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At least 991 records · Page 55Linked to original sources
PubMed2004

Promoter hypermethylation profile of kidney cancer.

PURPOSE: Promoter hypermethylation is an important mechanism of inactivation of tumor suppressor genes in cancer cells. Kidney tumors are heterogeneous in their histology, genetics, and clinical behavior. To gain insight into the role of epigenetic silencing of tumor suppressor and cancer genes in kidney tumorigenesis, we determined a hypermethylation profile of kidney cancer. EXPERIMENTAL DESIGN: We examined the promoter methylation status of 10 biologically significant tumor suppressor and cancer genes in 100 kidney tumors (50 clear cell, 20 papillary, 6 chromophobe, 5 collecting duct, 5 renal cell unclassified, 7 oncocytoma, 6 transitional cell carcinomas of the renal pelvis, and 1 Wilms' tumor) by methylation-specific PCR. The hypermethylation profile was examined with regard to clinicopathological characteristics of the kidney cancer patients. RESULTS: Hypermethylation of one or more genes was found in 93 (93%) of 100 tumors. A total of 33% of kidney tumors had one gene, 35% two genes, 14% three genes, and 11% four or more genes hypermethylated. The frequency of hypermethylation of the 10 genes in the 100 tumor DNAs was VHL 8% (all clear cell), p16(INK4a) 10%, p14(ARF) 17%, APC 14%, MGMT 7%, GSTP1 12%, RARbeta2 12%, RASSF1A 45%, E-cadherin 11%, and Timp-3 58%. Hypermethylation was observed in all of the histological cell types and grades and stages examined. No hypermethylation was observed in specimens of normal kidney or ureteral tissue from 15 patients. Hypermethylation of VHL was specific to clear cell tumors. RASSF1A methylation was detected at a significantly higher frequency in papillary renal cell tumors and in high-grade tumors of all cell types. MGMT methylation was more frequent in nonsmokers. Simultaneous methylation of five or more genes was observed in 3 (3%) of 100 tumors and may indicate a methylator phenotype in kidney cancer. In addition, the CpG island in the promoter of the fumarate hydratase (FH) tumor suppressor gene was bisulfite sequenced and was found to be unmethylated in 15 papillary renal tumors. CONCLUSIONS: Promoter hypermethylation is common, can occur relatively early, may disrupt critical pathways, and, thus, likely plays an important role in kidney tumorigenesis. A hypermethylation profile may be useful in predicting a patient's clinical outcome and provide molecular markers for diagnostic and prognostic approaches to kidney cancer.

Adult↗
PubMed2001

Cyclin D1 and p16 alterations in advanced premalignant lesions of the upper aerodigestive tract: role in response to chemoprevention and cancer development.

PURPOSE: To better understand the role of G(1)-S transition regulator abnormalities in the pathogenesis of advanced premalignant lesions of the upper aerodigestive tract and the biological effects of chemoprevention, we studied biopsies obtained sequentially from participants in a prospective trial using 13-cis retinoic acid, IFN-alpha, and alpha-tocopherol for 12 months. EXPERIMENTAL DESIGN: Cyclin D1 and p16 expression were analyzed by immunohistochemistry, loss of heterozygosity by polymerase chain reacting amplification, and then electrophoretic separation of the products, methylation of the p16 promoter by methylation-specific polymerase chain reacting, and cyclin D1 gene amplification by fluorescence in situ hybridization. RESULTS: Baseline dysregulation of cyclin D1 expression was found in 50% (14 of 28) and was reversed in 6 of 14 cases, whereas p16 expression was lost in 46% (13 of 28) and regained in 2 of 13 cases. Loss of heterozygosity at 9p21 occurred in 68% and p16(INK4a) promoter methylation occurred in 75% of cases, with increasing frequency from mild to severe dysplasia. Cyclin D1 gene amplification was identified in two cases. Cyclin D1 protein dysregulation at last follow-up alone and in combination with p16 loss was associated with histological progression and cancer development (P < 0.01). CONCLUSIONS: Additional study of these alterations in a larger sample and exploration of the upstream signaling partners of these cell cycle regulators in vivo is warranted to identify cancer risk profiles that would be meaningful targets for chemopreventive intervention.

