Alterations of (CA)n DNA repeats and tumor suppressor genes in human gastric cancer.

We have examined whether alterations of simple (CA)n DNA repeats, as observed in human colon cancers, occur during human gastric carcinogenesis and whether such alterations reflect genomic instability that could lead to other genetic changes. A total of 22 gastric cancer samples were analyzed: 15 well or moderately differentiated adenocarcinomas, 6 signet-ring cell carcinomas, and 1 poorly differentiated adenocarcinoma. When (CA)n repeat sequences were examined at 10 loci, one adenocarcinoma showed a loss of repeat sequences at five loci, three adenocarcinomas gained a repeat at one locus, and one adenocarcinoma had new, repeated sequences at five loci. Three samples showed mutations in the p53 gene, two in exon 5 (both GC to AT transition at a CpG dinucleotide) and one in exon 7 (AT to GC transition). Only one sample with a p53 mutation also showed altered (CA)n repeats. A putative tumor suppressor gene, connexin 32, was not altered as assessed by single-strand conformation polymorphism analysis. These results suggest that genomic instability revealed by (CA)n repeat changes does not seem to contribute to induction of point mutations in p53 or connexin 32 genes but may participate in loss of heterozygosity at APC/MCC loci. The results are consistent with the hypothesis that different mechanisms are involved in the gain and loss of (CA)n repeats.

Assay by inhibition of repair to measure O6-methylguanine in DNA.

A procedure for measuring the level of O6-methylguanine (O6-meG) in DNA is described. Repair of 32P-oligodeoxynucleotides containing O6-meG adducts by O6-alkylguanine alkyltransferase (AGT) was performed in the presence of different quantities of DNA containing unknown concentrations of O6-meG. Each methylated DNA sample inhibited the repair of oligodeoxynucleotide substrate to an extent dependent upon O6-meG concentration. Each DNA sample tested at different concentrations in the assay therefore had a characteristic inhibition curve and could be compared to the curves generated using reference DNA samples of known O6-meG concentration. We report the method of calculation of the O6-meG level in a given DNA sample by comparison of its inhibition curve with that of reference DNAs. This method of calculation does not require a knowledge of the exact quantity of the labelled substrate or AGT used. The method requires only 0.1-10 micrograms of DNA, with a limit of detection of 0.8 fmol of O6-meG per microgram of DNA.

Nonrandom distribution of O6-methylguanine in H-ras gene sequence from DNA modified with N-methyl-N-nitrosourea.

The distribution of O6-meG in the rat H-ras gene sequence was studied using PCR by transition of O6-meG to adenine during the reaction. In order to study the transition mutations the PCR product was cloned in a replicative form of phage M13mp18 and sequenced. The use of PCR for detection of O6-meG was validated by using oligonucleotides (61 bases) containing one O6-meG residue at a defined site. After treatment of rat liver DNA by N-methyl-N-nitrosourea in vitro, a striking nonrandom sequence distribution of O6-meG was observed. Sixty-eight per cent of O6-methylated Gs were found in the middle G of the sequences GGT and GGA in the H-ras gene whereas no methylation was found in the middle G of the sequences AGG, GGG, TGT, TGC, CGA and CGC. No O6-meG adduct was found in the 12th codon of H-ras (sequence GGA). The frequency of O6-meG formation as a function of two flanking nucleotides on each side of the target guanine was calculated as an approach to understanding more distant sequence effects. It was found that in the DNA sequence studied the formation of O6-meG was highest if the G was flanked by PyPu or PuPu on the 5' side (Py, pyrimidine and Pu, purine) whereas PuPu on the 3' side showed maximal inhibition of O6-meG formation.

[Genome instability and neoplasia]. / Nestabil'nost' genoma i neoplaziia.

Necessity of oncogene for the neoplastic cell transformation is substantiated. The oncogene may be introduced into the cell by a virus; be present in the cell from its formation but be repressed by products of regulatory genes; be arisen from separated DNA segments. The latter possibility is discussed in view of data on the presence of mobile elements and Sarc sequences in the cell genome.

[Repair in the nuclear matrix of DNA damaged by benz(a)pyrene]. / Reparatsiia na iadernom matrikse DNK, povrezhdennoi benz(a)pirenom.

