Free nucleotides in animal tissues

Consistency of genotyping data from simultaneously collected plasma circulating tumor DNA and tumor-DNA in lung cancer patients

Background

To clarify the rate of concordance between the results of concurrent sequencing of circulating tumor DNA (ctDNA) and tumor tissue samples based in clinic settings, and to explore potential factors influencing consistency.

Methods

A retrospective analysis of 27 patients with lung cancer who underwent gene sequencing at the Department of Biotherapy of Tianjin Medical University Cancer Hospital from February 2016 to April 2019, was conducted by synchronous sequencing of tumor and plasma DNA samples and the concordance of mutations in nine known driver genes was calculated.

Results

The overall concordance, sensitivity, and specificity for sequencing driver genes in plasma samples, were 85.2%, 87.0%, and 75%, respectively, relative to tumor samples. Concordance was 100% in patients with bone metastases, while the rate in those without bone metastases was 69.2%. Moreover, in patients where both the driver gene and TP53 mutations in plasma were detected, the findings of plasma sequencing of the driver gene were identical to those of tumor sequencing (concordance: 100%).

Conclusions

Overall, our data show that circulating tumor DNA (ctDNA) was able to identify 75% of the identical information in driver genes, with higher rates of concordance in lung cancer patients with bone metastases or TP53 mutation-positive plasma samples.

Simultaneous extraction of several metabolites of energy metabolism and related substances in mammalian cells: optimization using experimental design

As a basis for the development of predictive mathematical models in systems biology and a quantitative understanding of cellular metabolism, reliable experimental data sets of intracellular metabolites are indispensable. A prerequisite for the acquisition of such data is the identification of a suitable sample preparation method. In this work, the extraction procedure for the simultaneous measurement of a wide range of intracellular metabolites from adherent mammalian cells in culture was optimized. A screening of several commonly used extraction protocols with Madin-Darby canine kidney (MDCK) cells found the methanol/chloroform (MeOH/CHCl(3)) and MeOH/Boil methods to be promising candidates for further analysis by anion-exchange chromatography. Both methods were optimized based on experimental design techniques with four response variables: Nucleotide Content, Energy Charge, Fructose 1,6-Bisphosphate content (F16bP), and Absorption at 280 nm. After data evaluation and with the help of desirability functions, an overall optimum for the extraction conditions was found. Using optimal settings, the extraction performances for MDCK and Vero cell cultivations of both methods were compared. Both methods extracted nearly the same absolute amounts of intracellular metabolites, suggesting that these methods are equal. However, recoveries for nucleotide diphosphates were significantly above 100% for both methods. This most likely was due to remaining nucleotide kinase activity during extraction. After combining individual steps of both methods, recoveries close to 100% for all metabolites could be reached. Absolute values of intracellular metabolites extracted with this modified method are comparable to the results of the two previously optimized methods, indicating a good extraction procedure according to the chosen response variables.

Characterization of an ecto-5'-nucleotidase (EC 3.1.3.5) activity in intact trophozoites of Trichomonas gallinae

This study describes the enzymatic properties of an ecto-5'-nucleotidase in Trichomonas gallinae. The enzyme hydrolyzes nucleoside monophosphates at pH 7.2 and is activated by divalent cations, such as magnesium. Ecto-5'-nucleotidase activity was insensitive to levamisole, tetramisole (alkaline phosphatase inhibitors), and AMPCP (adenosine 5'-[alpha,beta-methylene]diphosphate), an ecto-5'-nucleotidase inhibitor, whereas 0.1mM ammonium molybdate (considered a potent inhibitor of 5'-nucleotidase activity) completely inhibited the enzyme activity. The apparent K(M) (Michaelis constant) and Vmax (maximum velocity) values for Mg2+-AMP were 466+/-57 microM and 3.7+/-0.59 nmolPi/min/10(6) trichomonads, respectively. Considering that trichomonads lack the ability to synthesize purines and pyrimidines de novo, the presence of an ecto-5'-nucleotidase in intact trophozoites of T. gallinae could be important in regulating the extracellular nucleotide levels and generating adenosine, essential for the survival strategies of the parasite.