Adult↗
PubMed2001

Tissue microdissection and degenerate oligonucleotide primed-polymerase chain reaction (DOP-PCR) is an effective method to analyze genetic aberrations in invasive tumors.

We amplified various amounts of DNA derived from frozen SF210 and U251NCI human glioblastoma cells, carried out comparative genomic hybridization (CGH) using degenerate oligonucleotide primed-PCR (DOP-PCR) products as test probes, and compared results to analyses performed with probes prepared by standard nick translation. Next we extracted DNA from hematoxylin-eosin (HE)- and methyl green (MG)-stained, microdissected sections of formalin-fixed and paraffin-embedded U251NCI cells, amplified and labeled it by DOP-PCR, and subjected it to CGH. Finally, we used the same methods in multiple samples from a single human mixed glioma tissue. DOP-PCR products from 50 pg to 250 ng of DNA were equally effective in generating the same CGH profiles as the standard method. DOP-PCR products from microdissected pieces of MG-stained cells were effective probes for CGH, but HE-stained samples were not desirable. As the proportion of HE-stained sample increased, CGH profiles deteriorated. DOP-PCR products from microdissected pieces of MG-stained paraffin sections of glioma tissue produced CGH profiles compatible with their histological features. CGH performed with DOP-PCR products from microdissected paraffin blocks allows for the accurate investigation of the cytogenetic characteristics from invasive tumors and of cytogenetic heterogeneity within neoplastic tissue.

Astrocytoma↗
PubMed2006

The Brucella abortus xthA-1 gene product participates in base excision repair and resistance to oxidative killing but is not required for wild-type virulence in the mouse model.

Exonuclease III, encoded by the xthA gene, plays a central role in the base excision pathway of DNA repair in bacteria. Studies with Escherichia coli xthA mutants have also shown that exonuclease III participates in the repair of oxidative damage to DNA. An isogenic xthA-1 mutant (designated CAM220) derived from virulent Brucella abortus 2308 exhibited increased sensitivity to the alkylating agent methyl methanesulfonate (MMS) compared to the parent strain. In contrast, 2308 and the isogenic xthA-1 mutant displayed similar levels of resistance to the DNA cross-linker mitomycin C. These phenotypic properties are those that would be predicted for a strain defective in base excision repair. The B. abortus xthA-1 mutant also displayed reduced resistance to killing by H2O2 and the ONOO(-)-generating compound 3-morpholinosydnonimine (SIN-1) compared to strain 2308, indicating that the xthA-1 gene product participates in protecting B. abortus 2308 from oxidative damage. Introducing a plasmid-borne copy of the parental xthA-1 gene into CAM220 restored wild-type resistance of this mutant to MMS, H2O2, and SIN-1. Although the B. abortus xthA-1 mutant exhibited increased sensitivity to oxidative killing compared to the parental strain in laboratory assays, CAM220 and 2308 displayed equivalent spleen colonization profiles in C57BL/6 [corrected] mice through 8 weeks postinfection and equivalent intracellular survival and replication profiles in cultured murine macrophages. Thus, although the xthA-1 gene product participates in base excision repair and resistance to oxidative killing in B. abortus 2308, XthA-1 is not required for wild-type virulence of this strain in the mouse model.

Animals↗
PubMedDate not supplied

Characterization of DNA adducts derived from (+/- )-trans-3,4-dihydroxy-anti-1,2-epoxy-1,2,3,4- tetrahydrodibenz[a,j]anthracene and (+/- )-7-methyl-trans-3,4-dihydroxy- anti-1,2-epoxy-1,2,3,4-tetrahydrodibenz[a,j]anthracene.