The confluent culture of hamster embryo cells was incubated with benzo(a)pyrene for 24 hours. Then the medium was replaced by maximal lacking both the serum and benzo(a)pyrene. The process of DNA repair was observed in four nuclear fractions according to two indexes: the disappearance of metabolites of benzo(a)pyrene covalently bound to DNA and the incorporation of 3H-thymidine to DNA in the period from I min to 72 hours. Hydroxyurea at the concentration of 5 mM was added 2-19 hours before 3H-thymidine. The highest concentration of benzo(a)pyrene metabolites was found in the DNA of nuclear matrix fraction throughout all the experiment. The initial concentration of 3H-thymidine right after its addition into the cell culture medium was the highest in DNA of nuclear matrix fraction and the lowest in DNA fraction soluble in the buffer with low ionic strength. Later on, the concentration of 3H-thymidine was decreased in matrix-bound fractions and increased in other fractions up to the total DNA level. The results suggest that the repair process requires joining of benzo(a)pyrene damaged DNA region to the nuclear matrix with the following reverse transition into the fraction where the fragment was initially located.

[The content of various active and inactive genes in chromatin fractions with different accessibilities of DNA to polycyclic aromatic hydrocarbons]. / Soderzhanie nekotorykh aktivnykh i neaktivnykh genov vo fraktsiiakh khromatina, razlichaiushchikhsia dostupnost'iu DNK k deistviiu politsiklicheskikh aromaticheskikh uglevodorodov.

Nuclear chromatin was separated into four fractions according to solubility in low (0.2 mM MgCl2, 10 mM Tris-HCl, pH 7.6) and high (2 M NaCl) ionic strengths after digestion of nuclear DNA with nucleases. In nuclear matrix DNA the ratio of active to inactive genes was always higher than that in the original total DNA, i.e., 25 times greater in rat liver nuclei. In DNA released from the nuclei into a low ionic strength buffer the active to inactive gene ratio was lower than in total DNA (3.7 times as low in case of rat liver nuclei). The amount of carcinogens in matrix DNA exceeded that of DNA soluble in a low ionic strength buffer (3-4 times in case of rat liver nuclei and 16 times in case of hamster embryo cells). The two other fractions occupied an intermediate position between the above said fractions of DNA. The experimental results suggest that the level of carcinogen-induced modifications may be increased in active genes, including transcribed protooncogenes.

[Protein composition of chromatin fractions differing in their attachment to nuclear structures at low ionic strength]. / Belkovyi sostav fraktsii khromatina, razlichaiushchikhsia po sviazy s iadernymi strukturami v usloviiakh nizkoi ionnoi sily.

Rat livers were disrupted in the TMS buffer (10 mM Tris-HCl, pH 7.6, 5 mM MgCl2, 0.25 M sucrose +70 microM beta-mercaptoethanol) and the nuclei were purified by sedimentation through 2.2 M sucrose with the same components as in TMS. Then the nuclei were resuspended and washed 3 times in TMS. After that the nuclei were resuspended to 1 mg DNA per ml in TM buffer (10 mM Tris-HCl, pH 7.6, 0.2 mM MgCl2) followed by centrifugation at low speed. About 60% of total nuclear DNP was recovered by this extraction. The protein/DNA ratio in the extracted chromatin fraction (DNPs) was about 1.1. The bulk of the non-extracted in TM residual chromatin fraction was released from the nuclear pellet after treatment with micrococcal nuclease. This matrix-associated chromatin fraction (DNPm) is significantly enriched in non-histone proteins as compared with the DNPs; hence the protein/DNA ratio of DNPm is at least two times higher than that of DNPs. The protein components of DNPs are represented by five histones containing negligible non-histone admixture. One of them was identified as protein A24, another--as non-dissociated from DNA in 0.6 M NaCl acid-soluble protein with m. w. of about 42,500. The possible structural features of these two distinguishable chromatin fractions are discussed.

[Characteristics of DNA during binding with polycyclic aromatic hydrocarbons in vitro]. / Kharakteristika DNK v protsesse sviazyvaniia politsiklicheskikh aromaticheskikh uglevodorodov in vitro.

Polycyclic aromatic hydrocarbons (PAH) were covalently bound to DNA by means of various activating systems. The following systems were used: the microsomal fraction of the rat liver, the system with I2, the system with ascorbic acid and FeSO4. Breaks in DNA due to the activating systems action appeared in all of these systems. Plateau of the PAH binding system curve in the microsomal system cannot be attributed either to the fall of the PAH metabolism rate to zero, or to the PAH binding sites in DNA. This plateau is the result of equalization of the rates of the two contrary-directed processes: the binding of metabolites and their removal due to DNA degradation. Because of the breaks in DNA caused by the activating systems, the authors failed to discover the changes in sedimentation data of DNA due to the covalently bound PAH.

[Proteins and the functional properties of the chromatin fractions from the nuclei of the normal liver and of experimental hepatomas]. / Belki i funktsional'nye svoistva fraktsii khromatina iz iader normal'noi pecheni i éksperimental'nykh gepatom.