Adenosine is the primary precursor of all purine nucleotides in Trichomonas vaginalis

Trichomonas vaginalis, a parasitic protozoan and the causative agent of trichomoniasis, lacks de novo purine nucleotide synthesis and possesses a unique purine salvage pathway, consisting of a bacterial type purine nucleoside phosphorylase and a purine nucleoside kinase. It is generally believed that adenine and guanine are converted to their corresponding nucleosides and then further phosphorylated to form AMP and GMP, respectively, as the main as well as the essential pathway of replenishing the purine nucleotide pool in the organism. Formycin A, an analogue of adenosine, inhibits both enzymes as well as the in vitro growth of T. vaginalis with an estimated IC(50) of 0.27 microM. This growth inhibition was reversed by adding adenine to the culture medium but not by adding guanine or hypoxanthine. Furthermore, T. vaginalis can grow in semi-defined medium supplemented with only adenine but not with guanine or hypoxanthine. Radiolabeling experiments followed by HPLC analysis of the purine nucleotide pool in T. vaginalis demonstrated incorporation of [8-14C]adenine into both adenine and guanine nucleotides, whereas [8-14C]guanine was incorporated only into guanine nucleotides. Substantial adenosine deaminase activity and significant IMP dehydrogenase and GMP synthetase activities were identified in T. vaginalis lysate, suggesting a pathway capable of converting adenine to GMP via adenosine. This purine salvage scheme depicts adenosine the primary precursor of the entire purine nucleotide pool in T. vaginalis and the purine nucleoside kinase one of the most pivotal enzymes in purine salvage and a potential target for anti-trichomoniasis chemotherapy.

Purine and pyrimidine compounds in murine peritoneal macrophages cultured in vitro

Extracts of murine peritoneal macrophages were analysed by ion-pair reversed-phase high-performance liquid chromatography during incubation at 37 degrees C in vitro. Four-step gradient elution was applied to an ODS column (250 x 4.6 mm I.D.) at a flow-rate of 1.3 ml/min, allowing the separation of hypoxanthine, inosine, guanosine, adenosine, IMP, CDP, AMP, GDP, UDP, ADP, CTP, GTP, UTP and ATP within 50 min. Samples of 0.4 . 10(6)-0.5 . 10(6) cells were washed twice with RPMI 1640 medium and extracted with perchloric acid. Nucleotide concentrations of murine peritoneal macrophages did not change during incubation for 4 days in vitro.

Purification of apyrase from yellow lupin cotyledons after extraction with perchloric acid

Neutralized 1 M perchloric acid (PCA) extracts of yellow lupin (Lupinus luteus) seedling cotyledons contain considerable amounts of apyrase (EC 3.6.1.5). Investigators who use PCA extraction for the estimation of nucleotide levels, particularly in plant tissues, should be aware of this danger. Only when the material is treated with 1.8-2 M PCA are the extracts obtained free of apyrase activity. Chromatography of neutralized 1 M extracts obtained from 7-day-old seedling cotyledons on DEAE-Sephacel and Sephadex G-100 yields almost homogeneous apyrase that shows a band of M(r) 51,000 on sodium dodecyl sulfate-polyacrylamide gel electrophoresis gels. The molecular weight of the native enzyme is also about 51,000. The apyrase preparation is free of nonspecific phosphatases, nucleotidases, and adenosine nucleosidase, as well as dinucleoside polyphosphate-degrading enzymes. The apyrase exhibits a broad pH optimum between 6 and 8. Mg2+ and Ca2+ are required for maximum activity; Zn2+ and Mn2+ are less effective and Co2+, Ni2+, and Cd2+ are without effect. The Km values for ATP and ADP are about 20 microM. All common 5'-nucleoside tri- and diphosphates as well as adenosine 5'-tetraphosphate are substrates.

Analysis of the effects of ethanol, fructose and nicotinamide on the free nucleotides of rat liver using high performance liquid chromatography

1. Rat liver nucleotides were separated on a weak anion-exchange HPLC column. The characteristic nucleotide profile could be modified by treatment of the rats with ethanol, at both acute and chronic dosages, by fructose and by nicotinamide. 2. The major effect observed after ethanol administration was a decrease in the concentration of ATP with increases in the concentrations of AMP and other nucleotide monophosphates. 3. These changes gradually reverted to normal values over a 30 min period. 4. Ingestion of 1 or 5% ethanol for 4 weeks caused similar changes in the nucleotide profile of liver. 5. Fructose administration caused a dramatic but reversible decrease in the size of the entire nucleotide pool. 6. Rats given daily injections of nicotinamide exhibited greatly elevated concentrations of liver NAD+, whereas the other pyridine nucleotides were relatively unaffected. 7. The results are discussed in relation to the known effect on metabolism of the compounds tested.

De novo pyrimidine nucleotide biosynthesis in isolated rat glomeruli

Uracil ribonucleotide-sugars and aminosugars are required for glomerular basement membrane (GBM) biosynthesis. Since these nucleotides are metabolic derivatives of uridine 5'-triphosphate (UTP), we have studied the cellular pools of uridine 5'-diphosphoglucose (UDPG), uridine 5'-diphosphoglucuronic acid (UDPGA), uridine 5'-diphospho-N-acetyl glucosamine (UDPAG) and UTP, and measured UTP synthesis de novo in isolated glomeruli incubated in vitro. Improved techniques for nucleotide quantitation were established and the optimal conditions for glomerular isolation and incubation determined. Substantial quantities of uracil ribonucleotide coenzymes and an active utilization of orotate for the synthesis of pyrimidine nucleotides were demonstrated. UTP synthesis and the pools of UDPG and UDPGA varied markedly with changes in the experimental conditions. The adverse effects of suboptimal conditions were more apparent in glomeruli from diabetic animals than in controls. The use of suboptimal conditions could provide misleading information on GBM metabolism in isolated glomeruli since uracil ribonucleotide coenzyme availability might be reduced.

