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PubMed1990

Genetic variability at the human tumor necrosis factor loci.

Variability in the structure of the human tumor necrosis factor (TNF-alpha) or lymphotoxin (TNF-beta) genes may contribute to the functional polymorphism of the HLA gene complex. We have characterized an allelic restriction fragment length polymorphism (RFLP) of the TNF-beta gene by using the restriction endonuclease NcoI. Digestion of genomic DNA with NcoI and Southern blotting by using TNF-alpha gene probes show 5.4-kb and 10.5-kb hybridizing fragments. In Caucasian populations, the 10.5-kb fragment is present in 64 to 72% of haplotypes. The polymorphic NcoI site is located within the first intron of the TNF-beta gene. Additional restriction fragment variability was demonstrated by digestion with AccI; however, this restriction fragment variability was not allelic in nature. Rather, it was a consequence of variable DNA methylation at AccI sites within and upstream of the TNF-beta gene. In peripheral blood leukocytes, methylation of the TNF-beta AccI sites was greatest in neutrophils (TNF-beta nonproducers), and lowest in T lymphocytes (the major producers of TNF-beta). These results suggest strongly that variation in DNA methylation may play an important role in regulation of the expression of the TNF-beta gene.

Azacitidine↗
PubMed1990

Effects of sodium butyrate and 5-azacytidine on DNA methylation in human tumor cell lines: variable response to drug treatment and withdrawal.

The effect of butyrate (Btr) and 5-azacytidine (azaC) on genomic DNA methylation was examined in a variety of human tumor cell lines. Butyrate treatment differentially affected 5-methylcytosine (m5C) content in a cell type-specific manner. For example, incubation of CBT cells (glioblastoma multiforme) for 48 h in medium containing 2 mM Btr resulted in the hypomethylation of their DNA; after removal of the drug, the m5C content was rapidly (24 h) restored to its original level. In contrast, when HeLa cells (cervical carcinoma) were cultured for 48 h in 3 mM Btr, their genomic DNA became more extensively methylated relative to the untreated control, and the hypermethylated state was maintained for long periods in culture. Treatment of HeLa cell lines with azaC resulted in extensive demethylation of their DNA. Following removal of the drug, the DNA was rapidly remethylated to levels equal to or greater than those of the untreated cells. The hypermethylated state has remained stable for over 180 generations. Together, the data suggest that cells respond rapidly to alter drug-induced reductions in the m5C content of their DNA, and this response can subsequently result in overmethylation. In contrast, when drug-induced hypermethylation of genomic DNA occurs, it may persist for many cell generations.

5-Methylcytosine↗
PubMed1986

Stability of DNA methylation of the human hypoxanthine phosphoribosyltransferase gene.

Methylation sensitive restriction enzymes were used to evaluate the methylation level of several restriction sites near human hypoxanthine phosphoribosyltransferase (HPRT) genes on active and inactive X chromosomes. DNA samples from leukocytes, from clonally derived fibroblasts, and from independent mouse-human hybrid lines isolated from the fusion of A-9 cells and these clonally derived human cells were studied. Comparison of the methylation patterns shows that restriction sites may show variable or constant methylation among tissues and clones, and heritability of methylation is also different among restriction sites. Methylation is more stable at sites whose methylation status correlate well with HPRT activity. Our results suggest that the methylation of certain cytosine residues may critically affect gene activity and that the methylation pattern of these sites is stably inherited.

Animals↗
PubMed1989

Cellular mosaicism in the methylation and expression of hemizygous loci in the mouse.

Proposed models for the inheritance of locus-specific methylation phenotypes in somatic cells include those in which there is stable inheritance of a methylation pattern such that all cells contain a similarly methylated locus, as well as models in which the inheritance of methylation can be variable. We investigated these possibilities by examining the methylation and expression of hemizygous loci in the mouse. Our results demonstrate that differences in both methylation and expression can exist between apparently identical cells and that such mosaicism is genetically controlled.

Animals↗
PubMed1986

Distribution of 5-methylcytosine-rich regions in the polytene chromosomes of Phaseolus coccineus embryo suspensor as shown by the immunoperoxidase technique.