Chromatin fragments generated in normal liver and solid hepatoma nuclei due to the action of endogenous nucleases and in ascites hepatomas nuclei treated with micrococcal nuclease differ in the ability to be released from the nuclei into a medium of low ionic strength. It is suggested that such a fractionation is based on different solubility of DNP fragments attached to the nuclear skeleton and of those that are not bound with it. DNP fragments extracted in a low-salt buffer contain all five histones with a negligible admixture of nonhistone proteins having the protein/DNA ratio about 1.1. No endogenous RNA-polymerase activity could be detected in these DNP fragments. The bulk of the RNA-polymerase activity is found in the matrix-associated DNP fragments that appear to be enriched in nonhistone proteins (their protein/DNA ratio amounted to 2.5). The possibility that transcribable DNP fragments are associated with the matrix through low-salt-stable linkages like those in the DNA-(RNA-polymerase-RNA or RNP)-matrix seems to be confirmed by the data obtained.

Preferential binding of polycyclic hydrocarbons to matrix-bound DNA in rat-liver nuclei.

The reactions of benzo[a]pyrene and 7,12-dimethylbenz[a]anthracene metabolites and of r-7,t-8-dihydroxy-t-9,10-oxy-7,8,9,10-tetrahydrobenzo[a]pyrene with the DNA of matrix-bound and released chromatin fractions of rat-liver nuclei have been examined. Qualitatively there were no differences between the DNA-bound metabolites in each fraction but more binding to matrix-bound DNA occurred. Evidence was obtained that the increased binding of hydrocarbon to matrix-bound DNA was not dependent upon the proximity of hydrocarbon-metabolizing enzymes and Sephadex LH20 chromatography showed that the differences between the fractions were not due to contamination of DNA with residual proteins. The conformation of the matrix-bound chromatin may make its DNA more accessible to reactive metabolites than that of released chromatin.

[Chromatin fractionation according to the strength of its matrix bond]. / Fraktsionirovanie khromatina po prochnosti ego sviazi s matriksom.

Extraction in low salt concentration followed by centrifugation allows rat liver nuclear chromatin to be divided into two fractions: the supernatant chromatin and matrix chromatin. The former fraction contains about 60-70% of initial DNA and about 15% of initial protein along with all five histones, and an insignificant amount of non-histone proteins. RNA synthesis in the matrix chromatin fraction is 2-3 times more intense than that in the original nuclei. The data on gradient centrifugation do not suggest the elongation of RNA molecules synthesized in the matrix fraction. The results obtained as compared with the literature data suggest that the matrix chromatin fraction is enriched with active genes.

The distribution of nuclear proteins and transcriptionally-active sequences in rat liver chromatin fractions.

Chromatin fractions from rat liver nuclei digested by nucleases were separated by differential solubility into several fractions. Material solubilized during digestion (predominantly monomer nucleosomes and polynucleosomes) had the highest HMG14 + 17/DNA ratios but were not enriched in active gene sequences (albumin and c-Ha-ras1 genes). Material soluble in a low ionic strength buffer containing 0.2 mM MgCl2 (monomer nucleosomes and polynucleosomes) contained in addition to the histones, HMG14 and 17 plus a 41K non-histone protein. This fraction was depleted in active gene sequences and enriched in inactive sequences. The insoluble material was highly enriched in active sequences and had the lowest HMG14 + 17/DNA ratio. This fraction could be further fractionated into a histone-containing 2 M NaCl-soluble fraction and a 2 M NaCl-insoluble matrix-bound fraction, both of which were enriched in active sequences. The results show that the HMG proteins do not partition with active sequences during fractionation of chromatin. The 41K protein may be associated with inactive chromatin fraction.

[Preferential modification of replicating DNA by benz(a)pyrene)]. / Preimushchestvennaia modifikatsiia replitsiruiushcheisia DNK benz(a)pirenom.

The nuclei of cells from regenerating rat liver were incubated with benzo(a)pyrene and the concentrations of the metabolites that covalently bound to DNA of different nuclear fractions were compared. It appeared that DNA associated with nuclear matrix (containing replicating DNA) is modified most intensively. The synchronized mouse embryo cells were incubated with benzo(a)pyrene during S phase and the levels of modifications in short and long single-stranded DNA fragments were compared. It has been observed that replicating DNA is represented in short fragments. These short DNA fragments were found to be modified by benzo(a)pyrene 4-9 times more intensively than total DNA. The possible mechanisms of both the increase in the number of DNA modifications in proliferating cells and the reason for the enhancement of carcinogenic effect on dividing cells are being discussed.

Microsatellite alterations in human and rat esophageal tumors at selective loci.