Frog rod outer segments with attached inner segment ellipsoids as an in vitro model for photoreceptors on the retina

Purified suspensions of frog rod outer segments still attached to the mitochondria-rich inner segment portion of the receptor cell (OS-IS) can be obtained in quantities (0.1 mg/retina) sufficient for chemical analysis. In oxygenated glucose-bicarbonate Ringer's medium with added Percoll, they display normal dark currents, light sensitivity, and photocurrent kinetics for several hours. Two millimolar cytoplasmic levels of ATP and GTP are maintained, fivefold higher than in isolated OS. The levels are not altered by abolition of the dark current with ouabain. Nucleoside triphosphates are more effectively buffered than in isolated OS, and their levels remain constant during changes in external calcium levels. 32Pi is incorporated into endogenous ATP and GTP pools twice as efficiently as in isolated OS, and is used in the phosphorylation of rhodopsin. OS-IS take up and release 45Ca++ by Na+-, Ca++-, and IBMX-sensitive mechanisms. Illumination causes release of 45Ca++, which confirms retinal studies by other groups using Ca++-sensitive electrodes. Thus, OS-IS suspensions model the behavior of photoreceptors still attached to the living retina. Their availability permits the simultaneous assay and correlation of electrophysiological and chemical changes occurring during excitation and adaptation.

Guanylate cyclase: assay and properties of the particulate and supernatant enzymes in mouse parotid

A new, very sensitive, rapid and reliable assay for guanylate cyclase has been established based on conversion of [32P]GTP to [32P]guanosine 3':5'-monophosphate and its separation on Dowex 50 and aluminium oxide columns. The optimum conditions for the assay of mouse parotid guanylate cyclase have been established and using this procedure the properties of the enzyme have been investigated. The enzyme was found in both the particulate and supernatant fractions. The particulate enzyme was activated 12-fold by Triton X-100 and the supernatant enzyme activity increased 2-fold. In the presence of detergent guanylate cyclase activity was distributed 85% in the particulate and 15% in the supernatant fractions, respectively. The particulate activity was localised in a plasma membrane fraction. Guanylate cyclase activity was also assayed in a wide variety of other tissues. In all cases enzymatic activity was found in both the particulate and supernatant fractions. The distribution varied with the tissue but only the intestinal mucosa had a greater proportion of total guanylate cyclase activity in the particulate fraction than the parotid. The two enzymes showed some similar properties. Their pH optima were pH 7.4, both enzymes were inhibited by ATP, dATP, dGTP and ITP, required Mn2+ for activity and plots of activity versus Mn2+ concentration were sigmoidal. However, in many properties the enzymes were dissimilar. The ratios of Mn2+ to GTP for optimum activity were 4 and 1.5 for the supernatant and plasma-bound enzymes, respectively. The slope of Hill plots for the supernatant enzyme with varying Mn2+ was 2. The particulate enzyme plots also had a slope of 2 at low Mn2+ concentration but at higher concentrations (above 0.7 mM) the Hill coefficient shifted abruptly to 4. Calcium ions reduced sigmoidicity of the kinetics lowering the Hill coefficient, activated the enzyme at all Mn2+ concentrations but had no effect on the Mn2+:GTP ratio with the supernatant enzyme while with the plasma membrane enzyme Ca2+ had no effect on the sigmoid form of the kinetics at low Mn2+ but prevented the shift to a greater Hill coefficient at higher Mn2+, inhibited the activity at low Mn2+ and shifted the Mn2+:GTP optimum ratio to 4. For the particulate enzyme plots of activity versus GTP concentration were sigmoid (n = 1.3), while the supernatant enzyme exhibited hyperbolic kinetics.

Short-lived messenger RNA in HeLa cells and its impace on the kinetics of accumulation of cytoplasmic polyadenylate

Accumulation of [3H]adenine in the acid-soluble pool and in nuclear and cytoplasmic poly(A) of HeLa cells shows that the nuclear poly(A) rises along a curve similar to that of the acid-soluble pool. By use of a [3H]guanosine pulse-chase experiment in adenine-grown cells, at least 35-50% of the pulse-labeled mRNA was found to have a half-life of about 1-2 hr. A mathematical model involving nuclear poly(A) synthesis and conservative transport to the cytoplasm has been derived from the new information about mRNA with a short half-life. This model predicts curves similar to those found for nuclear and cytoplasmic accumulation of poly(A). Thus, there is no necessity on kinetic grounds to invoke either nuclear turnover or cytoplasmic synthesis of poly(A).