5-Methylcytosine (5-mC) has been visualized in polytene chromosomes of Phaseolus coccineus, scarlet bean using specific antibodies to 5-mC and the immunoperoxidase technique. The results obtained indicate that most heterochromatic regions are methylated, even though the frequency of methylation is highly variable and sometimes low. A preferential binding of anti-5-mC to centromeric heterochromatic blocks was observed. Comparison between anti-5-mC binding and the results of hybridization with highly repetitive DNA and satellite DNA shows, moreover, that centrometric heterochromatic regions hybridize in particular with both DNAs. This finding is consistent with the fact that repetitive DNA and satellite DNA are methylated to a considerably greater extent than main band DNA, in line with many data to be found in the literature. The binding pattern of anti-5-mC that we observed also suggests that methylation does not occur in all classes of repetitive DNA. The high variability of band methylation frequency is discussed in relation to a possible characteristic DNA composition of the band.

5-Methylcytosine↗
PubMed1975

The methylated constituents of L cell messenger RNA: evidence for an unusual cluster at the 5' terminus.

An analysis of the methylated constituents of L cell mRNA by a combination of chromatographic methods and enzymatic treatments indicates that they comprise both 2'-O-methyl nucleosides and N6-methyl adenine, and/or 1-methyl adenine, and suggests that the 2'-O-methyl nucleotides, Ym, are part of an unusual class of sequences forming the 5' terminus of mRNA. These sequences seem to contain two 2'-O-methyl residues and a terminal residue that is not phosphorylated but, nevertheless, is blocked with respect to polynucleotid kinase reactivity. A strong candidate is a sequence of the type XppY1mpY2mpZp..., where X represents a blocking group which is itself occasionally methylated. The sequences isolated from total poly(A)+ mRNA contain all four species of 2'-O-methylated nucleoside, indicating some variability among different mRNA species. The methylated sequences do not appear to be enriched in the mRNA which hybridizes with repetitive DNA. The average L cell mRNA molecule also contains three residues of N6-methyl adenine. These residues are not part of the poly(A) segment, but appear to be located internal to the poly(A) near the 3' end of the mRNA molecules.

Adenine↗
PubMed1985

Methylation patterns in the gene for the alpha subunit of chorionic gonadotropin are inherited with variable fidelity in clonal lineages of human fibroblasts.

Cytosine methylation in DNA of an endogenous single-copy gene locus, the alpha-subunit of human chorionic gonadotropin (alpha-hCG), was assessed in a mass culture and individual clonal lineages of human diploid fibroblasts. Progressive hypomethylation at -CCGG- sites in this gene occurred during the replicative lifespan of the mass culture and was shown to arise randomly during clonal expansion. Thus, some clones and subclones lost -CCGG- methylation in the alpha-hCG gene region while others maintained essentially complete methylation. These data indicate significant interclonal variability in the fidelity with which DNA methylation is transmitted in an endogenous gene.

5-Methylcytosine↗
PubMed2024

Blood-based DNA methylation and exposure risk scores predict PTSD with high accuracy in military and civilian cohorts.

BACKGROUND: Incorporating genomic data into risk prediction has become an increasingly useful approach for rapid identification of individuals most at risk for complex disorders such as PTSD. Our goal was to develop and validate Methylation Risk Scores (MRS) using machine learning to distinguish individuals who have PTSD from those who do not. METHODS: Elastic Net was used to develop three risk score models using a discovery dataset (n = 1226; 314 cases, 912 controls) comprised of 5 diverse cohorts with available blood-derived DNA methylation (DNAm) measured on the Illumina Epic BeadChip. The first risk score, exposure and methylation risk score (eMRS) used cumulative and childhood trauma exposure and DNAm variables; the second, methylation-only risk score (MoRS) was based solely on DNAm data; the third, methylation-only risk scores with adjusted exposure variables (MoRSAE) utilized DNAm data adjusted for the two exposure variables. The potential of these risk scores to predict future PTSD based on pre-deployment data was also assessed. External validation of risk scores was conducted in four independent cohorts. RESULTS: The eMRS model showed the highest accuracy (92%), precision (91%), recall (87%), and f1-score (89%) in classifying PTSD using 3730 features. While still highly accurate, the MoRS (accuracy = 89%) using 3728 features and MoRSAE (accuracy = 84%) using 4150 features showed a decline in classification power. eMRS significantly predicted PTSD in one of the four independent cohorts, the BEAR cohort (beta = 0.6839, p-0.003), but not in the remaining three cohorts. Pre-deployment risk scores from all models (eMRS, beta = 1.92; MoRS, beta = 1.99 and MoRSAE, beta = 1.77) displayed a significant (p < 0.001) predictive power for post-deployment PTSD. CONCLUSION: Results, especially those from the eMRS, reinforce earlier findings that methylation and trauma are interconnected and can be leveraged to increase the correct classification of those with vs. without PTSD. Moreover, our models can potentially be a valuable tool in predicting the future risk of developing PTSD. As more data become available, including additional molecular, environmental, and psychosocial factors in these scores may enhance their accuracy in predicting the condition and, relatedly, improve their performance in independent cohorts.