Structural characterizations of the DNA adducts derived from reaction of the racemic bay region anti-diol epoxides of dibenz[a,j]anthracene and 7-methyldibenz[a,j]anthracene with calf thymus DNA are presented. Quantities of adducts necessary for spectroscopic characterization were obtained from reactions of the respective diol epoxides with individual deoxyribonucleotides. Both hydrocarbon diol epoxides showed similar adduct profiles upon reaction with calf thymus DNA in vitro which were composed mainly of three deoxyguanosine and four deoxyadenosine adducts. No significant modification of pyrimidine bases in DNA was detected with either of the diol epoxides. Approximately 3 times more deoxyguanosine than deoxyadenosine residues in the DNA were found to be modified by both diol epoxides. The DNA reactions showed very similar stereo- and enantioselectivities with both diol epoxides. The stereochemistries of addition of the purine bases to the diol epoxides were determined from analysis of the NMR spectra of individual adducts. The predominant adducts formed were products of trans addition of the exocyclic amino group of purines to the diol epoxides. The enantiomeric nature of the various adducts was determined from reaction of the individual deoxyribonucleotides with the pure (+)-anti-diol epoxide of dibenz[a,j]anthracene. The major deoxyguanosine and deoxyadenosine adducts from reactions with DNA were found to arise from the (+)-enantiomer of both hydrocarbon diol epoxides. The high reactivities of both diol epoxides (24-38%) with DNA in solution are consistent with the high tumor-initiating activity exhibited by the diol epoxide of dibenz[a,j]anthracene relative to the parent hydrocarbon.

Animals↗
PubMed1999

Constitutive expression of cytoplasmic activator protein-1 with DNA binding activity and responsiveness to ionotropic glutamate signals in the murine hippocampus.

Gel retardation electrophoresis revealed that cytosolic fractions contained DNA binding activity of the transcription factor activator protein-1 with profiles different from those reported in nuclear extracts in murine brain. In particular, activator protein-1 DNA binding was almost undetectable at 25 degrees C in the presence of both KCl and MgCl2 in cytosol fractions. Moreover, cytoplasmic activator protein-1 binding occurred at three different mobilities on the gel when determined at 2 degrees C in the absence of MgCl2. Systemic administration of N-methyl-D-aspartate and kainate led to marked potentiation of cytoplasmic activator protein-1 binding detected as slow bands in the murine hippocampus, without markedly affecting that as a fast band. Immunoblotting and supershift assays revealed much higher expression of both immunoreactive c-Jun and c-Fos in hippocampal cytosolic fractions in response to the administration of kainate than N-methyl-D-aspartate. These results suggest that activator protein-1 may be constitutively expressed in the cytoplasm with DNA binding activity and responsiveness to ionotropic glutamate signals in a manner different from that in the nucleus in the murine hippocampus.

Animals↗
PubMed2005

Gene expression in the preimplantation embryo: in-vitro developmental changes.

The regulation of early embryo development and the mechanism of implantation remains poorly understood, due to the large number of genes and the complexity of the systems involved. The effect of in-vitro culture on embryos also remains unclear, which raises concerns about the safety of assisted reproductive technology. Changes in the expression of several individual genes in cultured embryos have been reported previously, but a large-scale comparison has not yet been performed to investigate the effects of in-vitro culture systems on embryo development. This study investigated established gene expression profiles of more that 20,000 genes from in-vitro cultured mouse embryos at eight different stages (oocytes, zygote, 2-, 4-, 8-cell embryo, compacting embryo, morula and blastocyst) using microarray technology, and compared these profiles with in-vivo embryos. In most stages of development there was little significant difference in overall expression patterns between in-vitro and in-vivo embryos. In addition, the expression patterns of developmentally important genes from several different categories, such as apoptosis, glycolysis, adhesion and methylation, were examined and compared between in-vitro and in-vivo embryos. Among the genes examined, DNA methyltransferase 1 (DNMT1) shows a significantly higher (P < 0.05) expression level in cultured embryos. Cadherin-11 also demonstrates a slightly different pattern, although the difference is not statistically significant. All the other genes have remarkably similar expression patterns between in-vitro and in-vivo embryos throughout preimplantation stages.

