CRC and healthy controls in a small held-out test set. By integrating tissue methylation evidence with plasma cfDNA profiling, this study expands the repertoire of candidate region-level methylation markers for blood-based CRC detection.

Colorectal cancer (CRC)↗

[Investigations to the influence of tumor supressor gene p16 inactivation on the prognosis of head and neck squamous cell carcinoma].

BACKGROUND: The inactivation of the tumor suppressor gene p16 plays an important role in the development of malignant tumors. P16 loss can result from point mutations, loss of heterozygosity (LOH) or methylation of the promoter region. MATERIAL AND METHODS: A total of 67 samples of tumor tissue from squamous cell carcinomas of the oral cavity, the pharynx and the larynx were analysed for an inactivation of p16. The samples were obtained during surgery. In all cases there was a curative intention. Point mutations were detected by DNA sequencing. Methylation of the promotor region was explored with a methylation-specific PCR. A microsatellite analysis of the tumor tissue was used to search for LOH. RESULTS: The results of the molecularbiological investigations were correlated to the known clinical prognostic parameters (tumor stadium, grading, patho-histological differentiation, local and regional recurrence) after a follow-up period of approximately 3 years. Methylation of the promotor region and LOH were the main mechanisms of p16 inactivation encountered in this study. Point mutations presented as rare events. The methylation of the promotor region appeared frequently parallel with an LOH. An inactivation of p16 did not have any statistical influence on the tumor dependent survival, the lymphatic spread, the number and time delay of local and regional recurrences. Patients with an inactivated p16 gene by promotor methylation appeared to have a slightly lower tendency for local and regional recurrences. CONCLUSIONS: The inactivation of the tumor suppressor gene p16 plays a role in the carcinogenesis of squamous cell carcinomas of the oral cavity, the pharynx and the larynx. There is no influence on the tumor dependent prognosis. Tumors with an inactivated p16 gene tend to have a lower recurrence rate.

Carcinoma, Squamous Cell↗

[Analysis of methylation and loss of heterozygosity of RUNX3 gene in hepatocellular carcinoma and its clinical significance].

OBJECTIVE: In order to elucidate role of RUNX3 gene in hepatocarcinogenesis, we detected genetic and epigenetic alteration of RUNX3 gene in hepatocellular carcinoma (HCC). METHODS: PCR-SSCP, analysis of loss of heterozygosity (LOH), sequencing and methylation-specific PCR (MSP) were used to detect mutation, LOH and DNA methylation of RUNX3 gene in 90 HCCs. RESULTS: No mutation was found, but three single-nucleotide polymorphisms (SNP) were found and distributed over exon1 and exon4. 30.6% (11/36) of cases showed LOH; 54.4% (49/90) of cases was in hypermethylation. There is a significant correlation between LOH and major portal vein invasive or micro vessel invasion or intrahepatic metastasis. CONCLUSION: High frequent hypermethylation and LOH of RUNX3 gene were found in HCC. Aberrant RUNX3 gene may play an important role in the development of HCC.

Carcinoma, Hepatocellular↗

DNA methylation in rat tissues by a series of homologous aliphatic nitrosamines ranging from N-nitrosodimethylamine to N-nitrosomethyldodecylamine.