DNA methylation↗
PubMed2024

Blood-based DNA methylation and exposure risk scores predict PTSD with high accuracy in military and civilian cohorts.

BACKGROUND: Incorporating genomic data into risk prediction has become an increasingly popular approach for rapid identification of individuals most at risk for complex disorders such as PTSD. Our goal was to develop and validate Methylation Risk Scores (MRS) using machine learning to distinguish individuals who have PTSD from those who do not. METHODS: Elastic Net was used to develop three risk score models using a discovery dataset (n&#x2009;=&#x2009;1226; 314 cases, 912 controls) comprised of 5 diverse cohorts with available blood-derived DNA methylation (DNAm) measured on the Illumina Epic BeadChip. The first risk score, exposure and methylation risk score (eMRS) used cumulative and childhood trauma exposure and DNAm variables; the second, methylation-only risk score (MoRS) was based solely on DNAm data; the third, methylation-only risk scores with adjusted exposure variables (MoRSAE) utilized DNAm data adjusted for the two exposure variables. The potential of these risk scores to predict future PTSD based on pre-deployment data was also assessed. External validation of risk scores was conducted in four independent cohorts. RESULTS: The eMRS model showed the highest accuracy (92%), precision (91%), recall (87%), and f1-score (89%) in classifying PTSD using 3730 features. While still highly accurate, the MoRS (accuracy&#x2009;=&#x2009;89%) using 3728 features and MoRSAE (accuracy&#x2009;=&#x2009;84%) using 4150 features showed a decline in classification power. eMRS significantly predicted PTSD in one of the four independent cohorts, the BEAR cohort (beta&#x2009;=&#x2009;0.6839, p=0.006), but not in the remaining three cohorts. Pre-deployment risk scores from all models (eMRS, beta&#x2009;=&#x2009;1.92; MoRS, beta&#x2009;=&#x2009;1.99 and MoRSAE, beta&#x2009;=&#x2009;1.77) displayed a significant (p&#x2009;<&#x2009;0.001) predictive power for post-deployment PTSD. CONCLUSION: The inclusion of exposure variables adds to the predictive power of MRS. Classification-based MRS may be useful in predicting risk of future PTSD in populations with anticipated trauma exposure. As more data become available, including additional molecular, environmental, and psychosocial factors in these scores may enhance their accuracy in predicting PTSD and, relatedly, improve their performance in independent cohorts.

Humans↗
PubMed1991

Polymorphism and altered methylation of the lactoferrin gene in normal leukocytes, leukemic cells, and breast cancer.

Human lactoferrin has been found to be decreased or absent in most breast cancer and leukemia cells. In order to examine the lactoferrin gene for both structural alterations and the degree of methylation, we isolated a 2117-kilobase complementary DNA from human breast tissue. This complementary DNA was used to probe DNA extracted from normal peripheral blood, leukemia cells from patients, leukemia cell lines, and breast cancer cell lines. Immunocytochemical staining of these cells confirmed the decreased production of lactoferrin in malignancy. MspI restriction enzyme fragment patterns demonstrated genetic polymorphism which occurred in DNA from both normal and malignant cells. Polymorphism was also noted with XbaI. In this case, there were two fragment patterns that were only found in DNA from malignant cells. The degree of DNA methylation was also evaluated. The methylation pattern of DNA extracted from malignant cells was highly variable and generally less methylated than DNA extracted from normal WBCs. It is possible that the decrease in lactoferrin associated with cancer is multifactorial and includes gene structural changes as well as altered regulation. Further study is needed to determine whether the changes found in this study are the result of the malignancy or contribute to its onset or maintenance.

Amino Acid Sequence↗
PubMed1992

N-methyl-D-aspartate receptor complex in the hippocampus of elderly, normal individuals and those with Alzheimer's disease.