Animals↗
PubMed2006

Antibacterial agent discovery using thymidylate synthase biolibrary screening.

Thymidylate synthase (TS, ThyA) catalyzes the reductive methylation of 2'-deoxyuridine 5'-monophosphate to 2'-deoxythymidine 5'-monophosphate, an essential precursor for DNA synthesis. A specific inhibition of this enzyme induces bacterial cell death. As a second round lead optimization design, new 1,2-naphthalein derivatives have been synthesized and tested against a TS-based biolibrary, including human thymidylate synthase (hTS). Docking studies have been performed to rationalize the experimentally observed affinity profiles of 1,2-naphthalein compounds toward Lactobacillus casei TS and hTS. The best TS inhibitors have been tested against a number of clinical isolates of Gram-positive-resistant bacterial strains. Compound 3,3-bis(3,5-dibromo-4-hydroxyphenyl)-1H,3H-naphtho[1,2-c]furan-1-one (5) showed significant antibacterial activity, no in vitro toxicity, and dose-response effects against Staphylococcus epidermidis (MIC=0.5-2.5 microg/mL) clinical isolate strains, which are resistant to at least 17 of the best known antibacterial agents, including vancomycin. So far this compound can be regarded as a leading antibacterial agent.

Animals↗
PubMed2003

Analysis of gene expression profiles in pancreatic carcinoma by using cDNA microarray.

OBJECTIVES: To survey the gene expression profiles in pancreatic carcinoma by using cDNA microarray and detect target genes for further study. METHODS: Three mixed samples from 2 cases of normal pancreatic tissue and 4 cases of moderate-differentiated pancreatic carcinoma were studied by means of cDNA microarray consisting of 18 000 genes. RESULTS: 1484 and 1353 different expressed genes were observed in two cancer samples respectively. We identified 455 genes altered with the same tendency in both samples, including 102 up-regulated and 353 down-regulated genes. There were 274 known genes and 181 unknown genes; 27.8% and 52.0% genes respectively had an expression level in cancer that was 2-fold higher or lower than that in normal samples. Tumor suppressor genes, growth factors and receptor genes, signal conduction genes, transcription factor genes were identified. CONCLUSIONS: cDNA microarray is an efficient and high-throughout method to investigate gene expression profiles in pancreatic carcinoma. MBD1, EDG1 and gene hypermethylation mechanism would play an important role in the pathogenesis of pancreatic carcinoma.

DNA Methylation↗
PubMed2002

Protein-facilitated base flipping in DNA by cytosine-5-methyltransferase.

DNA methylation, various DNA repair mechanisms, and possibly early events in the opening of DNA as required for transcription and replication are initiated by flipping of a DNA base out of the DNA double helix. The energetics and structural mechanism of base flipping in the presence of the DNA-processing enzyme, cytosine 5-methyltransferase from HhaI (M.HhaI), were obtained through molecular dynamics based upon free-energy calculations. Free-energy profiles for base flipping show that, when in the closed conformation, M.HhaI lowers the free-energy barrier to flipping by 17 kcalmol and stabilizes the fully flipped state. Flipping is shown to occur via the major groove of the DNA. Structural analysis indicates that flipping is facilitated by destabilization of the DNA double-helical structure and substitution of DNA base-pairing and base-stacking interactions with DNA-protein interactions. The fully flipped state is stabilized by DNA-protein interactions that are enhanced upon binding of coenzyme. This study represents an atomic detail description of the mechanism by which a protein facilitates specific structural distortion in DNA.

Base Composition↗
PubMed2003

Predicting aberrant CpG island methylation.