Aliphatic N-nitrosomethylalkylamines exhibit a remarkable organ specificity in rats, the principal targets for tumour induction being liver, oesophagus, urinary bladder and lung. We have determined the extent of DNA methylation in these tissues following a single oral dose (0.1 mmol/kg; 6 h survival) of each of 12 homologues, ranging from N-nitrosodimethylamine (C1) to N-nitrosomethyldodecylamine (C12). Methylpurines (7- and O6-methylguanine) were determined by cation exchange HPLC with fluorescence detection. Highest levels of hepatic DNA methylation were found with N-nitrosodimethylamine (C1) and N-nitrosomethylethylamine (C2), the most potent hepatocarcinogens in this series. Concentrations of methylpurines in liver DNA decreased with increasing chain length for C1-C5. Administration of the higher homologues (C6-C12) caused levels of DNA methylation which by themselves were considered too low to account for their hepatocarcinogenicity. In rat oesophagus, DNA methylation closely paralleled carcinogenicity, the butyl and pentyl derivatives (C4, C5) being most effective. In rat lung, the extent of DNA methylation was generally lower and there was no apparent correlation with carcinogenicity. Methylation of kidney DNA also decreased with increasing chain length and was only detectable for C1-C5. In urinary bladder DNA, methylpurines were below or close to the limit of detection. It is concluded that the initiation of malignant transformation by DNA methylation alone (through hydroxylation at the methylene alpha-carbon) could be operative for C1 in kidney and lung, for C1 and C2 in liver, and C3-C5 in oesophagus. For the higher homologues, the extent of DNA methylation seems insufficient to explain the complex pattern of tissue specificity, suggesting that DNA modification other than, or in addition to, methylation may be responsible.

Animals↗

Gene promoter hypermethylation in tumors and lymph nodes of stage I lung cancer patients.

Promoter hypermethylation is an important pathway for repression of gene transcription in cancer cells and a promising marker for cancer detection. We tested five gene promoters [CDKN2A (p16), O(6)-methylguanine-DNA-methyltransferase, glutathione S-transferase P1 (GSTP1), adenomatous polyposis coli (APC), and death-associated protein kinase (DAPK)] by real-time methylation-specific PCR in primary tumors from 90 stage I lung cancer patients for aberrant DNA methylation. We then used the presence of tumor methylation as a marker to investigate the presence of occult metastasis in corresponding histologically negative lymph nodes. Of the primary tumors, 73 of 90 (81%) displayed promoter hypermethylation in at least one of the genes studied: 17% (15 of 90) at p16 (CDKN2A); 16% (14 of 90) at O(6)-methylguanine-DNA-methyltransferase; 8% (7 of 90) at GSTP1; 72% (65 of 90) at APC; and 17% (15 of 90) at DAPK. Squamous histology was predictive of worse overall survival (P = 0.074, log-rank test). APC methylation and GSTP1 methylation in the primary tumor were both correlated with nonsquamous histology (P = 0.02 and P = 0.01 likelihood ratio respectively). The presence of both APC methylation and DAPK methylation in the primary tumor predicted a worse outcome, with 7 of 13 (54%) deaths in this group compared with 21 of 77 (27%) deaths in cases without both genes methylated (P = 0.229, log-rank test). The same methylation pattern was detected in DNA from at least one of the corresponding lymph nodes in 11 of 73 (15%) cases. Five of 11 (45%) patients with occult metastasis detected by methylation analysis have died compared with 17 of 62 (27%) patients with negative lymph nodes, although survival analysis did not reach statistical significance (P = 0.632, log-rank test). Promoter hypermethylation is common in lung cancer and represents a promising marker for the molecular staging of lung cancer patients. Although this study showed important trends, a larger prospective study is required to better understand the value of methylation analysis in detecting occult metastasis.

Adenomatous Polyposis Coli Protein↗

DNA analysis by MALDI-TOF mass spectrometry.

The last decade has seen an increased demand for high-throughput DNA analysis. This is mainly due to the human genome sequencing project that is now completed. Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry was pinpointed early on as a technology that could be of great use for sequence variation analysis in the post-genome sequencing era. Applications developed first on this platform were for SNP genotyping. Several strategies for allele-discrimination (hybridization, cleavage, ligation, and primer extension) were combined with MALDI-TOF mass spectrometric detection. Nowadays, in practice, only primer extension methods are applied for large-scale SNP genotyping studies with MALDI-TOF detection. Problems surrounding the integration of SNP genotyping by MALDI-TOF mass spectrometry at high throughput are largely mastered now. Mass spectrometry geared presentations at the HUGO Mutation Detection Meeting in Palm Cove, Australia almost exclusively focused on novel applications that go beyond standard SNP genotyping. These applications are more demanding in terms of chemistry and molecular biology. Molecular haplotyping, expression profiling, DNA methylation analysis, and mutation detection are now being demonstrated.

DNA Mutational Analysis↗