The various ligand binding sites of the N-methyl-D-aspartate receptor complex in the hippocampal formation and parahippocampal gyrus of Alzheimer's disease patients and age-matched normal individuals were examined using quantitative autoradiography. The hippocampus and parahippocampal gyrus of the normal elderly brain exhibited virtually identical distributions of L-[3H]glutamate, [3H]5-methyl-10,11-dihydro-5H- dibenzo[a,d]cyclohepten-5,10-iminemaleate ([3H]MK-801), [3H][(+/-)2-carboxypiperazine-4-yl]propyl-1-phosphonic acid ([3H]CPP) and strychnine-insensitive [3H]glycine binding sites (r greater than 0.87) suggesting that binding occurred to different domains of the same receptor macromolecule. The binding of [3H]MK-801 to channel-associated phencyclidine sites appeared to be most severely impaired in Alzheimer's disease, especially at the anterior hippocampal level. When the data were averaged and the means for Alzheimer's disease and control group compared, a 34% decrease (P less than 0.01) in [3H]MK-801 binding was identified in the CA1 stratum pyramidale and a smaller decrease was found in the dentate gyrus molecular layer, parahippocampal gyrus and subiculum. The CA1 region exhibited a similar 35% reduction (P less than 0.05) in L-[3H]glutamate binding to N-methyl-D-aspartate-sensitive sites. This decrease most probably reflected a decline in receptor density. Binding of [3H]CPP to antagonist-preferring sites and [3H]glycine to glycine modulatory sites did not change significantly. However, a marked intersubject variability in N-methyl-D-aspartate receptor binding was observed in control and Alzheimer's disease groups. This variability was not related to age, sex or post mortem delay. Some Alzheimer's disease patients showed markedly reduced receptor binding levels, while others showed no changes or even increased binding. The loss of N-methyl-D-aspartate-sensitive sites did not correlate with a loss of neurons in the CA1 region (r = 0.286). Similarly, no correlation between the level of binding to N-methyl-D-aspartate-sensitive sites and the density of neuritic plaques and neurofibrillary tangles was found. Intersubject variability in N-methyl-D-aspartate receptor responses in the Alzheimer's disease group may partially explain conflicting reports in the literature on the N-methyl-D-aspartate receptor changes in Alzheimer's disease, and imply that caution should be exercised before making any generalizations about receptor changes in Alzheimer's disease based on mean values only. The analysis of the individual Alzheimer's disease cases may also be valuable in determining the mechanism(s) underlying the disease.

Aged↗
PubMed1991

Peptidyl (acyloxy)methyl ketones and the quiescent affinity label concept: the departing group as a variable structural element in the design of inactivators of cysteine proteinases.

(Acyloxy)methyl ketones, of general structure Z-[AA2]-[AA1]-CH2OCOAr, are potent inactivators of the cysteine proteinase cathepsin B. These reagents have been designed as affinity labels in which the dipeptidyl moiety serves as an affinity group (complementary to the S1 and S2 sites of the enzyme), while the (acyloxy)methyl ketone unit (-COCH2OCOR), containing a weak leaving group in the form of a carboxylate nucleofuge, functions as the potentially reactive entity that labels the enzyme. The inhibition is time dependent, active site directed, and irreversible. The apparent second-order rate constant kinact/Kinact, which characterizes the inhibition of cathepsin B by this series, spans several orders of magnitude and in certain cases exceeds 10(6) M-1 s-1. The activity of this series of inhibitors was found to be exquisitely sensitive to the nature of the carboxylate leaving group as well as the affinity group. A strong dependence of second-order inactivation rate on leaving group pKa was uncovered for Z-Phe-Ala (acyloxy)methyl ketones [log(k/K) = 1.1 (+/- 0.1) X pKa + 7.2 (+/- 0.4); r2 = 0.82, n = 26]. Heretofore in constructing affinity labels the choice of leaving group was quite restricted. The aryl carboxylate group thus offers considerable variation as a design element in that both its binding affinity and reactivity can be controlled by substituent effects. Specific peptidyl (acyloxy)methyl ketones thus represent prime examples of highly potent, chemically stable enzyme inhibitors with variable structural elements in both the affinity and departing groups.

Affinity Labels↗
PubMed1986

Variability and functional recovery in the N-methyl-4-phenyl-1,2,3,6-tetrahydropyridine model of parkinsonism in monkeys.