Modulation of guanine deaminase

1. Guanine deaminases purified from the 15000g supernatant fraction of iso-osmotic sucrose homogenates of rat and mouse liver and brain were tested for the influence of GTP and allantoin. 2. The suffixes A and B were assigned to the isoenzyme fractions eluted from DEAE-cellulose with the lower and the higher molarity of eluent respectively. Isoenzyme A from rat liver, the activity of which showed a sigmoid dependence on substrate saturation, was activated by GTP and inhibited by allantoin. Isoenzyme B, which had a hyperbolic substrate-saturation curve, was not influenced by GTP or allantoin. 3. Isoenzyme A from rat brain, the activity of which had a sigmoid dependence on substrate concentration, was stimulated by GTP. Isoenzyme B, which showed classical Michaelis-Menten kinetics, was inhibited by allantoin. 4. Mouse liver guanine deaminase was not influenced by either GTP or allantoin. 5. Isoenzyme A from mouse brain, which had a hyperbolic substrate-saturation curve, was not influenced by GTP or allantoin but isoenzyme B, with sigmoidal kinetics, was inhibited by allantoin. 6. Mg(2+) activated, or inhibited or did not have an effect on guanine deaminase, depending on the source of the enzyme. 7. The bearing of the above findings on the possible regulation of guanine deaminase activity in vivo is discussed.

3-phosphoglycerate kinase from Hydrogenomonas facilis

Phosphoglycerate kinase levels in Hydrogenomonas facilis were reasonably constant whether cells were utilizing or synthesizing hexose during growth. Specific enzyme activities (micromoles of 3-phosphoglycerate disappearing per minute per milligram of protein) at 30 C were 0.234, 0.391, 0.300, and 0.229 in the "soluble" fraction derived from cells grown on fructose, lactate, succinate, and glutamate, respectively. The enzyme was purified 300-fold from succinate-grown cells. The final preparation, which was not homogenous but was free from glyceraldehyde-3-phosphate dehydrogenase and adenylate kinase, had a specific activity at 30 C of 90 mumoles of 3-phosphoglycerate per min per mg of protein. K(m) values for adenosine triphosphate (ATP), 3-phosphoglycerate, and Mg(++) were 0.16, 0.83, and 0.4 mm, respectively, at pH 7.4 and 30 C. Adenosine monophosphate (AMP) inhibited 23% at a ratio of AMP to ATP of 2.4, and the possible physiological implications of this inhibition are discussed. No evidence was found for an enzyme which catalyzes ATP-dependent conversion of 3-phosphoglycerate to 1,3-diphosphoglycerate, AMP, and phosphate.

The effect of ether, pentobarbital, and decapitation on various metabolites of rat skeletal muscle

The concentrations of creatine phosphate, ATP, ADP, AMP, lactate, pyruvate, hexose monophosphate, and glycogen were examined in skeletal muscle obtained from decapitated rats, or animals anesthetized with ether or pentobarbital.The concentrations of ATP, creatine phosphate, and glycogen were highest in muscles from pentobarbital-treated rats, whereas those of AMP, ADP, lactate, and pyruvate were the lowest in these animals. The data suggest that changes in the concentration of metabolites in skeletal muscle were less when the tissue was isolated under pentobarbital anesthesia than when it was isolated from decapitated or ether-anesthetized rats.

Availability of bases and nucleosides as precursors of nucleic acids in L cells and in the agent of meningopneumonitis

Tribby, Ilse I. E. (University of Chicago, Chicago, Ill.), and James W. Moulder. Availability of bases and nucleosides as precursors of nucleic acids in L cells and in the agent of meningopneumonitis. J. Bacteriol. 91:2362-2367. 1966.-Uninfected L cells and the meningopneumonitis agent propagated in L cells utilized exogenous adenine, guanine, and their ribonucleosides and deoxyribonucleosides for synthesis of both deoxyribonucleic acid (DNA) and ribonucleic acid. Cytosine, cytidine, and uridine were also incorporated into the nucleic acids of both host and parasite. L cells and the meningopneumonitis agent incorporated uracil, thymine, and deoxyuridine very poorly. L cells utilized thymidine and deoxycytidine almost exclusively for DNA synthesis, but the meningopneumonitis agent did not incorporate these nucleosides at all. Since the L cell had previously been shown to convert added thymidine to its nucleotides, mainly the triphosphate, it was concluded that the meningopneumonitis agent can utilize neither the thymidine nor the thymidine nucleotides of the L-cell pool, and that it can probably synthesize the thymidine triphosphate needed for DNA synthesis from the uridine of the L-cell pool.