(CA)n simple repeats in DNA were examined at 17 loci in 18 human squamous cell carcinomas of the esophagus and compared with those in normal esophageal tissue from the same patients. Six loci were examined in 32 esophageal papillomas that had been induced by N-nitrosomethylbenzylamine in BD VI rats. Length-altered CA repeats were found in two human tumors and four rat papillomas. Loss of heterozygosity was observed in three human tumors; two rat papillomas had lost microsatellite bands that are common in inbred BD VI rats. Both (CA)n microsatellite length alteration and loss of heterozygosity were clustered at certain loci in the human tumor samples and in the chemically induced rat esophageal tumors. Our findings indicate that genomic instability that results in alteration of repeated sequences not only occurs in human tumors but may also be a consequence of chemical carcinogenesis in rodents.

[Proteins from nuclear fractions with different contents of active genes]. / Belki iz iadernykh fraktsii s razlichnym soderzhaniem aktivnykh genov.

The protein content in four nuclear fractions was compared. The nuclear fraction of rat liver deficient in active genes was characterized by a very low content of non-histone proteins whose mobility is less than that of histone H1.. The predominant protein of this fraction is an acid-soluble protein (Mr = 41 +/- 1 kD) designated as 41K. This protein was detected in acid nuclear extracts of rat lungs, kidney and spleen but was absent (or practically absent) in four murine and rat hepatomas under study. The decreased content of protein 41K was correlated with the diminution of the content of histone H1(0) fraction. It was shown that proteins HMG 14 and 17 are readily washed off during fractionation of nuclei and they bind to DNA fragments passing into solution irrespective of whether they contain active or inactive genes. The nuclear matrix fraction rich in active genes was heterogeneous according to its protein composition. Differences in the intensity of staining and in electrophoretic mobility of some polypeptides of this nuclear fraction in normal and hepatoma cells were revealed.

[Changes in RNA synthesis induced by n-methyl-nitrosourea]. / Izmeniia v sinteze RNK, vyzyvaemye N-metil-N-nitrozomochevinoi.

N-methyl- and N-nitrosourea (NMU) methylate and carbamoylate DNA, RNA and chromatin proteins. The paper is concerned with an analysis of the MNU-induced changes in the synthesis of RNA in isolated nuclei, chromatin, and in protein-free DNA. It was found that NMU decreases the rate of the RNA synthesis in all the templates used. It was also found that a 5-10 times greater concentration is required to attain the same effect in the nuclei as in chromatin. Comparison of the effects of NMU, KNCO and KCl on the template activity of chromatin allows the conclusion that the processes of methylation rather than of carbamoylation of the template are responsible for the decreased RNA synthesis. Sedimentation of the RNA synthesized over the saccharose density gradient demonstrated that the changes in the synthesis are a consequence of the decreased molecular mass of the RNA-transcript, while the number of the RNA molecules synthesized is approximately the same in control and experiment.

[Nature of RNA synthesis on embikhin-damaged templates]. / Kharakteristika sinteza RNK na povrezhdennykh émbikhinom matritsakh.

Embichin, a bifunctional alkylating mutagenic agent, inhibits RNA-synthesizing capacity of DNA and chromatin. The template capacity for decreasing the embichin-injured chromatin is caused by substantial reduction in the number of RNA molecules synthesized by this template. When DNA extracted from embichin-injured chromatin is used as a template, its template restriction is accounted for by an approximately 5-fold decrease in the RNA average molecular weight. The deoxyribonucleoprotein complexes reconstituted from embichin-injured DNA and control chromatic proteins had a lower template capacity compared with that of DNP reconstituted from control DNA. It is concluded that both links between DNA and proteins and DNA injuries are responsible for the inhibition of genome template capacity.

[Aggregation of fragmented chromatin associated with the synthesis of products of its treatment with nuclease]. / Agregatsiia fragmentirovannogo khromatina, sviazannaia s poiavleniem produktov ego nukleaznoi obrabotki.

Isolated cell nuclei were incubated with nucleases followed by extraction of chromatin with a low salt buffer. With an increase of nuclear chromatin degradation with DNAse I or micrococcal nuclease, solubilization of deoxyribonucleoprotein (DNP) by a low salt buffer increases, reaching a maximum upon hydrolysis with 2-4% nuclear DNA and then decreases appreciably after extensive treatment with nucleases. Soluble fragmented chromatin aggregates in the course of treatment with DNAase. I. Addition to gel chromatin preparations of exogenous products of nuclease treatment of isolated nuclei leads to its aggregation. Pretreatment of nuclear chromatin with RNAase prevents solubilization of DNP by low ionic strength solutions. Some experimental data obtained with the use of severe nuclease treatment are discussed; for a correct interpretation of these data the aggregation of fragmented chromatin by products of its nuclease degradation should be taken into consideration.