Fourteen macaque monkeys were injected intravenously with N-methyl-4-phenyl-1,2,3,6-tetrahydropyridine. All developed the cardinal signs of parkinsonism (akinesia, rigidity, etc.) in varying degrees; some required repeated series of injections of the drug, while others developed the syndrome readily after the first series. Most of the subjects that were kept for longer than 4 weeks after the first dose of the drug showed complete or partial recovery after that time. Measurement, in some of the subjects, of the neostriatal levels of dopamine and dihydroxyphenylacetic acid showed the expected depletion of these substances at the peak of the behavioral action of the drug, but no recovery when the animals had returned to, or near, pre-drug behavioral status. No firm conclusion can be reached at this time as to the reasons for the behavioral recovery or the variability of the effects of the drug across subjects.

1-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine↗
PubMed2025

Optimizing genetic ancestry adjustment in DNA methylation studies: a comparative analysis of approaches.

BACKGROUND: Genetic ancestry is an important factor to account for in DNA methylation studies because genetic variation influences DNA methylation patterns. One approach uses principal components (PCs) calculated from CpG sites that overlap with common SNPs to adjust for ancestry when genotyping data is not available. However, this method does not remove technical and biological variations, such as sex and age, prior to calculating the PCs. The first PC is therefore often associated with factors other than ancestry. METHODS: We developed and adapted the adapted EpiAnceR+&#x2009;approach, which includes (1) residualizing the CpG data overlapping with common SNPs for control probe PCs, sex, age, and cell type proportions to remove the effects of technical and biological factors, and (2) integrating the residualized data with genotype calls from the SNP probes (commonly referred to as rs probes) present on the arrays, before calculating PCs and evaluated the clustering ability and relationship to genetic ancestry. RESULTS: The PCs generated by EpiAnceR+&#x2009;led to improved clustering for repeated samples from the same individual and stronger associations with genetic ancestry groups predicted from genotype information compared to the original approach. EpiAnceR+&#x2009;also outperformed the use of DNA methylation PCs or surrogate variables for ancestry adjustment. CONCLUSIONS: We show that the EpiAnceR+&#x2009;approach improves the adjustment for genetic ancestry in DNA methylation studies. EpiAnceR+&#x2009;can be integrated into existing R pipelines for commercial methylation arrays, such as 450&#xa0;K, EPIC v1, and EPIC v2. The code is available on GitHub ( https://github.com/KiraHoeffler/EpiAnceR ).

DNA Methylation↗
PubMed1976

Dose-response of prolactin and thyrotropin to N3im-methyl-thyrotropin releasing hormone in euthyroid men.

The synthetic N3im-methyl analogue of thyrotropin releasing hormone (methyl-TRH) was administered intravenously to 15 euthyroid men, ages 36-62, in graded doses from 6.25 mug to 500 mug in order to establish the range of response of prolactin (PRL), TSH, T3 and T4 to various doses of methyl-TRH. There was a dose-related rise in serum TSH, PRL, T3, and T4 which gave a nearly linear relationship when the integrated area of response was used as an index of response to the various doses of methyl-TRH. All 15 men had a clear elevation in TSH, PRL, T3 and T4 following the lowest dose of methyl-TRH TESTED (6.25 mug). There was considerable variability in the response to methyl-TRH among the individuals. One hundred mug of methyl-TRH gave a maximum TSH response; a 25 mug dose elicited a maximum PRL response.

Adult↗
PubMedDate not supplied

[Coalpha/Cobeta-isomerism of corrinoids. Partial synthesis and Escherichia coli activity of further isomer pairs of the (Co-methyl)-corrinoids (author's transl)].

In 2-methyladenyl-(Cobeta-methyl)-cobamide and in adenyl-(cobeta-methyl)-cobamide the nucleotide base is coordinated to the cobalt atom in neutral and weak acidic aqueous solutions (in the corresponding adenosylcorrinoids the nucleotide base is not coordinated). 2-Methylthioadenyl-(Cobeta-methyl)-cobamide resembles, with regard to the coordination of the nucleotide base, the benzimidazole-corrinoids. The partial synthesis via cobalt (I) corrinoids results in a variable proportion: (Coalpha-methyl) isomer/(Cobeta-methyl) isomer, e. g. 7/93 (cobalamin) and 50/50 (p-cresylcobamide). This proportion is generally low, if in the corresponding cyanocorrinoid the nucleotide base is firmly coordinated; it is high, if the coordination in the corresponding cyanocorrinoid is weak or absent. These results are compatible with the assumption that in the cobalt (I) corrinoids the nucleotide base is to a certain extent coordinated. In Escherichia coli 113-3 the examined (Coalpha-methyl)-corrinoids show a weaker bioactivity than the corresponding (Cobeta-methyl)-corrinoids.

Cobalt↗