Epigenetic silencing associated with aberrant methylation of promoter region CpG islands is one mechanism leading to loss of tumor suppressor function in human cancer. Profiling of CpG island methylation indicates that some genes are more frequently methylated than others, and that each tumor type is associated with a unique set of methylated genes. However, little is known about why certain genes succumb to this aberrant event. To address this question, we used Restriction Landmark Genome Scanning to analyze the susceptibility of 1,749 unselected CpG islands to de novo methylation driven by overexpression of DNA cytosine-5-methyltransferase 1 (DNMT1). We found that although the overall incidence of CpG island methylation was increased in cells overexpressing DNMT1, not all loci were equally affected. The majority of CpG islands (69.9%) were resistant to de novo methylation, regardless of DNMT1 overexpression. In contrast, we identified a subset of methylation-prone CpG islands (3.8%) that were consistently hypermethylated in multiple DNMT1 overexpressing clones. Methylation-prone and methylation-resistant CpG islands were not significantly different with respect to size, C+G content, CpG frequency, chromosomal location, or promoter association. We used DNA pattern recognition and supervised learning techniques to derive a classification function based on the frequency of seven novel sequence patterns that was capable of discriminating methylation-prone from methylation-resistant CpG islands with 82% accuracy. The data indicate that CpG islands differ in their intrinsic susceptibility to de novo methylation, and suggest that the propensity for a CpG island to become aberrantly methylated can be predicted based on its sequence context.

Base Sequence↗
PubMed2026

Genetic and epigenetic contributors to cleft laterality: evidence from monozygotic mirror twins and replication cohorts.

Nonsyndromic cleft lip (nsCL) exhibits a non-random laterality pattern, with left-sided clefts occurring twice as frequently as right-sided clefts. The molecular mechanisms underlying this laterality bias remain poorly understood. We performed whole-genome sequencing and methylation profiling on a family comprising monozygotic twins with mirror-image nsCL, their affected mother, and unaffected father and brother. We conducted three independent replications via publicly available whole genome data; genome-wide methylation analysis in 38 individuals with unilateral cleft; and validation of methylation results in the top 3 candidate genes in 385 unrelated individuals with unilateral nonsyndromic cleft lip with or without cleft palate (nsCL/P) (DNA from blood or saliva). We identified a variant in FGF20 (p.Ile79Val) shared by the twins and their mother. We observed laterality and severity-associated methylation differences in three main genes. ARID5B showed higher methylation in left clefts (saliva, P&#x2009;=&#x2009;.001; blood, P&#x2009;=&#x2009;.032). ZFP57 demonstrated a strong cleft-extent effect, with cleft lip and palate (CLP) showing markedly higher methylation than cleft lip only (CL) (LCLP vs. RCL padj&#x2009;=&#x2009;0.0004; LCLP vs. LCL padj&#x2009;=&#x2009;0.019). HOOK2 displayed a cross-tissue cleft-extent effect in the opposite direction-CLP subtypes were hypomethylated relative to CL-only subtypes in blood (P&#x2009;<&#x2009;.0001) and saliva (P&#x2009;=&#x2009;.0008). This study provides evidence that DNA methylation patterns play a role in both the laterality and severity of cleft lip. ARID5B provides a consistent laterality signal across tissues, while ZFP57 and HOOK2 track palatal involvement independently of side. Together, these findings suggest that epigenetic variation acts downstream of genetic predisposition to shape cleft phenotypes.

Humans↗
PubMed1999

The enigma of arsenic carcinogenesis: role of metabolism.

Inorganic arsenic is considered a high-priority hazard, particularly because of its potential to be a human carcinogen. In exposed human populations, arsenic is associated with tumors of the lung, skin, bladder, and liver. While it is known to be a human carcinogen, carcinogenesis in laboratory animals by this metalloid has never been convincingly demonstrated. Therefore, no animal models exist for studying molecular mechanisms of arsenic carcinogenesis. The apparent human sensitivity, combined with our incomplete understanding about mechanisms of carcinogenic action, create important public health concerns and challenges in risk assessment, which could be met by understanding the role of metabolism in arsenic toxicity and carcinogenesis. This symposium summary covers three critical major areas involving arsenic metabolism: its biodiversity, the role of arsenic metabolism in molecular mechanisms of carcinogenesis, and the impact of arsenic metabolism on human risk assessment. In mammals, arsenic is metabolized to mono- and dimethylated species by methyltransferase enzymes in reactions that require S-adenosyl-methionine (SAM) as the methyl donating cofactor. A remarkable species diversity in arsenic methyltransferase activity may account for the wide variability in sensitivity of humans and animals to arsenic toxicity. Arsenic interferes with DNA methyltransferases, resulting in inactivation of tumor suppressor genes through DNA hypermethylation. Other studies suggest that arsenic-induced malignant transformation is linked to DNA hypomethylation subsequent to depletion of SAM, which results in aberrant gene activation, including oncogenes. Urinary profiles of arsenic metabolites may be a valuable tool for assessing human susceptibility to arsenic carcinogenesis. While controversial, the idea that unique arsenic metabolic properties may explain the apparent non-linear threshold response for arsenic carcinogenesis in humans. In order to address these outstanding issues, further efforts are required to identify an appropriate animal model to elucidate carcinogenic mechanisms of action, and to define dose-response relationships.

Animals↗
PubMed2025

Beyond parental lines: multi-omics analyses reveal epigenetic and transcriptional mechanisms underlying heterosis in Oryza sativa &#xd7; Oryza rufipogon hybrids.

Heterosis, or hybrid vigor, refers to the superior phenotypes of a hybrid compared with their parents and is widely exploited in agriculture. Interspecific hybrids within the Oryza genus demonstrate significant potential for the systematic improvement of rice varieties. Nevertheless, the mechanistic basis underlying heterosis in interspecific Oryza hybrids remains poorly understood. Here, we systematically performed phenotypic characterization, whole-genome bisulfite sequencing, RNA sequencing, and small RNA profiling using Oryza sativa L. ssp. japonica cv. Nipponbare (NIP), Oryza rufipogon Griff. acc. CWR, and their resulting F1 hybrid (named as NC). NIP and CWR showed distinct phenotypic and molecular differences. The interspecific hybrid, NC, exhibited significant yield heterosis. In the hybrid, most epigenetic and transcriptional features displayed additive inheritance patterns relative to parental lines. Analysis revealed that domestication-selected genes maintained relatively low DNA methylation coupled with high expression levels in both hybrid and parental lines. Additionally, we identified that non-additive miRNAs were potentially involved in regulating fertility, cell growth, and cell division processes in the hybrid. A significant negative correlation was observed between DNA methylation level and gene expression. Functional enrichment analysis revealed that hybrid-MPV DEGs were significantly associated with flowering time regulation, carbohydrate metabolism, photosynthesis, protein phosphorylation, seed development, and defense responses. Through weighted gene co-expression network analysis, we identified 102 functional gene modules, six of which were significantly associated with yield-related heterosis. Collectively, our results provide a multi-omics framework for understanding interspecific hybridization between elite cultivars and wild rice relatives, highlighting CWR as an untapped genetic reservoir for rice improvement.

Oryza↗
PubMed2005

Macroarray expression analysis of barley susceptibility and nonhost resistance to Blumeria graminis.

Different formae speciales of the grass powdery mildew fungus Blumeria graminis undergo basic-compatible or basic-incompatible (nonhost) interactions with barley. Background resistance in compatible interactions and nonhost resistance require common genetic and mechanistic elements of plant defense. To build resources for differential screening for genes that potentially distinguish a compatible from an incompatible interaction on the level of differential gene expression of the plant, we constructed eight dedicated cDNA libraries, established 13.000 expressed sequence tag (EST) sequences and designed DNA macroarrays. Using macroarrays based on cDNAs derived from epidermal peels of plants pretreated with the chemical resistance activating compound acibenzolar-S-methyl, we compared the expression of barley gene transcripts in the early host interaction with B. graminis f.sp. hordei or the nonhost pathogen B. graminis f.sp. tritici, respectively. We identified 102 spots corresponding to 94 genes on the macroarray that gave significant B. graminis-responsive signals at 12 and/or 24 h after inoculation. In independent expression analyses, we confirmed the macroarray results for 11 selected genes. Although the majority of genes showed a similar expression profile in compatible versus incompatible interactions, about 30 of the 94 genes were expressed on slightly different levels in compatible versus incompatible interactions.

Ascomycota↗
PubMed1987

Influence of N6-methylation of residue A(5) on the conformational behaviour of d(C-C-G-A-A-T-T-C-G-G) in solution studied by 1H-NMR spectroscopy. 2. The hairpin form.

The solution conformations of the oligonucleotides d(C-C-G-A-A-T-T-C-G-G) and d(C-C-G-A-m6A-T-T-C-G-G) as a function of temperature and sample concentration were investigated by means of 1H-NMR spectroscopy. The NMR spectra revealed that, at certain combinations of temperature and low sample and salt concentration, both compounds exist as a B-DNA-type duplex slowly (on the 1H-NMR time scale) interconverting with a monomeric species. From chemical shift data and imino-proton spectra, it is concluded that the monomeric species consists of a mixture of a hairpin form in rapid equilibrium with the random-coil form. The double-helical stem of the hairpin is formed by the six terminal cytidine and guanine residues, whereas the four core residues, -A-(m6)A-T-T-, partake in the loop. Thermodynamic analysis of the chemical shift of the resonances of the monomeric species vs temperature profiles of the two decamers and mutual comparison of these profiles indicate the following: the influence of N6-methylation of residue A(5) upon the local structure of the hairpin must be small; methylation decreases the stability of the duplex relative to the monomeric species: the temperature at which the fraction duplex equals 0.5 was found to be 312 K for the parent compound and 305 K for the methylated decamer at 2 mM sample concentration; methylation does not significantly alter the stability of the hairpin form relative to the random coil form: the Tm of the hairp----n equilibrium random-coil equilibrium is 308 K for the parent compound and 306 K for the methylated decamer. A higher fraction hairpin-like structure for the N6-methylated compound is observed under identical conditions of temperature and sample concentration: at 300 K, 2 mM sample concentration, the fraction hairpin form is 0.12 for d(C-C-G-A-A-T-T-C-G-G) and 0.20 for d(C-C-G-A-m6A-T-T-C-G-G). This finding appears to be a consequence of the reduced stability of the methylated dimeric species relative to the monomeric species, and to depend upon the sodium-ion concentration: it becomes more pronounced under low-salt conditions.

Magnetic Resonance Spectroscopy↗
PubMed2006

Wnt signaling promoter hypermethylation distinguishes lung primary adenocarcinomas from colorectal metastasis to the lung.

Promoter hypermethylation is responsible for gene inactivation during carcinogenesis. It has been proposed that there is some degree of specificity in the set of genes that become altered by this mechanism in distinct tumor types. To understand whether promoter hypermethylation may differentiate the site of origin, 49 lung adenocarcinomas from 31 lung primaries and 18 metastases from colorectal primaries, respectively, were tested for the presence of this alteration in the APC, CDH1, DAPK, GSTP1, MLH1, MGMT, P14, P16, RARbeta2, RASSF1, sFRP1 and WIF-1 genes. A distinct profile was apparent for the 2 groups of lung tumors and the frequencies of promoter hypermethylation at sFRP1 and WIF-1, 2 genes involved in Wnt signaling, and at CDH1 were significantly higher in colorectal metastases than in lung primaries, whereas methylation of the APC promoter was significantly more common in lung primary adenocarcinomas. Some tumors showed concomitant APC, sFRP1 and WIF-1 gene inactivation, indicating that multiple DNA methylation events must have occurred to definitively down-regulate the signaling through Wnt. However, promoter hypermethylation at the APC and CDH1 genes tended to be mutually exclusive (Fisher's exact test, p = 0.006), suggesting a similar role in carcinogenesis. In conclusion, we propose that inactivation by promoter hypermethylation at the APC, CDH1, sFRP1 and WIF-1 genes may contribute to the discrimination of lung primary adenocarcinomas from colorectal metastasis to the lung, and report the simultaneous presence of methylation at the promoters of multiple genes involved in the Wnt signaling. This may have biological consequences for carcinogenesis.

Adenocarcinoma↗